ISMB 2003 ASAD Poster

Tue Feb 11 06:58:04 2003 Number: 1 Name: Liu, Xiaole Shirley Affiliation: Harvard School of Public Health, Dana Farber Cancer Institute Address: 44 Binney Street, Mayer 1B28 City: Boston State/Provice: MA Postal/Zip Code: 02115 Country: USA Email: xsliu@jimmy.harvard.edu Phone: 617-632-2472 Fax: Category: Functional Genomics Poster Title: Integrating Regulatory Motif Discovery and Genome-wide Expression Analysis Poster Authors and organization: X. Shirley Liu¹, Erin Conlon², Jason Lieb, Jun Liu
¹xsliu@jimmy.harvard.edu, Harvard, DFCI; ²erin@bioinfo.stat.harvard.edu, Harvard Abstract: File: xsliuATjimmy.harvard.edu_1 ************************************************* Wed Feb 26 23:33:34 2003 Number: 2 Name: Yao, Xiang Affiliation: Johnson and Johnson PRD Address: 3210 Merryfield Row City: San Diego State/Provice: CA Postal/Zip Code: 92129 Country: USA Email: xyao@prdus.jnj.com Phone: 858 784 3125 Fax: I plan to use my laptop computer as part of my poster Category: Databases Poster Title: GeneView: A Dynamic Gene Annotation System and Its Application to Microarray Data Analysis Poster Authors and organization: Xiang Yao¹, Heng Dai², Bin Tian, David Zhao, Albert Leung, Simon Smith, and Jackson Wan
¹xyao@prdus.jnj.com, Johnson and Johnson PRD; ²hdai1@prdus.jnj.com, Johnson and Johnson PRD Abstract: I. We have developed a system that monitors various data sources, dynamically extracts gene information, comprehensively matches genes, and integrates them into a central database by categories, such as pathway, genetic mapping, phenotype, expression profile, domain structure, protein interaction, disease association, and references. The system achieves high performance when querying a large batch of genes together File: xyaoATprdus.jnj.com_2 ************************************************* Sun Mar 2 22:57:30 2003 Number: 4 Name: Hakobyan, Gagik Hovsep Affiliation: Yerevan State University Address: Al.Manoogyan.-1 City: Yerevan State/Provice: Armenia Postal/Zip Code: 375025 Country: Armenia Email: gaghakob@ysu.am Phone: 3741577649 Fax: 3741 554641 Category: Sequence Comparison Poster Title: The distance function for computing the continuous distance of biopolymer sequences Poster Authors and organization: G.H. Hakobyan¹, T.V. Margaryan²
¹gaghakob@ysu.am, YSU; ²gaghakob@ysu.am, YSU Abstract: In some applications of sequence comparison theories the actual items to be compared are not successions of discrete elements, but "continuous" functions of a continuous argument. The present paper is aimed to construct a "continuous" distance function with the help of the given "distance" matrix D. File: gaghakobATysu.am_3 ************************************************* Mon Mar 3 06:53:15 2003 Number: 3 Name: Sheng, Qizheng Affiliation: Katholieke Universiteit Leuven, Department of Electrical Engineering Address: Kasteelpark Arenberg 10 City: Leuven-Heverlee State/Provice: Vlaams-Brabant Postal/Zip Code: 3000 Country: Belgium Email: qizheng.sheng@esat.kuleuven.ac.be Phone: +32-16-321939 Fax: +32-16-321970 Category: Data Mining Poster Title: Biclustering Microarray Data by Gibbs Sampling Poster Authors and organization: Qizheng Sheng¹, Yves Moreau², Bart De Moor
¹qizheng.sheng@esat.kuleuven.ac.be, Katholieke Universiteit Leuven, Department of Electrical Engineering; ²yves.moreau@esat.kuleuven.ac.be, Katholieke Universiteit Leuven, Department of Electrical Engineering Abstract: We have adapted Gibbs sampling strategy, which has become a method of choice for the discovery of motifs in DNA and protein sequences, to the biclustering of discretized microarray data. In contrast with standard clustering, biclustering reveals similar expressional behavior of the genes over a subset of conditions in an microarray data set. File: qizheng.shengATesat.kuleuven.ac.be_3 ************************************************* Wed Mar 5 14:05:38 2003 UPDATE ----- Number: 4 Name: Hakobyan, Gagik Hovsep Affiliation: Yerevan State University Address: Al.Manoogyan City: Yerevan State/Provice: Armenia Postal/Zip Code: 375025 Country: Armenia Email: gaghakob@ysu.am Phone: 3741577649 Fax: 3741 554641 Category: Sequence Comparison Poster Title: The distance function for computing the continuous distance of biopolymer sequences Poster Authors and organization: G.H. Hakobyan¹, T.V. Margaryan²
¹gaghakob@ysu.am, YSU; ² gaghakob@ysu.am Abstract: In some applications of sequence comparison theories the actual items to be compared are not successions of discrete elements, but "continuous" functions of a continuous argument. The present paper is aimed to construct a "continuous" distance function with the help of the given "distance" matrix D. File: gaghakobATysu.am_4 ************************************************* Wed Mar 5 14:24:21 2003 UPDATE ----- Number: 4 Name: Hakobyan, Gagik Hovsep Affiliation: Yerevan State University Address: Al.Manoogyan.-1 City: Yerevan State/Provice: Armenia Postal/Zip Code: 375025 Country: Armenia Email: gaghakob@ysu.am Phone: 3741577649 Fax: 3741 554641 Category: Sequence Comparison Poster Title: The distance function for computing the continuous distance of biopolymer sequences Poster Authors and organization: G.H. Hakobyan¹, T.V. Margaryan²
¹gaghakob@ysu.am, YSU; ² gaghakob@ysu.am Abstract: In some applications of sequence comparison theories the actual items to be compared are not successions of discrete elements, but "continuous" functions of a continuous argument. The present paper is aimed to construct a "continuous" distance function with the help of the given "distance" matrix D. File: gaghakobATysu.am_4 ************************************************* Wed Mar 5 19:37:48 2003 UPDATE ----- Number: 3 Name: Sheng, Qizheng Affiliation: Katholieke Universiteit Leuven, Department of Electrical Engineering Address: Kasteelpark Arenberg 10 City: Leuven-Heverlee State/Provice: Vlaams-Brabant Postal/Zip Code: 3000 Country: Belgium Email: qizheng.sheng@esat.kuleuven.ac.be Phone: +32-16-321939 Fax: +32-16-321970 Category: Data Mining Poster Title: Biclustering Microarray Data by Gibbs Sampling Poster Authors and organization: Qizheng Sheng¹, Yves Moreau², Bart De Moor
¹qizheng.sheng@esat.kuleuven.ac.be, Katholieke Universiteit Leuven, Department of Electrical Engineering; ²y ves.moreau@esat.kuleuven.ac.be, Katholieke Universiteit Leuven, Department of Electrical Engineering Abstract: We have adapted Gibbs sampling strategy, which has become a method of choice for the discovery of motifs in DNA and protein sequences, to the biclustering of discretized microarray data. In contrast with standard clustering, biclustering reveals similar expressional behavior of the genes over a subset of conditions in an microarray data set. File: qizheng.shengATesat.kuleuven.ac.be_3 ************************************************* Wed Mar 5 23:43:56 2003 Number: 5 Name: Plewczynski, Dariusz M Affiliation: ICM UW, Interdisciplinary Center of Mathematical and Computational Modelling, Warsaw University Address: Pawinskiego 5a City: Warsaw State/Provice: CA Postal/Zip Code: 02-106 Country: POLAND Email: darman@icm.edu.pl Phone: +48-22-554-08-11 Fax: +48-22-554-08-01 Category: Predictive Methods Poster Title: Prediction of Local Structure of Proteins using Segments Profile Similarity. Poster Authors and organization: Dariusz Plewczynski¹, Adam Godzik², Lukasz Jaroszewski, Yuzhen Ye
¹darman@icm.edu.pl, ICM Warsaw University; ², The Burnham Institute Abstract: A novel method for prediction of local structure of proteins using sequence information is presented. Structures of local fragments of proteins are described in terms of phi/psi backbone dihedral angles. We predict local structure of proteins using this library of structure-sequence motifs by profile-profile matching algorithm. Our prediction algorithm is available as an http server at http://ffas.ljcrf.edu/Servers/frag.html. File: darmanATicm.edu.pl_5 ************************************************* Sun Mar 9 11:03:58 2003 Number: 6 Name: nawaz, zafar Affiliation: University of Karachi Address: university Road City: karachi State/Provice: sind Postal/Zip Code: 4400 Country: pakistan Email: zafarn1@hotmail.com Phone: 416-813-6612 Fax: 416-813-7732 Category: Systems Biology Poster Title: Regulation of Cytokines and G-protein gene expression by Cholera toxin Poster Authors and organization: zafar nawaz¹, Bukhtiar H Shah²
¹zafarn1@hotmail.com, University of karachi; ², Aga khan University Abstract: The molecular mechanism of Cholera toxin (CTX) action on Gas and Gaq, inflammatory cytokines and Nitric oxide gene regulation studied in mice intestinal epithelial cells File: zafarn1AThotmail.com_6 ************************************************* Sun Mar 9 20:11:30 2003 UPDATE ----- Number: 3 Name: Sheng, Qizheng Affiliation: Katholieke Universiteit Leuven, Department of Electrical Engineering Address: Kasteelpark Arenberg 10 City: Leuven-Heverlee State/Provice: Vlaams-Brabant Postal/Zip Code: 3000 Country: Belgium Email: qizheng.sheng@esat.kuleuven.ac.be Phone: +32-16-321939 Fax: +32-16-321970 Category: Data Mining Poster Title: Biclustering Microarray Data by Gibbs Sampling Poster Authors and organization: Qizheng Sheng¹, Yves Moreau², Bart De Moor
¹qizheng.sheng@esat.kuleuven.ac.be, Katholieke Universiteit Leuven, Department of Electrical Engineering; ²y ves.moreau@esat.kuleuven.ac.be, Katholieke Universiteit Leuven, Department of Electrical Engineering Abstract: We have adapted Gibbs sampling strategy, which has become a method of choice for the discovery of motifs in DNA and protein sequences, to the biclustering of discretized microarray data. In contrast with standard clustering, biclustering reveals similar expressional behavior of the genes over a subset of conditions in an microarray data set. File: qizheng.shengATesat.kuleuven.ac.be_3 ************************************************* Mon Mar 10 05:25:28 2003 Number: 7 Name: Gong, Yunchen Affiliation: McGill University Address: 21111 Lakeshore Rd. City: Ste-Anne-de-Bellevue State/Provice: Quebec Postal/Zip Code: H9X3V9 Country: Canada Email: ygong@po-box.mcgill.ca Phone: 1-514-398-7539 Fax: Category: Systems Biology Poster Title: Shc-dependent pathway is redundant but dominant in MAPK cascade activation by EGF receptors: a computational result Poster Authors and organization: Yunchen Gong¹, Xin Zhao²
¹ygong@po-box.mcgill.ca, McGill University; ²zhao@macdonald.mcgill.ca, McGill University Abstract: MAPK is activated by EGFR via Shc-dependent and -independent pathways. Exploring of an mathematical model revealed redundancy and dominance of Shc-dependent pathway. Its dominance results from the majority consumption of the common precursor. Results imply that organisms may use longer pathway rather than shorter alternative pathway for signal transduction. File: ygongATpo-box.mcgill.ca_7 ************************************************* Mon Mar 10 16:07:47 2003 UPDATE ----- Number: 3 Name: Sheng, Qizheng Affiliation: Katholieke Universiteit Leuven, Department of Electrical Engineering Address: Kasteelpark Arenberg 10 City: Leuven-Heverlee State/Provice: Vlaams-Brabant Postal/Zip Code: 3000 Country: Belgium Email: qizheng.sheng@esat.kuleuven.ac.be Phone: +32-16-321939 Fax: +32-16-321970 Category: Data Mining Poster Title: Biclustering Microarray Data by Gibbs Sampling Poster Authors and organization: Qizheng Sheng¹, Yves Moreau², Bart De Moor
¹qizheng.sheng@esat.kuleuven.ac.be, Katholieke Universiteit Leuven, Department of Electrical Engineering; ²yves.moreau@esat.kuleuven.ac.be, Katholieke Universiteit Leuven, Department of Electrical Engineering Abstract: We have adapted Gibbs sampling strategy, which has become a method of choice for the discovery of motifs in DNA and protein sequences, to the biclustering of discretized microarray data. In contrast with standard clustering, biclustering reveals similar expressional behavior of the genes over a subset of conditions in an microarray data set. File: qizheng.shengATesat.kuleuven.ac.be_3 ************************************************* Mon Mar 10 16:11:07 2003 UPDATE ----- Number: 5 Name: Plewczynski, Dariusz M Affiliation: ICM UW, Interdisciplinary Center of Mathematical and Computational Modelling, Warsaw University Address: Pawinskiego 5a City: Warsaw State/Provice: CA Postal/Zip Code: 02-106 Country: POLAND Email: darman@icm.edu.pl Phone: +48-22-554-08-11 Fax: +48-22-554-08-01 Category: Predictive Methods Poster Title: Prediction of Local Structure of Proteins using Segments Profile Similarity. Poster Authors and organization: Dariusz Plewczynski¹, Adam Godzik², Lukasz Jaroszewski, Yuzhen Ye
¹darman@icm.edu.pl, ICM Warsaw University; ²The Burnham Institute Abstract: A novel method for prediction of local structure of proteins using sequence information is presented. Structures of local fragments of proteins are described in terms of phi/psi backbone dihedral angles. We predict local structure of proteins using this library of structure-sequence motifs by profile-profile matching algorithm. Our prediction algorithm is available as an http server at http://ffas.ljcrf.edu/Servers/frag.html. File: darmanATicm.edu.pl_5 ************************************************* Mon Mar 10 16:15:37 2003 UPDATE ----- Number: 7 Name: Gong, Yunchen Affiliation: McGill University Address: 21111 Lakeshore Rd. City: Ste-Anne-de-Bellevue State/Provice: Quebec Postal/Zip Code: H9X3V9 Country: Canada Email: ygong@po-box.mcgill.ca Phone: 1-514-398-7539 Fax: Category: Systems Biology Poster Title: Shc-dependent pathway is redundant but dominant in MAPK cascade activation by EGF receptors: a computational result Poster Authors and organization: Yunchen Gong¹, Xin Zhao²
¹ygong@po-box.mcgill.ca, McGill University; ²zhao@macdonald.mcgill.ca, McGill University Abstract: MAPK is activated by EGFR via Shc-dependent and Shc-independent pathways. Exploration of a mathematical model revealed redundancy and dominance of Shc-dependent pathway. Its dominance results from the majority consumption of the common precursor. Results imply that organisms may use the longer pathway rather than the shorter alternative pathway for signal transduction. File: ygongATpo-box.mcgill.ca_7 ************************************************* Tue Mar 11 00:28:06 2003 Number: 8 Name: Rensing, Stefan A Affiliation: University of Freiburg, Plant Biotechnology Address: Sonnenstr. 5 City: Freiburg State/Provice: D Postal/Zip Code: 79104 Country: Germany Email: stefan.rensing@biologie.uni-freiburg.de Phone: +49 761 203-6974 Fax: +49 761 203-6990 Category: Genome Annotation Poster Title: In silico prediction of UTR repeats using clustered EST data Poster Authors and organization: Stefan Rensing¹, Daniel Lang², Ralf Reski
¹stefan.rensing@biologie.uni-freiburg.de, University of Freiburg, Plant Biotechnology; ²daniel.lang@biologie.uni-freiburg.de, University of Freiburg, Plant Biotechnology Abstract: Three approaches for the in silico prediction of UTR repeats have been used on a test data set, resulting in the detection of sequence stretches in ~5% of the input sequences during clustering and reduction in size of large clusters. Seven of those putative repeats have been proven to be repetitive in vivo by Southern blot analysis.
File: stefan.rensingATbiologie.uni-freiburg.de_8 ************************************************* Tue Mar 11 16:57:24 2003 Number: 9 Name: Cheung, Leo Wang-Kit Affiliation: Cancer Research Center of Hawaii, University of Hawaii Address: 1236 Lauhala City: Honolulu State/Provice: Hawaii Postal/Zip Code: 96813 Country: U.S.A. Email: lcheung@crch.hawaii.edu Phone: 808-586-5859 Fax: 808-586-2982 Category: Data Mining Poster Title: Hidden Multivariate Markov Models for Pattern Recognition in Genomic DNA Sequences Poster Authors and organization: Leo Wang-Kit Cheung¹
¹lcheung@crch.hawaii.edu, Cancer Research Center of Hawaii, University of Hawaii Abstract: Hidden Multivariate Markov Models (HM³s) are introduced for modeling multi-dimensional genomic DNA data. A bivariate version of HM³s is developed for studying the joint behavior of the C+G richness pattern and the bendability pattern of DNA. Applications of the bivariate HM³s for recognition/prediction of eukaryotic promoter regions are illustrated. File: lcheungATcrch.hawaii.edu_9 ************************************************* Wed Mar 12 10:03:27 2003 Number: 10 Name: Krivan, William Affiliation: ZymoGenetics, Inc. Address: 1201 Eastlake Ave E City: Seattle State/Provice: WA Postal/Zip Code: 98102 Country: USA Email: krivan@zgi.com Phone: +1 206 442 6663 Fax: +1 206 442 6608 Category: Predictive Methods Poster Title: Studies of the transcriptional regulation of the genes coding for the novel IL28A,B and IL29 protein family: Illustration of an in silico approach applicable on a genomic scale Poster Authors and organization: William Krivan¹, Brian Fox², Emily Cooper, Teresa Gilbert, Frank Grant, Betty
Haldeman, Katherine Henderson, Wayne Kindsvogel, Kevin Klucher, Gary
McKnight, Patrick O'Hara, Scott Presnell, Monica Tackett, David Taft, and
Paul Sheppard
¹krivan@zgi.com, ZymoGenetics, Inc.; ²bfox@zgi.com, ZymoGenetics, Inc. Abstract: We use the novel IL28A,B and IL29 protein family to illustrate an approach to the computational identification and characterization of putative transcriptional regulatory regions. Our technique consists of a combination of phylogenetic footprinting and detection of statistically significant clusters of binding sites and can be applied on a genomic scale. File: krivanATzgi.com_10 ************************************************* Wed Mar 12 13:16:39 2003 UPDATE ----- Number: 3 Name: Sheng, Qizheng Affiliation: Katholieke Universiteit Leuven, Department of Electrical Engineering Address: Kasteelpark Arenberg 10 City: Leuven-Heverlee State/Provice: Vlaams-Brabant Postal/Zip Code: 3000 Country: Belgium Email: qizheng.sheng@esat.kuleuven.ac.be Phone: +32-16-321939 Fax: +32-16-321970 Category: Data Mining Poster Title: Biclustering Microarray Data by Gibbs Sampling Poster Authors and organization: Qizheng Sheng¹, Yves Moreau², Bart De Moor
¹qizheng.sheng@esat.kuleuven.ac.be, Katholieke Universiteit Leuven, Department of Electrical Engineering; ²y ves.moreau@esat.kuleuven.ac.be, Katholieke Universiteit Leuven, Department of Electrical Engineering Abstract: We have adapted Gibbs sampling strategy, which has become a method of choice for the discovery of motifs in DNA and protein sequences, to the biclustering of discretized microarray data. In contrast with standard clustering, biclustering reveals similar expressional behavior of the genes over a subset of conditions in an microarray data set. File: qizheng.shengATesat.kuleuven.ac.be_3 ************************************************* Wed Mar 12 13:19:59 2003 UPDATE ----- Number: 3 Name: Sheng, Qizheng Affiliation: Katholieke Universiteit Leuven, Department of Electrical Engineering Address: Kasteelpark Arenberg 10 City: Leuven-Heverlee State/Provice: Vlaams-Brabant Postal/Zip Code: 3000 Country: Belgium Email: qizheng.sheng@esat.kuleuven.ac.be Phone: +32-16-321939 Fax: +32-16-321970 Category: Data Mining Poster Title: Biclustering Microarray Data by Gibbs Sampling Poster Authors and organization: Qizheng Sheng¹, Yves Moreau², Bart De Moor
¹qizheng.sheng@esat.kuleuven.ac.be, Katholieke Universiteit Leuven, Department of Electrical Engineering; ²yves.moreau@esat.kuleuven.ac.be, Katholieke Universiteit Leuven, Department of Electrical Engineering Abstract: We have adapted Gibbs sampling strategy, which has become a method of choice for the discovery of motifs in DNA and protein sequences, to the biclustering of discretized microarray data. In contrast with standard clustering, biclustering reveals similar expressional behavior of the genes over a subset of conditions in an microarray data set. File: qizheng.shengATesat.kuleuven.ac.be_3 ************************************************* Wed Mar 12 13:22:46 2003 UPDATE ----- Number: 3 Name: Sheng, Qizheng Affiliation: Katholieke Universiteit Leuven, Department of Electrical Engineering Address: Kasteelpark Arenberg 10 City: Leuven-Heverlee State/Provice: Vlaams-Brabant Postal/Zip Code: 3000 Country: Belgium Email: qizheng.sheng@esat.kuleuven.ac.be Phone: +32-16-321939 Fax: +32-16-321970 Category: Data Mining Poster Title: Biclustering Microarray Data by Gibbs Sampling Poster Authors and organization: Qizheng Sheng¹, Yves Moreau², Bart De Moor
¹qizheng.sheng@esat.kuleuven.ac.be, Katholieke Universiteit Leuven, Department of Electrical Engineering; ²yves.moreau@esat.kuleuven.ac.be, Katholieke Universiteit Leuven, Department of Electrical Engineering Abstract: We have adapted Gibbs sampling strategy, which has become a method of choice for the discovery of motifs in DNA and protein sequences, to the biclustering of discretized microarray data. In contrast with standard clustering, biclustering reveals similar expressional behavior of the genes over a subset of conditions in an microarray data set. File: qizheng.shengATesat.kuleuven.ac.be_3 ************************************************* Wed Mar 12 13:24:39 2003 UPDATE ----- Number: 3 Name: Sheng, Qizheng Affiliation: Katholieke Universiteit Leuven, Department of Electrical Engineering Address: Kasteelpark Arenberg 10 City: Leuven-Heverlee State/Provice: Vlaams-Brabant Postal/Zip Code: 3000 Country: Belgium Email: qizheng.sheng@esat.kuleuven.ac.be Phone: +32-16-321939 Fax: +32-16-321970 Category: Data Mining Poster Title: Biclustering Microarray Data by Gibbs Sampling Poster Authors and organization: Qizheng Sheng¹, Yves Moreau², Bart De Moor
¹qizheng.sheng@esat.kuleuven.ac.be, Katholieke Universiteit Leuven, Department of Electrical Engineering; ²yves.moreau@esat.kuleuven.ac.be, Katholieke Universiteit Leuven, Department of Electrical Engineering Abstract: We have adapted Gibbs sampling strategy, which has become a method of choice for the discovery of motifs in DNA and protein sequences, to the biclustering of discretized microarray data. In contrast with standard clustering, biclustering reveals similar expressional behavior of the genes over a subset of conditions in an microarray data set. File: qizheng.shengATesat.kuleuven.ac.be_3 ************************************************* Wed Mar 12 14:55:14 2003 UPDATE ----- Number: 3 Name: Sheng, Qizheng Affiliation: Katholieke Universiteit Leuven, Department of Electrical Engineering Address: Kasteelpark Arenberg 10 City: Leuven-Heverlee State/Provice: Vlaams-Brabant Postal/Zip Code: 3000 Country: Belgium Email: qizheng.sheng@esat.kuleuven.ac.be Phone: +32-16-321939 Fax: +32-16-321970 Category: Data Mining Poster Title: Biclustering Microarray Data by Gibbs Sampling Poster Authors and organization: Qizheng Sheng¹, Yves Moreau², Bart De Moor
¹qizheng.sheng@esat.kuleuven.ac.be, Katholieke Universiteit Leuven, Department of Electrical Engineering; ²yves.moreau@esat.kuleuven.ac.be, Katholieke Universiteit Leuven, Department of Electrical Engineering Abstract: We have adapted Gibbs sampling strategy, which has become a method of choice for the discovery of motifs in DNA and protein sequences, to the biclustering of discretized microarray data. In contrast with standard clustering, biclustering reveals similar expressional behavior of the genes over a subset of conditions in an microarray data set. File: qizheng.shengATesat.kuleuven.ac.be_3 ************************************************* Wed Mar 12 14:59:16 2003 UPDATE ----- Number: 3 Name: Sheng, Qizheng Affiliation: Katholieke Universiteit Leuven, Department of Electrical Engineering Address: Kasteelpark Arenberg 10 City: Leuven-Heverlee State/Provice: Vlaams-Brabant Postal/Zip Code: 3000 Country: Belgium Email: qizheng.sheng@esat.kuleuven.ac.be Phone: +32-16-321939 Fax: +32-16-321970 Category: Data Mining Poster Title: Biclustering Microarray Data by Gibbs Sampling Poster Authors and organization: Qizheng Sheng¹, Yves Moreau², Bart De Moor
¹qizheng.sheng@esat.kuleuven.ac.be, Katholieke Universiteit Leuven, Department of Electrical Engineering; ²yves.moreau@esat.kuleuven.ac.be, Katholieke Universiteit Leuven, Department of Electrical Engineering Abstract: We have adapted Gibbs sampling strategy, which has become a method of choice for the discovery of motifs in DNA and protein sequences, to the biclustering of discretized microarray data. In contrast with standard clustering, biclustering reveals similar expressional behavior of the genes over a subset of conditions in an microarray data set. File: qizheng.shengATesat.kuleuven.ac.be_3 ************************************************* Fri Mar 14 12:38:38 2003 Number: 11 Name: Cutler, Gene Affiliation: Tularik Inc Address: 2 Corporate Dr City: South San Francisco State/Provice: CA Postal/Zip Code: 94080 Country: USA Email: cutler@tularik.com Phone: 650 825-7489 Fax: 650 825-7318 Category: Microarrays Poster Title: Binned-Intensity Normalization Algorithm for Single-Dye Microarrays Poster Authors and organization: Gene Cutler¹
¹cutler@tularik.com, Tularik Inc Abstract: To generate meaningful mRNA expression ratios, data from separate arrays or probes must be normalized. Median normalization performs adequately only when differences between data sets are linear. To cope with non-linearities and noisy data, I have implemented a binned-intensity normalization algorithm which outperforms simple median normalization. File: cutlerATtularik.com_11 ************************************************* Sun Mar 16 20:31:30 2003 UPDATE ----- Number: 7 Name: Gong, Yunchen Affiliation: McGill University Address: 21111 Lakeshore Rd. City: Ste-Anne-de-Bellevue State/Provice: Quebec Postal/Zip Code: H9X3V9 Country: Canada Email: ygong@po-box.mcgill.ca Phone: 1-514-398-7539 Fax: Category: Systems Biology Poster Title: Shc-dependent pathway is redundant but dominant in MAPK cascade activation by EGF receptors: a computational result Poster Authors and organization: Yunchen Gong¹, Xin Zhao²
¹ygong@po-box.mcgill.ca, McGill University; ²zhao@macdonald.mcgill.ca, McGill University Abstract: MAPK is activated by EGFR via Shc-dependent and -independent pathways. Exploring a mathematical model revealed redundancy and dominance of the Shc-dependent pathway. Its dominance results from the majority consumption of the common precursor. Results imply that organisms may use the longer pathway rather than the shorter alternative pathway for signal transduction. File: ygongATpo-box.mcgill.ca_7 ************************************************* Tue Mar 18 00:04:17 2003 Number: 12 Name: Tan, Paul J Affiliation: Institute for Infocomm Research Address: 21 Heng Mui Keng Terrace City: Singapore State/Provice: Singapore Postal/Zip Code: 119613 Country: Singapore Email: tjtan@i2r.a-star.edu.sg Phone: 65-68748233 Fax: 65-67748056 Category: Predictive Methods Poster Title: Prediction of Protein Function from Primary Structure Poster Authors and organization: Paul J. Tan¹, Vladimir Brusic², Asif M. Khan, Judice L.Y. Koh, Seng-Hong Seah
¹tjtan@i2r.a-star.edu.sg, I2R; ²vladimir@i2r.a-star.edu.sg, I2R Abstract:

An approach was developed for predicting the presence of a specific functional effect for active peptides. It involved multiple steps: a) collection of protein sequences from multiple sources, b) data cleaning and functional annotation, c) definition of basic structure-function unit groups, and d) prediction of protein function by an intelligent agent.

File: tjtanATi2r.a-star.edu.sg_12 ************************************************* Tue Mar 18 02:54:57 2003 Number: 13 Name: van Baren, Marijke J Affiliation: Erasmus University Rotterdam Address: Dr. Molewaterplein 50 City: Rotterdam State/Provice: na Postal/Zip Code: 3015 GE Country: Netherlands Email: m.vanbaren@erasmusmc.nl Phone: 010-4088137 Fax: na Category: Data Mining Poster Title: The PCR Suite: batch primer design Poster Authors and organization: MJ van Baren ¹, P Heutink², na
¹m.vanbaren@erasmusmc.nl, Erasmus MC Rotterdam; ²p.heutink@erasmusmc.nl, Erasmus MC Rotterdam Abstract: The PCRSuite is an extension of the primer design program Primer3. It allows the design of primersets encompassing SNPs, all exons of a single gene, all open reading frames in a list of cDNAs or the creation of overlapping PCR products. The PCR Suite is available at www.eur.nl/fgg/kgen/primer File: m.vanbarenATerasmusmc.nl_13 ************************************************* Wed Mar 26 14:15:47 2003 Number: 14 Name: Xu, Qiang Affiliation: Molecular Biology Institute, Department of Chemistry and Biochemistry, UCLA Address: 611 Charles E. Young Dr. East, Boyer Hall, RM609 City: Los Angeles State/Provice: California Postal/Zip Code: 90095 Country: USA Email: qxu@chem.ucla.edu Phone: 1-310-794-4026 Fax: 1-310-267-0248 Category: Functional Genomics Poster Title: Cancer-Specific Alternative Splicing is prevalent in the Human Genome Poster Authors and organization: Qiang Xu¹, Christopher Lee²
¹qxu@chem.ucla.edu, Molecular Biology Institute, Department of Chemistry and Biochemistry, UCLA; ²leec@mbi.ucla.edu, Molecular Biology Institute, Department of Chemistry and Biochemistry, UCLA Abstract: We found strong evidence (p<0.01) of cancer-specific splice variants in 316 human genes through a genome-wide analysis of human expressed sequences. The majority of these genes have functions associated with cancer. For a large number of cancer-associated genes, it appears the normal form instead of the cancer form that is previously uncharacterized. File: qxuATchem.ucla.edu_14 ************************************************* Wed Mar 26 23:14:22 2003 Number: 15 Name: Jia, Li Affiliation: University of California Address: Computer Science Department City: Riverside State/Provice: CA Postal/Zip Code: 92521 Country: USA Email: lijia@cs.ucr.edu Phone: 909-787-2882 Fax: 909-787-4643 Category: Phylogeny and Evolution Poster Title: The Evaluation of Different Approaches to Infer Positive Selection Sites Poster Authors and organization: Li Jia¹, Tao Jiang², Michael Clegg
¹lijia@cs.ucr.edu, University of California; ²jiang@cs.ucr.edu, University of California Abstract: It is important to infer positive selection sites associated with a given gene family. Different approaches have been proposed to detect positive selection at single amino acid sites. The performance of these approaches was evaluated so that researchers should be able to apply an appropriate method to their research when certain circumstances meet. File: lijiaATcs.ucr.edu_15 ************************************************* Thu Mar 27 01:25:37 2003 Number: 16 Name: Sharma, Banshi Affiliation: Central Veterinary Laboratory Address: Tripureshwor City: Kathmandu State/Provice: Bagmati Postal/Zip Code: P. o. box 1640 Country: Nepal Email: banshisharma@yahoo.com Phone: 9774476527 Fax: 9774261938 I plan to use my laptop computer as part of my poster Category: Systems Biology Poster Title: Molecular characterization of NKR-p1 receptor in peripheral blood of pig Poster Authors and organization: Banshi sharma¹
¹sharmabanshi@hotmail.com, CVL Abstract: The aim of the work is to characterize the NKR-P1 receptor in the peripheral blood of pig. Total RNA was extracted from peripheral blood of pig as well as human. RT-PCR gives 573 bp PCR product in human. Similarly it gives 661 bp PCR product in pig. The PCR product is cloned in pPCR-script TM Amp SK (+) cloning vector. File: banshisharmaATyahoo.com_16 ************************************************* Thu Mar 27 05:05:03 2003 Number: 17 Name: Masso, Majid Affiliation: George Mason University Address: 8068 Stonewall Brigade Ct. 201 City: Manassas State/Provice: Virginia Postal/Zip Code: 20109 Country: USA Email: mmasso@gmu.edu Phone: 703-257-5756 Fax: Category: Structural Biology Poster Title: Analyzing Protein Structure-Function Correlations Using Statistical Geometry Poster Authors and organization: Majid Masso¹, Iosif Vaisman²
¹mmasso@gmu.edu, George Mason University; ²ivaisman@gmu.edu, George Mason University Abstract: An approach based on computational geometry is used to elucidate structural changes in an HIV-1 protease monomer caused by dimerization and inhibitor binding. A comprehensive mutational analysis of HIV-1 protease is also performed using this method and reveals a strong structure-function correlation. File: mmassoATgmu.edu_17 ************************************************* Sat Mar 29 09:41:21 2003 Number: 18 Name: Ratushny, Alexander V. Affiliation: Institute of Cytology and Genetics, SBRAS Address: 10 Lavrentiev Ave. City: Novosibirsk State/Provice: Novosibirsk Postal/Zip Code: 630090 Country: Russia Email: ratushny@bionet.nsc.ru Phone: 3832-333-119 Fax: 3832-331-278 Category: Systems Biology Poster Title: Theoretical analysis of mutations and evolution of gene networks Poster Authors and organization: Alexander V. Ratushny¹, Vitaly A. Likhoshvai², Yuri G. Matushkin, Nikolay A. Kolchanov
¹ratushny@bionet.nsc.ru, Institute of Cytology and Genetics, SBRAS; ²likho@bionet.nsc.ru, Institute of Cytology and Genetics, SBRAS Abstract:

The mathematical model simulating cholesterol biosynthesis in a cell and its exchange with blood plasma cholesterol was used for computer analysis of a mutational portrait and evolution of this gene network. The graphic interface of the gene network and its computer dynamic model can be accessed at http://wwwmgs.bionet.nsc.ru/mgs/gnw/gn_model/.

File: ratushnyATbionet.nsc.ru_18 ************************************************* Sun Mar 30 15:35:25 2003 UPDATE ----- Number: 15 Name: Jia, Li Affiliation: University of California Address: Computer Science Department City: Riverside State/Provice: CA Postal/Zip Code: 92521 Country: USA Email: lijia@cs.ucr.edu Phone: 909-787-2882 Fax: 909-787-4643 Category: Phylogeny and Evolution Poster Title: The Evaluation of Different Approaches to Infer Positive Selection Sites Poster Authors and organization: Li Jia¹, Tao Jiang², Michael Clegg
¹lijia@cs.ucr.edu, University of California; ²jiang@cs.ucr.edu, University of California Abstract: It is important to infer positive selection sites associated with a given gene family. Different approaches have been proposed to detect positive selection at single amino acid sites. The performance of these approaches was evaluated so that researchers should be able to apply an appropriate method to their research when certain circumstances are met. File: lijiaATcs.ucr.edu_15 ************************************************* Sun Mar 30 15:39:29 2003 UPDATE ----- Number: 13 Name: van Baren, Marijke J Affiliation: Erasmus University Rotterdam Address: Dr. Molewaterplein 50 City: Rotterdam State/Provice: Postal/Zip Code: 3015 GE Country: Netherlands Email: m.vanbaren@erasmusmc.nl Phone: 010-4088137 Fax: Category: Data Mining Poster Title: The PCR Suite: batch primer design Poster Authors and organization: MJ van Baren ¹, P Heutink²,
¹m.vanbaren@erasmusmc.nl, Erasmus MC Rotterdam; ²p.heutink@erasmusmc.nl, Erasmus MC Rotterdam Abstract: The PCRSuite is an extension of the primer design program Primer3. It allows the design of primersets encompassing SNPs, all exons of a single gene, all open reading frames in a list of cDNAs or the creation of overlapping PCR products. The PCR Suite is available at www.eur.nl/fgg/kgen/primer File: m.vanbarenATerasmusmc.nl_13 ************************************************* Sun Mar 30 15:40:56 2003 UPDATE ----- Number: 13 Name: van Baren, Marijke J Affiliation: Erasmus University Rotterdam Address: Dr. Molewaterplein 50 City: Rotterdam State/Provice: Postal/Zip Code: 3015 GE Country: Netherlands Email: m.vanbaren@erasmusmc.nl Phone: 010-4088137 Fax: Category: Data Mining Poster Title: The PCR Suite: batch primer design Poster Authors and organization: MJ van Baren ¹, P Heutink²
¹m.vanbaren@erasmusmc.nl, Erasmus MC Rotterdam; ²p.heutink@erasmusmc.nl, Erasmus MC Rotterdam Abstract: The PCRSuite is an extension of the primer design program Primer3. It allows the design of primersets encompassing SNPs, all exons of a single gene, all open reading frames in a list of cDNAs or the creation of overlapping PCR products. The PCR Suite is available at www.eur.nl/fgg/kgen/primer File: m.vanbarenATerasmusmc.nl_13 ************************************************* Sun Mar 30 15:44:08 2003 UPDATE ----- Number: 17 Name: Masso, Majid Affiliation: George Mason University Address: 8068 Stonewall Brigade Ct. 201 City: Manassas State/Provice: Virginia Postal/Zip Code: 20109 Country: USA Email: mmasso@gmu.edu Phone: 703-257-5756 Fax: Category: Structural Biology Poster Title: Analyzing Protein Structure-Function Correlations Using Statistical Geometry Poster Authors and organization: Majid Masso¹, Iosif Vaisman²
¹mmasso@gmu.edu, George Mason University; ²ivaisman@gmu.edu, George Mason University Abstract: An approach based on computational geometry is used to elucidate structural changes in a HIV-1 protease monomer caused by dimerization and inhibitor binding. A comprehensive mutational analysis of HIV-1 protease is also performed using this method and reveals a strong structure-function correlation. File: mmassoATgmu.edu_17 ************************************************* Mon Mar 31 23:39:45 2003 Number: 18 Name: Linding, Rune Affiliation: EMBL - Biocomputing Unit Address: Meyerhofstr 1 City: Heidelberg State/Provice: Baden-Wuerttemberg Postal/Zip Code: D-69117 Country: Germany Email: linding@embl.de Phone: +49 6221 387 451 Fax: +49 6221 387 417 I plan to use my laptop computer as part of my poster Category: Structural Biology Poster Title: http://globplot.embl.de - Exploring protein sequences for globularity and disorder Poster Authors and organization: Rune Linding¹, Rob Russell², Victor Neduva, Toby Gibson
¹linding@embl.de, EMBL; ²russell@embl.de, EMBL Abstract: We present here a new tool for discovery of such unstructured, or disordered regions within proteins. GlobPlot (http: //globplot.embl.de) is a web service that allows the user to plot the tendency within the query protein for order/globularity and disorder. File: lindingATembl.de_18 ************************************************* Tue Apr 1 09:47:39 2003 Number: 19 Name: Lombard, Vincent J.B. Affiliation: EMBL - EBI Address: Wellcome Trust Genome Campus City: Hinxton State/Provice: Cambridge Postal/Zip Code: CB10 1SD Country: United Kingdom Email: lombard@ebi.ac.uk Phone: 01223 494674 Fax: 01223 494468 Category: Databases Poster Title: Submission tools for EMBL-Bank, EMBL-Align and SWISS-PROT databases Poster Authors and organization: Vincent Lombard¹, Mary ann Tuli, Robert Vaughan, Minna Lehvaslaiho, Weimin Zhu and Rolf Apweiler
¹lombard@ebi.ac.uk, EBI Abstract:

Webin, Webin-Align and SPIN are the web-based tools for submitting nucleotide sequences, nucleotide sequence alignments and protein sequences respectively to EMBL-Bank, EMBL-Align, or SWISS-PROT databases. These tools guide you through a sequence of WWW forms allowing interactive submission. All the information required to create a database entry is collected during this process. All submission tools are available at http://www.ebi.ac.uk/Submissions/index.html

File: lombardATebi.ac.uk_19 ************************************************* Tue Apr 1 11:43:25 2003 Number: 19 Name: Bhattacharya, Soumyaroop Affiliation: University of Pittsburgh Address: 5230 Center Avenue, Cancer Pavilion 3rd Flr City: Pittsburgh State/Provice: PA Postal/Zip Code: 15232 Country: USA Email: bhattacharyas@msx.upmc.edu Phone: 4126237893 Fax: 4126475380 I plan to use my laptop computer as part of my poster Category: Microarrays Poster Title: Overcoming Confounded Controls in the Analysis of Gene Expression Data from Microarray Experiments Poster Authors and organization: Soumyaroop Bhattacharya¹, Dang Duc Long², James Lyons-Weiler
¹bhattacharyas@msx.upmc.edu, Benedum Oncology Informatics Center, University of Pittsburgh; ²Dang_Long@student.uml.edu, Center for Bioinformatics and Computational Biology, University of Massachusetts Lowell Abstract: The robust clustering of some normal samples within tumor groups and robust clustering of other normal samples in a separate, 'normal' group indicates the confounding of control samples. Our approach uses the maximum difference subset algorithm (MDSS) and bootstrap validation, which evaluates the difference in mean expression between two groups. File: bhattacharyasATmsx.upmc.edu_19 ************************************************* Tue Apr 1 15:26:32 2003 Number: 20 Name: Sandelin, Albin Affiliation: Center for Genomics and Bioinformatics, Karolinska Institutet Address: Berzelius vaeg 35 City: Solna State/Provice: Stockholm Postal/Zip Code: 17177 Country: Sweden Email: albin.sandelin@cgb.ki.se Phone: int + 8 728 61 32 Fax: Category: Predictive Methods Poster Title: HMM Frameworks for Nuclear Receptor Binding Sites Poster Authors and organization: Albin Sandelin¹, Wyeth Wasserman²
¹albin.sandelin@cgb.ki.se, Karolinska Institutet; ²wyeth@cmmt.ubc.ca, Univeristy of British Colombia Abstract:

Nuclear Receptors (NR) control diverse programs of gene expression. These transcription factors bind in homo- and heterodimeric forms to complex target sequences. Due to variable spacing and orientation of half-sites, standard profile models are inadequate. We construct an HMM framework for the prediction and classification of NR binding sites. File: albin.sandelinATcgb.ki.se_20 ************************************************* Wed Apr 2 00:35:28 2003 Number: 21 Name: Linding, Rune Affiliation: EMBL - Biocomputing Unit Address: Meyerhofstr 1 City: Heidelberg State/Provice: Baden-Wuerttemberg Postal/Zip Code: D-69117 Country: Germany Email: linding@embl.de Phone: +49 6221 387 451 Fax: +49 6221 387 417 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: http://elm.eu.org - ELM Resource for prediction of functional sites in proteins Poster Authors and organization: Rune Linding¹, ELM Consortium², ELM Consortium
¹linding@embl.de, EMBL; ²info@elm.eu.org, ELM Consortium Abstract: ELM is a resource for predicting functional sites in eukarytic proteins. Putative functional sites are identified by conventional methods, such as patterns (regular expressions) or HMM models. To improve the predictive power, context-based rules and logical filters will be developed and applied to reduce the amount of false positives. File: lindingATembl.de_21 ************************************************* Wed Apr 2 07:28:09 2003 Number: 22 Name: Williams, Allyson L Affiliation: EMBL - EBI Address: Wellcome Trust Genome Campus City: Hinxton State/Provice: Cambridgeshire Postal/Zip Code: CB10 1SD Country: UK Email: allyson@ebi.ac.uk Phone: +44 1223 494676 Fax: +44 1223 494468 Category: Databases Poster Title: UniProt: Universal Protein Databases for Protein Sequences and Function Poster Authors and organization: Allyson Williams¹, Maria Jesus Martin², Claire O'Donovan, Daniel Barrell, Alexander Fedotov, Rolf Apweiler
¹allyson@ebi.ac.uk, EMBL - EBI; ²martin@ebi.ac.uk, EMBL - EBI Abstract: The UniProt Consortium (European Bioinformatics Institute, Swiss Institute of Bioinformatics, and the Protein Information Resource) was created to merge Swiss-Prot, TrEMBL and PIR database activities into UniProt, a comprehensive resource of protein sequences and function. UniProt has three layers: protein sequence archive, protein knowledgebase, and non-redundant reference (NREF) databases. File: allysonATebi.ac.uk_22 ************************************************* Wed Apr 2 07:59:45 2003 Number: 22 Name: Varley, Andrew J Affiliation: University of Cambridge Address: Genetics Dept, Downing Street City: Cambridge State/Provice: Cambs Postal/Zip Code: CB2 3EH Country: UK Email: ajv12@cam.ac.uk Phone: +44 1223 333965 Fax: +44 1223 333992 Category: Databases Poster Title: FlyMine: An integrated database for Drosophila and Anopheles genomics Poster Authors and organization: Gos Micklem¹, Andrew Varley², Richard Smith, Rachel Lyne
¹gos@gen.cam.ac.uk, University of Cambridge; ²ajv12@cam.ac.uk, University of Cambridge Abstract: FlyMine is a project to build an integrated database of genomic, expression and protein data for Drosophila and Anopheles. Data are stored massively redundantly and arbitrary queries are allowed using a web interface or Java API. Queries are re-written in real time to make use of redundant tables. File: ajv12ATcam.ac.uk_22 ************************************************* Wed Apr 2 11:04:52 2003 Number: 23 Name: Betel, Doron Affiliation: Samuel Lunenfeld Research Institute, Mt. Sinai Hospital, Department of Biochemistry, University of Toronto Address: room 1060, 600 University Ave. City: Toronto State/Provice: Ontario Postal/Zip Code: M5G-1X5 Country: Canada Email: doron.betel@utoronto.ca Phone: 416-586-4800 ext. 2863 Fax: 416-586-8869 Category: Data Mining Poster Title: Domain-Domain correlations in Yeast protein complexes Poster Authors and organization: Doron Betel¹, Christopher W.V. Hogue²
¹doron.betel@utoronto.ca, Samuel Lunenfeld Research Institute, Mt. Sinai Hospital and Department of Biochemistry, University of Toronto; ²hogue@mshri.on.ca, Samuel Lunenfeld Research Institute, Mt. Sinai Hospital and Department of Biochemistry, University of Toronto Abstract: We introduce a new method for detecting statistically meaningful functional associations between domains from molecular complexes. Two random control sets were used to compute P-values for domain co-occurrences in complexes. Results from four different datasets show that many of the correlations are between domains of similar or associated function. File: doron.betelATutoronto.ca_23 ************************************************* Thu Apr 3 13:38:59 2003 Number: 24 Name: Pollastri, Gianluca Affiliation: University of California, Irvine Address: 442 ICS, UCI City: Irvine State/Provice: California Postal/Zip Code: 92612 Country: U.S.A. Email: gpollast@ics.uci.edu Phone: +1 949 854 3446 Fax: +1 949 824 4056 Category: Predictive Methods Poster Title: Protein structure from SCRATCH Poster Authors and organization: Gianluca Pollastri¹, Pierre Baldi²
¹gpollast@ics.uci.edu, University of California, Irvine; ²pfbaldi@ics.uci.edu, University of California, Irvine Abstract: The SCRATCH servers are a publicly available tool for ab initio prediction of protein structural features, and ultimately protein structure, by machine learning methods. The servers ranked among the best at the CASP4 and CASP5 experiments and have so far responded to over 60,000 queries from all over the world. File: gpollastATics.uci.edu_24 ************************************************* Thu Apr 3 17:18:14 2003 Number: 25 Name: Feldman, Howard J Affiliation: Samuel Lunenfeld Research Institute, Mount Sinai Hospital Address: Room 1060, 600 University Ave. City: North York State/Provice: Ontario Postal/Zip Code: M2M 1P4 Country: Canada Email: feldman@mshri.on.ca Phone: 1-416-586-4800 ext. 2416 Fax: 1-416-586-8869 I plan to use my laptop computer as part of my poster Category: Structural Biology Poster Title: Protein unfolding governed by geometric and steric principles Poster Authors and organization: Howard J Feldman¹, Christopher WV Hogue²
¹feldman@mshri.on.ca, Samuel Lunenfeld Research Institute, Mount Sinai Hospital; ²hogue@mshri.on.ca, Samuel Lunenfeld Research Institute, Mount Sinai Hospital Abstract: Using a novel physics-based approach, complete protein unfolding pathways for five distinct folds were computed and compared with published molecular dynamics and in-vitro experiments. Agreement was good and computation reduced by three orders of magnitude, suggesting that unfolding pathways of small globular proteins are largely constrained by geometry and sterics. File: feldmanATmshri.on.ca_25 ************************************************* Fri Apr 4 02:33:59 2003 Number: 26 Name: Couto, Francisco M. Affiliation: Faculdade de Ciencias, Universidade de Lisboa Address: Campo Grande City: Lisboa State/Provice: - Postal/Zip Code: 1749-016 Lisboa Country: Portugal Email: fjmc@di.fc.ul.pt Phone: +351918263676 Fax: +351217500084 I plan to use my laptop computer as part of my poster Category: Data Mining Poster Title: ReBIL : Relating Biological Information through Literature Poster Authors and organization: Francisco M. Couto¹, Pedro Coutinho², M�rio J. Silva
¹fjmc@di.fc.ul.pt, Faculdade de Ciencias, Universidade de Lisboa; ²pedro@afmb.cnrs-mrs.fr, UMR 6098, Architecture et Fonction des Macromol�cules Biologiques, CNRS Abstract: ReBIL aims to improve the efficiency of information extraction systems applied to biological literature. The project is based on the correlation between structural and functional classifications of gene products. We evaluate extracted information by checking if they preserve the correlation. More information about Rebil is available at http://xldb.fc.ul.pt/rebil/. File: fjmcATdi.fc.ul.pt_26 ************************************************* Fri Apr 4 04:31:57 2003 Number: 27 Name: Lottaz, Claudio Affiliation: Max-Planck-Institute for Molecular Genetics Address: Ihnestr. 73 City: Berlin State/Provice: Berlin Postal/Zip Code: 14195 Country: Germany Email: Claudio.Lottaz@molgen.mpg.de Phone: +49 30 8413 1177 Fax: +49 30 8413 1176 Category: Microarrays Poster Title: Gene Ontology Driven Classification of Gene Expression Patterns Poster Authors and organization: Claudio Lottaz¹, Renate Kirschner², Stefan Bentink, Christian Hagemeier and Rainer Spang
¹Claudio.Lottaz@molgen.mpg.de, Max-Planck-Institute for Molecular Genetics, Berlin; ²r.kirschner@charite.de, Medical Center Charit�, Berlin Abstract: We propose to structure analysis of microarry according to biological knowledge in order to provide an intuitive and biologically meaningful rationale for computational classification results. Thereby, we rely on the Gene Ontology to attribute genes to biological aspects and usual machine learning methods for classification. File: Claudio.LottazATmolgen.mpg.de_27 ************************************************* Sun Apr 6 19:56:59 2003 Number: 28 Name: Nathan, Sheila Affiliation: Universiti Kebangsaan Malaysia Address: Jalan Universiti City: Bangi State/Provice: Selangor Postal/Zip Code: 43600 Country: Malaysia Email: sheila@pkrisc.cc.ukm.my Phone: 60-3-89213862 Fax: 60-3-89252698 Category: Functional Genomics Poster Title: Identification of Novel Two-partner Secretion Family in Burkholderia pseudomallei Poster Authors and organization: Annapoorna Nimaggadda¹, Sheila Nathan², Rahmah Mohamed
¹anulins@yahoo.com, Universiti Kebangsaan Malaysia; ²sheila@pkrisc.cc.ukm.my, Universiti Kebangsaan Malaysia Abstract: Identification Of Novel Two-partner Secretion Family in Burkholderia pseudomallei Filamentous hemagglutinin belongs to the Two Partner Secretion (TPS) family. Sequence analysis indicated the presence of filamentous hemagglutinin (FhaB) and its transporter (FhaC) in an operon in Burkholderia pseudomallei. Motif recognition, phylogenetic analysis using N-J and PAM matrix methods provide more information of the functionality of the operon. File: sheilaATpkrisc.cc.ukm.my_28 ************************************************* Mon Apr 7 01:55:36 2003 Number: 29 Name: Mogno, Ilaria Affiliation: DIS, Universita di Roma La Sapienza Address: via Eudossiana, 18 City: Roma State/Provice: Roma Postal/Zip Code: 00184 Country: Italy Email: mogno@dis.uniroma1.it Phone: 0039 06 44585938 Fax: 0039 06 44585367 Category: Functional Genomics Poster Title: A Reconstruction Algorithm from Expression Data for Sparse Noninteracting Gene Networks Poster Authors and organization: Ilaria Mogno¹, Lorenzo Farina², Salvatore Monaco
¹mogno@dis.uniroma1.it, DIS, Universita di Roma La Sapienza; ²lorenzo.farina@uniroma1.it, DIS, Universita di Roma La Sapienza Abstract: We propose an algorithm, which reconstructs gene networks from expression data, trying to face the problem of "small" available data, assuming some reasonable biologically consistent hypotheses. We also evaluate algorithm performance on artificial problems. File: mognoATdis.uniroma1.it_29 ************************************************* Mon Apr 7 06:21:46 2003 Number: 29 Name: Lipson, Doron Affiliation: CS Department, Technion Address: Technion City: Haifa State/Provice: Haifa Postal/Zip Code: 32000 Country: Israel Email: dlipson@cs.technion.ac.il Phone: +972-4-8294927 Fax: Category: Functional Genomics Poster Title: Computational Design of Efficient PCR Multiplexing Schemes Poster Authors and organization: Doron Lipson¹, Zohar Yakhini²
¹dlipson@cs.technion.ac.il, CS Department, Technion, Haifa, Israel; ²zohar_yakhini@agilent.com PCR amplification is a major bottleneck in high-throughput DNA analysis techniques, e.g. SNP genotyping. We present an algorithm for computational design of a complete PCR multiplexing scheme (a selection of primers and division of the target fragments into reaction tubes) that maximizes the multiplexing rate – the number of fragments that may be co-amplified together.

File: dlipsonATcs.technion.ac.il_29 ************************************************* Mon Apr 7 12:14:02 2003 Number: 30 Name: bello, onimisi h Affiliation: bma tutorial oufit Address: no.6 zansi close City: off-iwaya road yaba State/Provice: lagos Postal/Zip Code: 340 Country: nigeria Email: hassanbello2001@yahoo.com Phone: none Fax: none Category: Predictive Methods Poster Title: The model representation of the mode of action of combination therapy of chloroquine,puritine an ascobic acid Poster Authors and organization: onimisi hassan bello¹
¹hassanbello2001@yahoo.com, bima tutorial outfit Abstract: The action of the combine therapy of chloroquine,putitine and ascobic acid has baffled biochemist for some times.but it is believe to potentiate its action based on the pertubation of the lipid bilayer surrounding the cells. but further studies to reveal the genetic conditions has not yielded much results. File: hassanbello2001ATyahoo.com_30 ************************************************* Mon Apr 7 12:59:51 2003 Number: 31 Name: Dumontier, Michel Affiliation: SLRI Address: 1060-600 University Avenue City: Toronto State/Provice: ON Postal/Zip Code: M5G1X5 Country: Canada Email: micheld@mshri.on.ca Phone: 416.586.4800x2416 Fax: 416.586.8869 Category: Sequence Comparison Poster Title: Species-Specific Substitution Matrices Poster Authors and organization: Michel Dumontier¹, Christopher W.V. Hogue²
¹micheld@mshri.on.ca, Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Ave.,Toronto, Ontario, Canada M5G 1X5; ²hogue@mshri.on.ca, Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Ave.,Toronto, Ontario, Canada M5G 1X5 Abstract: We derived and tested novel species-specific substitution matrices (SSSMs) for sequence alignment. Our results show increased alignment accuracy in the 20-30% sequence identity range, but decreased alignment length as compared to popular sequence alignment programs such as PSI-BLAST (using BLOSUM) using CASA�s SCOP based alignment test sets. File: micheldATmshri.on.ca_31 ************************************************* Mon Apr 7 13:02:53 2003 Number: 32 Name: Dumontier, Michel Affiliation: SLRI Address: 1060-600 University Avenue City: Toronto State/Provice: ON Postal/Zip Code: M5G1X5 Country: Canada Email: micheld@mshri.on.ca Phone: 416.586.4800x2416 Fax: 416.586.8869 Category: Predictive Methods Poster Title: Species-Specific Protein Sequence and Fold Optimizations Poster Authors and organization: Michel Dumontier¹, Katerina Michalickova², Christopher W.V. Hogue
¹micheld@mshri.on.ca, Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Ave.,Toronto, Ontario, Canada M5G 1X5; ²katerina@mshri.on.ca, Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Ave.,Toronto, Ontario, Canada M5G 1X5 Abstract: The ability of each and every organism to adapt its particular environmental niche is of fundamental importance to its survival and proliferation. We have identified species-specific protein sequence and fold optimizations, which we exploited to generate predictive scoring functions. These scoring functions will be used in future species-specific protein identification and optimization experiments. File: micheldATmshri.on.ca_32 ************************************************* Mon Apr 7 13:08:45 2003 Number: 33 Name: Dumontier, Michel Affiliation: SLRI Address: 1060-600 University Avenue City: Toronto State/Provice: ON Postal/Zip Code: M5G1X5 Country: Canada Email: micheld@mshri.on.ca Phone: 416.586.4800x2416 Fax: 416.586.8869 Category: Structural Biology Poster Title: Semi-Automated Homology Modeling Using A Modified TRADES Algorithm Poster Authors and organization: Michel Dumontier¹, Howard J. Feldman², Christopher W.V. Hogue
¹micheld@mshri.on.ca, Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Ave.,Toronto, Ontario, Canada M5G 1X5; ²feldman@mshri.on.ca, Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Ave.,Toronto, Ontario, Canada M5G 1X5 Abstract: We present a modified version of the TRADES algorithm for homology modeling of protein sequences given weak similarity to experimentally determined protein structure that generates realistic, all-atom models of non-idealized geometry as it incorporates backbone dependent rotamers, reasonable bond lengths, bond angles, torsion angles, minimized electrostatics and van der Waals forces. File: micheldATmshri.on.ca_33 ************************************************* Mon Apr 7 21:56:35 2003 Number: 34 Name: Arthur, Jonathan W Affiliation: Proteome Systems Ltd Address: Unit 1 35-41 Waterloo Rd City: North Ryde State/Provice: NSW Postal/Zip Code: 2113 Country: Australia Email: jonathan.arthur@proteomesystems.com Phone: 02 8877 8930 Fax: 02 9889 1805 I plan to use my laptop computer as part of my poster Category: Genome Annotation Poster Title: Using proteomics to mine genome sequences Poster Authors and organization: Jonathan W Arthur¹, Marc R Wilkins²
¹jonathan.arthur@proteomesystems.com, Proteome Systems Ltd; ²marc.wilkins@proteomesystems.com, Proteome Systems Ltd Abstract:

We present a hypothesis-independent method for identifying the region of a genome coding for a protein sequence using proteomic information. The method can be used to identify novel genes that were not found by other annotation techniques. It is demonstrated using theoretical and experimental data sets from prokaryotic and eukaryotic organsims.

File: jonathan.arthurATproteomesystems.com_34 ************************************************* Tue Apr 8 00:27:31 2003 Number: 35 Name: Jellema, Renger H Affiliation: TNO Nutrition and Food Research Address: P.O. Box 360 City: Zeist State/Provice: Utrecht Postal/Zip Code: 3700 AJ Country: The Netherlands Email: jellema@voeding.tno.nl Phone: +31 30 6944368 Fax: +31 30 6944077 Category: Microarrays Poster Title: Improving the reliability of transcriptomics data; The effect of quenching on RNA transcription profiles Poster Authors and organization: Bart Pieterse¹, Renger H. Jellema², Mari�t J. van der Werf
¹Pieterse@voeding.tno.nl, 1. Wageningen Centre for Food Sciences; ²jellema@voeding.tno.nl, 2. TNO Nutrition and Food Research Abstract:

We validated a quenching method for the harvesting of micro-organisms from liquid cultures for gene expression studies. The transcription profiles of quenched L. plantarum WCFS1 cells were compared with those of cells that were harvested by alternative methods. PCA analysis and hierarchal clustering of the resulting transcriptomics data show a clear effect of this quenching method on the transcription profiles.

File: jellemaATvoeding.tno.nl_35 ************************************************* Tue Apr 8 02:36:05 2003 Number: 36 Name: Huang, HsiangChi Affiliation: Institute for Information Industry Address: 22FL-A,NO.333,Sec2, DuenHua S.Rd. City: Taipei State/Provice: Taiwan Postal/Zip Code: 106 Country: Taiwan Email: illusion@iii.org.tw Phone: 886-2-8732-6222 ext 148 Fax: 886-2-8732-6271 I plan to use my laptop computer as part of my poster Category: Predictive Methods Poster Title: An evolving approach to finding Schemas for protein secondary structure prediction Poster Authors and organization: Huang,Hsiang Chi¹
¹illusion@iii.org.tw, Institute for Information Industry Abstract: A genetic algorithm has been applied to predict building schemas of protein secondary structure. Although the average Q3 of this research is not the highest score among researches, some fundamental and useful building schemas of protein secondary structure have been found. File: illusionATiii.org.tw_36 ************************************************* Tue Apr 8 09:17:03 2003 Number: 37 Name: Adoro, Stanley A Affiliation: Cellular Parasitology Programme, Department of Zoology, University of Ibadan Address: Oyo Road City: Ibadan State/Provice: Oyo State Postal/Zip Code: None Country: Nigeria Email: stanleyadoro@hotmail.com Phone: 234 2 8100822 Fax: 234 2 8100079 Category: Sequence Comparison Poster Title: Secondary structure interpretation of genetic sequence variation in Plasmodium falciparum cell surface antigens Poster Authors and organization: Stanley Adoro¹, Roseangela Nwuba, Chiaka Anumudu, Mark Nwagwu
¹stanleyadoro@hotmail.com, University of Ibadan Abstract: We have analyzed genetic and amino acid residue variation of Plasmodium falciparum cell surface antigens (merozoite surface proteins 1 and 2; circumsporozoite protein; stevor and rifin) in the context of their known or predicted secondary structures. Locations of structural motifs suggest the presence of functional domains or antigenic epitopes. File: stanleyadoroAThotmail.com_37 ************************************************* Tue Apr 8 22:38:13 2003 Number: 38 Name: Makhija, Mahindra T Affiliation: Western Australian Biomedical Research Institute, School of Biomedical Sciences, Curtin University of Technology, Address: GPO Box U1987, Perth City: Perth State/Provice: Western Australia Postal/Zip Code: 6845 Country: Australia Email: M.Makhija@exchange.curtin.edu.au Phone: 61 8 9266 7517 Fax: 61 8 9266 7485 Category: Predictive Methods Poster Title: Inhibitors of Glycogen Synthase Kinase-3beta and Cyclin-Dependent Kinases Modelled by 3D-QSAR Using a Novel Alignment Method Based on Electrostatic Potentials. Poster Authors and organization: Mahindra¹, Erik ²
¹M.Makhija@exchange.curtin.edu.au, Western Australian Biomedical Research Instittue, School of Biomedcial Sciences, Curtin University of Technology, Bentley, WA 6102, Australia; ²E.Helmerhorst@curtin.edu.au, Western Australian Biomedical Research Instittue, School of Biomedcial Sciences, Curtin University of Technology, Bentley, WA 6102, Australia Abstract: The ability of paullones and aloisines to inhibit glycogen synthase kinase-3β and cyclin-dependent kinases was well predicted by 3D-QSAR using CoMSIA in conjunction with a novel alignment method based on electrostatic potentials. The predictive value of this approach may lead to the development of better therapeutics for Alzheimer�s disease. File: M.MakhijaATexchange.curtin.edu.au_38 ************************************************* Tue Apr 8 23:38:52 2003 Number: 39 Name: Michael, Gromiha Affiliation: CBRC, AIST Address: 17F, Aomi Frontier Building City: 2-43 Aomi, Koto-ku State/Provice: Tokyo Postal/Zip Code: 135-0064 Country: Japan Email: michael-gromiha@aist.go.jp Phone: +81-3-3599-8046 Fax: +81-3-3599-8081 Category: Structural Biology Poster Title: Role of Long-range Interactions in the Transition and Folded Native states of Two-state Proteins Poster Authors and organization: M. Michael Gromiha¹, S. Selvaraj²
¹michael-gromiha@aist.go.jp, CBRC, AIST, Tokyo, Japan; ², Department of Physics, Bharathidasan University, Tiruchirapalli, India Abstract: We have proposed a novel parameter, long-range order (LRO) for a protein from the knowledge of long-range contacts in protein structure. LRO correlates very well with experimental protein folding rates. The short and medium-range non-bonded energy, long-range contacts, and helical/strand tendency are the major determinants for transition state structures of two-state proteins. File: michael-gromihaATaist.go.jp_39 ************************************************* Wed Apr 9 03:22:54 2003 Number: 40 Name: de Beer, Tjaart AP Affiliation: Univeristy of Pretoria Address: Lynnwood rd City: Pretoria State/Provice: Gauteng Postal/Zip Code: 0001 Country: South Africa Email: tjaart.de.beer@tuks.co.za Phone: 27 12 420 2990 Fax: 27 12 362 5302 Category: Structural Biology Poster Title: Homology modeling of dihydropteroate synthase from plasmodium falciparum Poster Authors and organization: T de Beer¹, F Joubert², AI Louw
¹tjaart.de.beer@tuks.co.za, University of Pretoria; ²fjoubert@postino.up.ac.za, University of Pretoria Abstract:

A homology model was constructed for the DHPS-PPPK bifunctional enzyme of Plasmodium falciparum. This enzyme plays a vital part in folate synthesis and is targeted by current, failing therapies. The LUDI/ACD and the NCI database was scanned against the models to identify new potential inhibitors.

File: tjaart.de.beerATtuks.co.za_40 ************************************************* Wed Apr 9 09:00:05 2003 Number: 41 Name: Shah, Nigam H Affiliation: Pennsylvania State University Address: 211 Wartik Labs City: University Park State/Provice: PA Postal/Zip Code: 16801 Country: USA Email: nigam@psu.edu Phone: 814-863-5720 Fax: I plan to use my laptop computer as part of my poster Category: New Frontiers Poster Title: HyBrow: A Hypothesis Space Browser Poster Authors and organization: Nigam Shah¹, Stephen Racunas², Nina V. Fedoroff, Penn State University, nvf1@psu.edu
¹nigam@psu.edu, Penn State University; ²sar147@psu.edu, Penn State University Abstract: HyBrow is a prototype computer system comprising an event-based ontology for biological processes, an associated database and programs to perform hypothesis evaluation using a wide variety of available data. We demonstrate the feasibility of HyBrow, using the galactose metabolism gene network in Saccharomyces cerevisiae as our test system, for ranking alternative hypotheses in an automated manner. File: nigamATpsu.edu_41 ************************************************* Wed Apr 9 23:52:44 2003 Number: 42 Name: Purevjav, Enkhbayar Affiliation: Hokkaido University Address: Kita-ku City: Sapporo State/Provice: Hokkaido Postal/Zip Code: 060-0810 Country: Japan Email: penkh@chem.agr.hokudai.ac.jp Phone: 81-11-611-2111 Fax: 81-11-612-3617 Category: Structural Biology Poster Title: 3D circle fitting of leucine-rich repeat proteins Poster Authors and organization: Purevjav Enkhbayar¹, Norio Matsushima², Mitsuru Osaki
¹penkh@chem.agr.hokudai.ac.jp, Hokkaido University; ²matusima@sapmed.ac.jp, Sapporo Medical University Abstract: The structure of leucine-rich repeat (LRR)-containing proteins had been regarded as a superhelix. We performed helix fitting and circle fitting using atomic coordinates of individual repeats in the known structures. Surprisingly, the result demonstrates that the LRR arch is satisfactorily fitted by a circle rather than a helix. File: penkhATchem.agr.hokudai.ac.jp_42 ************************************************* Thu Apr 10 06:55:11 2003 Number: 43 Name: Lu, Fu Affiliation: Celera Genomics Address: 45 West Gude Drive City: Rockville State/Provice: MD Postal/Zip Code: 20878 Country: USA Email: fu.lu@celera.com Phone: 2404530875 Fax: 2404533768 Category: Phylogeny and Evolution Poster Title: CompMapper: An Automatic Pipeline to Define Conserved Segments between Genomes Systematically Poster Authors and organization: Fu Lu¹, Zhenyuan Wang², Xiangqun Holly Zheng, Wenyan Zhong, Fei Zhong, Richard Mural
¹fu.lu@celera.com, Celera Genomics; ²jack.wang@celera.com, Celera Genomics Abstract: To overcome the limitations of comparative mapping using orthologous genes, we have developed a new paradigm and systematic approach to define conserved synteny between human and mouse directly from genomic sequence. The automatic pipeline should be applicable to compare any species with complete or draft genome sequence and within an appropriate phylogenetic distance. File: fu.luATcelera.com_43 ************************************************* Fri Apr 11 01:29:46 2003 Number: 44 Name: Mulder, Nicola J Affiliation: European Bioinformatics Institute Address: Wellcome Trust Genome Campus City: Hinxton State/Provice: Cambridgeshire Postal/Zip Code: CB10 1SD Country: United Kingdom Email: mulder@ebi.ac.uk Phone: +44 1223 494602 Fax: +44 1223 494468 Category: Databases Poster Title: InterPro, a protein functional classification resource Poster Authors and organization: Nicola Mulder¹, InterPro Consortium²
¹mulder@ebi.ac.uk, EBI; ²interpro@ebi.ac.uk, EBI Abstract: InterPro is an integrated protein signature resource for predicting protein families, domains and functional sites. It incorporates data from PROSITE, Pfam, Print, ProDom, SMART, TIGRFAMs, PIR Superfamilies and the structure-based SUPERFAMILY. InterPro classifies 80% of SWISS-PROT/TREMBL and provides links to the proteins, methods, specialised protein family resources and structural information. File: mulderATebi.ac.uk_44 ************************************************* Sat Apr 12 23:53:53 2003 Number: 45 Name: BEN-ZEEV, EFRAT Affiliation: WEIZMANN INSTITUTE OF SCIENCE Address: Department of Biological Chemistry City: REHOVOT State/Provice: Israel Postal/Zip Code: 76100 Country: ISRAEL Email: efrat.ben-zeev@weizmann.ac.il Phone: 972-8-9342434 Fax: 972-8-9468256 Category: Predictive Methods Poster Title: Weighted Geometric Docking with MolFit: Incorporating External Information in the Rotation-Translation Scan Poster Authors and organization: Efrat Ben-Zeev¹, Miriam Eisenstein²
¹efrat.ben-zeev@weizmann.ac.il, Weizmann Institute of Science; ²miriam.eisenstein@weizmann.ac.il, Weizmann Institute of Science Abstract: Weighted-geometric docking incorporates external data from different sources, such as biochemical and biophysical experiments and bioinformatics analyses, in the docking rotation-translation scan. The method is successful even when the weighted portion of the surface corresponded only partially and approximately to the binding site. Implemented in our program MolFit. File: efrat.ben-zeevATweizmann.ac.il_45 ************************************************* Sun Apr 13 12:51:10 2003 Number: 46 Name: Ramadass, Aroul S Affiliation: University of Cambridge Address: Room 2, 17 Bateman Street City: Cambridge State/Provice: Cambridgeshire Postal/Zip Code: CB2 1NB Country: United Kingdom Email: asr25@cam.ac.uk Phone: 0044-07786570766 Fax: 0044-01223-494919 Category: Data Mining Poster Title: POLII TRANSCRIPTION TERMINATION SIGNALS IN HUMAN Poster Authors and organization: Aroul Selvam¹, Thomas Down², Tim Hubbard
¹asr25@cam.ac.uk, The Wellcome Trust Sanger Institute; ²td2@sanger.ac.uk, The Wellcome Trust Sanger Institute Abstract: RNA polymerase II - although important as it transcribes all the protein coding genes in the cell, little is known about its termination process. This study focuses on identifying motifs that link to transcription termintion and polymerase relase process. File: asr25ATcam.ac.uk_46 ************************************************* Sun Apr 13 22:29:21 2003 Number: 47 Name: Suzuki, Harukazu Affiliation: RIKEN Genomic Sciences Center Address: 1-7-22, Suehiro-cho City: Tsurumi-ku State/Provice: Yokohama Postal/Zip Code: 230-0045 Country: JAPAN Email: harukazu@gsc.riken.go.jp Phone: 81-45-503-9222 Fax: 81-45-503-9216 Category: Genome Annotation Poster Title: Global insights into protein complexes through integrated analysis of the interactome and knockout lethality Poster Authors and organization: Harukazu Suzuki¹, Rintaro Saito ², Yoshihide Hayashizaki
¹harukazu@gsc.riken.go.jp, RIKEN Genomic Sciences Center ; ², RIKEN Genomic Sciences Center Abstract: We have developed the new interaction generality measure (IG2), which can be used to computationally assess the reliability of the interactome data. We performed an integrated analysis by using comprehensive phenotype dataset and IG2-treated interactome dataset from yeast, which yielded global insights into the biological features of the protein complexes. File: harukazuATgsc.riken.go.jp_47 ************************************************* Sun Apr 13 23:16:01 2003 Number: 48 Name: Lyakhovich, Alex Affiliation: University of Michigan Address: 1301 E.Catherine City: Ann Arbor State/Provice: MI Postal/Zip Code: 48109 Country: U.S.A. Email: alexlyak@umich.edu Phone: 1-734-913-8210 Fax: I plan to use my laptop computer as part of my poster Category: Predictive Methods Poster Title: Prediction of New Regulatory Properties For Proteins Sharing Different Functional Motifs Poster Authors and organization: Alex Lyakhovich¹, Anatoly Karp²
¹alexlyak@umich.edu, University of Michigan; ², University of Wisconsin-Madison Abstract: We suggest a new algorithm that allows prediction of additional regulatory functions for the proteins containing different structural motifs. This algorithm was successfully applied for a set of proteins containing ubiquitin motifs where we could also show their regulation by certain protein kinases. File: alexlyakATumich.edu_48 ************************************************* Mon Apr 14 00:29:38 2003 Number: 49 Name: Goffard, Nicolas ng Affiliation: Centre de Bioinformatique de Bordeaux Address: 146, rue Leo Saignat City: Bordeaux State/Provice: France Postal/Zip Code: 33076 Country: France Email: nicolas.goffard@pmtg.u-bordeaux2.fr Phone: 33 5 57 57 45 71 Fax: 33 5 57 57 90 16 Category: Functional Genomics Poster Title: Protein interactions and modular evolution of proteins Poster Authors and organization: Nicolas Goffard¹, Jerome Poix², Antoine de Daruvar
¹nicolas.goffard@pmtg.u-bordeaux2.fr, Centre de Bioinformatique de Bordeaux, Universite Bordeaux 2; ²jerome.poix@sm.u-bordeaux2.fr, Laboratoire Statistique Mathematique et ses Applications, EA 2961, Universite Bordeaux 2 Abstract: In order to investigate the mechanisms of molecular evolution involved in setting up protein- protein interactions we analysed pairs of interacting domains and domain composition of proteins. Our results show an over-representation of domain pairs that are found both involved in protein interaction and grouped together within proteins. File: nicolas.goffardATpmtg.u-bordeaux2.fr_49 ************************************************* Mon Apr 14 08:57:45 2003 Number: 50 Name: Burgoon, Lyle D Affiliation: Michigan State University Address: 223 Biochemistry Bldg, Michigan State University City: East Lansing State/Provice: MI Postal/Zip Code: 48824 Country: USA Email: burgoonl@msu.edu Phone: 517-353-1944 Fax: Category: Microarrays Poster Title: Statistical Promoter Regulatory Element Analysis of cDNA Microarray Data For the Prediction of cAMP Responsive Genes Poster Authors and organization: Lyle D Burgoon¹, Tim Zacharewski², Ken Y Kwan
¹burgoonl@msu.edu, Michigan State University; ²tzachare@msu.edu, Michigan State University Abstract: We have developed a method for predicting transcription factor responsive genes by combining response element prediction with cDNA microarray data. Our Statistical Promoter REgulatory Element (SPREE) application program identified cAMP responsive elements. SPREE output was combined with cDNA microarray data to design an SVM model for predicting cAMP responsive genes. File: burgoonlATmsu.edu_50 ************************************************* Mon Apr 14 09:11:02 2003 Number: 51 Name: Burgoon, Lyle D Affiliation: Michigan State University Address: 223 Biochemistry Bld, Wilson Road, Michigan State University City: East Lansing State/Provice: MI Postal/Zip Code: 48824 Country: USA Email: burgoonl@msu.edu Phone: 517-353-1944 Fax: Category: Databases Poster Title: dbZach: An Integrative Toxicogenomic Supportive Relational Database System Poster Authors and organization: Lyle D Burgoon¹, Paul C Boutros², Edward Dere, Shane Doran, Shraddha Pai, Raeka Aiyar, Jigger Vakharia, Rebecca Rotman, Tim Zacharewski
¹burgoonl@msu.edu, Michigan State University; ², Michigan State University Abstract: The dbZach System is a microarray information management system meant for local installation in labs or larger, enterprise environments. The dbZach database includes four core subsystems, and six modular subsystems. The system also includes GUI data mining tools, and an API. Source code will be available soon at: http://dbzach.fst.msu.edu. File: burgoonlATmsu.edu_51 ************************************************* Mon Apr 14 21:08:25 2003 Number: 52 Name: Wang, Yong Affiliation: the University of Hong Kong Address: Pok fulam City: Hong Kong State/Provice: Hong Kong Postal/Zip Code: 852 Country: China Email: wangyong@hkusua.hku.hk Phone: 22990817 Fax: Category: Genome Annotation Poster Title: An evaluation of new criteria for CpG islands in the human genome as gene markers Poster Authors and organization: Patrick, Yong Wang¹, Frederick, C. Leung²
¹wangyong@hkusua.hku.hk, HKU, Dept of Zoology; ²fcleung@hkucc.hku.hk, HKU, Dept of Zoology Abstract: Using the new criteria for CpG islands introduced by Takai and Jones, we investigated several association types between CpG islands and genes to further establish the importance of CpG islands as gene markers. Our investigation gave us a useful tool for evaluating the accuracy of gene annotation in human chromosomes. File: wangyongAThkusua.hku.hk_52 ************************************************* Mon Apr 14 22:07:27 2003 UPDATE ----- Number: 21 Name: Linding, Rune Affiliation: EMBL - Biocomputing Unit Address: Meyerhofstr 1 City: Heidelberg State/Provice: Baden-Wuerttemberg Postal/Zip Code: D-69117 Country: Germany Email: linding@embl.de Phone: +49 6221 387 451 Fax: +49 6221 387 417 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: http://elm.eu.org - ELM Resource for prediction of functional sites in proteins Poster Authors and organization: Rune Linding¹, ELM Consortium², ELM Consortium
¹linding@embl.de, EMBL; ²info@elm.eu.org, ELM Consortium Abstract: ELM is a resource for predicting functional sites in eukarytic proteins. Putative functional sites are identified by conventional methods, such as patterns (regular expressions) or hidden Markov models. To improve the predictive power, context-based rules and logical filters will be developed and applied to reduce the amount of false positives. File: lindingATembl.de_21 ************************************************* Mon Apr 14 22:11:09 2003 UPDATE ----- Number: 23 Name: Betel, Doron Affiliation: Samuel Lunenfeld Research Institute, Mt. Sinai Hospital, Department of Biochemistry, University of Toronto Address: room 1060, 600 University Ave. City: Toronto State/Provice: Ontario Postal/Zip Code: M5G-1X5 Country: Canada Email: doron.betel@utoronto.ca Phone: 416-586-4800 ext. 2863 Fax: 416-586-8869 Category: Data Mining Poster Title: Domain-Domain correlations in Yeast protein complexes Poster Authors and organization: Doron Betel¹, Christopher W.V. Hogue²
¹doron.betel@utoronto.ca, Samuel Lunenfeld Research Institute, Mt. Sinai Hospital and Department of Biochemistry, University of Toronto; ²hogue@mshri.on.ca, Samuel Lunenfeld Research Institute, Mt. Sinai Hospital and Department of Biochemistry, University of Toronto Abstract: We introduce a new method for detecting statistically meaningful functional associations between domains from molecular complexes. Two random control sets were used to compute P-values for domain co-occurrences in complexes. Results from four different datasets show that many of the correlations are between domains of similar or associated function. File: doron.betelATutoronto.ca_23 ************************************************* Mon Apr 14 22:29:57 2003 UPDATE ----- Number: 27 Name: Lottaz, Claudio Affiliation: Max-Planck-Institute for Molecular Genetics Address: Ihnestr. 73 City: Berlin State/Provice: Berlin Postal/Zip Code: 14195 Country: Germany Email: Claudio.Lottaz@molgen.mpg.de Phone: +49 30 8413 1177 Fax: +49 30 8413 1176 Category: Microarrays Poster Title: Gene Ontology Driven Classification of Gene Expression Patterns Poster Authors and organization: Claudio Lottaz¹, Renate Kirschner², Stefan Bentink, Christian Hagemeier and Rainer Spang
¹Claudio.Lottaz@molgen.mpg.de, Max-Planck-Institute for Molecular Genetics, Berlin; ²r.kirschner@charite.de, Medical Center Charit�, Berlin Abstract: We propose to structure analysis of microarry according to biological knowledge in order to provide an intuitive and biologically meaningful rationale for computational classification results. Thereby, we rely on the Gene Ontology to attribute genes to biological aspects and usual machine learning methods for classification. File: Claudio.LottazATmolgen.mpg.de_27 ************************************************* Mon Apr 14 22:32:15 2003 UPDATE ----- Number: 27 Name: Lottaz, Claudio Affiliation: Max-Planck-Institute for Molecular Genetics Address: Ihnestr. 73 City: Berlin State/Provice: Berlin Postal/Zip Code: 14195 Country: Germany Email: Claudio.Lottaz@molgen.mpg.de Phone: +49 30 8413 1177 Fax: +49 30 8413 1176 Category: Microarrays Poster Title: Gene Ontology Driven Classification of Gene Expression Patterns Poster Authors and organization: Claudio Lottaz¹, Renate Kirschner², Stefan Bentink, Christian Hagemeier and Rainer Spang
¹Claudio.Lottaz@molgen.mpg.de, Max-Planck-Institute for Molecular Genetics, Berlin; ²r.kirschner@charite.de, Medical Center Charit�, Berlin Abstract: We propose to structure analysis of microarry according to biological knowledge in order to provide an intuitive and biologically meaningful rationale for computational classification results. Thereby, we rely on the Gene Ontology to attribute genes to biological aspects and usual machine learning methods for classification. File: Claudio.LottazATmolgen.mpg.de_27 ************************************************* Mon Apr 14 22:35:17 2003 UPDATE ----- Number: 27 Name: Lottaz, Claudio Affiliation: Max-Planck-Institute for Molecular Genetics Address: Ihnestr. 73 City: Berlin State/Provice: Berlin Postal/Zip Code: 14195 Country: Germany Email: Claudio.Lottaz@molgen.mpg.de Phone: +49 30 8413 1177 Fax: +49 30 8413 1176 Category: Microarrays Poster Title: Gene Ontology Driven Classification of Gene Expression Patterns Poster Authors and organization: Claudio Lottaz¹, Renate Kirschner², Stefan Bentink, Christian Hagemeier and Rainer Spang
¹Claudio.Lottaz@molgen.mpg.de, Max-Planck-Institute for Molecular Genetics, Berlin; ²r.kirschner@charite.de, Medical Center Charit�, Berlin Abstract: We propose to structure analysis of microarry according to biological knowledge in order to provide an intuitive and biologically meaningful rationale for computational classification results. Thereby, we rely on the Gene Ontology to attribute genes to biological aspects and usual machine learning methods for classification. File: Claudio.LottazATmolgen.mpg.de_27 ************************************************* Tue Apr 15 05:01:11 2003 Number: 53 Name: de Lichtenberg, Ulrik Affiliation: Center for Biological Sequence Analysis, BioCentrum-DTU, The Technical University of Denmark Address: Kemitorvet, Building 208 City: Lyngby State/Provice: Denmark Postal/Zip Code: DK-2800 Country: Denmark Email: ulrik@cbs.dtu.dk Phone: +045-45252485 Fax: +045-45831585 Category: Systems Biology Poster Title: Protein Feature Based Identification of Cell Cycle Regulated Proteins Poster Authors and organization: Ulrik de Lichtenberg¹, Thomas Sk�t Jensen², Lars Juhl Jensen, Anders Fausb�ll, S�ren Brunak
¹ulrik@cbs.dtu.dk, Center for Biological Sequence Analysis, BioCentrum-DTU, The Technical University of Denmark; ²skot@cbs.dtu.dk, Center for Biological Sequence Analysis, BioCentrum-DTU, The Technical University of Denmark Abstract: We show that cell cycle regulated proteins can be identified via certain features, including protein phosphorylation, glycosylation, subcellular location and instability/degradation. We demonstrate that co-expressed, periodic genes encode proteins which share combinations of features, and provide an overview of the proteome dynamics during the cycle. File: ulrikATcbs.dtu.dk_53 ************************************************* Tue Apr 15 12:06:06 2003 Number: 54 Name: Wong, Sharyl L Affiliation: Harvard Medical School Address: 1353 Beacon St. Apt. 4 City: Brookline State/Provice: MA Postal/Zip Code: 02446 Country: USA Email: sharyl_wong@student.hms.harvard.edu Phone: 617-893-0490 Fax: 617-432-3557 Category: Predictive Methods Poster Title: Predicting Synthetic Lethality Poster Authors and organization: Sharyl L. Wong¹, Lan O. Zhang², Amy H. Tong, Debra S. Goldberg, Guillaume Lesage, Marc Vidal, Brenda Andrews, Howard Bussey, Charles Boone, Frederick P. Roth
¹sharyl_wong@student.hms.harvard.edu, Harvard Medical School; ²lan_zhang@student.hms.harvard.edu, Harvard Medical School Abstract: We successfully predicted synthetic lethal genes in Saccharomyces cerevisiae by integrating multiple data types including co-localization, correlated mRNA expression, physical interaction, protein function, and sequence homology. Our predictions may help identify redundant genes and pathways. Furthermore, gene pair characteristics important in generating predictions may better our understanding of genetic robustness. File: sharyl_wongATstudent.hms.harvard.edu_54 ************************************************* Tue Apr 15 12:08:48 2003 Number: 55 Name: Goesmann, Alexander Affiliation: Center for Genome Research, Bielefeld University Address: Keplerstrasse 15 City: Bielefeld State/Provice: NRW Postal/Zip Code: 33613 Country: Germany Email: Alexander.Goesmann@Genetik.Uni-Bielefeld.DE Phone: 0049 521 106 4813 Fax: 0049 521 106 5626 I plan to use my laptop computer as part of my poster Category: Functional Genomics Poster Title: BRIDGE - Building a Bioinformatics Ressource for the Integration of heterogeneous Data from Genomic Explorations into a platform for Systems Biology Poster Authors and organization: Alexander Goesmann¹, Folker Meyer², D. Bartels, L. Krause, B. Linke, O. Rupp, A. P�hler
¹Alexander.Goesmann@Genetik.Uni-Bielefeld.DE, Center for Genome Research, Bielefeld University; ²fm@Genetik.Uni-Bielefeld.DE, Center for Genome Research, Bielefeld University Abstract: We describe our concept for the integration of heterogeneous data into a platform for systems biology. We have implemented a Bioinformatics Resource for the Integration of heterogeneous Data from Genomic Explorations (BRIDGE) and illustrate the usability of our approach as a platform for systems biology for two sample applications. File: Alexander.GoesmannATGenetik.Uni-Bielefeld.DE_55 ************************************************* Tue Apr 15 14:10:52 2003 Number: 56 Name: Van Yper, Stefan JL Affiliation: Department of Applied Mathematics, Biometrics and Process Control, Ghent University Address: Coupure Links 653 City: Gent State/Provice: Oost-Vlaanderen Postal/Zip Code: B-9000 Country: Belgium Email: Stefan@biomath.rug.ac.be Phone: +32 9 264 61 79 Fax: +32 9 264 62 20 Category: New Frontiers Poster Title: Phylogenetic footprinting of co-expressed genes by Tree-Gibbs sampling Poster Authors and organization: Stefan Van Yper ¹, Olivier Thas ², Jean-Pierre Ottoy and Wim Van Criekinge
¹Stefan@biomath.rug.ac.be, Department of Applied Mathematics, Biometrics and Process Control, Ghent University; ²olivier.thas@rug.ac.be, Department of Applied Mathematics, Biometrics and Process Control, Ghent University Abstract: Using site/motif Gibbs sampling, transcription factor binding sites can be found by analysing either the promoter sequences of co-expressed genes or the promoter sequences of orthologous genes. Tree-Gibbs sampling combines both data sources in one algorithm. This way additional information is available, resulting in improved, both in speed and accuracy, motif finding File: StefanATbiomath.rug.ac.be_56 ************************************************* Tue Apr 15 16:28:45 2003 Number: 57 Name: Lewis, Kimberly N Affiliation: University of Toronto Address: Room 1060 10th Floor, Mt Sinai Hospital, 600 University Ave City: Toronto State/Provice: Ontario Postal/Zip Code: M5G 1X5 Country: Canada Email: lewis@mshri.on.ca Phone: 416-586-4800 x2863 Fax: 416-586-8869 Category: Databases Poster Title: MyMED - An Internal XML Relational Database Implementation of MEDLINE Citations Poster Authors and organization: K Lewis¹, CW Hogue²
¹lewis@mshri.on.ca, Samuel Lunenfeld Research Institute, Mt Sinai Hospital, Dept of Biochemistry, University of Toronto; ²hogue@mshri.on.ca, Samuel Lunenfeld Research Institute, Mt Sinai Hospital, Dept of Biochemistry, University of Toronto Abstract: MyMED is an internal relational XML database implementation of MEDLINE citations. The MyMED database is necessary to execute text mining algorithms and complex text searches in a fast, secure manner. Data is stored in a DB2 database that is enabled for the XML Extender and Text Information Extender. File: lewisATmshri.on.ca_57 ************************************************* Wed Apr 16 05:10:41 2003 Number: 58 Name: Beissbarth, Tim Affiliation: WEHI Address: 1G Royal Parade City: Parkville State/Provice: VIC Postal/Zip Code: 3050 Country: Australia Email: beissbarth@wehi.edu.au Phone: +61 3 9345 2629 Fax: Category: Data Mining Poster Title: GOstat: Find statistically overrepresented Gene GOstat: Find statistically overrepresented Gene Ontologies within a group of genes Poster Authors and organization: Tim Beissbarth¹, Terry Speed²
¹beissbarth@wehi.edu.au, WEHI; ²terry@wehi.adu.au, WEHI Abstract: GOstat provides a useful tool in order to find biological processes or annotations characteristic for a group of genes. This is greatly helpful in analyzing lists of genes resulting from high throughput screening experiments, such as microarrays, for their biological meaning. GOstat is accessible via the Internet at http://gostat.wehi.edu.au. File: beissbarthATwehi.edu.au_58 ************************************************* Wed Apr 16 08:51:18 2003 Number: 59 Name: Platzer, Ute Affiliation: German Cancer Research Centre Address: Im Neuenheimer Feld 280 City: Heidelberg State/Provice: Baden-Wuerttemberg Postal/Zip Code: 69120 Country: Germany Email: u.platzer@dkfz.de Phone: +49 6221 422355 Fax: +49 6221 422345 I plan to use my laptop computer as part of my poster Category: Systems Biology Poster Title: Gene-O-Matic: Regulatory Network Simulation in Multicellular Organisms Poster Authors and organization: Ute Platzer¹, Rolf Lohaus², Hans-Peter Meinzer
¹u.platzer@dkfz.de, German Cancer Research Centre; ²r.lohaus@dkfz.de, German Cancer Research Centre Abstract: Gene-O-Matic is a graphical tool for the construction and simulation of regulatory networks in multicellular organisms. A developmental process simulated successfully is embryonic development of the worm Caenorhabditis elegans. Gene-O-Matic is availabe on request from the authors, or by e-mail to cello@dkfz.de. The project's website can be found at http://mbi.dkfz-heidelberg.de/projects/cellsim/. File: u.platzerATdkfz.de_59 ************************************************* Wed Apr 16 13:36:56 2003 Number: 59 Name: Hughes, Aubrey D Affiliation: Medical College of Wisconsin Address: 8701 Watertown Plank Rd City: Milwaukee State/Provice: Wisconsin Postal/Zip Code: 53226 Country: USA Email: ahughes@mcw.edu Phone: 1 4144567506 Fax: 1 4144566190 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: RAT GENOME DATABASE - RGD - DISEASE ORIENTED RESEARCH RESOURCE Poster Authors and organization: Aubrey Hughes¹, Jedediah Mathis², Mary Shimoyama, Milton Datta, Simon Twigger, Charles W.Wang, Nataliya Nenasheva, Dean Pasko, Norberto de la Cruz, Victor Ruotti, Susan Bromberg, Chin-Fu Chen, Rajni Nigam, Gopal Gopinathrao, Angela Zuniga-Myer and Peter Tonellato
¹ahughes@mcw.edu, Medical College of Wisconsin; ²jmathis@mcw.edu, Medical College of Wisconsin Abstract: The Rat Genome Database (RGD) provides research groups� access to rat genomic and genetic data, including annotated sequence, related to particular diseases. DORR will help RGD answer the need of the rat community for access to curated data of interest. rgd.mcw.edu File: ahughesATmcw.edu_59 ************************************************* Wed Apr 16 14:00:45 2003 Number: 59 Name: Hughes, Aubrey D Affiliation: Medical College of Wisconsin Address: 8701 Watertown Plank Rd City: Milwaukee State/Provice: Wisconsin Postal/Zip Code: 53226 Country: USA Email: ahughes@mcw.edu Phone: 1 4144567506 Fax: 1 4144566190 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: RAT GENOME DATABASE - RGD - MAPPING DISEASE ONTO THE GENOME Poster Authors and organization: Aubrey Hughes¹, Jedediah Mathis², Mary Shimoyama, Norberto de la Cruz, Charles W. Wang, Nataliya Nenasheva, Dean Pasko, Jiali Chen, Lan Zhao, Chunyu Fan, Wenhua Wu, Chin-Fu Chen, Rajni Nigam, Gopal Gopinathrao, Angela Zuniga-Meyer, Susan Bromberg, Jessica Ginster, Anne Kwitek-Black, Janan Eppig, Lois Maltais, Donna Maglott, Greg Schuler, Simon Twigger, Howard Jacob and Peter Tonellato
¹ahughes@mcw.edu, Medical College of Wisconsin; ²jmathis@mcw.edu, Medical College of Wisconsin Abstract: The Rat Genome Database (RGD) is a disease centric resource of comprehensively curated data from rat genetic and genomic research. RGD�s goal is to provide information that will aid researchers in using the rat as a model organism for human disease studies. RGD is available at rgd.mcw.edu . File: ahughesATmcw.edu_59 ************************************************* Wed Apr 16 14:30:14 2003 Number: 59 Name: Hughes, Aubrey D Affiliation: Medical College of Wisconsin Address: 8701 Watertown Plank Rd City: Milwaukee State/Provice: Wisconsin Postal/Zip Code: 53226 Country: USA Email: ahughes@mcw.edu Phone: 1 4144567506 Fax: 1 4144566190 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: RAT GENOME DATABASE - RGD - DISEASE ORIENTED RESEARCH RESOURCE Poster Authors and organization: Aubrey Hughes¹, Jedediah Mathis², Mary Shimoyama, Milton Datta, Simon Twigger, Charles W.Wang, Nataliya Nenasheva, Dean Pasko, Norberto de la Cruz, Victor Ruotti, Susan Bromberg, Chin-Fu Chen, Rajni Nigam, Gopal Gopinathrao, Angela Zuniga-Myer and Peter Tonellato
¹ahughes@mcw.edu, Medical College of Wisconsin; ²jmathis@mcw.edu, Medical College of Wisconsin Abstract: The Rat Genome Database (RGD) provides research groups� access to rat genomic and genetic data, including annotated sequence, related to particular diseases. DORR will help RGD answer the need of the rat community for access to curated data of interest. rgd.mcw.edu File: ahughesATmcw.edu_59 ************************************************* Wed Apr 16 15:22:25 2003 Number: 59 Name: Hayes, Wayne B Affiliation: University of Maryland Address: IPST Building 224 City: College Park State/Provice: MD Postal/Zip Code: 20742 Country: USA Email: wayne@cs.toronto.edu Phone: 240-893-1612 Fax: 301-314-9363 Category: Sequence Comparison Poster Title: IMPROVING SEQUENCE ASSEMBLIES USING HIGH-QUALITY OVERLAPS Poster Authors and organization: Michael Roberts¹, James Yorke², Brian Hunt, Wayne Hayes, Aleksey Zimin, Cevat Ustun, Paul Havlak
¹tri@ipst.umd.edu, University of Maryland; ²yorke@ipst.umd.edu, University of Maryland Abstract: Finishing a genome costs as much as initial assembly. Since initial assembly gets about 95% of it, gaining just a few extra percent initially can save tens of millions of dollars in finishing costs. We present computational techniques for improving "overlaps" result in up to 5% additional sequence during initial assembly. File: wayneATcs.toronto.edu_59 ************************************************* Wed Apr 16 16:04:43 2003 UPDATE ----- Number: 50 Name: Burgoon, Lyle D Affiliation: Michigan State University Address: 223 Biochemistry Bldg, Michigan State University City: East Lansing State/Provice: MI Postal/Zip Code: 48824 Country: USA Email: burgoonl@msu.edu Phone: 517-353-1944 Fax: Category: Microarrays Poster Title: Statistical Promoter Regulatory Element Analysis of cDNA Microarray Data For the Prediction of cAMP Responsive Genes Poster Authors and organization: Lyle D Burgoon¹, Ken Y Kwan, Tim Zacharewski²
¹burgoonl@msu.edu, Michigan State University; ²tzachare@msu.edu, Michigan State University Abstract: We have developed a method for predicting transcription factor responsive genes by combining response element prediction with cDNA microarray data. Our Statistical Promoter REgulatory Element (SPREE) application program identified cAMP responsive elements. SPREE output was combined with cDNA microarray data to design an SVM model for predicting cAMP responsive genes. File: burgoonlATmsu.edu_50 ************************************************* Wed Apr 16 16:21:26 2003 UPDATE ----- Number: 27 Name: Lottaz, Claudio Affiliation: Max-Planck-Institute for Molecular Genetics Address: Ihnestr. 73 City: Berlin State/Provice: Berlin Postal/Zip Code: 14195 Country: Germany Email: Claudio.Lottaz@molgen.mpg.de Phone: +49 30 8413 1177 Fax: +49 30 8413 1176 Category: Microarrays Poster Title: Gene Ontology Driven Classification of Gene Expression Patterns Poster Authors and organization: Claudio Lottaz¹, Renate Kirschner², Stefan Bentink, Christian Hagemeier and Rainer Spang
¹Claudio.Lottaz@molgen.mpg.de, Max-Planck-Institute for Molecular Genetics, Berlin; ²r.kirschner@charite.de, Medical Center Charit�, Berlin Abstract: We propose to structure analysis of microarry according to biological knowledge in order to provide an intuitive and biologically meaningful rationale for computational classification results. Thereby, we rely on the Gene Ontology to attribute genes to biological aspects and usual machine learning methods for classification. File: Claudio.LottazATmolgen.mpg.de_27 ************************************************* Wed Apr 16 22:07:57 2003 Number: 67 Name: Gardy, Jennifer L Affiliation: Dept. of Molecular Biology and Biochemistry, Simon Fraser University Address: 8888 University Dr. City: Burnaby State/Provice: B.C. Postal/Zip Code: V5A 1S6 Country: Canada Email: jlgardy@sfu.ca Phone: 604-291-5414 Fax: 604-291-5583 Category: Predictive Methods Poster Title: PSORT-B: A Web-based Tool for Bacterial Subcellular Localization Prediction Poster Authors and organization: Jennifer L. Gardy¹, Cory A. Spencer², Fiona S.L. Brinkman
¹jlgardy@sfu.ca, Dept. of Molecular Biology and Biochemistry, Simon Fraser University; ²cspencer@sprocket.org, Dept. of Molecular Biology and Biochemistry, Simon Fraser University Abstract: We present PSORT-B (http://www.psort.org) - a subcellular localization predictor with a measured accuracy of 97% for Gram-negative bacteria. Issues including the handling of proteins resident at multiple localizations, the importance of the �unknown� result and the development of a Gram-positive version are discussed. Selected whole genome analysis is also presented. File: jlgardyATsfu.ca_67 ************************************************* Wed Apr 16 22:30:26 2003 Number: 68 Name: Cheung, Angel Y.M. Affiliation: Department of Computer Science, Chu Hai College Address: Yi Lok Street, Riviera Gardens, Tsuen Wan, Hong Kong City: Hong Kong State/Provice: Hong Kong Postal/Zip Code: Country: Hong Kong Email: angelymch@yahoo.com Phone: 852-9322-6370 Fax: Category: Data Mining Poster Title: Multi-Dynamic Bayesian Networks for Pattern Recognition in Genomic DNA Sequences Poster Authors and organization: Leo Wang-Kit Cheung¹, Angel Yee-Man Cheung²
¹lcheung@crch.hawaii.edu, Cancer Research lCenter of Hawaii, University of Hawaii ; ²angelymch@yahoo.com, Department of Computer Science, Chu Hai College Abstract:

Abstract (50-word Version):

Multi-Dynamic Bayesian Networks (MDBNs) are introduced for analyzing multi-dimensional genomic DNA data. A two-dimensional version of MDBNs is developed for learning and predicting the joint behavior of the C+G richness pattern and the bendability pattern of DNA. Applications of these MDBNs for recognition/prediction of eukaryotic promoter regions are illustrated.

File: angelymchATyahoo.com_68 ************************************************* Wed Apr 16 23:48:11 2003 UPDATE ----- Number: 34 Name: Arthur, Jonathan W Affiliation: Proteome Systems Ltd Address: Unit 1 35-41 Waterloo Rd City: North Ryde State/Provice: NSW Postal/Zip Code: 2113 Country: Australia Email: jonathan.arthur@proteomesystems.com Phone: 02 8877 8930 Fax: 02 9889 1805 I plan to use my laptop computer as part of my poster Category: Genome Annotation Poster Title: Using proteomics to mine genome sequences Poster Authors and organization: Jonathan W Arthur¹, Marc R Wilkins²
¹jonathan.arthur@proteomesystems.com, Proteome Systems Ltd; ²marc.wilkins@proteomesystems.com, Proteome Systems Ltd Abstract:

File: jonathan.arthurATproteomesystems.com_34 ************************************************* Thu Apr 17 00:08:54 2003 UPDATE ----- Number: 68 Name: Cheung, Angel Y Affiliation: Department of Computer Science, Chu Hai College Address: Yi Lok Street, Riviera Gardens, Tsuen Wan, Hong Kong City: Hong Kong State/Provice: Hong Kong Postal/Zip Code: Country: Hong Kong Email: angelymch@yahoo.com Phone: 852-9322-6370 Fax: Category: Data Mining Poster Title: Multi-Dynamic Bayesian Networks for Pattern Recognition in Genomic DNA Sequences Poster Authors and organization: Leo Wang-Kit Cheung¹, Angel Yee-Man Cheung²
¹lcheung@crch.hawaii.edu, Cancer Research lCenter of Hawaii, University of Hawaii ; ²angelymch@yahoo.com, Department of Computer Science, Chu Hai College Abstract: Multi-Dynamic Bayesian Networks (MDBNs) are introduced for analyzing multi-dimensional genomic DNA data. A two-dimensional version of MDBNs is developed for learning and predicting the joint behavior of the C+G richness pattern and the bendability pattern of DNA. Applications of these MDBNs for recognition/prediction of eukaryotic promoter regions are illustrated. File: angelymchATyahoo.com_68 ************************************************* Thu Apr 17 00:12:19 2003 UPDATE ----- Number: 68 Name: Cheung, Angel Y Affiliation: Department of Computer Science, Chu Hai College Address: Yi Lok Street, Riviera Gardens, Tsuen Wan, Hong Kong City: Hong Kong State/Provice: Hong Kong Postal/Zip Code: Country: Hong Kong Email: angelymch@yahoo.com Phone: 852-9322-6370 Fax: Category: Data Mining Poster Title: Multi-Dynamic Bayesian Networks for Pattern Recognition in Genomic DNA Sequences Poster Authors and organization: Leo Wang-Kit Cheung¹, Angel Yee-Man Cheung²
¹lcheung@crch.hawaii.edu, Cancer Research lCenter of Hawaii, University of Hawaii ; ²angelymch@yahoo.com, Department of Computer Science, Chu Hai College Abstract: Multi-Dynamic Bayesian Networks (MDBNs) are introduced for analyzing multi-dimensional genomic DNA data. A two-dimensional version of MDBNs is developed for learning and predicting the joint behavior of the C+G richness pattern and the bendability pattern of DNA. Applications of these MDBNs for recognition/prediction of eukaryotic promoter regions are illustrated. File: angelymchATyahoo.com_68 ************************************************* Thu Apr 17 00:31:36 2003 Number: 69 Name: Vilanova, David Affiliation: Nestle Research Center Address: VERS CHEZ LES BLANC City: Lausanne State/Provice: VAUD Postal/Zip Code: 1012 Country: Switzerland Email: david.vilanova@rdls.nestle.com Phone: +41217858723 Fax: +41217858925 Category: Data Mining Poster Title: Hight-throughput gene expression analysis with GATO Poster Authors and organization: David Vilanova¹, James holzwarth², Marie camille Zwahlen, Frank Desiere,Matthew Alan Roberts
¹david.vilanova@rdls.nestle.com, Nestle research center; ²james.holzwarth@rdls.nestle.com, Nestle research center Abstract: We present GATO (gene annotation tool) a tool to analyse gene expression data based on Ensembl database and Gene ontology. We describe how our tool can be utilized to rapidly mind gene expression data and drive biological interpretation using Affymetrix arrays. File: david.vilanovaATrdls.nestle.com_69 ************************************************* Thu Apr 17 07:08:13 2003 Number: 70 Name: Steinhoff, Christine Affiliation: Max Planck Institute for Molecular Genetics Address: Ihnestr. 73 City: Berlin State/Provice: Germany Postal/Zip Code: 14195 Country: Germany Email: christine.steinhoff@molgen.mpg.de Phone: +49 30 8413 1171 Fax: +49 30 8413 1152 Category: Functional Genomics Poster Title: Extraction of Pathways Involved in Microarray Time Course Experiments Poster Authors and organization: Steinhoff¹, Mueller², Hannes Luz, Martin Vingron
¹christine.steinhoff@molgen.mpg.de, Max Planck Institute; ²Tobias.Mueller@biozentrum.uni-wuerzburg.de, Biocenter, University W�rzburg Abstract: We present a procedure that integrates knowledge of multiple biological databases to recover potentially involved pathways from time course microarray experiments. Starting with a refined new clustering algorithm we group similarly behaving genes, followed by an integrated analysis of common transcription factor binding patterns, functional categories and biologically verified pathways. File: christine.steinhoffATmolgen.mpg.de_70 ************************************************* Thu Apr 17 11:38:23 2003 Number: 71 Name: Gerber, Georg K Affiliation: Massachusetts Institute of Technology, Laboratory for Computer Science Address: 200 Technology Square no. 775 City: Cambridge State/Provice: MA Postal/Zip Code: 02139 Country: USA Email: georg@mit.edu Phone: 617-764-1398 Fax: 617-253-7512 Category: Functional Genomics Poster Title: Computational Discovery of Gene Modules and Regulatory Networks Poster Authors and organization: Georg K. Gerber¹, Ziv-Bar Joseph², Tong Ihn Lee, Fran�ois Robert, D. Benjamin Gordon, Ernest Fraenkel, Itamar Simon, Tommi S. Jaakkola, Richard A. Young, David K. Gifford
¹georg@mit.edu, Massachusetts Institute of Technology, Laboratory for Computer Science; ²georg@mit.edu, Massachusetts Institute of Technology, Laboratory for Computer Science Abstract: We present an algorithm for combining genome-wide expression and protein-DNA binding data to discover co-regulated modules of genes and associated regulatory networks. Our algorithm operates on discovered networks to label transcription factors as activators or repressors, identify patterns of combinatorial regulation, and uncover sub-networks for biological processes in Saccharomyces cervisiae. File: georgATmit.edu_71 ************************************************* Thu Apr 17 13:47:18 2003 Number: 72 Name: Haenel, Petra Affiliation: Bielefeld University Address: Postfach 10 01 31 City: Bielefeld State/Provice: na Postal/Zip Code: 33501 Country: Germany Email: iphaenel@techfak.uni-bielefeld.de Phone: +49 521 106 2950 Fax: +49 521 106 2992 Category: Data Mining Poster Title: Continuous in situ Analysis of Cell Growth and Cell Viability Poster Authors and organization: Petra Haenel¹, Franz Kummert², Karl Friehs, Erwin Flaschel, Gerhard Sagerer
¹iphaenel@techfak.uni-bielefeld.de, Bielefeld University, Germany; ²franz@techfak.uni-bielefeld.de, Bielefeld University, Germany Abstract: We present an image analysis system to detect and count eukaryotic cells in darkfield microscopy images. Analyzing undiluted yeast suspension the tool differentiates between single, budding and cell clusters as well as dead and vital cells. The cells within a cluster are detected by active contours as well as the cell features which results in precise information for fermentation. File: iphaenelATtechfak.uni-bielefeld.de_72 ************************************************* Thu Apr 17 14:04:44 2003 Number: 73 Name: Sczyrba, Alexander Affiliation: Bielefeld University Address: Postfach 10 01 31 City: Bielefeld State/Provice: na Postal/Zip Code: 33501 Country: Germany Email: asczyrba@techfak.uni-bielefeld.de Phone: +49 521 106 2910 Fax: +49 521 106 6411 Category: Sequence Comparison Poster Title: The Bielefeld University Bioinformatics Server Poster Authors and organization: Alexander Sczyrba¹, Jan Krueger², Robert Giegerich
¹asczyrba@techfak.uni-bielefeld.de, Bielefeld University, Germany; ²jkrueger@techfak.uni-bielefeld.de, Bielefeld University, Germany Abstract: The Bielefeld University Bioinformatics Server (BiBiServ), http://bibiserv.techfak.uni-bielefeld.de, supports Internet-based collaborative research and education in bioinformatics. Currently, 15 software tools and various educational media are available. These include tools from different areas such as Genome Comparison, Alignments, Primer Design, RNA Structures, and Evolutionary Relationships. In 2002 approximate 14.000 users per month used BiBiServ services with rising tendency. File: asczyrbaATtechfak.uni-bielefeld.de_73 ************************************************* Thu Apr 17 14:20:44 2003 Number: 74 Name: Jiang, Tianzi Affiliation: Institute of Automation, Chinese Academy of Sciences Address: 95 Zhong Guan Cun Dong Lu City: Beijing State/Provice: Beijing Postal/Zip Code: 100080 Country: China Email: jiangtz@nlpr.ia.ac.cn Phone: +86-10 82614469 Fax: +86-10-6255 1993 Category: Structural Biology Poster Title: Protein Folding Simulations by Combining Tabu Search with Genetic Algorithms Based on HP Model Poster Authors and organization: Tianzi Jiang¹, Qinghua Cui², Guihua Shi, Songde Ma
¹jiangtz@nlpr.ia.ac.cn, Chinese Academy of Sciences; ²qhcui@nlpr.ia.ac.cn, Chinese Academy of Sciences Abstract: A hybrid algorithm of genetic algorithm and tabu search is presented. The hybrid algorithm can be successfully applied to protein folding based on hydrophobic-hydrophilic model. A protein structure database is also created. The results indicate that in all cases our method work better than genetic algorithm and tabu search alone. File: jiangtzATnlpr.ia.ac.cn_74 ************************************************* Thu Apr 17 16:50:17 2003 Number: 75 Name: Shilov, Boris V Affiliation: Siberian State Medical University Address: Solyanoi pereulok, 34, 2 City: Tomsk State/Provice: Russia Postal/Zip Code: 634003 Country: Russia Email: bvshilov@hotbox.ru Phone: +7-3822-650564 Fax: +7-3822-650564 Category: Predictive Methods Poster Title: Low-budgetary scheme for differentiation and DNA quantity investigation in blood lymphocytes of patients with chronical tonsillitis Poster Authors and organization: Boris V.Shilov¹, Dmitry A.Dolgun²
¹bvshilov@hotbox.ru, SSMU; ², SSMU Abstract: The nucleus belonging to any type of the cells was determined to estimate of atypical lymphocytes in patients with chronic tonsillitis, to analyze the vital cycle those cells on the base of classification of transformed cells stained according to Romanovsky-Gimza. Image segmentation process was adapted to condition of low-budgetary science File: bvshilovAThotbox.ru_75 ************************************************* Fri Apr 18 01:18:11 2003 Number: 76 Name: Keer, Dipinder S Affiliation: Georgia Institute of Technology Address: 325151 Georgia Tech Station City: Atlanta State/Provice: Georgia Postal/Zip Code: 30332 Country: USA Email: dipinder.keer@biology.gatech.edu Phone: 404-206-4160 Fax: I plan to use my laptop computer as part of my poster Category: Structural Biology Poster Title: Using Molecular Mechanics Algorithms in Computational Ab-Initio Folding for ssRNA Structure Determination in the Packaged Pariacotovirus Poster Authors and organization: Dipinder Keer¹
¹dipinder.keer@biology.gatech.edu, Georgia Institute of Technology Abstract: We present a model for the packaged structure of the ssRNA in pariacotovirus along with the development methodology for such a model. The computational ab-initio methodology uses molecular mechanics algorithms to model the folding of PaV RNA within the dodecahedral RNA cage. File: dipinder.keerATbiology.gatech.edu_76 ************************************************* Fri Apr 18 05:46:58 2003 Number: 77 Name: Schoenhuth, Alexander _ Affiliation: Center for Applied Computer Science, University Cologne Address: Weyertal 80 City: Koeln State/Provice: NRW Postal/Zip Code: 50931 Country: Germany Email: aschoen@zpr.uni-koeln.de Phone: 49 221 4706003 Fax: 49 221 4705160 Category: Data Mining Poster Title: Partially supervised clustering of gene expression time course data Poster Authors and organization: Alexander Schoenhuth¹, Alexander Schliep², Christine Steinhoff
¹aschoen@zpr.uni-koeln.de, Center for Applied Computer Science, University Cologne; ²schliep@molgen.mpg.de, Max Planck Institute for Molecular Genetics, Berlin Abstract: As the amount of genes with known function available is growing there is a need for classification methods which allow to use prior knowledge. Partially supervised clustering of time courses stemming from gene expression experiments addresses this problem. Here a model-based clustering approach using Hidden Markov Models is proposed. File: aschoenATzpr.uni-koeln.de_77 ************************************************* Sat Apr 19 00:32:19 2003 Number: 78 Name: Koike, Asako Affiliation: Human Genome Center, The Institute of Medical Science, The University of Tokyo Address: 4-6-1 Shirokane-dai City: Minto-ku State/Provice: Tokyo Postal/Zip Code: 108-8639 Country: Japan Email: akoike@ims.u-tokyo.ac.jp Phone: 81-3-5449-5611 Fax: 81-3-5449-5434 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: PRIME: automatically extracted PRotein Interactions and Molecular Information databasE. Poster Authors and organization: Asako Koike¹, Yoshiyuki Kobayashi², Toshihisa Takagi
¹akoike@ims.u-tokyo.ac.jp, Human Genome Center, The Institute of Medical Science, Univ. of Tokyo; ²yashi@ls.hitachi.co.jp, Life Science Group, Hitachi, Ltd. Abstract: PRIME(http://prime.ontology.ims.u-tokyo.ac.jp/) is an integrated database involving major completely sequenced eukaryotes. It contains the protein-protein/gene/compound interaction data extracted by natural language processing, domain information, structural information, protein kinase classification, and ortholog tables among organisms. The comparison and prediction of pathways are also available by an automatic pathway graphic image interface. File: akoikeATims.u-tokyo.ac.jp_78 ************************************************* Sat Apr 19 00:41:26 2003 Number: 79 Name: Koike, Asako Affiliation: Human Genome Center, The Institute of Medical Science, The University of Tokyo Address: 4-6-1 Shirokane-dai City: Minto-ku State/Provice: Tokyo Postal/Zip Code: 108-8639 Country: Japan Email: akoike@ims.u-tokyo.ac.jp Phone: 81-3-5449-5611 Fax: 81-3-5449-5434 Category: Structural Biology Poster Title: The analysis and prediction of protein-protein interacting sites. Poster Authors and organization: Asako Koike¹, Toshihisa Takagi²
¹akoike@ims.u-tokyo.ac.jp, Human Genome Center, The Institute of Medical Science, Univ. of Tokyo; ²takagi@ims.u-tokyo.ac.jp, Human Genome Center, The Institute of Medical Science, Univ. of Tokyo Abstract: We developed the prediction method of protein interaction sites using sequence profiles and accessible surface area of neighboring residues, surface patches, other physicochemical characteristic, and support vector machines. The relationship between the prediction accuracy and the characteristic of protein-protein interaction sites is discussed. File: akoikeATims.u-tokyo.ac.jp_79 ************************************************* Sun Apr 20 03:11:45 2003 UPDATE ----- Number: 76 Name: Keer, Dipinder S Affiliation: Georgia Institute of Technology Address: 325151 Georgia Tech Station City: Atlanta State/Provice: Georgia Postal/Zip Code: 30332 Country: USA Email: dipinder.keer@biology.gatech.edu Phone: 404-206-4160 Fax: I plan to use my laptop computer as part of my poster Category: Structural Biology Poster Title: Structural Modeling of RNA in the Packaged Pariacotovirus Using Molecular Mechanics Algorithms Poster Authors and organization: Dipinder Keer¹
¹dipinder.keer@biology.gatech.edu, Georgia Institute of Technology Abstract: We present a model for the packaged structure of the single stranded RNA in the pariacotovirus along with the development methodology for such a model. The computational methodology uses molecular mechanics algorithms to model the folding of PaV RNA within the dodecahedral RNA cage. File: dipinder.keerATbiology.gatech.edu_76 ************************************************* Sun Apr 20 03:23:40 2003 UPDATE ----- Number: 61 Name: Hughes, Aubrey D Affiliation: Medical College of Wisconsin Address: 8701 Watertown Plank Rd City: Milwaukee State/Provice: Wisconsin Postal/Zip Code: 53226 Country: USA Email: ahughes@mcw.edu Phone: 1 4144567506 Fax: 1 4144566190 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: RAT GENOME DATABASE - RGD - MAPPING DISEASE ONTO THE GENOME Poster Authors and organization: Aubrey Hughes¹, Jedediah Mathis², Mary Shimoyama, Norberto de la Cruz, Charles W. Wang, Nataliya Nenasheva, Dean Pasko, Jiali Chen, Lan Zhao, Chunyu Fan, Wenhua Wu, Chin-Fu Chen, Rajni Nigam, Gopal Gopinathrao, Angela Zuniga-Meyer, Susan Bromberg, Jessica Ginster, Anne Kwitek-Black, Janan Eppig, Lois Maltais, Donna Maglott, Greg Schuler, Simon Twigger, Howard Jacob and Peter Tonellato
¹ahughes@mcw.edu, Medical College of Wisconsin; ²jmathis@mcw.edu, Medical College of Wisconsin Abstract: The Rat Genome Database (RGD) is a disease centric resource of comprehensively curated data from rat genetic and genomic research. RGD's goal is to provide information that will aid researchers in using the rat as a model organism for human disease studies. RGD is available at rgd.mcw.edu . File: ahughesATmcw.edu_61 ************************************************* Sun Apr 20 03:26:09 2003 UPDATE ----- Number: 61 Name: Hughes, Aubrey D Affiliation: Medical College of Wisconsin Address: 8701 Watertown Plank Rd City: Milwaukee State/Provice: Wisconsin Postal/Zip Code: 53226 Country: USA Email: ahughes@mcw.edu Phone: 1 4144567506 Fax: 1 4144566190 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: RAT GENOME DATABASE - RGD - MAPPING DISEASE ONTO THE GENOME Poster Authors and organization: Aubrey Hughes¹, Jedediah Mathis², Mary Shimoyama, Norberto de la Cruz, Charles W. Wang, Nataliya Nenasheva, Dean Pasko, Jiali Chen, Lan Zhao, Chunyu Fan, Wenhua Wu, Chin-Fu Chen, Rajni Nigam, Gopal Gopinathrao, Angela Zuniga-Meyer, Susan Bromberg, Jessica Ginster, Anne Kwitek-Black, Janan Eppig, Lois Maltais, Donna Maglott, Greg Schuler, Simon Twigger, Howard Jacob and Peter Tonellato
¹ahughes@mcw.edu, Medical College of Wisconsin; ²jmathis@mcw.edu, Medical College of Wisconsin Abstract: The Rat Genome Database (RGD) is a disease centric resource of comprehensively curated data from rat genetic and genomic research. RGD's goal is to provide information that will aid researchers in using the rat as a model organism for human disease studies. RGD is available at rgd.mcw.edu . File: ahughesATmcw.edu_61 ************************************************* Sun Apr 20 22:32:14 2003 Number: 80 Name: SUN, YAN Affiliation: Bioinformatics Institute Address: 21 Heng Mui Keng Terrace City: Singapore State/Provice: Singapore Postal/Zip Code: 119613 Country: Singapore Email: sunyan@bii.a-star.edu.sg Phone: 65 6874 5526 Fax: 65 6778 1250 Category: Systems Biology Poster Title: Discovering novel regulatory controls of budding yeast cell cycle by Reverse Engineering and Bayesian Network Modeling Poster Authors and organization: Yan Sun¹, Pawan Dhar²
¹sunyan@bii.a-star.edu.sg, Bioinformatics Institute, 21 Heng Mui Keng Terrace, Singapore; ²pk@bii.a-star.edu.sg, Bioinformatics Institute, 21 Heng Mui Keng Terrace, Singapore Abstract: In this study, a Reverse Engineering and Bayesian Network Modeling (REBNM) approach has been used for inferring the cell cycle regulatory network from high-throughput gene expression data. The REBNM analyzer uses prior biological knowledge and supervised classification scheme for functionally grouping genes for downstream processing by Bayesian network modeling. File: sunyanATbii.a-star.edu.sg_80 ************************************************* Sun Apr 20 22:32:22 2003 Number: 81 Name: SUN, YAN Affiliation: Bioinformatics Institute Address: 21 Heng Mui Keng Terrace City: Singapore State/Provice: Singapore Postal/Zip Code: 119613 Country: Singapore Email: sunyan@bii.a-star.edu.sg Phone: 65 6874 5526 Fax: 65 6778 1250 Category: Systems Biology Poster Title: Discovering novel regulatory controls of budding yeast cell cycle by Reverse Engineering and Bayesian Network Modeling Poster Authors and organization: Yan Sun¹, Pawan Dhar²
¹sunyan@bii.a-star.edu.sg, Bioinformatics Institute, 21 Heng Mui Keng Terrace, Singapore; ²pk@bii.a-star.edu.sg, Bioinformatics Institute, 21 Heng Mui Keng Terrace, Singapore Abstract: In this study, a Reverse Engineering and Bayesian Network Modeling (REBNM) approach has been used for inferring the cell cycle regulatory network from high-throughput gene expression data. The REBNM analyzer uses prior biological knowledge and supervised classification scheme for functionally grouping genes for downstream processing by Bayesian network modeling. File: sunyanATbii.a-star.edu.sg_81 ************************************************* Mon Apr 21 05:12:51 2003 Number: 82 Name: Zou, Ming Yan Affiliation: School of Agriculture and Food Systems, University of Melbourne Address: Sneydes Road, Werribee City: Melbourne State/Provice: Victoria Postal/Zip Code: 3030 Country: Australia Email: y.zou@pgrad.unimelb.edu.au Phone: 61 3 92175204 Fax: 61 3 97419396 Category: Structural Biology Poster Title: Comparison between experimentally determined RNA secondary structures and computed structures with XNAfold Poster Authors and organization: Ming Yan Zou¹, Alan J. Hillier², P. Scott Chandry
¹y.zou@pgrad.unimelb.edu.au, School of Agriculture and Food Systems, University of Melbourne; ², School of Agriculture and Food Systems, University of Melbourne Abstract: XNAfold: a Java-C hybrid program for predicting RNA secondary structure and freely available at http://www.student.unimelb.edu.au/~yanmz/index.html The comparison between known secondary structures of RNA and structures computed with XNAfold is analysed. Among 133 different RNA from Protein Data Bank, 58% identified secondary structures match the predicted minimum free energy structure. File: y.zouATpgrad.unimelb.edu.au_82 ************************************************* Mon Apr 21 07:56:03 2003 Number: 83 Name: Veeramalai, Mallika Affiliation: Bioinformatics Research Centre, Dept. of Computing Science, University of Glasgow Address: 17, lilybank Gardens, University of Glasgow, City: Glasgow State/Provice: Scotland Postal/Zip Code: G12 8QQ Country: United Kingdom Email: mallika@dcs.gla.ac.uk Phone: +44 141 330 2421 Fax: +44 141 330 8627 Category: Structural Biology Poster Title: Incorporating Sequence and Biochemical Information in TOPS models - For Significant Pattern Matching and Pattern Discovery in Protein Structures Poster Authors and organization: Mallika Veeramalai¹, David Gilbert², David R Westhead
¹mallika@dcs.gla.ac.uk, Bioinformatics Research Centre, Dept. of Computing Science, University of Glasgow; ²drg@dcs.gla.ac.uk, Abstract: Incorporating sequence and biochemical features in TOPS (Topological Models of Protein Structures) for significant pattern matching and pattern discovery in protein structures. Interesting results would be valuable efforts to predict protein structure and function from the sequences, and these problems remain key challenges of direct relevance to projects in structural and functional genomics. TOPS database can be accessible from http://www.tops.leeds.ac.uk File: mallikaATdcs.gla.ac.uk_83 ************************************************* Mon Apr 21 13:54:09 2003 Number: 84 Name: Manduchi, Elisabetta Affiliation: University of Pennsylvania Address: 1428 Blockley Hall, 423 Guardian Drive City: Philadelphia State/Provice: PA Postal/Zip Code: 19104-6021 Country: USA Email: manduchi@pcbi.upenn.edu Phone: 215-573-4408 Fax: 215-573-3111 Category: Microarrays Poster Title: The RNA Abundance Database and its Annotation Web-Forms. Poster Authors and organization: Elisabetta Manduchi¹, G.R. Grant, Hongxian He, J. Liu, M.D. Mailman, A. Pizarro, P.L. Whetzel, C.J. Stoeckert Jr.
¹manduchi@pcbi.upenn.edu, Center for Bioinformatics, University of Pennsylvania Abstract: RAD and its web-based annotation forms are a system aimed at the collection, organization, and exchange of all relevant information pertaining to gene expression array (and SAGE) studies. The richness of information captured and the use of ontologies render RAD a very powerful infrastructure for querying and analysis ( http://www.cbil.upenn.edu/RAD3). File: manduchiATpcbi.upenn.edu_84 ************************************************* Mon Apr 21 14:30:02 2003 Number: 85 Name: Natasa, Przulj Affiliation: Department of Computer Science, University of Toronto Address: 10 Kings College Road City: Toronto State/Provice: Ontario Postal/Zip Code: M5S 3G4 Country: CANADA Email: natasha@cs.toronto.edu Phone: 416.946.3924 Fax: 416.978.1931 Category: Systems Biology Poster Title: Functional topology in a network of protein interactions Poster Authors and organization: Natasa Przulj¹, Dennis Wigle², Igor Jurisica, Department of Computer Science, University of Toronto, and Ontario Cancer Institute, Division of Cancer Informatics, Canada
¹natasha@cs.toronto.edu, Department of Computer Science, University of Toronto, Canada; ², Department of Surgery, University of Toronto, Canada Abstract: We systematically analyzed the S.cerevisiae protein-protein interaction network using graph theoretic tools to determine structure-function relationships. Constructed computational models describe and predict the properties of functional groups, protein complexes, signaling pathways, lethal and viable mutations, and proteins participating in genetic interactions. Our models offer insight into the complex wiring underlying cellular function. File: natashaATcs.toronto.edu_85 ************************************************* Mon Apr 21 17:33:19 2003 UPDATE ----- Number: 61 Name: Hughes, Aubrey D Affiliation: Medical College of Wisconsin Address: 8701 Watertown Plank Rd City: Milwaukee State/Provice: Wisconsin Postal/Zip Code: 53226 Country: USA Email: ahughes@mcw.edu Phone: 1 4144567506 Fax: 1 4144566190 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: RAT GENOME DATABASE - RGD - MAPPING DISEASE ONTO THE GENOME Poster Authors and organization: Aubrey Hughes¹, Jedediah Mathis², Mary Shimoyama, Norberto de la Cruz, Charles W. Wang, Nataliya Nenasheva, Dean Pasko, Jiali Chen, Lan Zhao, Chunyu Fan, Wenhua Wu, Chin-Fu Chen, Rajni Nigam, Gopal Gopinathrao, Angela Zuniga-Meyer, Susan Bromberg, Jessica Ginster, Anne Kwitek-Black, Janan Eppig, Lois Maltais, Donna Maglott, Greg Schuler, Simon Twigger, Howard Jacob and Peter Tonellato
¹ahughes@mcw.edu, Medical College of Wisconsin; ²jmathis@mcw.edu, Medical College of Wisconsin Abstract: The Rat Genome Database (RGD) is a disease centric resource of comprehensively curated data from rat genetic and genomic research. RGD's goal is to provide information that will aid researchers in using the rat as a model organism for human disease studies. RGD is available at rgd.mcw.edu . File: ahughesATmcw.edu_61 ************************************************* Mon Apr 21 17:35:11 2003 UPDATE ----- Number: 61 Name: Hughes, Aubrey D Affiliation: Medical College of Wisconsin Address: 8701 Watertown Plank Rd City: Milwaukee State/Provice: Wisconsin Postal/Zip Code: 53226 Country: USA Email: ahughes@mcw.edu Phone: 1 4144567506 Fax: 1 4144566190 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: RAT GENOME DATABASE - RGD - MAPPING DISEASE ONTO THE GENOME Poster Authors and organization: Aubrey Hughes¹, Jedediah Mathis², Mary Shimoyama, Norberto de la Cruz, Charles W. Wang, Nataliya Nenasheva, Dean Pasko, Jiali Chen, Lan Zhao, Chunyu Fan, Wenhua Wu, Chin-Fu Chen, Rajni Nigam, Gopal Gopinathrao, Angela Zuniga-Meyer, Susan Bromberg, Jessica Ginster, Anne Kwitek-Black, Janan Eppig, Lois Maltais, Donna Maglott, Greg Schuler, Simon Twigger, Howard Jacob and Peter Tonellato
¹ahughes@mcw.edu, Medical College of Wisconsin; ²jmathis@mcw.edu, Medical College of Wisconsin Abstract: The Rat Genome Database (RGD) is a disease centric resource of comprehensively curated data from rat genetic and genomic research. RGD's goal is to provide information that will aid researchers in using the rat as a model organism for human disease studies. RGD is available at rgd.mcw.edu . File: ahughesATmcw.edu_61 ************************************************* Mon Apr 21 22:11:40 2003 Number: 86 Name: Ohta, Yoshihiro Affiliation: HITACHI Central Research Laboratory Address: 1-280, Higashi-Koigakubo City: Kokubunji-shi State/Provice: Tokyo Postal/Zip Code: 185-8601 Country: Japan Email: yoh@crl.hitachi.co.jp Phone: +81-42-323-1111 Fax: Category: Data Mining Poster Title: ExMI: Extracting Molecular Interaction from Large Biomedical Literature Poster Authors and organization: Yoshihiro Ohta¹, Tohru Natume², Tetsuo Nishikawa, Hiroko Ohi, Tohru Hisamitsu
¹yoh@crl.hitachi.co.jp, HITACHI Central Research Laboratory; ²natsume@jbirc.aist.go.jp, National Institute of Advanced Industrial Science and Technology Abstract: Extracting molecular interactions from the rapidly growing biomedical literature is important to seek systematical explorations of relationships between genes and proteins. However, many of the existing computer-aided methods are not sufficiently capable of processing a huge amount of literature. Extraction techniques include molecule name detection, interaction event detection, and graphical interface construction. We explore these techniques and show system examples. File: yohATcrl.hitachi.co.jp_86 ************************************************* Mon Apr 21 23:38:12 2003 Number: 87 Name: Somani, Sandeep Affiliation: Bioinformatics Institute Address: Rm 03-11, 21, Heng Mui Keng Terrace City: Singapore State/Provice: Singapore Postal/Zip Code: 119613 Country: Singapore Email: ssomani@bii.a-star.edu.sg Phone: 65 6874 1279 Fax: 65 6778 1250 Category: Systems Biology Poster Title: Cellware: A Modeling and Simulation tool for Large Scale Biological Systems Poster Authors and organization: Sandeep Somani¹, Chee Meng², Li Ye, Anand Sairam, Zhu Hao,Mandar Chitre, Pawan Dhar
¹ssomani@bii.a-star.edu.sg, Bioinformatics Institute; ²cheemeng@bii.a-star.edu.sg, Bioinformatics Institute Abstract: A software tool for in-silico modeling and simulation of large scale biological networks is being developed. Stress is on using distributed computing and grid computing technologies and novel algorithmic development for meeting the computational challenge of simulating large scale networks. File: ssomaniATbii.a-star.edu.sg_87 ************************************************* Mon Apr 21 23:40:23 2003 Number: 88 Name: Tan, Chee M Affiliation: Bioinformatics Institute Address: 21 Heng Mui Keng Terrace City: Singapore State/Provice: Singapore Postal/Zip Code: 119613 Country: Singapore Email: cheemeng@bii.a-star.edu.sg Phone: 65-68741383 Fax: - Category: Systems Biology Poster Title: Parameter Estimation for Biochemical Pathways using Swarm Algorithm Poster Authors and organization: Tan Chee Meng¹, Sandeep Somani²
¹cheemeng@bii.a-star.edu.sg, Bioinformatics Institute; ²ssomani@bii.a-star.edu.sg, Bioinformatics Institute Abstract: Biological systems exhibit high robustness and operate at a broad range of kinetic parameters, it is important that optimization techniques capture this important property of cells. In this study, we present an optimization technique called SWARM that is capable of detecting multiple optimal solutions. File: cheemengATbii.a-star.edu.sg_88 ************************************************* Mon Apr 21 23:41:39 2003 Number: 89 Name: Tan, Keng H Affiliation: BioInformatics Institute Address: 21 Heng Mui Keng Terrace, 03-14 City: Singapore State/Provice: Singapore Postal/Zip Code: 119613 Country: Singapore Email: eric@bii.a-star.edu.sg Phone: +65 6874 6182 Fax: +65 6778 1250 Category: Sequence Comparison Poster Title: Evolutionary significance of G1/S checkpoint among Eukaryotes Poster Authors and organization: Keng Hwa Tan¹, Pawan Dhar²
¹eric@bii.a-star.edu.sg, BioInformatics Institute; ²pk@bii.a-star.edu.sg, BioInformatics Institute Abstract: Short Abstract: G1/S checkpoint plays a pivotal role during early stages of the cell cycle. Progression through G1/S boundary is controlled by a series of regulators. To explore the roles of these regulators and identify targets of CDKs, bioinformatics analysis are being done on DNA and protein sequences from different eukaryotic organisms. File: ericATbii.a-star.edu.sg_89 ************************************************* Tue Apr 22 06:10:47 2003 Number: 90 Name: Rouchka, Eric C Affiliation: University of Louisville Address: JB Speed Building Room 123 City: Louisville State/Provice: Kentucky Postal/Zip Code: 40292 Country: USA Email: eric.rouchka@louisville.edu Phone: 502-852-2581 Fax: 502-852-4713 Category: New Frontiers Poster Title: Statewide Bioinformatics in Kentucky Poster Authors and organization: Eric Rouchka¹, Nigel Cooper²
¹eric.rouchka@louisville.edu, University of Louisville; ²nigelcooper@louisville.edu, University of Louisville Abstract: Abbreviated Abstract The KBRIN bioinformatics core is attempting to create a Kentucky-wide network of bioinformatics expertise. This venture has led to the identification of knowledge- and compute-based resources. The core seeks to improve bioinformatics knowledge through research and the creation of bioinformatics courses, certificates, and degrees. The core web site is: http://www.kbrin.louisville.edu/about/bioinform_core.html File: eric.rouchkaATlouisville.edu_90 ************************************************* Tue Apr 22 06:14:53 2003 Number: 91 Name: Rouchka, Eric C Affiliation: University of Louisville Address: JB Speed Building Room 123 City: Louisville State/Provice: Kentucky Postal/Zip Code: 40292 Country: USA Email: eric.rouchka@louisville.edu Phone: 502-852-2581 Fax: 502-852-4713 Category: Microarrays Poster Title: MPRIME: Efficient Large Scale Multiple Primer Design for Customized Microarrays Poster Authors and organization: Eric Rouchka¹, Nigel Cooper², Abdelnaby Khalyfa
¹eric.rouchka@louisville.edu, University of Louisville; ²nigelcooper@louisville.edu, University of Louisville Abstract: Abbreviated Abstract

MPrime is a system for efficiently creating large sets of PCR primer pairs for use in designing products for custom cDNA microarrays. MPrime has allowed us to effectively design custom neurodegenerative microarray chips for humans as well as the rat and mouse genomes. MPrime is available at: href=http://kbrin.a-bldg.louisville.edu/Tools/MPrime/ File: eric.rouchkaATlouisville.edu_91 ************************************************* Tue Apr 22 07:54:22 2003 Number: 92 Name: Artamonova, Irena I Affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS Address: Miklukho-Maklaya 16-10 City: Moscow State/Provice: Moscow Postal/Zip Code: 117997 Country: Russia Email: irena@humgen.siobc.ras.ru Phone: 7-095-3307029 Fax: 7-095-3306538 Category: Phylogeny and Evolution Poster Title: Evolutionary analysis of long terminal repeats of human endogenous retroviruses Poster Authors and organization: Artamonova I.¹
¹irena@humgen.siobc.ras.ru, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16-10, Moscow, 117997, Russia Abstract: We analyzed locations of HERV-K LTRs in the human genome. Their distribution is not uniform among human chromosomes and among different regions of one chromosome. The majority of HERV-K LTRs are clustered. Positions of LTR clusters correlate with the Giemsa segmentation of human chromosomes. Most clusters are observed GC-rich regions. File: irenaAThumgen.siobc.ras.ru_92 ************************************************* Tue Apr 22 07:55:18 2003 Number: 93 Name: Artamonova, Irena I Affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS Address: Miklukho-Maklaya 16-10 City: Moscow State/Provice: Moscow Postal/Zip Code: 117997 Country: Russia Email: irena@humgen.siobc.ras.ru Phone: 7-095-3307029 Fax: 7-095-3306538 Category: Functional Genomics Poster Title: Non-conserved alternative splicing of human and mouse genes Poster Authors and organization: Artamonova I.¹, Gelfand M. ², Mironov A., Nurtdinov R.
¹irena@humgen.siobc.ras.ru, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16-10, Moscow, 117997, Russia; ²gelfand@ig-msk.ru, State Scientific Center GosNIIGenetika, 1st Dorozhny 1, Moscow 113545, Russia Abstract: We analyzed conservation of alternative splicing patterns in pairs of orthologous genes from the human and mouse genomes. Our results demonstrate considerable diversity of alternative splicing in these genomes: at least half of alternatively spliced genes have species-specific isoforms. Orthologs with non-conserved isoforms may play a role in species-specific development. File: irenaAThumgen.siobc.ras.ru_93 ************************************************* Tue Apr 22 08:58:18 2003 Number: 94 Name: Zdobnov, Evgeny M Affiliation: EMBL Address: Meyerhofstrasse 1 City: Heidelberg State/Provice: state Postal/Zip Code: Country: Germany Email: zdobnov@embl.de Phone: 496221387534 Fax: Category: Predictive Methods Poster Title: Biochemical networks and functional modules revealed by comparative genomics. Poster Authors and organization: Evgeny M. Zdobnov¹, Christian von Mering², Christos A. Ouzounis, Peer Bork.
¹zdobnov@embl.de, EMBL; ², EMBL Abstract: Functional associations among proteins predicted by genomic context (common phylogenetic coverage, conserved gene neighborhood and gene fusions) were used to infer functional modules using unsupervised clustering. We show that The predicted modules are able to recover Escherichia coli pathways with high accuracy and extend beyond metabolism. File: zdobnovATembl.de_94 ************************************************* Tue Apr 22 09:15:11 2003 Number: 95 Name: Wilke, Andreas Affiliation: Bielefeld University, Institute for Genomeresearch, Germany Address: Universitaetstrasse City: Bielefeld State/Provice: NRW Postal/Zip Code: D-33615 Country: Germany Email: andreas.wilke@genetik.uni-bielefeld.de Phone: 00495211064813 Fax: Category: Functional Genomics Poster Title: ProDB - Bioinformatics support for high throughput proteomics Poster Authors and organization: Andreas Wilke¹, Christian Rueckert², Sebastian Kespoh , Martina Mahne, Andrea T. Hueser, Folker Meyer
¹andreas.wilke@genetik.uni-bielefeld.de, UniversBielefeld University, Institute for Genome Research, Germany; ²christian.rueckert@genetik.uni-bielefeld.de, Int. NRW Grad. School in Bioinformatics Genome Research, Bielefeld Unive rsity, Germanyy Abstract: To cope with the need for automated data conversion, storage, and analysis in the field of proteomics, the open source system ProDB was developed. The system handles data conversion from different mass spectrometer software, automates data analysis, and will allow the annotation of MS spectra. File: andreas.wilkeATgenetik.uni-bielefeld.de_95 ************************************************* Tue Apr 22 13:20:51 2003 Number: 96 Name: Yung, Christina K Affiliation: Johns Hopkins University Address: 3400 N. Charles St., Rm. 202 Clark Hall City: Baltimore State/Provice: MD Postal/Zip Code: 21218 Country: USA Email: cyung@bme.jhu.edu Phone: 410-516-5466 Fax: 410-516-5294 Category: Microarrays Poster Title: Gene Expression Profiles in End-Stage Human Idiopathic Dilated Cardiomyopathy Poster Authors and organization: Christina K. Yung¹, Gordon F. Tomaselli², Raimond L. Winslow
¹cyung@bme.jhu.edu, Johns Hopkins University; ²gtomsel@jhmi.edu, Johns Hopkins University Abstract: High-density oligonucleotide microarrays are used to characterize expression profiles in end-stage idiopathic dilated cardiomyopathy. Multiple algorithms for data normalization and computation of expression level are evaluated using a spike-in data set. Statistical analyses accounting for intensity-dependent variances identify 165 genes that potentially constitute the genetic signature of heart failure. File: cyungATbme.jhu.edu_96 ************************************************* Tue Apr 22 18:59:49 2003 Number: 97 Name: Gill, John C Affiliation: Victorian Bioinformatics Consortium, Monash University Address: Wellington rd. City: Clayton State/Provice: Victoria Postal/Zip Code: 3800 Country: Australia Email: john.gill@med.monash.edu.au Phone: 9 905 9274 Fax: Category: Databases Poster Title: Automating Data Collection And Categorisation Using The CAS Software Poster Authors and organization: John Gill¹
¹john.gill@monash.edu.au, Victorian Bioinformatics Consortium, Monash University Abstract: 50 Word Abstract:

CAS is a data integration system that allows for the creation of categories and integrated data sets. Each category consists of a set of attributes and methods, which act as an object item. Incoming data, obtained manually or through the automated data collection component, is linked to category attributes according to user defined rules and conditions File: john.gillATmed.monash.edu.au_97 ************************************************* Tue Apr 22 19:30:44 2003 UPDATE ----- Number: 30 Name: bello, onimisi h Affiliation: bma tutorial oufit Address: no.6 zansi close City: off-iwaya road yaba State/Provice: lagos Postal/Zip Code: 340 Country: nigeria Email: hassanbello2001@yahoo.com Phone: none Fax: none Category: Predictive Methods Poster Title: The model representation of the mode of action of combination therapy of chloroquine,puritine an ascobic acid Poster Authors and organization: onimisi hassan bello¹
¹hassanbello2001@yahoo.com, bima tutorial outfit Abstract: The action of the combine therapy of chloroquine,putitine and ascobic acid has baffled biochemist for some times.but it is believe to potentiate its action based on the pertubation of the lipid bilayer surrounding the cells. but further studies to reveal the genetic conditions has not yielded much results. File: hassanbello2001ATyahoo.com_30 ************************************************* Tue Apr 22 19:32:29 2003 UPDATE ----- Number: 30 Name: bello, onimisi h Affiliation: bma tutorial oufit Address: no.6 zansi close City: off-iwaya road yaba State/Provice: lagos Postal/Zip Code: 340 Country: nigeria Email: hassanbello2001@yahoo.com Phone: none Fax: none Category: Predictive Methods Poster Title: The model representation of the mode of action of combination therapy of chloroquine,puritine an ascobic acid Poster Authors and organization: onimisi hassan bello¹
¹hassanbello2001@yahoo.com, bima tutorial outfit Abstract: The action of the combine therapy of chloroquine,putitine and ascobic acid has baffled biochemist for some times.but it is believe to potentiate its action based on the pertubation of the lipid bilayer surrounding the cells. but further studies to reveal the genetic conditions has not yielded much results. File: hassanbello2001ATyahoo.com_30 ************************************************* Tue Apr 22 19:35:34 2003 UPDATE ----- Number: 30 Name: bello, onimisi h Affiliation: bma tutorial oufit Address: no.6 zansi close City: off-iwaya road yaba State/Provice: lagos Postal/Zip Code: 340 Country: nigeria Email: hassanbello2001@yahoo.com Phone: none Fax: none Category: Predictive Methods Poster Title: The model representation of the mode of action of combination therapy of chloroquine,puritine an ascobic acid Poster Authors and organization: onimisi hassan bello¹
¹hassanbello2001@yahoo.com, bima tutorial outfit Abstract: The action of the combine therapy of chloroquine,putitine and ascobic acid has baffled biochemist for some times.but it is believe to potentiate its action based on the pertubation of the lipid bilayer surrounding the cells. but further studies to reveal the genetic conditions has not yielded much results. File: hassanbello2001ATyahoo.com_30 ************************************************* Wed Apr 23 01:48:57 2003 Number: 98 Name: Park, Sung-Hee Affiliation: Chungbuk National University Address: 48 Gashin-Dong HoungDuk-Ku City: Cheongju State/Provice: Chungbuk Postal/Zip Code: 361763 Country: Korea Email: shpark@dblab.chungbuk.ac.kr Phone: +82432672250 Fax: +82432752254 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: Building a Database of Protein Structure Using a Geographic Model based on Topological Consistency Poster Authors and organization: Sung-Hee Park¹, Keun Ho Ryu², Byeong-Jin Jeong Hyeon S. Son
¹shpark@dblab.chungbuk.ac.kr, Chungbuk National University; ²khryu@dblab.chungbuk.ac.kr, Chungbuk National University Abstract: We propose protein structure modeling using a geographic model and build a structure database which includes thematic information and geometry of protein. In the modeling, geometry is represented by spatial types and thematic information includes the physico-chemical data. We state queries to retrieve topological relationship between structural elements with spatial operators. File: shparkATdblab.chungbuk.ac.kr_98 ************************************************* Wed Apr 23 01:51:51 2003 Number: 99 Name: Park, Sung-Hee Affiliation: Chungbuk National University Address: 48 Gashin-Dong HoungDuk-Ku City: Cheongju State/Provice: Chungbuk Postal/Zip Code: 361763 Country: Korea Email: shpark@dblab.chungbuk.ac.kr Phone: +82432672250 Fax: +82432752254 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: Version Management of a Genomic Sequence Database Using Active Rules and Temporal Concepts Poster Authors and organization: Sung-Hee Park¹, Keun Ho Ryu², Byeong-Jin Jeong Hyeon S. Son
¹shpark@dblab.chungbuk.ac.kr, Chungbuk National University; ²khryu@dblab.chungbuk.ac.kr, Chungbuk National University Abstract: We propose modeling of sequence versions for sequence changes of the same piece of DNA using a time stamp attribute in a temporal data model and mechanism of management of sequence versions in a sequence database by applying trigger rules(Event-Condition-Action) in an active database system. File: shparkATdblab.chungbuk.ac.kr_99 ************************************************* Wed Apr 23 02:11:41 2003 Number: 100 Name: del Val, Coral Affiliation: DKFZ, German Cancer Research Center Address: Im Neuenheimer Feld 580 City: Heidelberg State/Provice: Baden-Wuttemberg Postal/Zip Code: 69120 Country: Germany Email: c.delval@dkfz.de Phone: 00496221422349 Fax: 496221439633 Category: Genome Annotation Poster Title: cDNA2Genome: A TOOL FOR MAPPING AND ANNOTATING cDNAS Poster Authors and organization: Coral del Val¹, Karl-Heinz Glatting², S.Suhai
¹c.delval@dkfz.de, Department of Molecular Biophysics DKFZ, German Cancer Research Center; ²glatting@dkfz.de, Department of Molecular Biophysics DKFZ, German Cancer Research Center Abstract:

cDNA2Genome is a web tool for automatic high-throughput mapping and characterization of cDNAs. It uses already existing annotation data and improves them when possible in the case of ESTs, proteins and mRNAs. It is focussed on the determination of the cDNA exon-intron structure. The final result of cDNA2Genome is an XML file with all information obtained by the task.

File: c.delvalATdkfz.de_100 ************************************************* Wed Apr 23 03:41:16 2003 Number: 101 Name: Ao, Hiroko Affiliation: Takagi Laboratory, Department of Computational Biology, University of Tokyo Address: 5-1-5, Kashiwanoha City: Kashiwa-shi State/Provice: Chiba Postal/Zip Code: 277-8561 Country: Japan Email: aohiroko@ims.u-tokyo.ac.jp Phone: +81-4-7136-3973 Fax: +81-4-7136-3975 Category: Data Mining Poster Title: An algorithm to select abstracts from MEDLINE concerning UV-regulated genes Poster Authors and organization: Hiroko Ao¹, Toshihisa Takagi²
¹aohiroko@hotmail.com, Department of Computational Biology, University of Tokyo, and Basic Research Laboratory, Kenebo, LTD.; ²tt@k.u-tokyo.ac.jp, Department of Computational Biology, University of Tokyo Abstract: With a rapid growth of machine-readable literature, such like MEDLINE database, a search for articles is an important assignment. Therefore, we propose an efficient algorithm to select information from results of a PubMed search. When taking 487 UV-regulated genes, it extracted sentences containing the query with 97% precision and 97% recall. File: aohirokoATims.u-tokyo.ac.jp_101 ************************************************* Wed Apr 23 03:45:21 2003 Number: 102 Name: Yamamoto, Yasunori Affiliation: Takagi Laboratory, Human Genome Center, Department of Computer Science, University of Tokyo Address: 4-6-1 Shirokane-dai City: Minato-ku State/Provice: Tokyo Postal/Zip Code: 108-8639 Country: Japan Email: yayamamo@ims.u-tokyo.ac.jp Phone: +81-3-5449-5611 Fax: +81-3-5449-5434 Category: Data Mining Poster Title: TextLens: A Fast and Practical Partial Parser for Biomedical Literature Poster Authors and organization: Yasunori Yamamoto¹, Hiroko Ao², Toshihisa Takagi
¹yayamamo@ims.u-tokyo.ac.jp, Department of Computer Science, University of Tokyo; ²aohiroko@ims.u-tokyo.ac.jp, Department of Computational Biology Abstract: TextLens Partial Parser is a parser to catch a pair of main subject and predicate of a sentence. It aims at an improvement of information extraction by appropriately capturing each chunk of words and a structure of a sentence. It uses a rule-based algorithm which makes an abstract expression of a sentence. File: yayamamoATims.u-tokyo.ac.jp_102 ************************************************* Wed Apr 23 10:21:58 2003 Number: 103 Name: Al-Shahib, Ali W Affiliation: Department of Computing Science, University of Glasgow Address: 17 Lilybank Gardens City: Glasgow State/Provice: Scotland Postal/Zip Code: G12 8QQ Country: UK Email: alshahib@dcs.gla.ac.uk Phone: 0044 7932 626 015 Fax: 0044 141 330 3690 Category: Functional Genomics Poster Title: Functional Annotation in the Twilight Zone using Machine Learning Poster Authors and organization: Ali Al-Shahib¹, David Gilbert²
¹alshahib@dcs.gla.ac.uk, University of Glasgow; ²drg@dcs.gla.ac.uk, University of Glasgow Abstract: In functional genomics, many are worried at the number of functionally unknown genes we have. One of the areas that we think has contributed to this is the uncertainty in low sequence alignments (twilight zone). Our work involves the development of a rule-based system that allows us to accurately assign functional annotation in the twilight zone. File: alshahibATdcs.gla.ac.uk_103 ************************************************* Wed Apr 23 11:52:55 2003 Number: 104 Name: Ohler, Uwe Affiliation: MIT Address: 77 Massachusetts Ave 68-223 City: Cambridge State/Provice: MA Postal/Zip Code: 02144 Country: USA Email: ohler@mit.edu Phone: 617-253-7039 Fax: 617-452-2936 Category: Predictive Methods Poster Title: New features for microRNA gene finding Poster Authors and organization: Uwe Ohler¹, Chris Burge², David Bartel
¹ohler@mit.edu, MIT; ²cburge@mit.edu, MIT Abstract: MicroRNAs are a class of tiny RNA genes excised from precursor hairpin structures. We identified a highly specific conserved motif upstream of precursors that might be involved in miRNA transcription, and describe how much this motif, plus features of general upstream and downstream conservation, aid in miRNA gene finding. File: ohlerATmit.edu_104 ************************************************* Wed Apr 23 17:40:34 2003 Number: 105 Name: Zhang, Lan Affiliation: Harvard University Address: 250 Longwood Ave., SGM 322 City: Boston State/Provice: MA Postal/Zip Code: 02115 Country: USA Email: lan_zhang@student.hms.harvard.edu Phone: 6176948655 Fax: 6174323557 Category: Functional Genomics Poster Title: Predicting Co-Complexed Protein Pairs Using Genomic and Proteomic Data Integration Poster Authors and organization: Lan Zhang¹, Sharyl L. Wong², Frederick P. Roth
¹lan_zhang@student.hms.harvard.edu, Harvard University; ²sharyl_wong@student.hms.harvard.edu, Harvard University Abstract: We took a probabilistic decision tree approach to predict protein pairs present in the same complex (CCPs) through integrating high-throughput protein-protein interaction screens with various genomic and proteomic information. Our method made predictions more sensitive and specific than high-throughput experiments, and is also promising in detecting unknown CCPs. File: lan_zhangATstudent.hms.harvard.edu_105 ************************************************* Wed Apr 23 20:07:28 2003 Number: 106 Name: Goldberg, Debra S Affiliation: Harvard Medical School Address: 250 Longwood Ave, SGM-322 City: Boston State/Provice: MA Postal/Zip Code: 02466 Country: USA Email: debg@hms.harvard.edu Phone: 617-432-3552 Fax: 617-432-3557 Category: Functional Genomics Poster Title: Protein Function Prediction Using Probabilistic Protein Interaction Networks Poster Authors and organization: Debra S. Goldberg¹, Sharyl Wong², Frederick P. Roth
¹debg@hms.harvard.edu, Harvard Medical School; ²sharyl_wong@student.hms.harvard.edu, Harvard Medical School Abstract: To improve protein function prediction from high-throughput, error-prone data, we compute a posterior probability for the validity of each interaction. These edge weights are based on the experimental data and how well each observation fits the expected network topology. Our function predictions compare favorably to previously published methods. File: debgAThms.harvard.edu_106 ************************************************* Wed Apr 23 21:27:25 2003 Number: 107 Name: Gladwin, Benjamin A Affiliation: University of Queensland, Department of mathematics Address: stlucia City: brisbane State/Provice: QLD Postal/Zip Code: 4067 Country: Australia Email: gladwin@maths.uq.edu.au Phone: 0733461430 Fax: Category: Predictive Methods Poster Title: Long time scale simulations of Molecular Systems Poster Authors and organization: Benjamin Gladwin¹, Dr Thomas Huber²
¹gladwin@maths.uq.edu.au, University of Queensland Department of Mathematics.; ²huber@maths.uq.edu.au, University of Queensland Department of Mathematics. Abstract: Long time scale simulation of molecular pathways can be achieved using least action pathways. In this work we look at the simulation of transitional paths of molecules over long simulation times. File: gladwinATmaths.uq.edu.au_107 ************************************************* Wed Apr 23 23:42:48 2003 UPDATE ----- Number: 30 Name: bello, onimisi h Affiliation: bma tutorial oufit Address: no.6 zansi close City: off-iwaya road yaba State/Provice: lagos Postal/Zip Code: 340 Country: nigeria Email: hassanbello2001@yahoo.com Phone: none Fax: none Category: Predictive Methods Poster Title: The model representation of the mode of action of combination therapy of chloroquine,puritine an ascobic acid Poster Authors and organization: onimisi hassan bello¹
¹hassanbello2001@yahoo.com, bima tutorial outfit Abstract: The action of the combine therapy of chloroquine,putitine and ascobic acid has baffled biochemist for some times.but it is believe to potentiate its action based on the pertubation of the lipid bilayer surrounding the cells. but further studies to reveal the genetic conditions has not yielded much results. File: hassanbello2001ATyahoo.com_30 ************************************************* Wed Apr 23 23:44:42 2003 UPDATE ----- Number: 30 Name: bello, onimisi h Affiliation: bma tutorial oufit Address: no.6 zansi close City: off-iwaya road yaba State/Provice: lagos Postal/Zip Code: 340 Country: nigeria Email: hassanbello2001@yahoo.com Phone: none Fax: none Category: Predictive Methods Poster Title: The model representation of the mode of action of combination therapy of chloroquine,puritine an ascobic acid Poster Authors and organization: onimisi hassan bello¹
¹hassanbello2001@yahoo.com, bima tutorial outfit Abstract: The action of the combine therapy of chloroquine,putitine and ascobic acid has baffled biochemist for some times.but it is believe to potentiate its action based on the pertubation of the lipid bilayer surrounding the cells. but further studies to reveal the genetic conditions has not yielded much results. File: hassanbello2001ATyahoo.com_30 ************************************************* Wed Apr 23 23:45:05 2003 UPDATE ----- Number: 27 Name: Lottaz, Claudio Affiliation: Max-Planck-Institute for Molecular Genetics Address: Ihnestr. 73 City: Berlin State/Provice: Berlin Postal/Zip Code: 14195 Country: Germany Email: Claudio.Lottaz@molgen.mpg.de Phone: +49 30 8413 1177 Fax: +49 30 8413 1176 Category: Microarrays Poster Title: Gene Ontology Driven Classification of Gene Expression Patterns Poster Authors and organization: Claudio Lottaz¹, Renate Kirschner², Stefan Bentink, Christian Hagemeier and Rainer Spang
¹Claudio.Lottaz@molgen.mpg.de, Max-Planck-Institute for Molecular Genetics, Berlin; ²r.kirschner@charite.de, Medical Center Charit�, Berlin Abstract: We propose to structure analysis of microarry according to biological knowledge in order to provide an intuitive and biologically meaningful rationale for computational classification results. Thereby, we rely on the Gene Ontology to attribute genes to biological aspects and usual machine learning methods for classification. File: Claudio.LottazATmolgen.mpg.de_27 ************************************************* Wed Apr 23 23:46:01 2003 UPDATE ----- Number: 30 Name: bello, onimisi h Affiliation: bma tutorial oufit Address: no.6 zansi close City: off-iwaya road yaba State/Provice: lagos Postal/Zip Code: 340 Country: nigeria Email: hassanbello2001@yahoo.com Phone: none Fax: none Category: Predictive Methods Poster Title: The model representation of the mode of action of combination therapy of chloroquine,puritine an ascobic acid Poster Authors and organization: onimisi hassan bello¹
¹hassanbello2001@yahoo.com, bima tutorial outfit Abstract: The action of the combine therapy of chloroquine,putitine and ascobic acid has baffled biochemist for some times.but it is believe to potentiate its action based on the pertubation of the lipid bilayer surrounding the cells. but further studies to reveal the genetic conditions has not yielded much results. File: hassanbello2001ATyahoo.com_30 ************************************************* Wed Apr 23 23:46:05 2003 Number: 108 Name: Nelson, Eric J Affiliation: Univ. of Colorado HSC, Dept. of Pharmacology Address: 4200 East 9th Ave., Box C236 City: Denver State/Provice: CO Postal/Zip Code: 80262 Country: USA Email: eric.nelson@uchsc.edu Phone: 303-315-6809 Fax: 303-315-7097 Category: Predictive Methods Poster Title: Identification of PKC Phosphorylation Sites on AC7 using a Directed Bioinformatics Approach. Poster Authors and organization: Eric J. Nelson¹, John VanHoven², Vlad Verkhusha, Tonny deBeer, and Boris Tabakoff.
¹eric.nelson@uchsc.edu, Univ. of Colorado; ²john.vanhoven@uchsc.edu, Univ. of Colorado Abstract: A bioinformatics approach is presented that can bypass in some instances the traditional means of phosphopeptide mapping a radiologically labeled target protein to identify PKC phosphorylation sites. This directed bioinformatics approach utilizes comparative sequence analysis, molecular modeling, and machine learning techniques to assist in the discovery of PKC phosphorylation sites. File: eric.nelsonATuchsc.edu_108 ************************************************* Wed Apr 23 23:46:33 2003 UPDATE ----- Number: 30 Name: bello, onimisi h Affiliation: bma tutorial oufit Address: no.6 zansi close City: off-iwaya road yaba State/Provice: lagos Postal/Zip Code: 340 Country: nigeria Email: hassanbello2001@yahoo.com Phone: none Fax: none Category: Predictive Methods Poster Title: The model representation of the mode of action of combination therapy of chloroquine,puritine an ascobic acid Poster Authors and organization: onimisi hassan bello¹
¹hassanbello2001@yahoo.com, bima tutorial outfit Abstract: The action of the combine therapy of chloroquine,putitine and ascobic acid has baffled biochemist for some times.but it is believe to potentiate its action based on the pertubation of the lipid bilayer surrounding the cells. but further studies to reveal the genetic conditions has not yielded much results. File: hassanbello2001ATyahoo.com_30 ************************************************* Wed Apr 23 23:47:50 2003 UPDATE ----- Number: 30 Name: bello, onimisi h Affiliation: bma tutorial oufit Address: no.6 zansi close City: off-iwaya road yaba State/Provice: lagos Postal/Zip Code: 340 Country: nigeria Email: hassanbello2001@yahoo.com Phone: none Fax: none Category: Predictive Methods Poster Title: The model representation of the mode of action of combination therapy of chloroquine,puritine an ascobic acid Poster Authors and organization: onimisi hassan bello¹
¹hassanbello2001@yahoo.com, bima tutorial outfit Abstract: The action of the combine therapy of chloroquine,putitine and ascobic acid has baffled biochemist for some times.but it is believe to potentiate its action based on the pertubation of the lipid bilayer surrounding the cells. but further studies to reveal the genetic conditions has not yielded much results. File: hassanbello2001ATyahoo.com_30 ************************************************* Wed Apr 23 23:49:26 2003 UPDATE ----- Number: 27 Name: Lottaz, Claudio Affiliation: Max-Planck-Institute for Molecular Genetics Address: Ihnestr. 73 City: Berlin State/Provice: Berlin Postal/Zip Code: 14195 Country: Germany Email: Claudio.Lottaz@molgen.mpg.de Phone: +49 30 8413 1177 Fax: +49 30 8413 1176 Category: Microarrays Poster Title: Gene Ontology Driven Classification of Gene Expression Patterns Poster Authors and organization: Claudio Lottaz¹, Renate Kirschner², Stefan Bentink, Christian Hagemeier and Rainer Spang
¹Claudio.Lottaz@molgen.mpg.de, Max-Planck-Institute for Molecular Genetics, Berlin; ²r.kirschner@charite.de, Medical Center Charit�, Berlin Abstract: We propose to structure analysis of microarry according to biological knowledge in order to provide an intuitive and biologically meaningful rationale for computational classification results. Thereby, we rely on the Gene Ontology to attribute genes to biological aspects and usual machine learning methods for classification. File: Claudio.LottazATmolgen.mpg.de_27 ************************************************* Wed Apr 23 23:50:54 2003 UPDATE ----- Number: 27 Name: Lottaz, Claudio Affiliation: Max-Planck-Institute for Molecular Genetics Address: Ihnestr. 73 City: Berlin State/Provice: Berlin Postal/Zip Code: 14195 Country: Germany Email: Claudio.Lottaz@molgen.mpg.de Phone: +49 30 8413 1177 Fax: +49 30 8413 1176 Category: Microarrays Poster Title: Gene Ontology Driven Classification of Gene Expression Patterns Poster Authors and organization: Claudio Lottaz¹, Renate Kirschner², Stefan Bentink, Christian Hagemeier and Rainer Spang
¹Claudio.Lottaz@molgen.m_pg.de, Max-Planck-Institute for Molecular Genetics, Berlin; ²r.kirschner@charite.de, Medical Center Charit�, Berlin Abstract: We propose to structure analysis of microarry according to biological knowledge in order to provide an intuitive and biologically meaningful rationale for computational classification results. Thereby, we rely on the Gene Ontology to attribute genes to biological aspects and usual machine learning methods for classification. File: Claudio.LottazATmolgen.mpg.de_27 ************************************************* Wed Apr 23 23:52:22 2003 UPDATE ----- Number: 27 Name: Lottaz, Claudio Affiliation: Max-Planck-Institute for Molecular Genetics Address: Ihnestr. 73 City: Berlin State/Provice: Berlin Postal/Zip Code: 14195 Country: Germany Email: Claudio.Lottaz@imb.uq.edu.au Phone: +49 30 8413 1177 Fax: +49 30 8413 1176 Category: Microarrays Poster Title: Gene Ontology Driven Classification of Gene Expression Patterns Poster Authors and organization: Claudio Lottaz¹, Renate Kirschner², Stefan Bentink, Christian Hagemeier and Rainer Spang
¹Claudio.Lottaz@molgen.m_pg.de, Max-Planck-Institute for Molecular Genetics, Berlin; ²r.kirschner@charite.de, Medical Center Charit�, Berlin Abstract: We propose to structure analysis of microarry according to biological knowledge in order to provide an intuitive and biologically meaningful rationale for computational classification results. Thereby, we rely on the Gene Ontology to attribute genes to biological aspects and usual machine learning methods for classification. File: Claudio.LottazATimb.uq.edu.au_27 ************************************************* Wed Apr 23 23:56:05 2003 UPDATE ----- Number: 27 Name: Lottaz, Claudio Affiliation: Max-Planck-Institute for Molecular Genetics Address: Ihnestr. 73 City: Berlin State/Provice: Berlin Postal/Zip Code: 14195 Country: Germany Email: r.kirschner@charite.de Phone: +49 30 8413 1177 Fax: +49 30 8413 1176 Category: Microarrays Poster Title: Gene Ontology Driven Classification of Gene Expression Patterns Poster Authors and organization: Claudio Lottaz¹, Renate Kirschner², Stefan Bentink, Christian Hagemeier and Rainer Spang
¹Claudio.Lottaz@molgen.mpg.de, Max-Planck-Institute for Molecular Genetics, Berlin; ²r.kirschner@charite.de, Medical Center Charit�, Berlin Abstract: We propose to structure analysis of microarry according to biological knowledge in order to provide an intuitive and biologically meaningful rationale for computational classification results. Thereby, we rely on the Gene Ontology to attribute genes to biological aspects and usual machine learning methods for classification. File: r.kirschnerATcharite.de_27 ************************************************* Wed Apr 23 23:56:23 2003 UPDATE ----- Number: 30 Name: bello, onimisi h Affiliation: bma tutorial oufit Address: no.6 zansi close City: off-iwaya road yaba State/Provice: lagos Postal/Zip Code: 340 Country: nigeria Email: hassanbello2001@yahoo.com Phone: none Fax: none Category: Predictive Methods Poster Title: The model representation of the mode of action of combination therapy of chloroquine,puritine an ascobic acid Poster Authors and organization: onimisi hassan bello¹
¹hassanbello2001@yahoo.com, bima tutorial outfit Abstract: The action of the combine therapy of chloroquine,putitine and ascobic acid has baffled biochemist for some times.but it is believe to potentiate its action based on the pertubation of the lipid bilayer surrounding the cells. but further studies to reveal the genetic conditions has not yielded much results. File: hassanbello2001ATyahoo.com_30 ************************************************* Wed Apr 23 23:56:56 2003 UPDATE ----- Number: 30 Name: bello, onimisi h Affiliation: bma tutorial oufit Address: no.6 zansi close City: off-iwaya road yaba State/Provice: lagos Postal/Zip Code: 340 Country: nigeria Email: hassanbello2001@yahoo.com Phone: none Fax: none Category: Predictive Methods Poster Title: The model representation of the mode of action of combination therapy of chloroquine,puritine an ascobic acid Poster Authors and organization: onimisi hassan bello¹
¹hassanbello2001@yahoo.com, bima tutorial outfit Abstract: The action of the combine therapy of chloroquine,putitine and ascobic acid has baffled biochemist for some times.but it is believe to potentiate its action based on the pertubation of the lipid bilayer surrounding the cells. but further studies to reveal the genetic conditions has not yielded much results. File: hassanbello2001ATyahoo.com_30 ************************************************* Wed Apr 23 23:57:20 2003 UPDATE ----- Number: 30 Name: bello, onimisi h Affiliation: bma tutorial oufit Address: no.6 zansi close City: off-iwaya road yaba State/Provice: lagos Postal/Zip Code: 340 Country: nigeria Email: hassanbello2001@yahoo.com Phone: none Fax: none Category: Predictive Methods Poster Title: The model representation of the mode of action of combination therapy of chloroquine,puritine an ascobic acid Poster Authors and organization: onimisi hassan bello¹
¹hassanbello2001@yahoo.com, bima tutorial outfit Abstract: The action of the combine therapy of chloroquine,putitine and ascobic acid has baffled biochemist for some times.but it is believe to potentiate its action based on the pertubation of the lipid bilayer surrounding the cells. but further studies to reveal the genetic conditions has not yielded much results. File: hassanbello2001ATyahoo.com_30 ************************************************* Thu Apr 24 00:11:42 2003 UPDATE ----- Number: 101 Name: Ao, Hiroko Affiliation: Takagi Laboratory, Department of Computational Biology, University of Tokyo Address: 5-1-5, Kashiwanoha City: Kashiwa-shi State/Provice: Chiba Postal/Zip Code: 277-8561 Country: Japan Email: aohiroko@ims.u-tokyo.ac.jp Phone: +81-4-7136-3973 Fax: +81-4-7136-3975 Category: Data Mining Poster Title: An algorithm to select abstracts from MEDLINE concerning UV-regulated genes Poster Authors and organization: Hiroko Ao¹, Toshihisa Takagi²
¹aohiroko@ims.u-tokyo.ac.jp, Department of Computational Biology, University of Tokyo, and Basic Research Laboratory, Kanebo, LTD.; ²tt@k.u-tokyo.ac.jp, Department of Computational Biology, University of Tokyo Abstract: With the rapid growth of machine-readable literature, such like MEDLINE database, a search for articles is an important assignment. Therefore, we propose an efficient algorithm to select information from results of a PubMed search. When taking 487 UV-regulated genes, it extracted sentences containing the query with 97% precision and 97% recall. File: aohirokoATims.u-tokyo.ac.jp_101 ************************************************* Thu Apr 24 00:20:12 2003 UPDATE ----- Number: 61 Name: Hughes, Aubrey D Affiliation: Medical College of Wisconsin Address: 8701 Watertown Plank Rd City: Milwaukee State/Provice: Wisconsin Postal/Zip Code: 53226 Country: USA Email: ahughes@mcw.edu Phone: 1 4144567506 Fax: 1 4144566190 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: RAT GENOME DATABASE - RGD - MAPPING DISEASE ONTO THE GENOME Poster Authors and organization: Aubrey Hughes¹, Jedediah Mathis², Mary Shimoyama, Norberto de la Cruz, Charles W. Wang, Nataliya Nenasheva, Dean Pasko, Jiali Chen, Lan Zhao, Chunyu Fan, Wenhua Wu, Chin-Fu Chen, Rajni Nigam, Gopal Gopinathrao, Angela Zuniga-Meyer, Susan Bromberg, Jessica Ginster, Anne Kwitek-Black, Janan Eppig, Lois Maltais, Donna Maglott, Greg Schuler, Simon Twigger, Howard Jacob and Peter Tonellato
¹ahughes@mcw.edu, Medical College of Wisconsin; ²jmathis@mcw.edu, Medical College of Wisconsin Abstract: The Rat Genome Database (RGD) is a disease centric resource of comprehensively curated data from rat genetic and genomic research. RGD's goal is to provide information that will aid researchers in using the rat as a model organism for human disease studies. RGD is available at rgd.mcw.edu . File: ahughesATmcw.edu_61 ************************************************* Thu Apr 24 00:20:45 2003 UPDATE ----- Number: 62 Name: Hayes, Wayne B Affiliation: University of Maryland Address: IPST Building 224 City: College Park State/Provice: MD Postal/Zip Code: 20742 Country: USA Email: wayne@cs.toronto.edu Phone: 240-893-1612 Fax: 301-314-9363 Category: Sequence Comparison Poster Title: IMPROVING SEQUENCE ASSEMBLIES USING HIGH-QUALITY OVERLAPS Poster Authors and organization: Michael Roberts¹, James Yorke², Brian Hunt, Wayne Hayes, Aleksey Zimin, Cevat Ustun, Paul Havlak
¹tri@ipst.umd.edu, University of Maryland; ²yorke@ipst.umd.edu, University of Maryland Abstract: Finishing a genome costs as much as initial assembly. Since initial assembly gets about 95% of it, gaining just a few extra percent initially can save tens of millions of dollars in finishing costs. We present computational techniques for improving "overlaps" resulting in up to 5% additional sequence during initial assembly. File: wayneATcs.toronto.edu_62 ************************************************* Thu Apr 24 00:21:10 2003 UPDATE ----- Number: 61 Name: Hughes, Aubrey D Affiliation: Medical College of Wisconsin Address: 8701 Watertown Plank Rd City: Milwaukee State/Provice: Wisconsin Postal/Zip Code: 53226 Country: USA Email: ahughes@mcw.edu Phone: 1 4144567506 Fax: 1 4144566190 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: RAT GENOME DATABASE - RGD - MAPPING DISEASE ONTO THE GENOME Poster Authors and organization: Aubrey Hughes¹, Jedediah Mathis², Mary Shimoyama, Norberto de la Cruz, Charles W. Wang, Nataliya Nenasheva, Dean Pasko, Jiali Chen, Lan Zhao, Chunyu Fan, Wenhua Wu, Chin-Fu Chen, Rajni Nigam, Gopal Gopinathrao, Angela Zuniga-Meyer, Susan Bromberg, Jessica Ginster, Anne Kwitek-Black, Janan Eppig, Lois Maltais, Donna Maglott, Greg Schuler, Simon Twigger, Howard Jacob and Peter Tonellato
¹ahughes@mcw.edu, Medical College of Wisconsin; ²jmathis@mcw.edu, Medical College of Wisconsin Abstract: The Rat Genome Database (RGD) is a disease centric resource of comprehensively curated data from rat genetic and genomic research. RGD's goal is to provide information that will aid researchers in using the rat as a model organism for human disease studies. RGD is available at rgd.mcw.edu . File: ahughesATmcw.edu_61 ************************************************* Thu Apr 24 00:21:24 2003 UPDATE ----- Number: 62 Name: Hayes, Wayne B Affiliation: University of Maryland Address: IPST Building 224 City: College Park State/Provice: MD Postal/Zip Code: 20742 Country: USA Email: wayne@cs.toronto.edu Phone: 240-893-1612 Fax: 301-314-9363 Category: Sequence Comparison Poster Title: IMPROVING SEQUENCE ASSEMBLIES USING HIGH-QUALITY OVERLAPS Poster Authors and organization: Michael Roberts¹, James Yorke², Brian Hunt, Wayne Hayes, Aleksey Zimin, Cevat Ustun, Paul Havlak
¹tri@ipst.umd.edu, University of Maryland; ²yorke@ipst.umd.edu, University of Maryland Abstract: Finishing a genome costs as much as initial assembly. Since initial assembly gets about 95% of it, gaining just a few extra percent initially can save tens of millions of dollars in finishing costs. We present computational techniques for improving "overlaps" resulting in up to 5% additional sequence during initial assembly. File: wayneATcs.toronto.edu_62 ************************************************* Thu Apr 24 00:22:53 2003 UPDATE ----- Number: 61 Name: Hughes, Aubrey D Affiliation: Medical College of Wisconsin Address: 8701 Watertown Plank Rd City: Milwaukee State/Provice: Wisconsin Postal/Zip Code: 53226 Country: USA Email: ahughes@mcw.edu Phone: 1 4144567506 Fax: 1 4144566190 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: RAT GENOME DATABASE - RGD - MAPPING DISEASE ONTO THE GENOME Poster Authors and organization: Aubrey Hughes¹, Jedediah Mathis², Mary Shimoyama, Norberto de la Cruz, Charles W. Wang, Nataliya Nenasheva, Dean Pasko, Jiali Chen, Lan Zhao, Chunyu Fan, Wenhua Wu, Chin-Fu Chen, Rajni Nigam, Gopal Gopinathrao, Angela Zuniga-Meyer, Susan Bromberg, Jessica Ginster, Anne Kwitek-Black, Janan Eppig, Lois Maltais, Donna Maglott, Greg Schuler, Simon Twigger, Howard Jacob and Peter Tonellato
¹ahughes@mcw.edu, Medical College of Wisconsin; ²jmathis@mcw.edu, Medical College of Wisconsin Abstract: The Rat Genome Database (RGD) is a disease centric resource of comprehensively curated data from rat genetic and genomic research. RGD's goal is to provide information that will aid researchers in using the rat as a model organism for human disease studies. RGD is available at rgd.mcw.edu . File: ahughesATmcw.edu_61 ************************************************* Thu Apr 24 00:24:34 2003 UPDATE ----- Number: 61 Name: Hughes, Aubrey D Affiliation: Medical College of Wisconsin Address: 8701 Watertown Plank Rd City: Milwaukee State/Provice: Wisconsin Postal/Zip Code: 53226 Country: USA Email: ahughes@mcw.edu Phone: 1 4144567506 Fax: 1 4144566190 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: RAT GENOME DATABASE - RGD - MAPPING DISEASE ONTO THE GENOME Poster Authors and organization: Aubrey Hughes¹, Jedediah Mathis², Mary Shimoyama, Norberto de la Cruz, Charles W. Wang, Nataliya Nenasheva, Dean Pasko, Jiali Chen, Lan Zhao, Chunyu Fan, Wenhua Wu, Chin-Fu Chen, Rajni Nigam, Gopal Gopinathrao, Angela Zuniga-Meyer, Susan Bromberg, Jessica Ginster, Anne Kwitek-Black, Janan Eppig, Lois Maltais, Donna Maglott, Greg Schuler, Simon Twigger, Howard Jacob and Peter Tonellato
¹ahughes@mcw.edu, Medical College of Wisconsin; ²jmathis@mcw.edu, Medical College of Wisconsin Abstract: The Rat Genome Database (RGD) is a disease centric resource of comprehensively curated data from rat genetic and genomic research. RGD's goal is to provide information that will aid researchers in using the rat as a model organism for human disease studies. RGD is available at rgd.mcw.edu . File: ahughesATmcw.edu_61 ************************************************* Thu Apr 24 00:25:42 2003 UPDATE ----- Number: 61 Name: Hughes, Aubrey D Affiliation: Medical College of Wisconsin Address: 8701 Watertown Plank Rd City: Milwaukee State/Provice: Wisconsin Postal/Zip Code: 53226 Country: USA Email: ahughes@imb.uq.edu.au Phone: 1 4144567506 Fax: 1 4144566190 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: RAT GENOME DATABASE - RGD - MAPPING DISEASE ONTO THE GENOME Poster Authors and organization: Aubrey Hughes¹, Jedediah Mathis², Mary Shimoyama, Norberto de la Cruz, Charles W. Wang, Nataliya Nenasheva, Dean Pasko, Jiali Chen, Lan Zhao, Chunyu Fan, Wenhua Wu, Chin-Fu Chen, Rajni Nigam, Gopal Gopinathrao, Angela Zuniga-Meyer, Susan Bromberg, Jessica Ginster, Anne Kwitek-Black, Janan Eppig, Lois Maltais, Donna Maglott, Greg Schuler, Simon Twigger, Howard Jacob and Peter Tonellato
¹ahughes@mcw.edu, Medical College of Wisconsin; ²jmathis@mcw.edu, Medical College of Wisconsin Abstract: The Rat Genome Database (RGD) is a disease centric resource of comprehensively curated data from rat genetic and genomic research. RGD's goal is to provide information that will aid researchers in using the rat as a model organism for human disease studies. RGD is available at rgd.mcw.edu . File: ahughesATimb.uq.edu.au_61 ************************************************* Thu Apr 24 00:27:59 2003 UPDATE ----- Number: 61 Name: Hughes, Aubrey D Affiliation: Medical College of Wisconsin Address: 8701 Watertown Plank Rd City: Milwaukee State/Provice: Wisconsin Postal/Zip Code: 53226 Country: USA Email: ahughes@mcw.edu Phone: 1 4144567506 Fax: 1 4144566190 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: freddofrog Poster Authors and organization: Aubrey Hughes¹, Jedediah Mathis², Mary Shimoyama, Norberto de la Cruz, Charles W. Wang, Nataliya Nenasheva, Dean Pasko, Jiali Chen, Lan Zhao, Chunyu Fan, Wenhua Wu, Chin-Fu Chen, Rajni Nigam, Gopal Gopinathrao, Angela Zuniga-Meyer, Susan Bromberg, Jessica Ginster, Anne Kwitek-Black, Janan Eppig, Lois Maltais, Donna Maglott, Greg Schuler, Simon Twigger, Howard Jacob and Peter Tonellato
¹ahughes@mcw.edu, Medical College of Wisconsin; ²jmathis@mcw.edu, Medical College of Wisconsin Abstract: The Rat Genome Database (RGD) is a disease centric resource of comprehensively curated data from rat genetic and genomic research. RGD's goal is to provide information that will aid researchers in using the rat as a model organism for human disease studies. RGD is available at rgd.mcw.edu . File: ahughesATmcw.edu_61 ************************************************* Thu Apr 24 00:30:09 2003 UPDATE ----- Number: 65 Name: Williams, Allyson L Affiliation: EMBL - EBI Address: Wellcome Trust Genome Campus City: Hinxton State/Provice: Cambridgeshire Postal/Zip Code: CB10 1SD Country: UK Email: allyson@ebi.ac.uk Phone: +44 1223 494676 Fax: +44 1223 494468 Category: Databases Poster Title: UniProt: Universal Protein Databases for Protein Sequences and Function Poster Authors and organization: Allyson Williams¹, Maria Jesus Martin², Claire O'Donovan, Daniel Barrell, Alexander Fedotov, Rolf Apweiler
¹allyson@ebi.ac.uk, EMBL - EBI; ²martin@ebi.ac.uk, EMBL - EBI Abstract: The UniProt Consortium (European Bioinformatics Institute, Swiss Institute of Bioinformatics, and the Protein Information Resource) was created to merge Swiss-Prot, TrEMBL and PIR database activities into UniProt, a comprehensive resource of protein sequences and function. UniProt has three layers: protein sequence archive, protein knowledgebase, and non-redundant reference (NREF) databases. File: allysonATebi.ac.uk_65 ************************************************* Thu Apr 24 00:30:35 2003 UPDATE ----- Number: 65 Name: Williams, Allyson L Affiliation: EMBL - EBI Address: Wellcome Trust Genome Campus City: Hinxton State/Provice: Cambridgeshire Postal/Zip Code: CB10 1SD Country: UK Email: allyson@ebi.ac.uk Phone: +44 1223 494676 Fax: +44 1223 494468 Category: Databases Poster Title: UniProt: Universal Protein Databases for Protein Sequences and Function Poster Authors and organization: Allyson Zippi Williams¹, Maria Jesus Martin², Claire O'Donovan, Daniel Barrell, Alexander Fedotov, Rolf Apweiler
¹allyson@ebi.ac.uk, EMBL - EBI; ²martin@ebi.ac.uk, EMBL - EBI Abstract: The UniProt Consortium (European Bioinformatics Institute, Swiss Institute of Bioinformatics, and the Protein Information Resource) was created to merge Swiss-Prot, TrEMBL and PIR database activities into UniProt, a comprehensive resource of protein sequences and function. UniProt has three layers: protein sequence archive, protein knowledgebase, and non-redundant reference (NREF) databases. File: allysonATebi.ac.uk_65 ************************************************* Thu Apr 24 00:32:16 2003 UPDATE ----- Number: 62 Name: Hayes, Wayne B Affiliation: University of Maryland Address: IPST Building 224 City: College Park State/Provice: MD Postal/Zip Code: 20742 Country: USA Email: wayne@cs.toronto.edu Phone: 240-893-1612 Fax: 301-314-9363 Category: Sequence Comparison Poster Title: IMPROVING SEQUENCE ASSEMBLIES USING HIGH-QUALITY OVERLAPS Poster Authors and organization: Michael Roberts¹, James Yorke², Brian Hunt, Wayne Hayes, Aleksey Zimin, Cevat Ustun, Paul Havlak
¹tri@ipst.umd.edu, University of Maryland; ²yorke@ipst.umd.edu, University of Maryland Abstract: Finishing a genome costs as much as initial assembly. Since initial assembly gets about 95% of it, gaining just a few extra percent initially can save tens of millions of dollars in finishing costs. We present computational techniques for improving "overlaps" result in up to 5% additional sequence during initial assembly. File: wayneATcs.toronto.edu_62 ************************************************* Thu Apr 24 00:32:19 2003 UPDATE ----- Number: 59 Name: Platzer, Ute Affiliation: German Cancer Research Centre Address: Im Neuenheimer Feld 280 City: Heidelberg State/Provice: Baden-Wuerttemberg Postal/Zip Code: 69120 Country: Germany Email: u.platzer@dkfz.de Phone: +49 6221 422355 Fax: +49 6221 422345 I plan to use my laptop computer as part of my poster Category: Systems Biology Poster Title: Gene-O-Matic: Regulatory Network Simulation in Multicellular Organisms Poster Authors and organization: Ute Platzer¹, Rolf Lohaus², Hans-Peter Meinzer
¹u.platzer@dkfz.de, German Cancer Research Centre; ²r.lohaus@dkfz.de, German Cancer Research Centre Abstract: Gene-O-Matic is a graphical tool for the construction and simulation of regulatory networks in multicellular organisms. A developmental process simulated successfully is embryonic development of the worm Caenorhabditis elegans. Gene-O-Matic is availabe on request from the authors, or by e-mail to cello@dkfz.de. The project's website can be found at http://mbi.dkfz-heidelberg.de/projects/cellsim/. File: u.platzerATdkfz.de_59 ************************************************* Thu Apr 24 00:32:59 2003 UPDATE ----- Number: 59 Name: Platzer, Ute Affiliation: German Cancer Research Centre Address: Im Neuenheimer Feld 280 City: Heidelberg State/Provice: Baden-Wuerttemberg Postal/Zip Code: 69120 Country: Germany Email: u.platzer@dkfz.de Phone: +49 6221 422355 Fax: +49 6221 422345 I plan to use my laptop computer as part of my poster Category: Systems Biology Poster Title: Gene-O-Matic: Regulatory Network Simulation in Multicellular Organisms Poster Authors and organization: Ute Platzer¹, Rolf Lohaus², Hans-Peter Meinzer
¹u.platzer@dkfz.de, German Cancer Research Centre; ²r.lohaus@dkfz.de, German Cancer Research Centre Abstract: Gene-O-Matic is a graphical tool for the construction and simulation of regulatory networks in multicellular organisms. A developmental process simulated successfully is embryonic development of the worm Caenorhabditis elegans. Gene-O-Matic is availabe on request from the authors, or by e-mail to cello@dkfz.de. The project's website can be found at http://mbi.dkfz-heidelberg.de/projects/cellsim/. File: u.platzerATdkfz.de_59 ************************************************* Thu Apr 24 00:33:34 2003 Number: 109 Name: Dejori, Mathaeus Affiliation: Siemens Address: Otto-Hahn-Ring 6 City: Munich State/Provice: Bavaria Postal/Zip Code: 81739 Country: Germany Email: mathaeus.dejori.external@mchp.siemens.de Phone: ++49 89 636 47373 Fax: ++49 89 636 49767 Category: Microarrays Poster Title: Estimation of oncogenes by Bayesian inverse modeling of gene-expression patterns Poster Authors and organization: Mathaeus Dejori¹, Martin Stetter²
¹mathaeus.dejori.external@mchp.siemens.de, TUM; ²stetter@siemens.com, Siemens AG Abstract: We train a Bayesian network to represent statistical dependencies between gene-expression levels from DNA-microarray datasets. The trained network is used to predict the effect of pathologically altered expression levels on the global expression pattern (inverse modeling). By use of this ability we can powerfully predict new genes involved in pathogenesis. File: mathaeus.dejori.externalATmchp.siemens.de_109 ************************************************* Thu Apr 24 00:33:40 2003 UPDATE ----- Number: 65 Name: Williams, Allyson L Affiliation: EMBL - EBI Address: Wellcome Trust Genome Campus City: Hinxton State/Provice: Cambridgeshire Postal/Zip Code: CB10 1SD Country: UK Email: allyson@ebi.ac.uk Phone: +44 1223 494676 Fax: +44 1223 494468 Category: Databases Poster Title: UniProt: Universal Protein Databases for Protein Sequences and Function Poster Authors and organization: Allyson Williams¹, Maria Jesus Martin², Claire O'Donovan, Daniel Barrell, Alexander Fedotov, Rolf Apweiler
¹allyson@ebi.ac.uk, EMBL - EBI; ²martin@ebi.ac.uk, EMBL - EBI Abstract: The UniProt Consortium (European Bioinformatics Institute, Swiss Institute of Bioinformatics, and the Protein Information Resource) was created to merge Swiss-Prot, TrEMBL and PIR database activities into UniProt, a comprehensive resource of protein sequences and function. UniProt has three layers: protein sequence archive, protein knowledgebase, and non-redundant reference (NREF) databases. File: allysonATebi.ac.uk_65 ************************************************* Thu Apr 24 00:34:16 2003 UPDATE ----- Number: 65 Name: Williams, Allyson L Affiliation: EMBL - EBI Address: Wellcome Trust Genome Campus City: Hinxton State/Provice: Cambridgeshire Postal/Zip Code: CB10 1SD Country: UK Email: allyson@ebi.ac.uk Phone: +44 1223 494676 Fax: +44 1223 494468 Category: Databases Poster Title: UniProt: Universal Protein Databases for Protein Sequences and Function Poster Authors and organization: Allyson Zippy Williams¹, Maria Jesus Martin², Claire O'Donovan, Daniel Barrell, Alexander Fedotov, Rolf Apweiler
¹allyson@ebi.ac.uk, EMBL - EBI; ²martin@ebi.ac.uk, EMBL - EBI Abstract: The UniProt Consortium (European Bioinformatics Institute, Swiss Institute of Bioinformatics, and the Protein Information Resource) was created to merge Swiss-Prot, TrEMBL and PIR database activities into UniProt, a comprehensive resource of protein sequences and function. UniProt has three layers: protein sequence archive, protein knowledgebase, and non-redundant reference (NREF) databases. File: allysonATebi.ac.uk_65 ************************************************* Thu Apr 24 00:38:33 2003 UPDATE ----- Number: 69 Name: Vilanova, David Affiliation: Nestle Research Center Address: VERS CHEZ LES BLANC City: Lausanne State/Provice: VAUD Postal/Zip Code: 1012 Country: Switzerland Email: david.vilanova@rdls.nestle.com Phone: +41217858723 Fax: +41217858925 Category: Data Mining Poster Title: Hight-throughput gene expression analysis with GATO Poster Authors and organization: David Vilanova¹, James holzwarth², Marie Camille Zwahlen, Frank Desiere,Matthew Alan Roberts
¹david.vilanova@rdls.nestle.com, Nestle research center; ²james.holzwarth@rdls.nestle.com, Nestle research center Abstract: We present GATO (gene annotation tool) a tool to analyse gene expression data based on Ensembl database and Gene Ontology. We describe how our tool can be utilized to rapidly mine gene expression data and drive biological interpretation using Affymetrix arrays. File: david.vilanovaATrdls.nestle.com_69 ************************************************* Thu Apr 24 00:38:50 2003 Number: 110 Name: Dejori, Mathaeus Affiliation: Siemens Address: Otto-Hahn-Ring 6 City: Munich State/Provice: Bavaria Postal/Zip Code: 81739 Country: Germany Email: mathaeus.dejori.external@mchp.siemens.de Phone: ++49 89 636 47373 Fax: ++49 89 636 49767 Category: Microarrays Poster Title: Using scale-free topology to estimate critical genes from regulatory networks Poster Authors and organization: Mathaeus Dejori¹, Martin Stetter²
¹mathaeus.dejori.external@mchp.siemens.de, TUN; ²stetter@siemens.com, Siemens AG Abstract: We present a method for estimating key regulatory genes of genetic networks by analyzing their summed biological signal throughput (load). In networks learned from childhood leukemia microarray datasets we find a small number of genes with a high load such as POU2AF1 that may contribute to B-cell tumorigenesis. File: mathaeus.dejori.externalATmchp.siemens.de_110 ************************************************* Thu Apr 24 00:40:08 2003 Number: 111 Name: Zhu, Jingchun Affiliation: University of California at San Francisco Address: 503 Font Blvd. City: San Francisco State/Provice: california Postal/Zip Code: 94132 Country: USA Email: jzhu@itsa.ucsf.edu Phone: 4153372017 Fax: Category: Microarrays Poster Title: Using bayesian network learning to model yeast transcriptional response to nitrogen oxide Poster Authors and organization: Jingchun Zhu¹, Joe DeRisi²
¹jzhu@itsa.ucsf.edu, UCSF; ²joe@derisilab.ucsf.edu, UCSF Abstract: We used Bayesian Network learning to analyze microarray transcriptional response profiles of yeast to nitrogen oxide. Using gene clusters as network nodes, the learned transcription response networks are consistent with the proposed biological hypotheses. The model also revealed a previously unknown link between galactose input and a fzf1 dependent cluster. File: jzhuATitsa.ucsf.edu_111 ************************************************* Thu Apr 24 00:47:18 2003 UPDATE ----- Number: 78 Name: Koike, Asako Affiliation: Human Genome Center, The Institute of Medical Science, The University of Tokyo Address: 4-6-1 Shirokane-dai City: Minto-ku State/Provice: Tokyo Postal/Zip Code: 108-8639 Country: Japan Email: akoike@ims.u-tokyo.ac.jp Phone: 81-3-5449-5611 Fax: 81-3-5449-5434 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: PRIME: automatically extracted PRotein Interactions and Molecular Information databasE. Poster Authors and organization: Asako Koike¹, Yoshiyuki Kobayashi², Toshihisa Takagi
¹akoike@ims.u-tokyo.ac.jp, Human Genome Center, The Institute of Medical Science, Univ. of Tokyo; ²yashi@ls.hitachi.co.jp, Life Science Group, Hitachi, Ltd. Abstract: PRIME(http://prime.ontology.ims.u-tokyo.ac.jp/) is an integrated database involving major completely sequenced eukaryotes. It contains the protein-protein/gene/compound interaction data extracted by natural language processing, domain information, structural information, protein kinase classification, and ortholog tables among organisms. The comparison and prediction of pathways are also available by an automatic pathway graphic image interface. File: akoikeATims.u-tokyo.ac.jp_78 ************************************************* Thu Apr 24 04:54:24 2003 Number: 112 Name: Splendiani, Andrea Affiliation: Genopolis, Univ.-Milano Bicocca. Address: Piazza della scienza 2 City: Milano State/Provice: MI Postal/Zip Code: 20126 Country: Italy Email: andrea.splendiani@unimib.it Phone: 39 2 6448 4521 Fax: 39 2 6448 4580 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: GCC: a database system for immune cells transcriptomes Poster Authors and organization: Andrea Splendiani¹, C.Vizzardelli,N.Pavelka,M.Pelizzola,M.Capozzoli,O.Beretta,F.Granucci,P.Ricciardi-Castagnoli
¹andrea.splendiani@unimib.it, Univ. Milano Bicocca Abstract: GCC is a database for immune cells transcriptomes. It is based on a database system (built using opensource technologies) that allows for data storage and intelligent retrieval. It is targeted at the affymetrix platform and allows for MIAME compliant experimental annotation and supports adoption of ontologies. File: andrea.splendianiATunimib.it_112 ************************************************* Thu Apr 24 05:13:07 2003 Number: 113 Name: Giegerich, Robert K Affiliation: Bielefeld University Address: Postfach 100131 City: Bielefeld State/Provice: NRW Postal/Zip Code: 33501 Country: Germany Email: robert@techfak.uni-bielefeld.de Phone: +49-521-1062913 Fax: +49-521-1066411 Category: Predictive Methods Poster Title: Evaluating the Predictability of RNA Pseudoknots Poster Authors and organization: J. Reeder¹, R. Giegerich²
¹robert@techfak.uni-bielefeld.de, Bielefeld University; ²jreeder@techfak.uni-bielefeld.de, Bielefeld University Abstract: We define a new class of pseudoknots and present algorithms for thermodynamic folding of RNA secondary structures including such pseudoknots. Their time/space complexity is O(n^4) and O(n^2). We also compute the best structure guaranteed to contain a pseudoknot, and the most tightly knotted substructure. An extensive evaluation of Pseudobase is performed. File: robertATtechfak.uni-bielefeld.de_113 ************************************************* Thu Apr 24 05:18:41 2003 Number: 114 Name: Garcia-Rizo, Carolina Affiliation: Max-Planck Institute Biochemistry Address: Am Klopferspitz 18a City: Martinsried State/Provice: Muenchen Postal/Zip Code: D-82152 Country: Germany Email: rizo@biochem.mpg.de Phone: 089-8578-2386 Fax: Category: Structural Biology Poster Title: A bioinformatic toolbox for postprocessing of MASCOT results and its application to the proteome of Halobacterium salinarum Poster Authors and organization: Carolina Garcia-Rizo¹, Cristian Klein², Pfeiffer, Siedler, Oesterhelt
¹klein@biochem.mpg.de, Max-Planck Institute Biochemistry; ²rizo@biochem.mpg.de, Max-Planck Institute Biochemistry Abstract: We present a bioinformatic toolbox for postprocessing of proteomic data obtained by peptide fingerprint analysis. This toolbox permits to (i) increase the reliability of protein identifications, (ii) detect additional annotation information and (iii) correct or validate start codon assignments by gene finders. The toolbox was developed for and applied to the proteomic of Halobacterium salinarum strain R1 (www.halolex.mpg.de) File: rizoATbiochem.mpg.de_114 ************************************************* Thu Apr 24 05:32:35 2003 Number: 115 Name: Garcia-Rizo, Carolina Affiliation: Max-Planck Institute Biochemistry Address: Am Klopferspitz 18a City: Martinsried State/Provice: Muenchen Postal/Zip Code: D-82152 Country: Germany Email: rizo@biochem.mpg.de Phone: 089-8578-2386 Fax: Category: Structural Biology Poster Title: Theoretical prediction of the feasibility of identifing membrane proteins by MALDI-TOF Poster Authors and organization: Carolina Garcia-Rizo¹, Cristian Klein², Pfeiffer, Siedler, Oesterhelt
¹klein@biochem.mpg.de, Max-Planck Institute Biochemistry; ²rizo@biochem.mpg.de, Max-Planck Institute Biochemistry Abstract: In the set of proteins of H. salinarum identified by MALDI-TOF peptide fingerprints, membrane proteins are severely underrepresented. Besides the technical problems encountered in their analysis by 2D gel electrophoresis, an �inherent data analysis problem� is found by statistical analysis. The degree to which this effect aggravates problems in detection ratio of membrane proteins varies from organism to organism. File: rizoATbiochem.mpg.de_115 ************************************************* Thu Apr 24 06:18:51 2003 Number: 116 Name: Jacques, Pierre-Etienne Affiliation: Universite de Sherbrooke, Departement de Biologie et Departement de Mathematiques-Informatique Address: 2500 Boul de l,Universite City: Sherbrooke State/Provice: Quebec Postal/Zip Code: J1K 2R1 Country: Canada Email: pierre-etienne.jacques@hermes.usherb.ca Phone: 819-821-8000-2082 Fax: 819-821-8049 Category: Predictive Methods Poster Title: A sequence-independent strategy for the prediction of prokaryotic promoters Poster Authors and organization: Pierre-Etienne Jacques¹, Sebastien Rodrigue², Jocelyn Beaucher, Jean-Fran�ois Jacques, Luc Gaudreau, Jean Goulet and Ryszard Brzezinski
¹pierre-etienne.jacques@hermes.usherb.ca, Universite de Sherbrooke; ², Universite de Sherbrooke Abstract: Our strategy is based on the biological fact which show that promoters are localized in the upstream regulatory regions of genes. The possibility for a particular sequence to be a bona fide promoter can be evaluated from its mismatch distribution amongst the various areas of the genome. File: pierre-etienne.jacquesAThermes.usherb.ca_116 ************************************************* Thu Apr 24 07:08:42 2003 Number: 117 Name: Julenius, Karin Affiliation: Center for Biological Sequence Analysis Address: Technical University of Denmark, Building 208 City: Lyngby State/Provice: NA Postal/Zip Code: DK-2800 Country: Denmark Email: kj@cbs.dtu.dk Phone: +45-45252472 Fax: +45-45931585 Category: Predictive Methods Poster Title: NetOGlyc 3.0: Prediction of mucin type O-glycosylation sites from sequence and sequence-derived features. Poster Authors and organization: Karin Julenius¹, Ramneek Gupta, Kristoffer Rapacki, Lars Juhl Jensen, S�ren Brunak
¹kj@cbs.dtu.dk, Center for Biological Sequence Analysis, BioCentrum-DTU Abstract: NetOGlyc 3.0 is a predictor of mucin type O-glycosylation sites, predicting from the protein sequence alone. NetOGlyc 3.0 show much better generalization behaviour (the ability of the network to correctly predict for completely new examples) than its predecessor and is available at www.cbs.dtu.dk/services/NetOGlyc/ File: kjATcbs.dtu.dk_117 ************************************************* Thu Apr 24 08:45:35 2003 Number: 118 Name: Poulin, Brett W Affiliation: University of Alberta Address: 10730 83 Ave Apt.202 City: Edmonton State/Provice: AB Postal/Zip Code: T6E 2E4 Country: Canada Email: poulin@cs.ualberta.ca Phone: 780-433-6128 Fax: 780-492-1071 Category: Data Mining Poster Title: Clustering Proteins in Non-metric Space Poster Authors and organization: Brett Poulin¹, Marianne Morris², Joerg Sander
¹poulin@cs.ualberta.ca, University of Alberta; ²marianne@cs.ualberta.ca, University of Alberta Abstract: Clustering techniques may be used to efficiently group protein sequences into functionally similar classes. Typical clustering algorithms assume that the measure of distance between sequences is a metric but common measures of local similarity do not satisfy this assumption. We examine challenges and techniques of clustering in a non-metric space. File: poulinATcs.ualberta.ca_118 ************************************************* Thu Apr 24 08:45:45 2003 Number: 119 Name: Poulin, Brett W Affiliation: University of Alberta Address: 10730 83 Ave Apt.202 City: Edmonton State/Provice: AB Postal/Zip Code: T6E 2E4 Country: Canada Email: poulin@cs.ualberta.ca Phone: 780-433-6128 Fax: 780-492-1071 Category: Data Mining Poster Title: Clustering Proteins in a Non-metric Space Poster Authors and organization: Brett Poulin¹, Marianne Morris², Joerg Sander
¹poulin@cs.ualberta.ca, University of Alberta; ²marianne@cs.ualberta.ca, University of Alberta Abstract: Clustering techniques may be used to efficiently group protein sequences into functionally similar classes. Typical clustering algorithms assume that the measure of distance between sequences is a metric but common measures of local similarity do not satisfy this assumption. We examine challenges and techniques of clustering in a non-metric space. File: poulinATcs.ualberta.ca_119 ************************************************* Thu Apr 24 09:36:09 2003 Number: 120 Name: Bartels, Daniela Affiliation: Center for Genome Research, Bielefeld University Address: Babenhauserstr. 324 City: Bielefeld State/Provice: NRW Postal/Zip Code: 33619 Country: Germany Email: Daniela.Bartels@Genetik.Uni-Bielefeld.DE Phone: 05211064813 Fax: 05211065626 I plan to use my laptop computer as part of my poster Category: Functional Genomics Poster Title: GOPArcII - new features of the GeneOntology and Pathways Architecture Poster Authors and organization: Daniela Bartels¹, Alexander Goesmann², Oliver Rupp, Folker Meyer
¹Daniela.Bartels@Genetik.Uni-Bielefeld.DE, Center for Genome Research, Bielefeld University; ²Alexander.Goesmann@Genetik.Uni-Bielefeld.DE, Center for Genome Research, Bielefeld University Abstract: We present GOPArcII, a new version of our comprehensive, open source framework for the integration of functional classifications and metabolic pathways. GOPArcII is based on a relational database. It enables a user to search and handle data like genome data from the perspective of functional categories and metabolic pathways. File: Daniela.BartelsATGenetik.Uni-Bielefeld.DE_120 ************************************************* Thu Apr 24 12:45:03 2003 Number: 121 Name: Lee, Lawrence C Affiliation: University of California San Francisco Address: 600 16th Street, N476 Box 2240 City: San Francisco State/Provice: CA Postal/Zip Code: 94143-2240 Country: USA Email: lle8@itsa.ucsf.edu Phone: 1-415-502-5649 Fax: 1-415-476-6515 Category: Data Mining Poster Title: MutationMiner: A Graph Theoretic Approach to Extract Point Mutation Data from Biomedical Literature Poster Authors and organization: Lawrence C. Lee¹, Florence Horn², Fred E. Cohen
¹lle8@itsa.ucsf.edu, University of California San Francisco; ²horn@cmpharm.ucsf.edu, University of California San Francisco Abstract: MutationMiner is a program which automates extraction of point mutation data from biomedical literature. It uses regular expressions and a graph theoretic approach to find point mutations in the text and then confirms the mutations with SwissProt data. MutationMiner can search over one thousand journal articles in 24 hours. File: lle8ATitsa.ucsf.edu_121 ************************************************* Thu Apr 24 14:41:12 2003 Number: 122 Name: Lea, Rod A Affiliation: Victoria University Address: Salamanca Avenue City: Wellington State/Provice: Wellington Postal/Zip Code: PO Box 600 Country: New Zealand Email: Rod.Lea@vuw.ac.nz Phone: 0211887876 Fax: 6444635331 Category: Systems Biology Poster Title: Population Genetic Structure in the South Pacific: Prospects for Identifying Disease Susceptibility Genes in New Zealanders with Polynesian Ancestry Poster Authors and organization: Rodney Lea¹, Geoffrey Chambers²
¹Rod.Lea@vuw.ac.nz, Institute of Molecular Systematics; ²Geoff.Chambers@vuw.ac.nz, Institute of Molecular Systematics Abstract: Understanding population genetic structure has important implications for identifying disease susceptibility genes. Our study will utilises multi-locus genotype data from unlinked microsatellite markers to describe the genetic structure in different Polynesian (Maori, Samoan, Tongan), European and admixed populations. File: Rod.LeaATvuw.ac.nz_122 ************************************************* Thu Apr 24 14:54:57 2003 Number: 123 Name: Yeo, Gene Affiliation: MIT Address: 77 Massachusetts Avenue 68-211 City: Cambridge State/Provice: MA Postal/Zip Code: 02139 Country: USA Email: geneyeo@mit.edu Phone: 617 2537039 Fax: Category: Predictive Methods Poster Title: Genomics of Vertebrate Splicing Regulatory Elements Poster Authors and organization: Gene Yeo¹, Shawn Hoon², Chris Burge
¹geneyeo@mit.edu, MIT; ²shawnh@fugu-sg.org, IMCB, Singapore Abstract: We find differences in the distribution and conservation of vertebrate splicing regulatory elements and relevant trans-factors given the availability of large-scale genomic data for Homo Sapiens, Mus musculus and Fugu rubripes. File: geneyeoATmit.edu_123 ************************************************* Thu Apr 24 14:58:46 2003 Number: 124 Name: Przybylski, Dariusz S Affiliation: Columbia University Address: 630 West 168 Street City: New York State/Provice: NY Postal/Zip Code: 10032 Country: USA Email: dudek@cubic.bioc.columbia.edu Phone: 212-305-4018 Fax: Category: Structural Biology Poster Title: Correlated errors of neural network predictions improve fold recognition. Poster Authors and organization: Dariusz Przybylski¹, Burkhard Rost²
¹dudek@cubic.bioc.columbia.edu, Columbia Univeristy; ²rost@columbia.edu, Columbia University Abstract: We present a fold recognition method that uses predicted secondary structure and solvent accessibility in a way that significantly improves both specificity and sensitivity of fold assignments compared to PSI-BLAST. The method can readily be used for high quality/throughput database annotations. File: dudekATcubic.bioc.columbia.edu_124 ************************************************* Thu Apr 24 15:10:57 2003 Number: 125 Name: Mathis, Jedidiah R Affiliation: Medical College of Wisconsin Address: 8701 Watertown Plank Rd. City: Milwaukee State/Provice: Wisconsin Postal/Zip Code: 53226 Country: USA Email: jmathis@mcw.edu Phone: 414-456-7507 Fax: 414-456-6190 Category: Data Visualisation Poster Title: Automated Construction of Comparative Maps between Zebrafish, Human, Rat and Mouse Poster Authors and organization: Jedidiah Mathis¹, Victor Ruotti², Jeff Nie, Dan Chen, John Postlethwait, Monte Westerfield, Michael Thomas, Michael Carvan, Peter Tonellato
¹jmathis@mcw.edu, Medical College of Wisconsin; ²vruotti@mcw.edu, Medical College of Wisconsin Abstract: Radiation hybrid maps coupled with the mapping of expressed sequence tags and their organization into UniGene clusters, has revolutionized the way comparative maps are built and maintained. We have used publicly available rat, mouse, human, and zebrafish data to build completely integrated comparative maps. File: jmathisATmcw.edu_125 ************************************************* Thu Apr 24 15:19:09 2003 Number: 126 Name: Mathis, Jedidiah R Affiliation: Medical College of Wisconsin Address: 8701 Watertown Plank Rd City: Milwaukee State/Provice: Wisconsin Postal/Zip Code: 53226 Country: USA Email: jmathis@mcw.edu Phone: 414-456-7507 Fax: 414-456-6190 Category: Genome Annotation Poster Title: Identifying and Annotating Disease Specific Rat Genome Sequences Poster Authors and organization: Jedidiah Mathis¹, Mary Shimoyama², Aubrey Hughes, Norberto Dela Cruz, Charles Wang, Simon Twigger, Michael Jensen-Seamen, Michelle Feldmann, Artur Rangel Filho, Jozef Lazar, Howard Jacob, Peter Tonellato
¹jmathis@mcw.edu, Medical College of Wisconsin; ²shimoyma@mcw.edu, Medical College of Wisconsin Abstract: Disease related Genomic Regions Of Interest (GROI) were submitted to the Rat Genome Sequencing Consortium for prioritized sequencing. These areas were analyzed to determine whether greater coverage facilitated denser and more accurate annotation. Functional annotation of genes in these regions was achieved using datamining of public databases and manual curation. File: jmathisATmcw.edu_126 ************************************************* Thu Apr 24 15:48:48 2003 Number: 127 Name: McLysaght, Aoife F Affiliation: University of California, Irvine Address: 321 Steinhaus Hall City: Irvine State/Provice: CA Postal/Zip Code: 92697-2525 Country: USA Email: amclysag@uci.edu Phone: 1-949-8247703 Fax: 1-949-8242181 Category: Phylogeny and Evolution Poster Title: In silico exploitation of genetic maps: detection of hidden synteny through multiple genome comparisons Poster Authors and organization: Aoife McLysaght¹, Brandon Gaut²
¹amclysag@uci.edu, UCI; ²bgaut@uci.edu, UCI Abstract: Genetic maps are expensive and time consuming to produce, yet they contain only partial genomic data. Here we present a method to maximise the value of genetic maps in silico through multiple genome comparison. Using this method we can detect regions conserved synteny that are not detectable through simple pairwise comparisons. File: amclysagATuci.edu_127 ************************************************* Thu Apr 24 18:12:00 2003 Number: 128 Name: Krebs, Werner G Affiliation: University of California, San Diego Address: 9500 Gilman Drive Department 0505 City: La Jolla State/Provice: CA Postal/Zip Code: 92093-0505 Country: USA Email: wernerkrebs@yahoo.com Phone: 8588223620 Fax: 5032109164 Category: Data Mining Poster Title: Statistically Rigorous Automated Gene Annotation and Classification using Gene Ontology Terms Poster Authors and organization: Werner G. Krebs¹, Philip E. Bourne²
¹wernerkrebs@yahoo.com, UCSD; ²bourne@sdsc.edu, UCSD Abstract: We have developed a robust, U.S.-patent-pending statistical method for annotation of clustered genes into an ontology. Here, we apply our method to annotate several databases into the Gene Ontology, including PDB and NR. We provide quantitative evidence in support of our method and demonstrate powerful web querying systems. File: wernerkrebsATyahoo.com_128.html ************************************************* Thu Apr 24 18:43:54 2003 Number: 129 Name: Gill, John C Affiliation: Victorian Bioinformatics Consortium, Monash University Address: Wellington rd. City: Clayton State/Provice: Victoria Postal/Zip Code: 3800 Country: Australia Email: john.gill@med.monash.edu.au Phone: 9 905 9274 Fax: Category: Data Visualisation Poster Title: GET3D, A Genomic Exploration Tool in 3D Poster Authors and organization: John Gill¹
¹john.gill@monash.edu.au, Victorian Bioinformatics Consortium, Monash University Abstract: 50 Word Abstract:

The GET3D, Genomic Exploration Tool in 3D, software tool is a complimentary product to the CAS, Categorised Annotation Set, system. Through 3D visualization and interaction techniques it allows for the manipulate of the CAS dataset, including the highlighting and exploration of data relationships, and for adding new information and relationships. File: john.gillATmed.monash.edu.au_129.html ************************************************* Thu Apr 24 20:53:49 2003 Number: 130 Name: Nair, Rajesh R Affiliation: Columbia University Address: 630W, 168th St ,Black Bldg 217 City: New York State/Provice: NY Postal/Zip Code: 10027 Country: USA Email: nair@cubic.bioc.columbia.edu Phone: 1 212 305 4018 Fax: 1 212 305 3773 Category: Functional Genomics Poster Title: LOC3D: annotate sub-cellular localization for protein structures Poster Authors and organization: Rajesh Nair¹, Burkhard Rost²
¹nair@cubic.bioc.columbia.edu, Columbia University; ²rost@columbia.edu, Columbia University Abstract: LOC3D is both a database and a web server for predicting the sub-cellular localization of eukaryotic proteins of known structure. Localization is predicted using a combination of four different methods; prediction of nuclear localization signals, through sequence homology to proteins with known localization, automatic text analysis of SWISS-PROT keywords and using neural networks. File: nairATcubic.bioc.columbia.edu_130.html ************************************************* Fri Apr 25 01:38:20 2003 Number: 131 Name: Dopazo, Joaquin Affiliation: Bioinformatics Unit, Spanish National Cancer Center, CNIO. Address: Melchor Fernandez Almagro 3 City: Madrid State/Provice: Madrid Postal/Zip Code: 28029 Country: Spain Email: jdopazo@cnio.es Phone: 34 912246919 Fax: 34 912246972 Category: Microarrays Poster Title: GEPAS, a web-based resource for microarray gene expression data analysis Poster Authors and organization: Javier Herrero¹, Fatima Al-Shahrour², Ramon Diaz-Uriarte, Alvaro Mateos, Juan M. Vaquerizas, Javier Santoyo, Joaquin Dopazo
¹jherrero@cnio.es, CNIO; ²falshahrour@cnio.es, CNIO Abstract: GEPAS is a web-based pipeline for microarray gene expression profile analysis, freely available at http://gepas.bioinfo.cnio.es. The most commonly used tools for the processing and management of different functional genomics data are included in GEPAS as interconnected modules that exchange information in a user friendly manner. File: jdopazoATcnio.es_131.html ************************************************* Fri Apr 25 01:51:30 2003 Number: 132 Name: Dopazo, Joaquin Affiliation: Bioinformatics Unit, Spanish Natonal Cancer Center, CNIO. Address: Melchor Fernandez Almagro 3 City: Madrid State/Provice: Madrid Postal/Zip Code: 28029 Country: Spain Email: jdopazo@cnio.es Phone: 34 912246919 Fax: 34 912246972 Category: Data Mining Poster Title: FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes Poster Authors and organization: Fatima Al-Shahrour¹, Ramon Diaz-Uriarte², Joaquin Dopazo
¹falshahrour@cnio.es, Bioinformatics Unit, Spanish Natonal Cancer Center, CNIO.; ²rdiaz@cnio.es, Bioinformatics Unit, Spanish Natonal Cancer Center, CNIO. Abstract: FatiGO (http://fatigo.bioinfo.cnio.es) is a simple but powerful procedure to extract Gene Ontology terms that result(upon the application of a statistical test) significantly over or under-represented in sets of genes within the context of a genome-scale experiments (DNA microarray, proteomics, etc.). File: jdopazoATcnio.es_132.html ************************************************* Fri Apr 25 03:10:46 2003 Number: 133 Name: OHTA, Tomoko Affiliation: CREST, JST Address: 7-3-1 Hongo City: Bunkyo-ku State/Provice: Tokyo Postal/Zip Code: 113-0033 Country: Japan Email: okap@is.s.u-tokyo.ac.jp Phone: +81-3-5841-4124 Fax: +81-3-5802-8872 Category: Data Mining Poster Title: Current status of the GENIA Corpus: an Annotated Corpus in Molecular Biology Domain Poster Authors and organization: Tomoko OHTA¹, Jin-Dong Kim², Yuka Tateisi, Masayoshi Tsuruoka, Jun'ichi Tsujii
¹okap@is.s.u-tokyo.ac.jp, CREST, JST; ²jkdim@is.s.u-tokyo.ac.jp, University of Tokyo Abstract: GENIA corpus 3.0p and 3.01, consisting of 2,000 MEDLINE abstracts, have been released with linguistically rich annotations including sentence boundaries, term boundaries, term classifications, semi-structured coordinated clauses, recovered ellipsis in terms, part-of-speech, etc. This poster is intended to provide the current status of the GENIA corpus. File: okapATis.s.u-tokyo.ac.jp_133.html ************************************************* Fri Apr 25 06:35:47 2003 Number: 134 Name: Tammi, Martti T. Affiliation: Center for Genomics and Bioinformatics, Karolinska Institutet Address: Berzeliusv 35 City: Stockholm State/Provice: NA Postal/Zip Code: 17177 Country: Sweden Email: martti.tammi@cgb.ki.se Phone: +46-8-7283986 Fax: +46-8-31160 Category: Sequence Comparison Poster Title: Efficient algorithms for sequence comparison and overlap detection - Correcting errors in shotgun sequence reads Poster Authors and organization: Martti T. Tammi¹, Erik Arner², Ellen Kindlund, Bj�rn Andersson
¹martti.tammi@cgb.ki.se, Center for Genomics and Bioinformatics, Karolinska Institutet; ²erik.arner@cgb.ki.se, Center for Genomics and Bioinformatics, Karolinska Institute Abstract: We developed a rapid approximate pattern matching algorithm and a linear time algorithm for multiple alignment construction, with no previous pairwise matching of sequences required. These are implemented in a program for shotgun sequence error correction able to correct 99% of sequencing errors. This is significantly better than previous methods. File: martti.tammiATcgb.ki.se_134.html ************************************************* Fri Apr 25 06:47:29 2003 Number: 135 Name: Tammi, Martti T. Affiliation: Center for Genomics and Bioinformatics, Karolinska Institutet Address: Berzeliusv 35 City: Stockholm State/Provice: NA Postal/Zip Code: 17177 Country: Sweden Email: martti.tammi@cgb.ki.se Phone: +46-8-7283986 Fax: +46-8-31160 Category: Genome Annotation Poster Title: Assembly and finishing tools for repeated and polymorphic genomes Poster Authors and organization: Martti T. Tammi¹, Erik Arner², Ellen Kindlund, Bj�rn Andersson
¹martti.tammi@cgb.ki.se, Center for Genomics and Bioinformatics, Karolinska Institutet; ²erik.arner@cgb.ki.se, Center for Genomics and Bioinformatics, Karolinska Institutet Abstract: DNPTrapper is a graphical tool specifically designed for finishing shotgun assemblies containing complex repeated regions. DNPTrapper allows visualization of sequences and sequence features, e.g DNPs, mate-pairs, repeat boundaries, chromatograms, etc. in horizontal and vertical representation, followed by manual and semi-automatic manipulation, which greately simplifies finishing. File: martti.tammiATcgb.ki.se_135.html ************************************************* Fri Apr 25 09:31:49 2003 Number: 136 Name: Voit, Eberhard O Affiliation: Medical University of S. Carolina Address: 135 Cannon Street, 303K City: Charleston State/Provice: South Carolina Postal/Zip Code: 29425 Country: U.S.A. Email: VoitEO@MUSC.edu Phone: 001-843-876-1122 Fax: 001-843-876-1126 Category: Systems Biology Poster Title: Data Preprocessing Facilitates Metabolic Pathway Identification from Time Profiles Poster Authors and organization: Eberhard O. Voit¹, Jonas S. Almeida²
¹VoitEO@MUSC.edu, Medical University of S. Carolina; ²almeidaj@musc.edu, Medical University of S. Carolina Abstract: The identification of metabolic pathway structure is a challenging problem that must be solved for the analysis of metabolic time profiles. Twofold data preprocessing significantly speeds up this identification. First, we model and smooth the data with an artificial neural network, and second, we replace differentials with estimated slopes. File: VoitEOATMUSC.edu_136.html ************************************************* Fri Apr 25 11:09:51 2003 Number: 137 Name: Jacobs, Jonathan L Affiliation: University of Maryland Address: 2135 Microbiology City: College Park State/Provice: MD Postal/Zip Code: 20742 Country: USA Email: jacobsjo@wam.umd.edu Phone: 3014051758 Fax: 3103149489 Category: Predictive Methods Poster Title: The Significance of Putative Programmed -1 Ribosomal Frameshift Signals Found in Eukaryotic Genomes Poster Authors and organization: Jonathan L. Jacobs¹, Jonathan D. Dinman, Ph.D.²
¹jacobsjo@wam.umd.edu, University of Maryland; ²jd280@umail.umd.edu, University of Maryland Abstract: We find that putative programmed �1 ribosomal frameshift signals are found in several higher eukaryotic genomes at statistically significant levels. Standard RNA sequence and structure analysis methods were integrated to identify PRF signals. Here we present our results as they pertain to 14 closely related yeast genomes. File: jacobsjoATwam.umd.edu_137.html ************************************************* Fri Apr 25 20:44:04 2003 UPDATE ----- Number: 30 Name: bello, onimisi h Affiliation: bma tutorial oufit Address: no.6 zansi close City: off-iwaya road yaba State/Provice: lagos Postal/Zip Code: 340 Country: nigeria Email: hassanbello2001@yahoo.com Phone: none Fax: none Category: Predictive Methods Poster Title: The model representation of the mode of action of combination therapy of chloroquine,puritine an ascobic acid Poster Authors and organization: onimisi hassan bello¹
¹hassanbello2001@yahoo.com, bima tutorial outfit Abstract: The action of the combine therapy of chloroquine,putitine and ascobic acid has baffled biochemist for some times.but it is believe to potentiate its action based on the pertubation of the lipid bilayer surrounding the cells. but further studies to reveal the genetic conditions has not yielded much results. File: hassanbello2001ATyahoo.com_30 ************************************************* Fri Apr 25 20:46:41 2003 UPDATE ----- Number: 30 Name: bello, onimisi h Affiliation: bma tutorial oufit Address: no.6 zansi close City: off-iwaya road yaba State/Provice: lagos Postal/Zip Code: 340 Country: nigeria Email: hassanbello2001@yahoo.com Phone: none Fax: none Category: Predictive Methods Poster Title: The model representation of the mode of action of combination therapy of chloroquine,puritine an ascobic acid Poster Authors and organization: onimisi hassan bello¹
¹hassanbello2001@yahoo.com, bima tutorial outfit Abstract: The action of the combine therapy of chloroquine,putitine and ascobic acid has baffled biochemist for some times.but it is believe to potentiate its action based on the pertubation of the lipid bilayer surrounding the cells. but further studies to reveal the genetic conditions has not yielded much results. File: hassanbello2001ATyahoo.com_30 ************************************************* Fri Apr 25 20:50:26 2003 UPDATE ----- Number: 30 Name: bello, onimisi h Affiliation: bma tutorial oufit Address: no.6 zansi close City: off-iwaya road yaba State/Provice: lagos Postal/Zip Code: 340 Country: nigeria Email: hassanbello2001@yahoo.com Phone: none Fax: none Category: Predictive Methods Poster Title: The model representation of the mode of action of combination therapy of chloroquine,puritine an ascobic acid Poster Authors and organization: onimisi hassan bello¹
¹hassanbello2001@yahoo.com, bima tutorial outfit Abstract: The action of the combine therapy of chloroquine,putitine and ascobic acid has baffled biochemist for some times.but it is believe to potentiate its action based on the pertubation of the lipid bilayer surrounding the cells. but further studies to reveal the genetic conditions has not yielded much results. File: hassanbello2001ATyahoo.com_30 ************************************************* Fri Apr 25 20:53:52 2003 UPDATE ----- Number: 30 Name: bello, onimisi h Affiliation: bma tutorial oufit Address: no.6 zansi close City: off-iwaya road yaba State/Provice: lagos Postal/Zip Code: 340 Country: nigeria Email: hassanbello2001@yahoo.com Phone: none Fax: none Category: Predictive Methods Poster Title: The model representation of the mode of action of combination therapy of chloroquine,puritine an ascobic acid Poster Authors and organization: onimisi hassan bello¹
¹hassanbello2001@yahoo.com, bima tutorial outfit Abstract: The action of the combine therapy of chloroquine,putitine and ascobic acid has baffled biochemist for some times.but it is believe to potentiate its action based on the pertubation of the lipid bilayer surrounding the cells. but further studies to reveal the genetic conditions has not yielded much results. File: hassanbello2001ATyahoo.com_30 ************************************************* Fri Apr 25 20:56:15 2003 UPDATE ----- Number: 30 Name: bello, onimisi h Affiliation: bma tutorial oufit Address: no.6 zansi close City: off-iwaya road yaba State/Provice: lagos Postal/Zip Code: 340 Country: nigeria Email: hassanbello2001@yahoo.com Phone: none Fax: none Category: Predictive Methods Poster Title: The model representation of the mode of action of combination therapy of chloroquine,puritine an ascobic acid Poster Authors and organization: onimisi hassan bello¹
¹hassanbello2001@yahoo.com, bima tutorial outfit Abstract: The action of the combine therapy of chloroquine,putitine and ascobic acid has baffled biochemist for some times.but it is believe to potentiate its action based on the pertubation of the lipid bilayer surrounding the cells. but further studies to reveal the genetic conditions has not yielded much results. File: hassanbello2001ATyahoo.com_30 ************************************************* Fri Apr 25 20:57:11 2003 UPDATE ----- Number: 30 Name: bello, onimisi h Affiliation: bma tutorial oufit Address: no.6 zansi close City: off-iwaya road yaba State/Provice: lagos Postal/Zip Code: 340 Country: nigeria Email: hassanbello2001@yahoo.com Phone: none Fax: none Category: Predictive Methods Poster Title: The model representation of the mode of action of combination therapy of chloroquine,puritine an ascobic acid Poster Authors and organization: onimisi hassan bello¹
¹hassanbello2001@yahoo.com, bima tutorial outfit Abstract: The action of the combine therapy of chloroquine,putitine and ascobic acid has baffled biochemist for some times.but it is believe to potentiate its action based on the pertubation of the lipid bilayer surrounding the cells. but further studies to reveal the genetic conditions has not yielded much results. File: hassanbello2001ATyahoo.com_30 ************************************************* Fri Apr 25 20:58:58 2003 UPDATE ----- Number: 30 Name: bello, onimisi h Affiliation: bma tutorial oufit Address: no.6 zansi close City: off-iwaya road yaba State/Provice: lagos Postal/Zip Code: 340 Country: nigeria Email: hassanbello2001@yahoo.com Phone: none Fax: none Category: Predictive Methods Poster Title: The model representation of the mode of action of combination therapy of chloroquine,puritine an ascobic acid Poster Authors and organization: onimisi hassan bello¹
¹hassanbello2001@yahoo.com, bima tutorial outfit Abstract: The action of the combine therapy of chloroquine,putitine and ascobic acid has baffled biochemist for some times.but it is believe to potentiate its action based on the pertubation of the lipid bilayer surrounding the cells. but further studies to reveal the genetic conditions has not yielded much results. File: hassanbello2001ATyahoo.com_30 ************************************************* Fri Apr 25 21:01:28 2003 UPDATE ----- Number: 30 Name: bello, onimisi h Affiliation: bma tutorial oufit Address: no.6 zansi close City: off-iwaya road yaba State/Provice: lagos Postal/Zip Code: 340 Country: nigeria Email: hassanbello2001@yahoo.com Phone: none Fax: none Category: Predictive Methods Poster Title: The model representation of the mode of action of combination therapy of chloroquine,puritine an ascobic acid Poster Authors and organization: onimisi hassan bello¹
¹hassanbello2001@yahoo.com, bima tutorial outfit Abstract: The action of the combine therapy of chloroquine,putitine and ascobic acid has baffled biochemist for some times.but it is believe to potentiate its action based on the pertubation of the lipid bilayer surrounding the cells. but further studies to reveal the genetic conditions has not yielded much results. File: hassanbello2001ATyahoo.com_30 ************************************************* Fri Apr 25 21:04:06 2003 UPDATE ----- Number: 30 Name: bello, onimisi h Affiliation: bma tutorial oufit Address: no.6 zansi close City: off-iwaya road yaba State/Provice: lagos Postal/Zip Code: 340 Country: nigeria Email: hassanbello2001@yahoo.com Phone: none Fax: none Category: Predictive Methods Poster Title: The model representation of the mode of action of combination therapy of chloroquine,puritine an ascobic acid Poster Authors and organization: onimisi hassan bello¹
¹hassanbello2001@yahoo.com, bima tutorial outfit Abstract: The action of the combine therapy of chloroquine,putitine and ascobic acid has baffled biochemist for some times.but it is believe to potentiate its action based on the pertubation of the lipid bilayer surrounding the cells. but further studies to reveal the genetic conditions has not yielded much results. File: hassanbello2001ATyahoo.com_30 ************************************************* Fri Apr 25 21:05:01 2003 UPDATE ----- Number: 30 Name: bello, onimisi h Affiliation: bma tutorial oufit Address: no.6 zansi close City: off-iwaya road yaba State/Provice: lagos Postal/Zip Code: 340 Country: nigeria Email: hassanbello2001@yahoo.com Phone: none Fax: none Category: Predictive Methods Poster Title: The model representation of the mode of action of combination therapy of chloroquine,puritine an ascobic acid Poster Authors and organization: onimisi hassan bello¹
¹hassanbello2001@yahoo.com, bima tutorial outfit Abstract: The action of the combine therapy of chloroquine,putitine and ascobic acid has baffled biochemist for some times.but it is believe to potentiate its action based on the pertubation of the lipid bilayer surrounding the cells. but further studies to reveal the genetic conditions has not yielded much results. File: hassanbello2001ATyahoo.com_30 ************************************************* Fri Apr 25 21:05:59 2003 UPDATE ----- Number: 30 Name: bello, onimisi h Affiliation: bma tutorial oufit Address: no.6 zansi close City: off-iwaya road yaba State/Provice: lagos Postal/Zip Code: 340 Country: nigeria Email: hassanbello2001@yahoo.com Phone: none Fax: none Category: Predictive Methods Poster Title: The model representation of the mode of action of combination therapy of chloroquine,puritine an ascobic acid Poster Authors and organization: onimisi hassan bello¹
¹hassanbello2001@yahoo.com, bima tutorial outfit Abstract: The action of the combine therapy of chloroquine,putitine and ascobic acid has baffled biochemist for some times.but it is believe to potentiate its action based on the pertubation of the lipid bilayer surrounding the cells. but further studies to reveal the genetic conditions has not yielded much results. File: hassanbello2001ATyahoo.com_30 ************************************************* Fri Apr 25 21:08:11 2003 UPDATE ----- Number: 16 Name: Sharma, Banshi Affiliation: Central Veterinary Laboratory Address: Tripureshwor City: Kathmandu State/Provice: Bagmati Postal/Zip Code: P. o. box 1640 Country: Nepal Email: banshisharma@yahoo.com Phone: 9774476527 Fax: 9774261938 I plan to use my laptop computer as part of my poster Category: Systems Biology Poster Title: Molecular characterization of NKR-p1 receptor in peripheral blood of pig Poster Authors and organization: Banshi sharma¹
¹sharmabanshi@hotmail.com, CVL Abstract: The aim of the work is to characterize the NKR-P1 receptor in the peripheral blood of pig. Total RNA was extracted from peripheral blood of pig as well as human. RT-PCR gives 573 bp PCR product in human. Similarly it gives 661 bp PCR product in pig. The PCR product is cloned in pPCR-script TM Amp SK (+) cloning vector. File: banshisharmaATyahoo.com_16 ************************************************* Fri Apr 25 21:10:49 2003 UPDATE ----- Number: 70 Name: Steinhoff, Christine Affiliation: Max Planck Institute for Molecular Genetics Address: Ihnestr. 73 City: Berlin State/Provice: Germany Postal/Zip Code: 14195 Country: Germany Email: christine.steinhoff@molgen.mpg.de Phone: +49 30 8413 1171 Fax: +49 30 8413 1152 Category: Functional Genomics Poster Title: Extraction of Pathways Involved in Microarray Time Course Experiments Poster Authors and organization: Steinhoff¹, Mueller², Hannes Luz, Martin Vingron
¹christine.steinhoff@molgen.mpg.de, Max Planck Institute; ²Tobias.Mueller@biozentrum.uni-wuerzburg.de, Biocenter, University W�rzburg Abstract: We present a procedure that integrates knowledge of multiple biological databases to recover potentially involved pathways from time course microarray experiments. Starting with a refined new clustering algorithm we group similarly behaving genes, followed by an integrated analysis of common transcription factor binding patterns, functional categories and biologically verified pathways. File: christine.steinhoffATmolgen.mpg.de_70 ************************************************* Fri Apr 25 21:12:07 2003 UPDATE ----- Number: 70 Name: Steinhoff, Christine Affiliation: Max Planck Institute for Molecular Genetics Address: Ihnestr. 73 City: Berlin State/Provice: Germany Postal/Zip Code: 14195 Country: Germany Email: christine.steinhoff@molgen.mpg.de Phone: +49 30 8413 1171 Fax: +49 30 8413 1152 Category: Functional Genomics Poster Title: Extraction of Pathways Involved in Microarray Time Course Experiments Poster Authors and organization: Steinhoff¹, Mueller², Hannes Luz, Martin Vingron
¹christine.steinhoff@molgen.mpg.de, Max Planck Institute; ²Tobias.Mueller@biozentrum.uni-wuerzburg.de, Biocenter, University W�rzburg Abstract: We present a procedure that integrates knowledge of multiple biological databases to recover potentially involved pathways from time course microarray experiments. Starting with a refined new clustering algorithm we group similarly behaving genes, followed by an integrated analysis of common transcription factor binding patterns, functional categories and biologically verified pathways. File: christine.steinhoffATmolgen.mpg.de_70 ************************************************* Fri Apr 25 21:20:27 2003 UPDATE ----- Number: 82 Name: Zou, Ming Y Affiliation: School of Agriculture and Food Systems, University of Melbourne Address: Sneydes Road, Werribee City: Melbourne State/Provice: Victoria Postal/Zip Code: 3030 Country: Australia Email: y.zou@pgrad.unimelb.edu.au Phone: 61 3 92175204 Fax: 61 3 97419396 Category: Structural Biology Poster Title: Comparison between experimentally determined RNA secondary structures and computed structures with XNAfold Poster Authors and organization: Ming Yan Zou¹, Alan J. Hillier², P. Scott Chandry
¹y.zou@pgrad.unimelb.edu.au, School of Agriculture and Food Systems, University of Melbourne; ², School of Agriculture and Food Systems, University of Melbourne Abstract: XNAfold: a Java-C hybrid program for predicting RNA secondary structure and freely available at http://www.student.unimelb.edu.au/~yanmz/index.html The comparison between known secondary structures of RNA and structures computed with XNAfold is analysed. Among 133 different RNA from Protein Data Bank, 58% identified secondary structures match the predicted minimum free energy structure. File: y.zouATpgrad.unimelb.edu.au_82 ************************************************* Fri Apr 25 21:21:39 2003 UPDATE ----- Number: 82 Name: Zou, Ming Y Affiliation: School of Agriculture and Food Systems, University of Melbourne Address: Sneydes Road, Werribee City: Melbourne State/Provice: Victoria Postal/Zip Code: 3030 Country: Australia Email: y.zou@pgrad.unimelb.edu.au Phone: 61 3 92175204 Fax: 61 3 97419396 Category: Structural Biology Poster Title: Comparison between experimentally determined RNA secondary structures and computed structures with XNAfold Poster Authors and organization: Ming Yan Zou¹, Alan J. Hillier², P. Scott Chandry
¹y.zou@pgrad.unimelb.edu.au, School of Agriculture and Food Systems, University of Melbourne; ², School of Agriculture and Food Systems, University of Melbourne Abstract: XNAfold: a Java-C hybrid program for predicting RNA secondary structure and freely available at http://www.student.unimelb.edu.au/~yanmz/index.html The comparison between known secondary structures of RNA and structures computed with XNAfold is analysed. Among 133 different RNA from Protein Data Bank, 58% identified secondary structures match the predicted minimum free energy structure. File: y.zouATpgrad.unimelb.edu.au_82 ************************************************* Fri Apr 25 21:25:08 2003 UPDATE ----- Number: 84 Name: Manduchi, Elisabetta Affiliation: University of Pennsylvania Address: 1428 Blockley Hall, 423 Guardian Drive City: Philadelphia State/Provice: PA Postal/Zip Code: 19104-6021 Country: USA Email: manduchi@pcbi.upenn.edu Phone: 215-573-4408 Fax: 215-573-3111 Category: Microarrays Poster Title: The RNA Abundance Database and its Annotation Web-Forms. Poster Authors and organization: Elisabetta Manduchi¹, G.R. Grant, Hongxian He, J. Liu, M.D. Mailman, A. Pizarro, P.L. Whetzel, C.J. Stoeckert Jr.
¹manduchi@pcbi.upenn.edu, Center for Bioinformatics, University of Pennsylvania Abstract: RAD and its web-based annotation forms are a system aimed at the collection, organization, and exchange of all relevant information pertaining to gene expression array (and SAGE) studies. The richness of information captured and the use of ontologies render RAD a very powerful infrastructure for querying and analysis ( http://www.cbil.upenn.edu/RAD3). File: manduchiATpcbi.upenn.edu_84 ************************************************* Fri Apr 25 21:26:29 2003 UPDATE ----- Number: 84 Name: Manduchi, Elisabetta Affiliation: University of Pennsylvania Address: 1428 Blockley Hall, 423 Guardian Drive City: Philadelphia State/Provice: PA Postal/Zip Code: 19104-6021 Country: USA Email: manduchi@pcbi.upenn.edu Phone: 215-573-4408 Fax: 215-573-3111 Category: Microarrays Poster Title: The RNA Abundance Database and its Annotation Web-Forms. Poster Authors and organization: Elisabetta Manduchi¹, G.R. Grant, Hongxian He, J. Liu, M.D. Mailman, A. Pizarro, P.L. Whetzel, C.J. Stoeckert Jr.
¹manduchi@pcbi.upenn.edu, Center for Bioinformatics, University of Pennsylvania Abstract: RAD and its web-based annotation forms are a system aimed at the collection, organization, and exchange of all relevant information pertaining to gene expression array (and SAGE) studies. The richness of information captured and the use of ontologies render RAD a very powerful infrastructure for querying and analysis ( http://www.cbil.upenn.edu/RAD3). File: manduchiATpcbi.upenn.edu_84 ************************************************* Fri Apr 25 21:27:23 2003 UPDATE ----- Number: 84 Name: Manduchi, Elisabetta Affiliation: University of Pennsylvania Address: 1428 Blockley Hall, 423 Guardian Drive City: Philadelphia State/Provice: PA Postal/Zip Code: 19104-6021 Country: USA Email: manduchi@pcbi.upenn.edu Phone: 215-573-4408 Fax: 215-573-3111 Category: Microarrays Poster Title: The RNA Abundance Database and its Annotation Web-Forms. Poster Authors and organization: Elisabetta Manduchi¹, G.R. Grant, Hongxian He, J. Liu, M.D. Mailman, A. Pizarro, P.L. Whetzel, C.J. Stoeckert Jr.
¹manduchi@pcbi.upenn.edu, Center for Bioinformatics, University of Pennsylvania Abstract: RAD and its web-based annotation forms are a system aimed at the collection, organization, and exchange of all relevant information pertaining to gene expression array (and SAGE) studies. The richness of information captured and the use of ontologies render RAD a very powerful infrastructure for querying and analysis ( http://www.cbil.upenn.edu/RAD3). File: manduchiATpcbi.upenn.edu_84 ************************************************* Fri Apr 25 21:27:49 2003 UPDATE ----- Number: 84 Name: Manduchi, Elisabetta Affiliation: University of Pennsylvania Address: 1428 Blockley Hall, 423 Guardian Drive City: Philadelphia State/Provice: PA Postal/Zip Code: 19104-6021 Country: USA Email: manduchi@pcbi.upenn.edu Phone: 215-573-4408 Fax: 215-573-3111 Category: Microarrays Poster Title: The RNA Abundance Database and its Annotation Web-Forms. Poster Authors and organization: Elisabetta Manduchi¹, G.R. Grant, Hongxian He, J. Liu, M.D. Mailman, A. Pizarro, P.L. Whetzel, C.J. Stoeckert Jr.
¹manduchi@pcbi.upenn.edu, Center for Bioinformatics, University of Pennsylvania Abstract: RAD and its web-based annotation forms are a system aimed at the collection, organization, and exchange of all relevant information pertaining to gene expression array (and SAGE) studies. The richness of information captured and the use of ontologies render RAD a very powerful infrastructure for querying and analysis ( http://www.cbil.upenn.edu/RAD3). File: manduchiATpcbi.upenn.edu_84 ************************************************* Fri Apr 25 21:33:34 2003 UPDATE ----- Number: 89 Name: Tan, Keng H Affiliation: BioInformatics Institute Address: 21 Heng Mui Keng Terrace, 03-14 City: Singapore State/Provice: Singapore Postal/Zip Code: 119613 Country: Singapore Email: eric@bii.a-star.edu.sg Phone: +65 6874 6182 Fax: +65 6778 1250 Category: Sequence Comparison Poster Title: Evolutionary significance of G1/S checkpoint among Eukaryotes Poster Authors and organization: Keng Hwa Tan¹, Pawan Dhar²
¹eric@bii.a-star.edu.sg, BioInformatics Institute; ²pk@bii.a-star.edu.sg, BioInformatics Institute Abstract: Short Abstract: G1/S checkpoint plays a pivotal role during early stages of the cell cycle. Progression through G1/S boundary is controlled by a series of regulators. To explore the roles of these regulators and identify targets of CDKs, bioinformatics analysis are being done on DNA and protein sequences from different eukaryotic organisms. File: ericATbii.a-star.edu.sg_89 ************************************************* Fri Apr 25 21:42:51 2003 UPDATE ----- Number: 100 Name: del Val, Coral Affiliation: DKFZ, German Cancer Research Center Address: Im Neuenheimer Feld 580 City: Heidelberg State/Provice: Baden-Wuttemberg Postal/Zip Code: 69120 Country: Germany Email: c.delval@dkfz.de Phone: 00496221422349 Fax: 496221439633 Category: Genome Annotation Poster Title: cDNA2Genome: A TOOL FOR MAPPING AND ANNOTATING cDNAS Poster Authors and organization: Coral del Val¹, Karl-Heinz Glatting², S.Suhai
¹c.delval@dkfz.de, Department of Molecular Biophysics DKFZ, German Cancer Research Center; ²glatting@dkfz.de, Department of Molecular Biophysics DKFZ, German Cancer Research Center Abstract:

File: c.delvalATdkfz.de_100 ************************************************* Fri Apr 25 22:06:58 2003 UPDATE ----- Number: 136 Name: Voit, Eberhard O Affiliation: Medical University of S. Carolina Address: 135 Cannon Street, 303K City: Charleston State/Provice: South Carolina Postal/Zip Code: 29425 Country: U.S.A. Email: VoitEO@MUSC.edu Phone: 001-843-876-1122 Fax: 001-843-876-1126 Category: Systems Biology Poster Title: Data Preprocessing Facilitates Metabolic Pathway Identification from Time Profiles Poster Authors and organization: Eberhard O. Voit¹, Jonas S. Almeida²
¹VoitEO@MUSC.edu, Medical University of S. Carolina; ²almeidaj@musc.edu, Medical University of S. Carolina Abstract: The identification of metabolic pathway structure is a challenging problem that must be solved for the analysis of metabolic time profiles. Twofold data preprocessing significantly speeds up this identification. First, we model and smooth the data with an artificial neural network, and second, we replace differentials with estimated slopes. File: VoitEOATMUSC.edu_136 ************************************************* Fri Apr 25 22:07:29 2003 UPDATE ----- Number: 136 Name: Voit, Eberhard O Affiliation: Medical University of S. Carolina Address: 135 Cannon Street, 303K City: Charleston State/Provice: South Carolina Postal/Zip Code: 29425 Country: U.S.A. Email: VoitEO@MUSC.edu Phone: 001-843-876-1122 Fax: 001-843-876-1126 Category: Systems Biology Poster Title: Data Preprocessing Facilitates Metabolic Pathway Identification from Time Profiles Poster Authors and organization: Eberhard O. Voit¹, Jonas S. Almeida²
¹VoitEO@MUSC.edu, Medical University of S. Carolina; ²almeidaj@musc.edu, Medical University of S. Carolina Abstract: The identification of metabolic pathway structure is a challenging problem that must be solved for the analysis of metabolic time profiles. Twofold data preprocessing significantly speeds up this identification. First, we model and smooth the data with an artificial neural network, and second, we replace differentials with estimated slopes. File: VoitEOATMUSC.edu_136 ************************************************* Fri Apr 25 23:41:54 2003 Number: 138 Name: Lyakhovich, Alex Affiliation: University of Michigan Address: 1301 E.Catherine City: Ann Arbor State/Provice: MI Postal/Zip Code: 48109 Country: U.S.A. Email: alexlyak@umich.edu Phone: 1-734-913-8210 Fax: I plan to use my laptop computer as part of my poster Category: Predictive Methods Poster Title: REMmatch program: finding potential hormone responsive elements Poster Authors and organization: Alex Lyakhovich¹, Nickolai Aksenov²
¹alexlyak@umich.edu, University of Michigan, Ann Arbor, U.S.A.; ², Umea University, Umea, Sweden Abstract: REMmatch program is designed for preliminary screening of any sequence database for searching potential hormone responsive elements (HRE) and is comparable with other known programs (TESS, Match). REMmatch is available at ( http://www.math.wisc.edu/~karp/REMmatch.exe) File: alexlyakATumich.edu_138.html ************************************************* Sun Apr 27 15:43:28 2003 Number: 139 Name: Watson, James R Affiliation: The University of Queensland Address: none City: Brisbane State/Provice: QLD Postal/Zip Code: 4072 Country: Australia Email: jwatson@itee.uq.edu.au Phone: 07 33658302 Fax: Category: Systems Biology Poster Title: Towards more biological mutation operators in models of gene regulation Poster Authors and organization: James Watson¹, Nicholas Geard², Janet Wiles
¹jwatson@itee.uq.edu.au, University of Queensland; ²nic@itee.uq.edu.au, University of Queensland Abstract: Gene regulation is often studied through models of directed graphs. Mutation operators applied to such networks impose limitations on how the models evolve. A method to extract a regulation network from an artificial nucleotide sequence is presented, and the impact of sequence-level mutations on network-level structure is discussed. File: jwatsonATitee.uq.edu.au_139.html ************************************************* Sun Apr 27 17:13:05 2003 UPDATE ----- Number: 61 Name: Hughes, Aubrey D Affiliation: Medical College of Wisconsin Address: 8701 Watertown Plank Rd City: Milwaukee State/Provice: Wisconsin Postal/Zip Code: 53226 Country: USA Email: ahughes@mcw.edu Phone: 1 4144567506 Fax: 1 4144566190 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: RAT GENOME DATABASE - RGD - MAPPING DISEASE ONTO THE GENOME Poster Authors and organization: Aubrey Hughes¹, Jedediah Mathis², Mary Shimoyama, Norberto de la Cruz, Charles W. Wang, Nataliya Nenasheva, Dean Pasko, Jiali Chen, Lan Zhao, Chunyu Fan, Wenhua Wu, Chin-Fu Chen, Rajni Nigam, Gopal Gopinathrao, Angela Zuniga-Meyer, Susan Bromberg, Jessica Ginster, Anne Kwitek-Black, Janan Eppig, Lois Maltais, Donna Maglott, Greg Schuler, Simon Twigger, Howard Jacob and Peter Tonellato
¹ahughes@mcw.edu, Medical College of Wisconsin; ²jmathis@mcw.edu, Medical College of Wisconsin Abstract: The Rat Genome Database (RGD) is a disease centric resource of comprehensively curated data from rat genetic and genomic research. RGD's goal is to provide information that will aid researchers in using the rat as a model organism for human disease studies. RGD is available at rgd.mcw.edu . File: ahughesATmcw.edu_61 ************************************************* Sun Apr 27 17:14:20 2003 UPDATE ----- Number: 61 Name: Hughes, Aubrey D Affiliation: Medical College of Wisconsin Address: 8701 Watertown Plank Rd City: Milwaukee State/Provice: Wisconsin Postal/Zip Code: 53226 Country: USA Email: ahughes@mcw.edu Phone: 1 4144567506 Fax: 1 4144566190 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: RAT GENOME DATABASE - RGD - MAPPING DISEASE ONTO THE GENOME Poster Authors and organization: Aubrey Hughes¹, Jedediah Mathis², Mary Shimoyama, Norberto de la Cruz, Charles W. Wang, Nataliya Nenasheva, Dean Pasko, Jiali Chen, Lan Zhao, Chunyu Fan, Wenhua Wu, Chin-Fu Chen, Rajni Nigam, Gopal Gopinathrao, Angela Zuniga-Meyer, Susan Bromberg, Jessica Ginster, Anne Kwitek-Black, Janan Eppig, Lois Maltais, Donna Maglott, Greg Schuler, Simon Twigger, Howard Jacob and Peter Tonellato
¹ahughes@mcw.edu, Medical College of Wisconsin; ²jmathis@mcw.edu, Medical College of Wisconsin Abstract: The Rat Genome Database (RGD) is a disease centric resource of comprehensively curated data from rat genetic and genomic research. RGD's goal is to provide information that will aid researchers in using the rat as a model organism for human disease studies. RGD is available at rgd.mcw.edu . File: ahughesATmcw.edu_61 ************************************************* Sun Apr 27 17:17:03 2003 UPDATE ----- Number: 37 Name: Adoro, Stanley A Affiliation: Cellular Parasitology Programme, Department of Zoology, University of Ibadan Address: Oyo Road City: Ibadan State/Provice: Oyo State Postal/Zip Code: None Country: Nigeria Email: stanleyadoro@hotmail.com Phone: 234 2 8100822 Fax: 234 2 8100079 Category: Sequence Comparison Poster Title: Secondary structure interpretation of genetic sequence variation in Plasmodium falciparum cell surface antigens Poster Authors and organization: Stanley Adoro¹, Roseangela Nwuba, Chiaka Anumudu, Mark Nwagwu
¹stanleyadoro@hotmail.com, University of Ibadan Abstract: We have analyzed genetic and amino acid residue variation of Plasmodium falciparum cell surface antigens (merozoite surface proteins 1 and 2; circumsporozoite protein; stevor and rifin) in the context of their known or predicted secondary structures. Locations of structural motifs suggest the presence of functional domains or antigenic epitopes. File: stanleyadoroAThotmail.com_37 ************************************************* Sun Apr 27 17:19:43 2003 UPDATE ----- Number: 39 Name: Michael, Gromiha Affiliation: CBRC, AIST Address: 17F, Aomi Frontier Building City: 2-43 Aomi, Koto-ku State/Provice: Tokyo Postal/Zip Code: 135-0064 Country: Japan Email: michael-gromiha@aist.go.jp Phone: +81-3-3599-8046 Fax: +81-3-3599-8081 Category: Structural Biology Poster Title: Role of Long-range Interactions in the Transition and Folded Native states of Two-state Proteins Poster Authors and organization: M. Michael Gromiha¹, S. Selvaraj²
¹michael-gromiha@aist.go.jp, CBRC, AIST, Tokyo, Japan; ², Department of Physics, Bharathidasan University, Tiruchirapalli, India Abstract: We have proposed a novel parameter, long-range order (LRO) for a protein from the knowledge of long-range contacts in protein structure. LRO correlates very well with experimental protein folding rates. The short and medium-range non-bonded energy, long-range contacts, and helical/strand tendency are the major determinants for transition state structures of two-state proteins. File: michael-gromihaATaist.go.jp_39 ************************************************* Sun Apr 27 17:24:49 2003 UPDATE ----- Number: 41 Name: Shah, Nigam H Affiliation: Pennsylvania State University Address: 211 Wartik Labs City: University Park State/Provice: PA Postal/Zip Code: 16801 Country: USA Email: nigam@psu.edu Phone: 814-863-5720 Fax: I plan to use my laptop computer as part of my poster Category: New Frontiers Poster Title: HyBrow: A Hypothesis Space Browser Poster Authors and organization: Nigam Shah¹, Stephen Racunas², Nina V. Fedoroff, Penn State University
¹nigam@psu.edu, Penn State University; ²sar147@psu.edu, Penn State University Abstract: HyBrow is a prototype computer system comprising an event-based ontology for biological processes, an associated database and programs to perform hypothesis evaluation using a wide variety of available data. We demonstrate the feasibility of HyBrow, using the galactose metabolism gene network in Saccharomyces cerevisiae as our test system, for ranking alternative hypotheses in an automated manner. File: nigamATpsu.edu_41 ************************************************* Sun Apr 27 17:33:47 2003 UPDATE ----- Number: 43 Name: Lu, Fu Affiliation: Celera Genomics Address: 45 West Gude Drive City: Rockville State/Provice: MD Postal/Zip Code: 20878 Country: USA Email: fu.lu@celera.com Phone: 2404530875 Fax: 2404533768 Category: Phylogeny and Evolution Poster Title: CompMapper: An Automatic Pipeline to Define Conserved Segments between Genomes Systematically Poster Authors and organization: Fu Lu¹, Zhenyuan Wang², Xiangqun Holly Zheng, Wenyan Zhong, Fei Zhong, Richard Mural
¹fu.lu@celera.com, Celera Genomics; ²jack.wang@celera.com, Celera Genomics Abstract: To overcome the limitations of comparative mapping using orthologous genes, we have developed a new paradigm and systematic approach to define conserved synteny between human and mouse directly from genomic sequence. The automatic pipeline should be applicable to compare any species with complete or draft genome sequence and within an appropriate phylogenetic distance. File: fu.luATcelera.com_43 ************************************************* Sun Apr 27 20:27:45 2003 UPDATE ----- Number: 107 Name: Gladwin, Benjamin A Affiliation: University of Queensland, Department of mathematics Address: stlucia City: brisbane State/Provice: QLD Postal/Zip Code: 4067 Country: Australia Email: gladwin@maths.uq.edu.au Phone: 0733461430 Fax: Category: Predictive Methods Poster Title: Long time scale simulations of Molecular Systems Poster Authors and organization: Benjamin Gladwin¹, Dr Thomas Huber²
¹gladwin@maths.uq.edu.au, University of Queensland Department of Mathematics.; ²huber@maths.uq.edu.au, University of Queensland Department of Mathematics. Abstract: Modelling large bio-molecules is still primarily limited to the simulation of short timeframes, which in many cases are not biologically significant. The goal is of this project is to�use the optimisation of Hamiltonian paths to enable calculation of the behaviour of molecular systems over large time frames. File: gladwinATmaths.uq.edu.au_107 ************************************************* Sun Apr 27 20:31:24 2003 UPDATE ----- Number: 139 Name: Watson, James R Affiliation: The University of Queensland Address: The University of Queensland City: Brisbane State/Provice: QLD Postal/Zip Code: 4072 Country: Australia Email: jwatson@itee.uq.edu.au Phone: 07 33658302 Fax: Category: Systems Biology Poster Title: Towards more biological mutation operators in models of gene regulation Poster Authors and organization: James Watson¹, Nicholas Geard², Janet Wiles
¹jwatson@itee.uq.edu.au, University of Queensland; ²nic@itee.uq.edu.au, University of Queensland Abstract: Gene regulation is often studied through models of directed graphs. Mutation operators applied to such networks impose limitations on how the models evolve. A method to extract a regulation network from an artificial nucleotide sequence is presented, and the impact of sequence-level mutations on network-level structure is discussed. File: jwatsonATitee.uq.edu.au_139 ************************************************* Sun Apr 27 20:41:20 2003 Number: 140 Name: Valuev, Vadim P Affiliation: Institute of Cytology and Genetics Address: Lavrentieva ave 10 City: Novosibirsk State/Provice: Postal/Zip Code: 630090 Country: Russia Email: gease@mail.ru Phone: +7 3832 333119 Fax: +73832331278 Category: Structural Biology Poster Title: Protein class recognition with neural networks Poster Authors and organization: Vadim Valuev¹
¹valuev@bionet.nsc.ru, Institute of Cytology and Genetics Abstract: There exist several classes of protein structure that are determined by predominance of one of elements of secondary structure. Their recognition starting from aminoacid composition gives some insight into the nature of this classification. Class recognition methods are built by means of neural networks. The accuracy of recognition reached 75%. File: geaseATmail.ru_140.html ************************************************* Sun Apr 27 20:40:35 2003 Number: 141 Name: Valuev, Vadim P Affiliation: Institute of Cytology and Genetics Address: Lavrentieva ave 10 City: Novosibirsk State/Provice: Postal/Zip Code: 630090 Country: Russia Email: R.teasdale@imb.uq.edu.au Phone: +7 3832 333119 Fax: +73832331278 Category: Structural Biology Poster Title: Protein class recognition with neural networks Poster Authors and organization: Vadim Valuev¹
¹valuev@bionet.nsc.ru, Institute of Cytology and Genetics Abstract: There exist several classes of protein structure that are determined by predominance of one of elements of secondary structure. Their recognition starting from aminoacid composition gives some insight into the nature of this classification. Class recognition methods are built by means of neural networks. The accuracy of recognition reached 75%. File: R.teasdaleATimb.uq.edu.au_141.html ************************************************* Sun Apr 27 22:41:51 2003 UPDATE ----- Number: 45 Name: BEN-ZEEV, EFRAT Affiliation: WEIZMANN INSTITUTE OF SCIENCE Address: Department of Biological Chemistry City: REHOVOT State/Provice: Israel Postal/Zip Code: 76100 Country: ISRAEL Email: efrat.ben-zeev@weizmann.ac.il Phone: 972-8-9342434 Fax: 972-8-9468256 Category: Predictive Methods Poster Title: Weighted Geometric Docking with MolFit: Incorporating External Information in the Rotation-Translation Scan Poster Authors and organization: Efrat Ben-Zeev¹, Miriam Eisenstein²
¹efrat.ben-zeev@weizmann.ac.il, Weizmann Institute of Science; ²miriam.eisenstein@weizmann.ac.il, Weizmann Institute of Science Abstract: Weighted-geometric docking incorporates external data from different sources, such as biochemical and biophysical experiments and bioinformatics analyses, in the docking rotation-translation scan. The method is successful even when the weighted portion of the surface corresponded only partially and approximately to the binding site. The method is implemented in our program MolFit. File: efrat.ben-zeevATweizmann.ac.il_45 ************************************************* Sun Apr 27 22:44:18 2003 UPDATE ----- Number: 47 Name: Suzuki, Harukazu Affiliation: RIKEN Genomic Sciences Center Address: 1-7-22, Suehiro-cho City: Tsurumi-ku State/Provice: Yokohama Postal/Zip Code: 230-0045 Country: JAPAN Email: harukazu@gsc.riken.go.jp Phone: 81-45-503-9222 Fax: 81-45-503-9216 Category: Genome Annotation Poster Title: Global insights into protein complexes through integrated analysis of the interactome and knockout lethality Poster Authors and organization: Harukazu Suzuki¹, Rintaro Saito ², Yoshihide Hayashizaki
¹harukazu@gsc.riken.go.jp, RIKEN Genomic Sciences Center ; ², RIKEN Genomic Sciences Center Abstract: We have developed the new interaction generality measure (IG2), which can be used to computationally assess the reliability of the interactome data. We performed an integrated analysis by using comprehensive phenotype dataset and IG2-treated interactome dataset from yeast, which yielded global insights into the biological features of the protein complexes. File: harukazuATgsc.riken.go.jp_47 ************************************************* Sun Apr 27 23:22:01 2003 UPDATE ----- Number: 141 Name: Davis, Melissa J Affiliation: Institute of Molecular Biosciences Address: University of Queensland, St. Lucia City: Brisbane State/Provice: Queensland Postal/Zip Code: 4067 Country: Australia Email: m.davis@imb.uq.edu.au Phone: +7 33662608 Fax: - Category: Predictive Methods Poster Title: An automated protocol for membrane protein prediction and annotation Poster Authors and organization: Melissa Davis, Zheng Yuan, Shane Fashang Zhang and Rohan Teasdale¹
¹m.davis@imb.uq.edu.au, Institute of Molecular Biosciences Abstract: In order to annotate the membrane organization of whole-proteome datasets, we have developed a consensus annotation protocol automated for high through-put analysis. This protocol predicts the presence of alpha-helical transmembrane domains, ER signal peptides and GPI anchor sites. These features are combined to generate a prediction of membrane organization that provides a biological context for any further functional annotation. File: m.davisATimb.uq.edu.au_141 ************************************************* Sun Apr 27 23:23:47 2003 UPDATE ----- Number: 16 Name: Sharma, Banshi Affiliation: Central Veterinary Laboratory Address: Tripureshwor City: Kathmandu State/Provice: Bagmati Postal/Zip Code: P. o. box 1640 Country: Nepal Email: banshisharma@yahoo.com Phone: 9774476527 Fax: 9774261938 I plan to use my laptop computer as part of my poster Category: Systems Biology Poster Title: Molecular characterization of NKR-p1 receptor in peripheral blood of pig Poster Authors and organization: Banshi sharma¹
¹sharmabanshi@hotmail.com, CVL Abstract: The aim of the work is to characterize the NKR-P1 receptor in the peripheral blood of pig. Total RNA was extracted from peripheral blood of pig as well as human. RT-PCR gives 573 bp PCR product in human. Similarly it gives 661 bp PCR product in pig. The PCR product is cloned in pPCR-script TM Amp SK (+) cloning vector. File: banshisharmaATyahoo.com_16 ************************************************* Sun Apr 27 23:23:44 2003 UPDATE ----- Number: 141 Name: Davis, Melissa J Affiliation: Institute of Molecular Biosciences Address: University of Queensland, St. Lucia City: Brisbane State/Provice: Queensland Postal/Zip Code: 4067 Country: Australia Email: m.davis@imb.uq.edu.au Phone: +7 33662608 Fax: - Category: Predictive Methods Poster Title: An automated protocol for membrane protein prediction and annotation Poster Authors and organization: Melissa Davis, Zheng Yuan, Shane Fashang Zhang and Rohan Teasdale¹
¹m.davis@imb.uq.edu.au, Institute of Molecular Biosciences Abstract: In order to annotate the membrane organization of whole-proteome datasets, we have developed a consensus annotation protocol automated for high through-put analysis. This protocol predicts the presence of transmembrane domains, signal peptides and GPI anchors. These features are combined to generate a prediction of membrane organization. File: m.davisATimb.uq.edu.au_141 ************************************************* Sun Apr 27 23:25:28 2003 UPDATE ----- Number: 141 Name: Davis, Melissa J Affiliation: Institute of Molecular Biosciences Address: University of Queensland, St. Lucia City: Brisbane State/Provice: Queensland Postal/Zip Code: 4067 Country: Australia Email: m.davis@imb.uq.edu.au Phone: +7 33662608 Fax: - Category: Predictive Methods Poster Title: An automated protocol for membrane protein prediction and annotation Poster Authors and organization: Melissa Davis¹, Zheng Yuan, Shane Fashang Zhang and Rohan Teasdale
¹m.davis@imb.uq.edu.au, Institute of Molecular Biosciences Abstract: In order to annotate the membrane organization of whole-proteome datasets, we have developed a consensus annotation protocol automated for high through-put analysis. This protocol predicts the presence of transmembrane domains, signal peptides and GPI anchors. These features are combined to generate a prediction of membrane organization. File: m.davisATimb.uq.edu.au_141 ************************************************* Sun Apr 27 23:42:12 2003 Number: 142 Name: Bottomley, Steve Affiliation: Western Australian Biomedical Research Institute, School of Biomedical Sciences, Curtin University of Technology Address: Hayman Road City: Bentley State/Provice: WA Postal/Zip Code: 6102 Country: Australia Email: S.Bottomley@curtin.edu.au Phone: +618 9266 4369 Fax: +618 9266 2342 Category: Functional Genomics Poster Title: Identification of putative insulin binding motifs of the insulin receptor Poster Authors and organization: Steve Bottomley¹, Jessica Mitchell², Brian Plewright, Erik Helmerhorst
¹S.Bottomley@curtin.edu.au, Western Australian Biomedical Research Institute, School of Biomedical Sciences, Curtin University of Technology; ²MITCHEJM@ses.curtin.edu.au, Western Australian Biomedical Research Institute, School of Biomedical Sciences, Curtin University of Technology Abstract: Overlapping 9 and 15mer peptides covering the insulin receptor alpha-subunit sequence were synthesised and measured for their ability to specifically bind ¹²⁵I-insulin. The insulin binding sequences were analysed to identify putative insulin-binding regions of the receptor, insulin-binding motifs, and develop a preliminary insulin-binding scoring matrix. File: S.BottomleyATcurtin.edu.au_142.html ************************************************* Sun Apr 27 23:53:52 2003 UPDATE ----- Number: 69 Name: Vilanova, David Affiliation: Nestle Research Center Address: VERS CHEZ LES BLANC City: Lausanne State/Provice: VAUD Postal/Zip Code: 1012 Country: Switzerland Email: david.vilanova@rdls.nestle.com Phone: +41217858723 Fax: +41217858925 Category: Data Mining Poster Title: Hight-throughput gene expression analysis with GATO Poster Authors and organization: David Vilanova¹, James holzwarth², Marie Camille Zwahlen, Frank Desiere,Matthew Alan Roberts
¹david.vilanova@rdls.nestle.com, Nestle research center; ²james.holzwarth@rdls.nestle.com, Nestle research center Abstract: We present GATO (gene annotation tool) a tool to analyse gene expression data based on Ensembl database and Gene Ontology. We describe how our tool can be utilized to rapidly mine gene expression data and drive biological interpretation using Affymetrix arrays. File: david.vilanovaATrdls.nestle.com_69 ************************************************* Sun Apr 27 23:54:50 2003 UPDATE ----- Number: 69 Name: Vilanova, David Affiliation: Nestle Research Center Address: VERS CHEZ LES BLANC City: Lausanne State/Provice: VAUD Postal/Zip Code: 1012 Country: Switzerland Email: david.vilanova@rdls.nestle.com Phone: +41217858723 Fax: +41217858925 Category: Data Mining Poster Title: Hight-throughput gene expression analysis with GATO Poster Authors and organization: David Vilanova¹, James holzwarth², Marie Camille Zwahlen, Frank Desiere,Matthew Alan Roberts
¹david.vilanova@rdls.nestle.com, Nestle research center; ²james.holzwarth@rdls.nestle.com, Nestle research center Abstract: We present GATO (gene annotation tool) a tool to analyse gene expression data based on Ensembl database and Gene Ontology. We describe how our tool can be utilized to rapidly mine gene expression data and drive biological interpretation using Affymetrix arrays. File: david.vilanovaATrdls.nestle.com_69 ************************************************* Sun Apr 27 23:58:36 2003 Number: 143 Name: Panek, Josef Affiliation: University of Queensland Address: Research Rd. City: Brisbane State/Provice: Queensland Postal/Zip Code: Qld 4072 Country: Australia Email: j.panek@imb.uq.edu.au Phone: 33462606 Fax: Category: Structural Biology Poster Title: Quantifying the similarities among proteins using features based on distribution of physico-chemical properties of amino acids Poster Authors and organization: Josef Panek¹
¹j.panek@imb.uq.edu.au, University of Queensland Abstract: A computational approach is presented to explore similarity in the distribution of amino acid properties in proteins. The approach uses features derived from the properties of amino acids to model the distribution. A feature space based on the proposed features is employed to indentify functional protein groups and the features that are specific for the groups. File: j.panekATimb.uq.edu.au_143.html ************************************************* Mon Apr 28 00:33:17 2003 Number: 144 Name: Fang, Yi Affiliation: Centre for Bioinformation Science, The Australian National University Address: John Dedman Mathematical Sciences Building City: Canberra State/Provice: ACT Postal/Zip Code: 0200 Country: Australia Email: yi@maths.anu.edu.au Phone: 02-61250725 Fax: 02-61255549 I plan to use my laptop computer as part of my poster Category: Predictive Methods Poster Title: A Mathematical Model for Protein Folding Poster Authors and organization: Yi Fang¹, Warren Kaplan²
¹yi@maths.anu.edu.au, CBiS, ANU; ²w.kaplan@garvan.org.au, Garvan Institute Abstract:

We mimic the major geometric features of the native structures of globular proteins: compactness, hydrophobic core, and smaller surface area. We hypothesize that the native structure of a globular protein should minimize all above three geometric features simultaneously and coherently among all conformations satisfying a relaxed steric condition.

File: yiATmaths.anu.edu.au_144.html ************************************************* Mon Apr 28 01:18:19 2003 Number: 145 Name: Matsuno, Hiroshi Affiliation: Yamaguchi University Address: 1677-1, Yoshida, City: Yamaguchi State/Provice: Yamaguchi Postal/Zip Code: 753-8512 Country: Japan Email: matsuno@sci.yamaguchi-u.ac.jp Phone: +81 83 933 5697 Fax: +81 83 933 5697 I plan to use my laptop computer as part of my poster Category: Systems Biology Poster Title: BioPACS: BioPathway Automatic Convert System for Genomic Object Net Poster Authors and organization: Masao Nagasaki ¹, Atsushi Doi², Hiroshi Matsuno, Satoru Miyano
¹masao@ims.u-tokyo.ac.jp, Human Genome Center, University of Tokyo; ²atsushi@ib.sci.yamaguchi-u.ac.jp, Faculty of Science, Yamaguchi University Abstract: For the modeling and simulation of a biopathway, suitable information selection from public biopathway databases, such as KEGG and BioCyc, would be useful. We have developed a method to transform these pathway databases so that the converted biopathways can run on Genomic Object Net (http://www.GenomicObject.Net). File: matsunoATsci.yamaguchi-u.ac.jp_145.html ************************************************* Mon Apr 28 09:02:26 2003 Number: 146 Name: Wilson, William J Affiliation: Karolinska Institute Address: Berzeliusvag 35 City: Stockholm State/Provice: Postal/Zip Code: 171 77 Country: Sweden Email: bill.wilson@cgb.ki.se Phone: +46 8 728 6142 Fax: Category: Functional Genomics Poster Title: A Functional Annotation Project for Novel and Uncharacterised Genes Poster Authors and organization: William Wilson¹, Emily Hodges², Ivana Novak, Claes Wahlestedt, Christer H��g, Boris Lenhard
¹bill.wilson@cgb.ki.se, Karolinska Institute; ²emily.hodges@cgb.ki.se, Karolinska Institute Abstract: Annotation of novel genes is a challenge to genome sequencing efforts. We streamlined the process for genes with novel protein-coding domains by integrating web-based databases and annotation tools with gene data from diverse sources. We show examples of how our approach enhances experimental design and leads to accurate gene annotation. File: bill.wilsonATcgb.ki.se_146.html ************************************************* Mon Apr 28 10:00:57 2003 Number: 147 Name: cootes, adrian p Affiliation: Imperial College, London Address: Exhibition Rd City: London State/Provice: London Postal/Zip Code: SW7 2AY Country: England Email: a.cootes@ic.ac.uk Phone: +44 20 7594 5715 Fax: +44 20 7594 5789 Category: Data Mining Poster Title: The automatic discovery of structural principles describing protein fold space Poster Authors and organization: adrian p cootes¹, michael je sternberg², stephen h muggleton
¹a.cootes@ic.ac.uk, Imperial College; ²m.sternberg@ic.ac.uk, Imperial College Abstract: The rapid increase in protein structures produced by structural-genomics projects will make it increasingly difficult to analyse and understand the distribution of proteins in fold space. We have applied a machine-learning strategy to automatically determine the structural principles describing 45 folds. File: a.cootesATic.ac.uk_147.html ************************************************* Mon Apr 28 13:55:22 2003 Number: 148 Name: Verspoor, Cornelia M Affiliation: Los Alamos National Laboratory Address: PO Box 1663, MS B256 City: Los Alamos State/Provice: NM Postal/Zip Code: 87545 Country: USA Email: verspoor@lanl.gov Phone: 1-505-667-5086 Fax: 1-505-667-1126 Category: Data Mining Poster Title: A Constructional Approach to Extraction Poster Authors and organization: Cornelia M. Verspoor¹, George J. Papcun², Kari Sentz
¹verspoor@lanl.gov, Los Alamos National Laboratory; ²gjp@lanl.gov, Los Alamos National Laboratory Abstract: We present a prototype implementation of a system for extracting protein/gene interactions from biological literature which is motivated by the theory of Construction Grammar.� CG provides a powerful framework for combining domain-specific terminology management with patterns incorporating generic linguistic structural constraints. File: verspoorATlanl.gov_148.html ************************************************* Mon Apr 28 14:56:46 2003 UPDATE ----- Number: 42 Name: Purevjav, Enkhbayar Affiliation: Hokkaido University Address: Kita-ku City: Sapporo State/Provice: Hokkaido Postal/Zip Code: 060-0810 Country: Japan Email: penkh@chem.agr.hokudai.ac.jp Phone: 81-11-611-2111 Fax: 81-11-612-3617 Category: Structural Biology Poster Title: 3D circle fitting of leucine-rich repeat proteins Poster Authors and organization: Purevjav Enkhbayar¹, Norio Matsushima², Mitsuru Osaki
¹penkh@chem.agr.hokudai.ac.jp, Hokkaido University; ²matusima@sapmed.ac.jp, Sapporo Medical University Abstract: Three dimensional circle fitting using atomic coordinate was performed to all known structures of leucine-rich repeat (LRR)-containing proteins. The analysis results indicate that there is a regular relationship between the radius of the LRR arc and the rotation angle about the central axis of the arc per repeating unit. File: penkhATchem.agr.hokudai.ac.jp_42 ************************************************* Mon Apr 28 14:59:33 2003 Number: 149 Name: Zhou, Yingyao Affiliation: Genomics Institute of the Novartis Research Foundation Address: 10675 John Jay Hopkins Dr City: San Diego State/Provice: CA Postal/Zip Code: 92121 Country: USA Email: zhou@gnf.org Phone: 858-812-1568 Fax: 858-812-1570 Category: New Frontiers Poster Title: Developing Analysis and Visualization Tools for Lead Discovery Poster Authors and organization: Dimitri¹, Shumei², Andrey Santrosyan, Hayk Asatryan, Kaisheng Chen, Chris Benner, Robert Downs, John Isbell, Yingyao Zhou
¹dpetrov@gnf.org, Petrov; ²sjiang@gnf.org, Jiang Abstract: Genomics Institute of the Novartis Research Foundation (GNF) is developing data analysis and visualization tools on top of a web-based informatics system for its lead discovery biomedical research. Recent tools include: dose-response data fitting and visualization, structural similarity-based compound hierarchical clustering, ring component-based compound diversity analysis, LCMS data visualization, etc. File: zhouATgnf.org_149.html ************************************************* Mon Apr 28 15:14:24 2003 Number: 150 Name: Zhou, Yingyao Affiliation: Genomics Institute of the Novartis Research Foundation Address: 10675 John Jay Hopkins Dr City: San Diego State/Provice: CA Postal/Zip Code: 92121 Country: USA Email: zhou@gnf.org Phone: 858-812-1568 Fax: 858-812-1570 Category: Microarrays Poster Title: Robust k-means Clustering of Gene Expression Poster Authors and organization: Chris¹, Dimitri², Yong-Chuan Tao, Karine G. Le Roch, Garret Hampton, Elizabeth A. Winzeler, Jiayu Liao, Guangzhou Zou, Peter Schultz, Yingyao Zhou
¹cbenner@gnf.org, Benner; ²dpetrov@gnf.org, Petrov Abstract: The existing k-means clustering algorithm for gene expression data suffers from its uncertainty and ambiguity. This robust k-means clustering algorithm demonstrates how both variations in data sources and the intrinsic indeterminacy of clustering procedures can be overcome and that reliable, informative, and optimal clustering results can be achieved. File: zhouATgnf.org_150.html ************************************************* Mon Apr 28 15:36:18 2003 Number: 151 Name: Lea, Rod A Affiliation: Genomics Research Centre Address: Parklands Drive City: Gold Coast State/Provice: Queensland Postal/Zip Code: 9726 Country: Australia Email: r.lea@griffith.edu.au Phone: 07 55528863 Fax: 07 55529081 Category: Functional Genomics Poster Title: Interacting Determinants of Migraine Susceptibility Poster Authors and organization: Rod Lea¹, Lyn Griffiths²
¹r.lea@griffith.edu.au, Genomics Research Centre, Griffith University; ²l.griffiths@griffith.edu.au, Genomics Research Centre, Griffith University Abstract: It is likely that multiple genetic variants interact to confer susceptibility to complex disease. We have shown that functional variants in the MTHFR and ACE genes interact to increase risk of migraine. File: r.leaATgriffith.edu.au_151.html ************************************************* Mon Apr 28 16:27:55 2003 UPDATE ----- Number: 63 Name: Ratushny, Alexander V Affiliation: Institute of Cytology and Genetics, SBRAS Address: 10 Lavrentiev Ave. City: Novosibirsk State/Provice: Novosibirsk Postal/Zip Code: 630090 Country: Russia Email: ratushny@bionet.nsc.ru Phone: 3832-333-119 Fax: 3832-331-278 Category: Systems Biology Poster Title: Theoretical analysis of mutations and evolution of gene networks Poster Authors and organization: Alexander V. Ratushny¹, Vitaly A. Likhoshvai², Yuri G. Matushkin, Nikolay A. Kolchanov
¹ratushny@bionet.nsc.ru, Institute of Cytology and Genetics, SBRAS; ²likho@bionet.nsc.ru, Institute of Cytology and Genetics, SBRAS Abstract:

File: ratushnyATbionet.nsc.ru_63 ************************************************* Mon Apr 28 16:51:43 2003 UPDATE ----- Number: 75 Name: Shilov, Boris V Affiliation: Siberian State Medical University Address: Solyanoi pereulok, 34, 2 City: Tomsk State/Provice: Russia Postal/Zip Code: 634003 Country: Russia Email: bvshilov@hotbox.ru Phone: +7-3822-650564 Fax: +7-3822-650564 Category: Predictive Methods Poster Title: Low-budgetary scheme for differentiation and DNA quantity investigation in blood lymphocytes of patients with chronical tonsillitis Poster Authors and organization: Boris V.Shilov¹, Dmitry A.Dolgun²
¹bvshilov@hotbox.ru, SSMU; ², SSMU Abstract: The nucleus belonging to any type of the cells was determined to estimate of atypical lymphocytes in patients with chronic tonsillitis, to analyze the vital cycle those cells on the base of classification of transformed cells stained according to Romanovsky-Gimza. Image segmentation process was adapted to condition of low-budgetary science File: bvshilovAThotbox.ru_75 ************************************************* Mon Apr 28 16:54:45 2003 UPDATE ----- Number: 77 Name: Schoenhuth, Alexander _ Affiliation: Center for Applied Computer Science, University Cologne Address: Weyertal 80 City: Koeln State/Provice: NRW Postal/Zip Code: 50931 Country: Germany Email: aschoen@zpr.uni-koeln.de Phone: 49 221 4706003 Fax: 49 221 4705160 Category: Data Mining Poster Title: Partially supervised clustering of gene expression time course data Poster Authors and organization: Alexander Schoenhuth¹, Alexander Schliep², Christine Steinhoff
¹aschoen@zpr.uni-koeln.de, Center for Applied Computer Science, University Cologne; ²schliep@molgen.mpg.de, Max Planck Institute for Molecular Genetics, Berlin Abstract: As the amount of genes with known function available is growing there is a need for classification methods which allow the use of prior knowledge. Partially supervised clustering of time courses stemming from gene expression experiments addresses this problem. Here a model-based clustering approach using Hidden Markov Models is proposed. File: aschoenATzpr.uni-koeln.de_77 ************************************************* Mon Apr 28 17:04:19 2003 UPDATE ----- Number: 141 Name: Davis, Melissa J Affiliation: Institute of Molecular Biosciences Address: University of Queensland, St. Lucia City: Brisbane State/Provice: Queensland Postal/Zip Code: 4067 Country: Australia Email: m.davis@imb.uq.edu.au Phone: +7 33662608 Fax: - Category: Predictive Methods Poster Title: An automated protocol for membrane protein prediction and annotation Poster Authors and organization: Melissa Davis¹, Zheng Yuan, Shane Fashang Zhang and Rohan Teasdale
¹m.davis@imb.uq.edu.au, Institute of Molecular Biosciences Abstract: In order to annotate the membrane organization of whole-proteome datasets, we have developed a consensus annotation protocol automated for high through-put analysis. This protocol predicts the presence of transmembrane domains, signal peptides and GPI anchors. These features are combined to generate a prediction of membrane organization. File: m.davisATimb.uq.edu.au_141 ************************************************* Mon Apr 28 17:06:47 2003 UPDATE ----- Number: 141 Name: Davis, Melissa J Affiliation: Institute of Molecular Biosciences Address: University of Queensland, St. Lucia City: Brisbane State/Provice: Queensland Postal/Zip Code: 4067 Country: Australia Email: m.davis@imb.uq.edu.au Phone: +7 33662608 Fax: - Category: Predictive Methods Poster Title: An automated protocol for membrane protein prediction and annotation Poster Authors and organization: Melissa Davis¹, Zheng Yuan, Shane Fashang Zhang and Rohan Teasdale
¹m.davis@imb.uq.edu.au, Institute of Molecular Biosciences Abstract: In order to annotate the membrane organization of whole-proteome datasets, we have developed a consensus annotation protocol automated for high through-put analysis. This protocol predicts the presence of transmembrane domains, signal peptides and GPI anchors. These features are combined to generate a prediction of membrane organization. File: m.davisATimb.uq.edu.au_141 ************************************************* Mon Apr 28 17:15:18 2003 UPDATE ----- Number: 79 Name: Koike, Asako Affiliation: Human Genome Center, The Institute of Medical Science, The University of Tokyo Address: 4-6-1 Shirokane-dai City: Minto-ku State/Provice: Tokyo Postal/Zip Code: 108-8639 Country: Japan Email: akoike@ims.u-tokyo.ac.jp Phone: 81-3-5449-5611 Fax: 81-3-5449-5434 Category: Structural Biology Poster Title: The analysis and prediction of protein-protein interacting sites. Poster Authors and organization: Asako Koike¹, Toshihisa Takagi²
¹akoike@ims.u-tokyo.ac.jp, Human Genome Center, The Institute of Medical Science, Univ. of Tokyo; ²takagi@ims.u-tokyo.ac.jp, Human Genome Center, The Institute of Medical Science, Univ. of Tokyo Abstract: We developed a prediction method for protein interaction sites using sequence profiles and accessible surface area of neighboring residues, surface patches, other physicochemical characteristics, and support vector machines. The relationship between the prediction accuracy and the characteristic of protein-protein interaction sites is discussed. File: akoikeATims.u-tokyo.ac.jp_79 ************************************************* Mon Apr 28 17:29:15 2003 UPDATE ----- Number: 83 Name: Veeramalai, Mallika Affiliation: Bioinformatics Research Centre, Dept. of Computing Science, University of Glasgow Address: 17, lilybank Gardens, University of Glasgow, City: Glasgow State/Provice: Scotland Postal/Zip Code: G12 8QQ Country: United Kingdom Email: mallika@dcs.gla.ac.uk Phone: +44 141 330 2421 Fax: +44 141 330 8627 Category: Structural Biology Poster Title: Incorporating Sequence and Biochemical Information in TOPS models - For Poster Authors and organization: Mallika Veeramalai¹, David Gilbert², David R Westhead
¹mallika@dcs.gla.ac.uk, Bioinformatics Research Centre, Dept. of Computing Science, University of Glasgow; ²drg@dcs.gla.ac.uk, Abstract: Incorporating sequence and biochemical features in TOPS (Topological Models of Protein Structures) is significant for pattern matching and pattern discovery in protein structures. Interesting results would be valuable for efforts to predict protein structure and function from sequences. These problems remain key challenges of direct relevance to projects in structural and functional genomics. TOPS is available at http://www.tops.leeds.ac.uk File: mallikaATdcs.gla.ac.uk_83 ************************************************* Mon Apr 28 17:34:24 2003 UPDATE ----- Number: 89 Name: Tan, Keng H Affiliation: BioInformatics Institute Address: 21 Heng Mui Keng Terrace, 03-14 City: Singapore State/Provice: Singapore Postal/Zip Code: 119613 Country: Singapore Email: eric@bii.a-star.edu.sg Phone: +65 6874 6182 Fax: +65 6778 1250 Category: Sequence Comparison Poster Title: Evolutionary significance of G1/S checkpoint among Eukaryotes Poster Authors and organization: Keng Hwa Tan¹, Pawan Dhar²
¹eric@bii.a-star.edu.sg, BioInformatics Institute; ²pk@bii.a-star.edu.sg, BioInformatics Institute Abstract: G1/S checkpoint plays a pivotal role during early stages of the cell cycle. Progression through G1/S boundary is controlled by a series of regulators. To explore the roles of these regulators and identify targets of CDKs, bioinformatics analysis are being done on DNA and protein sequences from different eukaryotic organisms. File: ericATbii.a-star.edu.sg_89 ************************************************* Mon Apr 28 17:35:07 2003 UPDATE ----- Number: 90 Name: Rouchka, Eric C Affiliation: University of Louisville Address: JB Speed Building Room 123 City: Louisville State/Provice: Kentucky Postal/Zip Code: 40292 Country: USA Email: eric.rouchka@louisville.edu Phone: 502-852-2581 Fax: 502-852-4713 Category: New Frontiers Poster Title: Statewide Bioinformatics in Kentucky Poster Authors and organization: Eric Rouchka¹, Nigel Cooper²
¹eric.rouchka@louisville.edu, University of Louisville; ²nigelcooper@louisville.edu, University of Louisville Abstract: The KBRIN bioinformatics core is attempting to create a Kentucky-wide network of bioinformatics expertise. This venture has led to the identification of knowledge- and compute-based resources. The core seeks to improve bioinformatics knowledge through research and the creation of bioinformatics courses, certificates, and degrees. The core web site is: http://www.kbrin.louisville.edu/about/bioinform_core.html File: eric.rouchkaATlouisville.edu_90 ************************************************* Mon Apr 28 17:36:14 2003 UPDATE ----- Number: 91 Name: Rouchka, Eric C Affiliation: University of Louisville Address: JB Speed Building Room 123 City: Louisville State/Provice: Kentucky Postal/Zip Code: 40292 Country: USA Email: eric.rouchka@louisville.edu Phone: 502-852-2581 Fax: 502-852-4713 Category: Microarrays Poster Title: MPRIME: Efficient Large Scale Multiple Primer Design for Customized Microarrays Poster Authors and organization: Eric Rouchka¹, Nigel Cooper², Abdelnaby Khalyfa
¹eric.rouchka@louisville.edu, University of Louisville; ²nigelcooper@louisville.edu, University of Louisville Abstract: MPrime is a system for efficiently creating large sets of PCR primer pairs for use in designing products for custom cDNA microarrays. MPrime has allowed us to effectively design custom neurodegenerative microarray chips for humans as well as the rat and mouse genomes. MPrime is available at: href=http://kbrin.a-bldg.louisville.edu/Tools/MPrime/ File: eric.rouchkaATlouisville.edu_91 ************************************************* Mon Apr 28 17:37:05 2003 UPDATE ----- Number: 90 Name: Rouchka, Eric C Affiliation: University of Louisville Address: JB Speed Building Room 123 City: Louisville State/Provice: Kentucky Postal/Zip Code: 40292 Country: USA Email: eric.rouchka@louisville.edu Phone: 502-852-2581 Fax: 502-852-4713 Category: New Frontiers Poster Title: Statewide Bioinformatics in Kentucky Poster Authors and organization: Eric Rouchka¹, Nigel Cooper²
¹eric.rouchka@louisville.edu, University of Louisville; ²nigelcooper@louisville.edu, University of Louisville Abstract: The KBRIN bioinformatics core is attempting to create a Kentucky-wide network of bioinformatics expertise. This venture has led to the identification of knowledge- and compute-based resources. The core seeks to improve bioinformatics knowledge through research and the creation of bioinformatics courses, certificates, and degrees. The core web site is: http://www.kbrin.louisville.edu/about/bioinform_core.html File: eric.rouchkaATlouisville.edu_90 ************************************************* Mon Apr 28 17:38:48 2003 UPDATE ----- Number: 141 Name: Davis, Melissa J Affiliation: Institute of Molecular Biosciences Address: University of Queensland, St. Lucia City: Brisbane State/Provice: Queensland Postal/Zip Code: 4067 Country: Australia Email: m.davis@imb.uq.edu.au Phone: +7 33662608 Fax: - Category: Predictive Methods Poster Title: An automated protocol for membrane protein prediction and annotation Poster Authors and organization: Melissa Davis¹, Zheng Yuan, Shane Fashang Zhang and Rohan D. Teasdale
¹m.davis@imb.uq.edu.au, Institute of Molecular Biosciences Abstract: In order to annotate the membrane organization of whole-proteome datasets, we have developed a consensus annotation protocol automated for high through-put analysis. This protocol predicts the presence of transmembrane domains and signal peptides. These features are combined to generate a prediction of membrane organization. File: m.davisATimb.uq.edu.au_141 ************************************************* Mon Apr 28 17:40:01 2003 UPDATE ----- Number: 93 Name: Artamonova, Irena I Affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS Address: Miklukho-Maklaya 16-10 City: Moscow State/Provice: Moscow Postal/Zip Code: 117997 Country: Russia Email: irena@humgen.siobc.ras.ru Phone: 7-095-3307029 Fax: 7-095-3306538 Category: Functional Genomics Poster Title: Non-conserved alternative splicing of human and mouse genes Poster Authors and organization: I. Artamonova¹, M. Gelfand², A. Mironov, R. Nurtdinov.
¹irena@humgen.siobc.ras.ru, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16-10, Moscow, 117997, Russia; ²gelfand@ig-msk.ru, State Scientific Center GosNIIGenetika, 1st Dorozhny 1, Moscow 113545, Russia Abstract: We analyzed conservation of alternative splicing patterns in pairs of orthologous genes from the human and mouse genomes. Our results demonstrate considerable diversity of alternative splicing in these genomes: at least half of alternatively spliced genes have species-specific isoforms. Orthologs with non-conserved isoforms may play a role in species-specific development. File: irenaAThumgen.siobc.ras.ru_93 ************************************************* Mon Apr 28 17:41:13 2003 UPDATE ----- Number: 95 Name: Wilke, Andreas Affiliation: Bielefeld University, Institute for Genomeresearch, Germany Address: Universitaetstrasse City: Bielefeld State/Provice: NRW Postal/Zip Code: D-33615 Country: Germany Email: andreas.wilke@genetik.uni-bielefeld.de Phone: 00495211064813 Fax: Category: Functional Genomics Poster Title: ProDB - Bioinformatics support for high throughput proteomics Poster Authors and organization: Andreas Wilke¹, Christian Rueckert², Sebastian Kespoh , Martina Mahne, Andrea T. Hueser, Folker Meyer
¹andreas.wilke@genetik.uni-bielefeld.de, UniversBielefeld University, Institute for Genome Research, Germany; ²christian.rueckert@genetik.uni-bielefeld.de, Int. NRW Grad. School in Bioinformatics Genome Research, Bielefeld Unive rsity, Germanyy Abstract: To cope with the need for automated data conversion, storage, and analysis in the field of proteomics, the open source system ProDB was developed. The system handles data conversion from different mass spectrometer software, automates data analysis, and will allow the annotation of MS spectra. File: andreas.wilkeATgenetik.uni-bielefeld.de_95 ************************************************* Mon Apr 28 17:42:43 2003 UPDATE ----- Number: 97 Name: Gill, John C Affiliation: Victorian Bioinformatics Consortium, Monash University Address: Wellington rd. City: Clayton State/Provice: Victoria Postal/Zip Code: 3800 Country: Australia Email: john.gill@med.monash.edu.au Phone: 9 905 9274 Fax: Category: Databases Poster Title: Automating Data Collection And Categorisation Using The CAS Software Poster Authors and organization: John Gill¹
¹john.gill@monash.edu.au, Victorian Bioinformatics Consortium, Monash University Abstract: CAS is a data integration system that allows for the creation of categories and integrated data sets. Each category consists of a set of attributes and methods, which act as an object item. Incoming data, obtained manually or through the automated data collection component, is linked to category attributes according to user defined rules and conditions. File: john.gillATmed.monash.edu.au_97 ************************************************* Mon Apr 28 17:54:47 2003 UPDATE ----- Number: 107 Name: Gladwin, Benjamin A Affiliation: University of Queensland, Department of mathematics Address: stlucia City: brisbane State/Provice: QLD Postal/Zip Code: 4067 Country: Australia Email: gladwin@maths.uq.edu.au Phone: 0733461430 Fax: Category: Predictive Methods Poster Title: Long time scale simulations of Molecular Systems Poster Authors and organization: Benjamin Gladwin¹, Dr Thomas Huber²
¹gladwin@maths.uq.edu.au, University of Queensland Department of Mathematics.; ²huber@maths.uq.edu.au, University of Queensland Department of Mathematics. Abstract: Modelling large bio-molecules is still primarily limited to the simulation of short timeframes, which in many cases are not biologically significant. The goal of this project is to use the optimisation of Hamiltonian paths to enable calculation of the behaviour of molecular systems over large time frames. File: gladwinATmaths.uq.edu.au_107 ************************************************* Mon Apr 28 17:55:54 2003 UPDATE ----- Number: 107 Name: Gladwin, Benjamin A Affiliation: University of Queensland, Department of mathematics Address: stlucia City: brisbane State/Provice: QLD Postal/Zip Code: 4067 Country: Australia Email: gladwin@maths.uq.edu.au Phone: 0733461430 Fax: Category: Predictive Methods Poster Title: Long time scale simulations of Molecular Systems Poster Authors and organization: Benjamin Gladwin¹, Dr Thomas Huber²
¹gladwin@maths.uq.edu.au, University of Queensland Department of Mathematics.; ²huber@maths.uq.edu.au, University of Queensland Department of Mathematics. Abstract: Modelling large bio-molecules is still primarily limited to the simulation of short timeframes, which in many cases are not biologically significant. The goal of this project is to use the optimisation of Hamiltonian paths to enable calculation of the behaviour of molecular systems over large time frames. File: gladwinATmaths.uq.edu.au_107 ************************************************* Mon Apr 28 18:32:07 2003 Number: 152 Name: Zeng, Yujing Affiliation: University of Delaware Address: 140, Evans Hall City: Newark State/Provice: DE Postal/Zip Code: 19716 Country: USA Email: zeng@eecis.udel.edu Phone: 302-831-3610 Fax: 302-831-4316 Category: Systems Biology Poster Title: A Novel Bayesian Network Model for the Study of Genetic Regulatory Networks Poster Authors and organization: Y. Zeng¹, J. Garcia-Frias²
¹zeng@eecis.udel.edu, University of Delaware; ²jgarcia@eecis.udel.edu, University of Delaware Abstract: We propose the use of Bayesian networks (BNs) with continuous valued variables, modeled by Student distributions, to simulate the cellular regulatory mechanism. Experimental results show the robustness of the proposed approach, which outperforms previous existing schemes based on BNs with either discrete variables or continuous variables with Gaussian distribution. File: zengATeecis.udel.edu_152.html ************************************************* Mon Apr 28 18:32:59 2003 Number: 153 Name: Zhu, Weirong Affiliation: University of Delaware Address: 326 Dupont Hall, University of Delaware City: Newark State/Provice: Delaware Postal/Zip Code: 19716 Country: U.S.A. Email: weirong@capsl.udel.edu Phone: 1-302-831-0327 Fax: 1-302-831-4316 Category: Sequence Comparison Poster Title: Parallel Implementation of Hmm-pfam on EARTH platform Using THREADED-C Poster Authors and organization: Weirong Zhu¹, Yanwei Niu², Jizhu Lu, Guang R. Gao
¹weirong@capsl.udel.edu, University of Delaware; ²niu@capsl.udel.edu, University of Delaware Abstract:

Abstract (50 words short version)

A parallel HMM-pfam is implemented on EARTH - an event-driven fine-grain multi-threaded program execution model. It demonstrated significant performance improvement over another PVM based version. On a cluster of 128 dual-CPU nodes, the execution time of a representative testbench is reduced from 15.9 hours to 4.3 minutes.

File: weirongATcapsl.udel.edu_153.html ************************************************* Mon Apr 28 19:18:24 2003 UPDATE ----- Number: 111 Name: Zhu, Jingchun Affiliation: University of California at San Francisco Address: 503 Font Blvd. City: San Francisco State/Provice: california Postal/Zip Code: 94132 Country: USA Email: jzhu@itsa.ucsf.edu Phone: 4153372017 Fax: Category: Microarrays Poster Title: Using bayesian network learning to model yeast transcriptional response to nitrogen oxide Poster Authors and organization: Jingchun Zhu¹, Joe DeRisi²
¹jzhu@itsa.ucsf.edu, UCSF; ²joe@derisilab.ucsf.edu, UCSF Abstract: We used a Bayesian Network learning technique to analyze microarray transcriptional response profiles of yeast to nitrogen oxide. Using gene clusters as network nodes, the learned transcription response networks are consistent with the proposed biological hypotheses. The model also revealed a previously unknown link between galactose input and a fzf1 dependent cluster. File: jzhuATitsa.ucsf.edu_111 ************************************************* Mon Apr 28 19:28:36 2003 UPDATE ----- Number: 117 Name: Julenius, Karin Affiliation: Center for Biological Sequence Analysis Address: Technical University of Denmark, Building 208 City: Lyngby State/Provice: NA Postal/Zip Code: DK-2800 Country: Denmark Email: kj@cbs.dtu.dk Phone: +45-45252472 Fax: +45-45931585 Category: Predictive Methods Poster Title: NetOGlyc 3.0: Prediction of mucin type O-glycosylation sites from sequence and sequence-derived features. Poster Authors and organization: Karin Julenius¹, Ramneek Gupta, Kristoffer Rapacki, Lars Juhl Jensen, S�ren Brunak
¹kj@cbs.dtu.dk, Center for Biological Sequence Analysis, BioCentrum-DTU Abstract: NetOGlyc 3.0 is a predictor of mucin type O-glycosylation sites, predicting from the protein sequence alone. NetOGlyc 3.0 shows much better generalization behaviour (the ability of the network to correctly predict for completely new examples) than its predecessor and is available at www.cbs.dtu.dk/services/NetOGlyc/ File: kjATcbs.dtu.dk_117 ************************************************* Mon Apr 28 19:39:48 2003 UPDATE ----- Number: 127 Name: McLysaght, Aoife F Affiliation: University of California, Irvine Address: 321 Steinhaus Hall City: Irvine State/Provice: CA Postal/Zip Code: 92697-2525 Country: USA Email: amclysag@uci.edu Phone: 1-949-8247703 Fax: 1-949-8242181 Category: Phylogeny and Evolution Poster Title: In silico exploitation of genetic maps: detection of hidden synteny through multiple genome comparisons Poster Authors and organization: Aoife McLysaght¹, Brandon Gaut²
¹amclysag@uci.edu, UCI; ²bgaut@uci.edu, UCI Abstract: Genetic maps are expensive and time consuming to produce, yet they contain only partial genomic data. Here we present a method to maximise the value of genetic maps in silico through multiple genome comparison. Using this method we can detect regions of conserved synteny that are not detectable through simple pairwise comparisons. File: amclysagATuci.edu_127 ************************************************* Mon Apr 28 19:40:33 2003 UPDATE ----- Number: 127 Name: McLysaght, Aoife F Affiliation: University of California, Irvine Address: 321 Steinhaus Hall City: Irvine State/Provice: CA Postal/Zip Code: 92697-2525 Country: USA Email: amclysag@uci.edu Phone: 1-949-8247703 Fax: 1-949-8242181 Category: Phylogeny and Evolution Poster Title: In silico exploitation of genetic maps: detection of hidden synteny through multiple genome comparisons Poster Authors and organization: Aoife McLysaght¹, Brandon Gaut²
¹amclysag@uci.edu, UCI; ²bgaut@uci.edu, UCI Abstract: Genetic maps are expensive and time consuming to produce, yet they contain only partial genomic data. Here we present a method to maximise the value of genetic maps in silico through multiple genome comparison. Using this method we can detect regions of conserved synteny that are not detectable through simple pairwise comparisons. File: amclysagATuci.edu_127 ************************************************* Mon Apr 28 19:46:48 2003 UPDATE ----- Number: 129 Name: Gill, John C Affiliation: Victorian Bioinformatics Consortium, Monash University Address: Wellington rd. City: Clayton State/Provice: Victoria Postal/Zip Code: 3800 Country: Australia Email: john.gill@med.monash.edu.au Phone: 9 905 9274 Fax: Category: Data Visualisation Poster Title: GET3D, A Genomic Exploration Tool in 3D Poster Authors and organization: John Gill¹
¹john.gill@monash.edu.au, Victorian Bioinformatics Consortium, Monash University Abstract: The GET3D, Genomic Exploration Tool in 3D, software tool is a complimentary product to the CAS, Categorised Annotation Set, system. Through 3D visualization and interaction techniques it allows for the manipulate of the CAS dataset, including the highlighting and exploration of data relationships, and for adding new information and relationships. File: john.gillATmed.monash.edu.au_129 ************************************************* Mon Apr 28 19:46:10 2003 Number: 154 Name: Nair, Murlidharan Teasdale Affiliation: San Diego Supercomputer Center Address: 9500 Gilman Dr City: La Jolla State/Provice: CA Postal/Zip Code: 92093 Country: USA Email: R.teasdale@imb.uq.edu.au Phone: 858-822-0887 Fax: 858-822-0873 Category: Functional Genomics Poster Title: On the Sequence Pattern Distribution in Splice Junctions. An Analysis Using Information Theoretic and Machine Learning Poster Authors and organization: Christina Zheng¹, Virginia R de Sa², Michael Gribskov, T. Murlidharan Nair
¹R.teasdale@imb.uq.edu.au, UCSD SDSC; ²desa@cogsci.ucsd.edu, UCSD Abstract: The computational recognition of precise splice junctions are a challenge faced in the analysis of newly sequenced genomes. To understand the sequence signatures at the splice junctions, comparative analysis using both neural network based calliper randomization and information theoretic based feature selection approaches have been used. File: R.teasdaleATimb.uq.edu.au_154.html ************************************************* Mon Apr 28 19:48:54 2003 UPDATE ----- Number: 133 Name: OHTA, Tomoko Affiliation: CREST, JST Address: 7-3-1 Hongo City: Bunkyo-ku State/Provice: Tokyo Postal/Zip Code: 113-0033 Country: Japan Email: okap@is.s.u-tokyo.ac.jp Phone: +81-3-5841-4124 Fax: +81-3-5802-8872 Category: Data Mining Poster Title: Current status of the GENIA Corpus: an Annotated Corpus in Molecular Biology Domain Poster Authors and organization: Tomoko OHTA¹, Jin-Dong Kim², Yuka Tateisi, Masayoshi Tsuruoka, Jun'ichi Tsujii
¹okap@is.s.u-tokyo.ac.jp, CREST, JST; ²jkdim@is.s.u-tokyo.ac.jp, University of Tokyo Abstract: GENIA corpus 3.0p and 3.01, consisting of 2,000 MEDLINE abstracts, have been released with linguistically rich annotations including sentence boundaries, term boundaries, term classifications, semi-structured coordinated clauses, recovered ellipsis in terms, part-of-speech, etc. This poster is intended to provide the current status of the GENIA corpus. File: okapATis.s.u-tokyo.ac.jp_133 ************************************************* Mon Apr 28 19:54:54 2003 UPDATE ----- Number: 141 Name: Davis, Melissa J Affiliation: Institute of Molecular Biosciences Address: University of Queensland, St. Lucia City: Brisbane State/Provice: Queensland Postal/Zip Code: 4067 Country: Australia Email: m.davis@imb.uq.edu.au Phone: +7 33662608 Fax: - Category: Predictive Methods Poster Title: An automated protocol for membrane protein prediction and annotation Poster Authors and organization: Melissa Davis¹, Zheng Yuan, Shane Fashang Zhang and Rohan D. Teasdale
¹m.davis@imb.uq.edu.au, Institute of Molecular Biosciences Abstract: In order to annotate the membrane organization of whole-proteome datasets, we have developed a consensus annotation protocol automated for high through-put analysis. This protocol predicts the presence of transmembrane domains, gpi-modifications and signal peptides. These features are combined to generate a prediction of membrane organization. File: m.davisATimb.uq.edu.au_141 ************************************************* Mon Apr 28 20:00:33 2003 UPDATE ----- Number: 141 Name: Davis, Melissa J Affiliation: Institute of Molecular Biosciences Address: University of Queensland, St. Lucia City: Brisbane State/Provice: Queensland Postal/Zip Code: 4067 Country: Australia Email: m.davis@imb.uq.edu.au Phone: +7 33662608 Fax: - Category: Predictive Methods Poster Title: An automated protocol for membrane protein prediction and annotation Poster Authors and organization: Melissa J. Davis¹, Zheng Yuan, Shane Fashang Zhang and Rohan D. Teasdale
¹m.davis@imb.uq.edu.au, Institute of Molecular Biosciences Abstract: In order to annotate the membrane organization of whole-proteome datasets, we have developed a consensus annotation protocol automated for high through-put analysis. This protocol predicts the presence of transmembrane domains, gpi-modifications and signal peptides. These features are combined to generate a prediction of membrane organization. File: m.davisATimb.uq.edu.au_141 ************************************************* Mon Apr 28 20:03:31 2003 UPDATE ----- Number: 145 Name: Matsuno, Hiroshi Affiliation: Yamaguchi University Address: 1677-1, Yoshida, City: Yamaguchi State/Provice: Yamaguchi Postal/Zip Code: 753-8512 Country: Japan Email: matsuno@sci.yamaguchi-u.ac.jp Phone: +81 83 933 5697 Fax: +81 83 933 5697 I plan to use my laptop computer as part of my poster Category: Systems Biology Poster Title: BioPACS: BioPathway Automatic Convert System for Genomic Object Net Poster Authors and organization: Masao Nagasaki ¹, Atsushi Doi², Hiroshi Matsuno, Satoru Miyano
¹masao@ims.u-tokyo.ac.jp, Human Genome Center, University of Tokyo; ²atsushi@ib.sci.yamaguchi-u.ac.jp, Faculty of Science, Yamaguchi University Abstract: For the modeling and simulation of a biopathway, suitable information selection from public biopathway databases, such as KEGG and BioCyc, would be useful. We have developed a method to transform these pathway databases so that the converted biopathways can run on Genomic Object Net (http://www.GenomicObject.Net). File: matsunoATsci.yamaguchi-u.ac.jp_145 ************************************************* Mon Apr 28 20:07:59 2003 UPDATE ----- Number: 153 Name: Zhu, Weirong Affiliation: University of Delaware Address: 326 Dupont Hall, University of Delaware City: Newark State/Provice: Delaware Postal/Zip Code: 19716 Country: U.S.A. Email: weirong@capsl.udel.edu Phone: 1-302-831-0327 Fax: 1-302-831-4316 Category: Sequence Comparison Poster Title: Parallel Implementation of Hmm-pfam on EARTH platform Using THREADED-C Poster Authors and organization: Weirong Zhu¹, Yanwei Niu², Jizhu Lu, Guang R. Gao
¹weirong@capsl.udel.edu, University of Delaware; ²niu@capsl.udel.edu, University of Delaware Abstract: A parallel HMM-pfam is implemented on EARTH - an event-driven fine-grain multi-threaded program execution model. It demonstrated significant performance improvement over another PVM based version. On a cluster of 128 dual-CPU nodes, the execution time of a representative testbench is reduced from 15.9 hours to 4.3 minutes. File: weirongATcapsl.udel.edu_153 ************************************************* Mon Apr 28 20:09:06 2003 UPDATE ----- Number: 153 Name: Zhu, Weirong Affiliation: University of Delaware Address: 326 Dupont Hall, University of Delaware City: Newark State/Provice: Delaware Postal/Zip Code: 19716 Country: U.S.A. Email: weirong@capsl.udel.edu Phone: 1-302-831-0327 Fax: 1-302-831-4316 Category: Sequence Comparison Poster Title: Parallel Implementation of Hmm-pfam on EARTH platform Using THREADED-C Poster Authors and organization: Weirong Zhu¹, Yanwei Niu², Jizhu Lu, Guang R. Gao
¹weirong@capsl.udel.edu, University of Delaware; ²niu@capsl.udel.edu, University of Delaware Abstract: A parallel HMM-pfam is implemented on EARTH - an event-driven fine-grain multi-threaded program execution model. It demonstrated significant performance improvement over another PVM based version. On a cluster of 128 dual-CPU nodes, the execution time of a representative testbench is reduced from 15.9 hours to 4.3 minutes. File: weirongATcapsl.udel.edu_153 ************************************************* Mon Apr 28 20:25:48 2003 Number: 155 Name: Liu, Haifeng Affiliation: DSO National Laboratories Address: 20 Science Park Drive City: Singapore State/Provice: Singapore Postal/Zip Code: 118230 Country: Singapore Email: lhaifeng@dso.org.sg Phone: 65-67728220 Fax: Category: Databases Poster Title: dbSTR: A Database for Short Tandem Repeats Poster Authors and organization: Haifeng Liu¹, Loo Nin Teow², Eric Yap, Linda Gan, Hui Min Wu, Sock Hoon Ng
¹lhaifeng@dso.org.sg, DSO National Laboratories, Singapore; ²tloonin@dso.org.sg, DSO National Laboratories, Singapore Abstract: dbSTR is a repository of short tandem repeats (microsatellites) whose polymorphisms have either been predicted using machine learning or verified using wet-lab methods. These STRs could be useful markers for high resolution linkage and association studies. dbSTR is freely available at http://www.dbstr.org. File: lhaifengATdso.org.sg_155.html ************************************************* Mon Apr 28 21:07:44 2003 Number: 156 Name: Pritchard, Lindsay I Affiliation: AAHL CSIRO Address: 5 Portarlington Rd Geelong City: Geelong State/Provice: Victoria Postal/Zip Code: 3220 Country: Australia Email: ian.pritchard@csiro.au Phone: 03 52 275468 Fax: 03 52275555 Category: Data Visualisation Poster Title: Application of Q-Gene software for the quantitation on Nipah virus in experimental animals using real-time PCR Poster Authors and organization: L.I. Pritchard¹, Y. Kaku², G. Crameri, B.T. Eaton, D.B. Boyle
¹ian.pritchard@csiro.au, AAHL CSIRO; ², NIAH Japan Abstract: Quantitative real-time PCR represents a highly sensitive and powerful technique for the high-throughput analysis of virus load and gene expression. We used the Q-Gene software (Muller et al., 2002) to expedite the statistical analysis, graphical presentation and evaluation of the real-time PCR quantitation of Nipah virus in experimental animals. File: ian.pritchardATcsiro.au_156.html ************************************************* Mon Apr 28 22:22:00 2003 Number: 157 Name: Kim, Jin Sik Affiliation: KAIST Address: 373-1 Guseong-dong Yuseong-gu City: Daejeon State/Provice: Postal/Zip Code: 305-701 Country: Republic of Korea Email: jskim@mail.kaist.ac.kr Phone: +82-42-869-5970 Fax: +82-42-869-8800 Category: Databases Poster Title: Integration and representation of heterogeneous metabolic databases for the analysis of metabolism: BIOSILICO Poster Authors and organization: Jin Sik Kim¹, Ji Hoon Jun², Yong Wook Kim, Sujin Chae, Mira Roh, Yong-Ho In and Sang Yup Lee
¹jskim@mail.kaist.ac.kr, KAIST; ²gene2@bioinfomatix.com, Bioinfomatix Inc. Abstract: BIOSILICO is a web-based database system that facilitates the search and analysis of metabolic pathways. BIOSILICO allows efficient retrieval of all available information on enzymes, compounds, reactions and pathways by integrating the heterogeneous metabolic databases and generates well-designed view pages showing retrieved data in a systematic way for easy understanding. File: jskimATmail.kaist.ac.kr_157.html ************************************************* Tue Apr 29 02:11:11 2003 Number: 158 Name: Blossey, Ralf Affiliation: Interdisciplinary Research Institute Address: Cite Scientifique- Avenue Poincare City: Villeneuve d Ascq State/Provice: Department du Nord Postal/Zip Code: 59652 Country: France Email: blossey@bioinf.uni-sb.de Phone: +49 681 302 64708 Fax: +49 681 302 64719 Category: Predictive Methods Poster Title: Reparametrizing loop entropy weights: effect on DNA melting curves Poster Authors and organization: Ralf Blossey¹, Enrico Carlon²
¹blossey@bioinf.uni-sb.de, IRI; ²carlon@lusi.uni-sb.de, IRI Abstract: We report an analysis of melting curves for genomic DNA. Our in-house software employs novel estimates for the weights of loop entropy factors. As test-cases, we studied D. Discoideum and synthetic sequences inserted in a linearized plasmid to compare with experiment. We find that the cooperativity parameter may be one order of magnitude larger than its consensus value. File: blosseyATbioinf.uni-sb.de_158.html ************************************************* Tue Apr 29 04:09:35 2003 Number: 159 Name: Morett, Enrique Affiliation: Instituto de of Biotecnologia Address: Universidad Nacional Autonoma de Mexico City: Cuernavaca Mor State/Provice: Postal/Zip Code: 62250 Country: Mexico Email: emorett@ibt.unam.mx Phone: +52 777 3291665 Fax: +52 777 3172388 Category: Data Mining Poster Title: Discovery of Analog Enzymes in Thiamin Biosynthesis by Anticorrelation Poster Authors and organization: Enrique Morett¹, J. Korbel², 1K. Emmanuvel Rajan, 1G. Saab-Rincon, 1L. Olvera, 1M. Olvera, 2B. Snel, 2S. Schmidt, and 2P. Bork.
¹emorett@ibt.unam.mx, 1Instituto de of Biotecnologia, Universidad Nacional Autonoma de Mexico, AP 510-3, Cuernavaca Mor. 62250.Mexico; ², European Molecular Biology Laboratory, Meyerhofstrasse 1. Heidelberg 69117. Germany. Abstract: Prediction of gene function is one of the most challenging tasks in genomic science when there is no clear sequence similarity to annotated genes. Here we present a new method denominated Anticorrelation of Gene Presence to predict gene function. Using this methd we identified four new genes involved in thiami biosynthesis File: emorettATibt.unam.mx_159.html ************************************************* Tue Apr 29 05:10:12 2003 Number: 160 Name: Fleming, Keiran P Affiliation: Imperial College London Address: Biochemistry Building, Deparment of Biological Sciences, Imperial College City: London State/Provice: London Postal/Zip Code: SW7 2AZ Country: UK Email: k.fleming@imperial.ac.uk Phone: 020 7594 5737 Fax: 020 7597 5789 Category: Genome Annotation Poster Title: e-PROTEIN: A Distributed Pipeline for Structure-based Proteome Annotation using Grid Technology Poster Authors and organization: Keiran Fleming¹, Liam McGuffin², Stefano Street, Andreas Kahari, Tim Massingham, Steven Newhouse, James Cuff, Ewan Birney, Soren Sorenson, Christine Orengo, John Darlington, David Jones, Janet Thornton, Michael Sternberg
¹k.fleming@imperial.ac.uk, Imperial College London; ²l.mcguffin@cs.ucl.ac.uk, University College London Abstract:

The e-Protein project aims to provide structure-based annotations of proteins in the major genomes by linking resources via Grid technology at 3 sites; Imperial College London, University College London, and the EBI. At the end of the first 6 months we have established a pre-prototype using GLOBUS/Grid technology.

File: k.flemingATimperial.ac.uk_160.html ************************************************* Tue Apr 29 06:28:42 2003 Number: 161 Name: Sato, Misaki Affiliation: Laboratory for Bioinformatics, Institute for Advanced Biosciences, Keio University Address: 5322 Endo City: Fujisawa State/Provice: Kanagawa Postal/Zip Code: 252-8520 Country: Japan Email: s00457ms@sfc.keio.ac.jp Phone: +81-466-47-5099 Fax: +81-466-47-5099 Category: Functional Genomics Poster Title: Computational analysis of stop codon readthrough in D.melanogaster Poster Authors and organization: Misaki Sato¹, Hitomi Umeki², Rintaro Saito, Akio Kanai, Masaru Tomita
¹s00457ms@sfc.keio.ac.jp, Laboratory for Bioinformatics, Institute for Advanced Biosciences, Keio University; ²t01513hu@sfc.keio.ac.jp, Laboratory for Bioinformatics, Institute for Advanced Biosciences, Keio University Abstract: We constructed a system that lists candidates of readthrough genes based on the existence of a �protein motif� at the 3�UTR. Using this system, we extracted 85 candidates in Drosophila melanogaster, and found features in those sequences which are known to have an effect on readthrough events. File: s00457msATsfc.keio.ac.jp_161.html ************************************************* Tue Apr 29 11:06:22 2003 Number: 162 Name: Megy, Karine Affiliation: University of Cambridge Address: Dpt of Pathology - Tennis Court Road City: Cambridge State/Provice: Cambridge Postal/Zip Code: CB2 1QP Country: United Kingdom Email: km369@cam.ac.uk Phone: 004401223333713 Fax: 004401223333346 Category: Data Mining Poster Title: EST based method to identify differentially expressed gene clusters along chromosmes Poster Authors and organization: Megy¹, Audic², J.M. Claverie
¹km369@cam.ac.uk, University of Cambridge; ²audic@igs.cnrs-mrs.fr, CNRS Abstract: 50-word abstract:

We developped a method based on a statistical analysis of Expressed Sequence Tags (ESTs) to evaluate the positionnal clustering of differentially expressed genes. Human chromosomes 20, 21 and 22 were analysed with this method and show clusters of specificaly expressed genes tml> File: km369ATcam.ac.uk_162.html ************************************************* Tue Apr 29 11:13:43 2003 Number: 163 Name: Commins, Jennifer Affiliation: Bioinformatics Lab , NUI Maynooth Address: North Campus City: Maynooth State/Provice: Co. Kildare Postal/Zip Code: N/A Country: Ireland Email: jennifer.commins@may.ie Phone: 00353 87 6494765 Fax: 00353 1 7083845 Category: Phylogeny and Evolution Poster Title: Novel Heterogeneous Maximum Likelihood Methods for The Detection of Adaptive Evolution. Poster Authors and organization: Jennifer Commins¹, Dr. James O. McInerney ²
¹jennifer.commins@may.ie, NUI, Maynooth; ²james.o.mcinerney@may.ie, NUI, Maynooth Abstract: Maximum Likelihood methods are popular for analysing sequences to detect adaptive evolution. We have designed new methods for robustly inferring the evolutionary history of extant sequences and identifying signatures of adaptive evolution, performing analyses of multiple sequence alignments in ways closer to biological reality than existing methods. Available at http://bioinf.may.ie/likelihood. File: jennifer.comminsATmay.ie_163.html ************************************************* Tue Apr 29 12:24:53 2003 Number: 164 Name: Fulmer, Andy W Affiliation: The Procter and Gamble Company Address: 11810 Miami River Road City: cincinnati State/Provice: OH Postal/Zip Code: 45252 Country: USA Email: fulmer.aw@pg.com Phone: 513-627-1267 Fax: I plan to use my laptop computer as part of my poster Category: Genome Annotation Poster Title: Gene Ontology Toolkit: A Comprehensive Software Package for Working with Gene Ontology Poster Authors and organization: Jing Ding¹, Jun Xu², Andy W. Fulmer
¹dingjing@iastate.edu, Iowa State University; ²xu.j.1@pg.com, The Procter and Gamble Company Abstract: Gene Ontology Toolkit is a Java GUI for working with the Gene Ontology (GO). Its three integrated components (editor, annotator and merger) enable biologists to visualize and extend GO, annotate gene products with GO terms, and merge the extensions and/or the annotations with new release of GO or others� extensions. File: fulmer.awATpg.com_164.html ************************************************* Tue Apr 29 12:48:53 2003 Number: 165 Name: Kreil, David P Affiliation: University of Cambridge Address: Downing Street City: Cambridge State/Provice: Cambs Postal/Zip Code: CB2 3EH Country: England, U.K. Email: ISMB03@Kreil.Org Phone: 0044 1223 764107 Fax: 0044 1223 333992 FOA D P Kreil Category: Microarrays Poster Title: Quantitative microarray spot profile optimization: A systematic evaluation of buffer/slide combinations Poster Authors and organization: D P Kreil¹, R P Auburn², L A Meadows, S Russell, G Micklem
¹ISMB03@Kreil.Org, University of Cambridge; ², Abstract: Selection of spotting-buffer and slide-chemistry is critical for the reliability of microarray-hybridization-experiments. Comparisons, however, have tended to be subjective, not suitable for systematic study. We present a novel approach, objectively assessing spot-morphology and -variance by measuring average (variance) of radial spot-pixel-intensity-profiles. It is successfully demonstrated comparing over 24x6 buffer/slide combinations. File: ISMB03ATKreil.Org_165.html ************************************************* Tue Apr 29 13:35:02 2003 Number: 166 Name: Madsen, Dennis Affiliation: Novo Nordisk Address: Novo Nordisk Park City: Maaloev State/Provice: Postal/Zip Code: 2760 Country: Denmark Email: dnnm@novonordisk.com Phone: +45 44436959 Fax: +45 44437171 Category: Data Mining Poster Title: Surfing data sources in drug discovery Poster Authors and organization: Dennis Madsen¹
¹dnnm@novonordisk.com, Novo Nordisk Abstract: A data integration generalist tool has been developed allowing simultaneous query in several data sources. The query is restricted to specific types such as project or metabolite name. The hits are displayed with links to the originating data source and an option to use the hit as the next query. File: dnnmATnovonordisk.com_166.html ************************************************* Tue Apr 29 15:44:12 2003 Number: 167 Name: Warren, Christopher L. Affiliation: University of Wisconsin - Madison Address: 4817 Sheboygan Apt. 707 City: Madison State/Provice: WI Postal/Zip Code: 53705 Country: USA Email: clwarren2@wisc.edu Phone: 608-274-2305 Fax: Category: Predictive Methods Poster Title: Computational Analysis of Homeodomain Protein Interaction Interfaces Poster Authors and organization: Christopher Warren¹, Mary Brezinski², Aseem Ansari
¹clwarren2@wisc.edu, University of Wisconsin - Madison; ², University of Wisconsin - Madison Abstract: Ubx and Exd are homeodomain transcriptional factors in Drosophila that cooperatively bind DNA to regulate cell differentiation. Using FADE, we discovered an interaction between these proteins that is nearly absent in the human homologs. Through chemical analysis we find that this interaction may increase binding in fly, but don\'t expect this in human. File: clwarren2ATwisc.edu_167.html ************************************************* Tue Apr 29 18:26:25 2003 Number: 168 Name: Kim, Yang Affiliation: Bioinformatics Unit, ISTECH Inc. Address: No.506, Hyundai Town Vill 848-1, Janghangdong, Ilsan City: Goyang State/Provice: Gyunggido Postal/Zip Code: 411-380 Country: Republic of Korea Email: yskim@istech21.com Phone: 82-31-903-1155 Fax: 82-31-903-1152 Category: Functional Genomics Poster Title: GOODIES: Gene Ontology-based Data-mining Tool for Biological Interpretation and Functional Classification on a Group of Biological Entities Poster Authors and organization: Sung Geun Lee¹, Wan Seon Lee²
¹sglee@istech21.com, Bioinformatics Unit, ISTECH Inc.; ²konan@istech21.com, Bioinformatics Unit, ISTECH Inc. Abstract: GOODIES is a Gene Ontology-based data-mining tool for effective functional classification. Given biological entities, GOODIES classifies them along their annotational attributes and selects optimal GO candidate terms from combinatorially many choices for overall biological interpretation, with intuitive visualization. The major applications of GOODIES include biologically-oriented cluster analysis and functional categorization. File: yskimATistech21.com_168.html ************************************************* Tue Apr 29 19:12:47 2003 Number: 169 Name: Segal, Eran Affiliation: Stanford University Address: Gates building 1A City: Stanford State/Provice: CA Postal/Zip Code: 94305 Country: USA Email: eran@cs.stanford.edu Phone: 650-725-8784 Fax: Category: Microarrays Poster Title: Module Networks: Identifying Regulatory Modules and their Condition Specific Regulators from Gene Expression Data Poster Authors and organization: Eran Segal¹, Aviv Regev², Dana Pe'er, Michael Shapira, David Botstein, Daphne Koller, Nir Friedman
¹eran@cs.stanford.edu, Stanford; ²ARegev@CGR.Harvard.edu, CGR Abstract: We present a probabilistic method for identifying regulatory modules from gene expression data. Our procedure identifies modules of coregulated genes, their regulators and the conditions under which regulation occurs, generating testable hypotheses in the form �regulator X regulates module Y under conditions W �. We present microarray experiments supporting three novel predictions,suggesting regulatory roles for previously uncharacterized proteins. File: eranATcs.stanford.edu_169.html ************************************************* Tue Apr 29 21:24:46 2003 Number: 170 Name: Huang, Yen-Chen S Affiliation: The Centre for Molecular Biodiscovery, University of Auckland Address: Private Bag 92019 City: Auckland State/Provice: Postal/Zip Code: Country: New Zealand Email: yc.huang@auckland.ac.nz Phone: +64-9-3737599 Ext. 86519 Fax: I plan to use my laptop computer as part of my poster Category: Functional Genomics Poster Title: Generation and Clustering of Phylogenetic Profiles for automatic Functional Annotation of Proteins Poster Authors and organization: Yen-Chen Steven Huang¹, Vic Arcus, Ted Baker, Shaun Lott, Patricia Riddle, Chris Triggs
¹yc.huang@auckland.ac.nz, The Centre for Molecular Biodiscovery, University of Auckland Abstract: phylogenetic profile analysis assigns functional clues to proteins in a manner that is indepent of sequence similarity. We present an improved algorithm that constructs the phylogenetic profiles of proteins based on the unambiguous Smith-Waterman Alignment algorithm. We used MetaCyc metabolic pathway clusters to estimate the prediction accuracy of the method. File: yc.huangATauckland.ac.nz_170.html ************************************************* Tue Apr 29 21:51:18 2003 Number: 171 Name: Arthur, Jonathan W Affiliation: Proteome Systems Address: Unit 1, 35 Waterloo Road City: Sydney State/Provice: NSW Postal/Zip Code: 2113 Country: Australia Email: Jonathan.Arthur@proteomesystems.com Phone: +61 2 9889 1830 Fax: +61 2 9889 1805 Category: Databases Poster Title: GlycoSuiteDB: A curated relational database of glycoprotein glycan structures Poster Authors and organization: Hiren J. Joshi¹, Sarah Jarvis², Jonathan W Arthur, Mathew J. Harrison, Marc R. Wilkins, Nicolle H. Packer, Catherine A. Cooper
¹hirenj@proteomesystems.com, Proteome Systems; ²sjarvis@proteomesystems.com, Proteome Systems Abstract: GlycoSuiteDB is a relational database of published glycan structures designed to assist researchers in the analysis of glycans. GlycoSuiteDB can be accessed from http://www.glycosuite.com File: Jonathan.ArthurATproteomesystems.com_171.html ************************************************* Tue Apr 29 22:35:43 2003 UPDATE ----- Number: 161 Name: Sato, Misaki Affiliation: Laboratory for Bioinformatics, Institute for Advanced Biosciences, Keio University Address: 5322 Endo City: Fujisawa State/Provice: Kanagawa Postal/Zip Code: 252-8520 Country: Japan Email: s00457ms@sfc.keio.ac.jp Phone: +81-466-47-5099 Fax: +81-466-47-5099 Category: Functional Genomics Poster Title: Computational analysis of stop codon readthrough in D.melanogaster Poster Authors and organization: Misaki Sato¹, Hitomi Umeki², Rintaro Saito, Akio Kanai, Masaru Tomita
¹s00457ms@sfc.keio.ac.jp, Laboratory for Bioinformatics, Institute for Advanced Biosciences, Keio University; ²t01513hu@sfc.keio.ac.jp, Laboratory for Bioinformatics, Institute for Advanced Biosciences, Keio University Abstract: We constructed a system that lists candidates of readthrough genes based on the existence of a “protein motif” at the 3’UTR. Using this system, we extracted 85 candidates in Drosophila melanogaster, and found features in those sequences which are known to have an effect on readthrough events. File: s00457msATsfc.keio.ac.jp_161 ************************************************* Tue Apr 29 22:41:37 2003 UPDATE ----- Number: 163 Name: Commins, Jennifer Affiliation: Bioinformatics Lab , NUI Maynooth Address: North Campus City: Maynooth State/Provice: Co. Kildare Postal/Zip Code: N/A Country: Ireland Email: jennifer.commins@may.ie Phone: 00353 87 6494765 Fax: 00353 1 7083845 Category: Phylogeny and Evolution Poster Title: Novel Heterogeneous Maximum Likelihood Methods for The Detection of Adaptive Evolution. Poster Authors and organization: Jennifer Commins¹, Dr. James O. McInerney ²
¹jennifer.commins@may.ie, NUI, Maynooth; ²james.o.mcinerney@may.ie, NUI, Maynooth Abstract: Maximum Likelihood methods are popular for analysing sequences to detect adaptive evolution. We have designed new methods for robustly inferring the evolutionary history of extant sequences and identifying signatures of adaptive evolution, performing analyses of multiple sequence alignments in ways closer to biological reality than existing methods. Available at http://bioinf.may.ie/likelihood. File: jennifer.comminsATmay.ie_163 ************************************************* Tue Apr 29 22:46:40 2003 UPDATE ----- Number: 81 Name: Miranda, Kevin Affiliation: Institute for Molecular Bioscience Address: Queensland Bioscience Precinct City: Brisbane State/Provice: Queensland Postal/Zip Code: 4072 Country: Australia Email: k.miranda@imb.uq.edu.au Phone: 61-7-33462347 Fax: 61-7-33462101 Category: Systems Biology Poster Title: Discovering novel regulatory controls of budding yeast cell cycle by Reverse Engineering and Bayesian Network Modeling Poster Authors and organization: Yan Sun¹, Pawan Dhar²
¹sunyan@bii.a-star.edu.sg, Bioinformatics Institute, 21 Heng Mui Keng Terrace, Singapore; ²pk@bii.a-star.edu.sg, Bioinformatics Institute, 21 Heng Mui Keng Terrace, Singapore Abstract: In this study, a Reverse Engineering and Bayesian Network Modeling (REBNM) approach has been used for inferring the cell cycle regulatory network from high-throughput gene expression data. The REBNM analyzer uses prior biological knowledge and supervised classification scheme for functionally grouping genes for downstream processing by Bayesian network modeling. File: k.mirandaATimb.uq.edu.au_81 ************************************************* Tue Apr 29 22:53:49 2003 UPDATE ----- Number: 162 Name: Megy, Karine Affiliation: University of Cambridge Address: Dpt of Pathology - Tennis Court Road City: Cambridge State/Provice: Cambridge Postal/Zip Code: CB2 1QP Country: United Kingdom Email: km369@cam.ac.uk Phone: 004401223333713 Fax: 004401223333346 Category: Data Mining Poster Title: EST based method to identify differentially expressed gene clusters along chromosmes Poster Authors and organization: Megy¹, Audic², J.M. Claverie
¹km369@cam.ac.uk, University of Cambridge; ²audic@igs.cnrs-mrs.fr, CNRS Abstract: 50-word abstract:

We developped a method based on a statistical analysis of Expressed Sequence Tags (ESTs) to evaluate the positionnal clustering of differentially expressed genes. Human chromosomes 20, 21 and 22 were analysed with this method and show clusters of specificaly expressed genes tml> File: km369ATcam.ac.uk_162 ************************************************* Tue Apr 29 23:01:39 2003 UPDATE ----- Number: 162 Name: Megy, Karine Affiliation: University of Cambridge Address: Dpt of Pathology - Tennis Court Road City: Cambridge State/Provice: Cambridge Postal/Zip Code: CB2 1QP Country: United Kingdom Email: km369@cam.ac.uk Phone: 004401223333713 Fax: 004401223333346 Category: Data Mining Poster Title: EST based method to identify differentially expressed gene clusters along chromosmes Poster Authors and organization: Megy¹, Audic², J.M. Claverie
¹km369@cam.ac.uk, University of Cambridge; ²audic@igs.cnrs-mrs.fr, CNRS Abstract: Expressed Sequence Tags File: km369ATcam.ac.uk_162 ************************************************* Tue Apr 29 23:04:14 2003 UPDATE ----- Number: 167 Name: Warren, Christopher L Affiliation: University of Wisconsin - Madison Address: 4817 Sheboygan Apt. 707 City: Madison State/Provice: WI Postal/Zip Code: 53705 Country: USA Email: clwarren2@wisc.edu Phone: 608-274-2305 Fax: Category: Predictive Methods Poster Title: Computational Analysis of Homeodomain Protein Interaction Interfaces Poster Authors and organization: Christopher Warren¹, Mary Brezinski, Aseem Ansari
¹clwarren2@wisc.edu, University of Wisconsin - Madison Abstract: Ubx and Exd are homeodomain transcriptional factors in Drosophila that cooperatively bind DNA to regulate cell differentiation. Using FADE, we discovered an interaction between these proteins that is nearly absent in the human homologs. Through chemical analysis we find that this interaction may increase binding in fly, but don't expect this in human. File: clwarren2ATwisc.edu_167 ************************************************* Tue Apr 29 23:29:50 2003 UPDATE ----- Number: 162 Name: Megy, Karine Affiliation: University of Cambridge Address: Dpt of Pathology - Tennis Court Road City: Cambridge State/Provice: Cambridge Postal/Zip Code: CB2 1QP Country: United Kingdom Email: km369@cam.ac.uk Phone: 004401223333713 Fax: 004401223333346 Category: Data Mining Poster Title: EST based method to identify differentially expressed gene clusters along chromosmes Poster Authors and organization: Megy¹, Audic², J.M. Claverie
¹km369@cam.ac.uk, University of Cambridge; ²audic@igs.cnrs-mrs.fr, CNRS Abstract: We developed a method based on a statistical analysis of Expressed Sequence Tags (ESTs) to evaluate the positional clustering of differentially expressed genes. Human chromosomes 20, 21 and 22 were analysed with this method and show clusters of specifically expressed genes File: km369ATcam.ac.uk_162 ************************************************* Wed Apr 30 00:03:58 2003 Number: 172 Name: Lee, Mi Young Affiliation: Korea Institute of Oriental Medicine Address: 129-11 Chungdam-dong City: Kangam-Ku State/Provice: Seoul Postal/Zip Code: 135-100 Country: S.Korea Email: mylee2020@hanmail.net Phone: 822-3442-1994-232 Fax: 822-3447-7985 Category: Phylogeny and Evolution Poster Title: Development of SCAR marker for the Discrimination of Bang-Poong species of Herbal Medicine Poster Authors and organization: Mi Young Lee¹, Byong Seob Ko², Seong Mi Hong, Jung Eun Kim, Sung Jin Lee
¹mylee2020@hanmail.net, Korea Institute of Oriental Medicine; ²bsko@kiom.re.kr, Korea Institute of Oriental Medicine Abstract: Bang-Poong species is one of the important herbal medicine. We could apply of molecular approach to development of SCAR marker and can be applied to dried herbal medicine. File: mylee2020AThanmail.net_172.html ************************************************* Wed Apr 30 01:12:00 2003 Number: 173 Name: Xue, Hong Affiliation: Applied Genomics Center, Hong Kong Bioinformatics Center, ParmacoGenetics Ltd, Department of Biochemistry, Hong Kong University of Science and Technology Address: Hong Kong University of Science and Technology, Clear Water Bay City: Kowloon State/Provice: Postal/Zip Code: Country: Hong Kong Email: hxue@ust.hk Phone: 23588707 Fax: Category: Databases Poster Title: SNP PrimerPicker Poster Authors and organization: Yip-Kuen Lau¹, Ching-Fun Lau², Henry Yiu-Hang Fu, Hong Xue
¹henryfu@ust.hk, Applied Genomics Center, Hong Kong Bioinformatics Center, ParmacoGenetics Ltd, Department of Biochemistry, Hong Kong University of Science and Technology; ²carolau@ust.hk, Applied Genomics Center, Hong Kong Bioinformatics Center, ParmacoGenetics Ltd, Department of Biochemistry, Hong Kong University of Science and Technology Abstract: SNP PrimerPicker is a software system for designing primers. Sequences in record are aligned with the source using bl2seq. It utilizes Primer3 to find primers and blastcl3 to compare similarity with the chromosomes. The components are integrated to make the procedure convenient. It is web accessible at bcz099.ust.hk/primerpicker. File: hxueATust.hk_173.html ************************************************* Wed Apr 30 01:33:57 2003 Number: 174 Name: Sklyar, Nataliya Affiliation: University of Leipzig Address: Feldstr. 88 City: Greifswald State/Provice: Postal/Zip Code: 17489 Country: Germany Email: sklyar@informatik.uni-leipzig.de Phone: +491752116289 Fax: +493834515239 Category: New Frontiers Poster Title: Using Web Services as part of the 2D gel analysis workflow Poster Authors and organization: Nataliya Sklyar¹, Matthias Berth ², Dirk Lewerentz
¹sklyar@informatik.uni-leipzig.de, University of Leipzig; ²berth@decodon.com , DECODON GmbH Abstract: We present the integration of web services into Delta2D, an end-user 2D gel analysis application. With Delta2D\'s web services plugins, users can access data from external sources and display it alongside the image analysis results in a uniform way. We describe the plugin architecture and first experiences in its use. File: sklyarATinformatik.uni-leipzig.de_174.html ************************************************* Wed Apr 30 01:58:42 2003 Number: 175 Name: Gilbert, David Affiliation: Bioinformatics Research Centre, Department of Computing Science, University of Glasgow Address: 17 Lilybank Gardens City: Glasgow State/Provice: Postal/Zip Code: G12 8QQ Country: UK Email: drg@brc.dcs.gla.ac.uk Phone: 44 1413302563 Fax: 44 1413303690 Category: Structural Biology Poster Title: Protein structure comparison based on profiles of topological motifs Poster Authors and organization: Juris Viksna¹, David Gilbert², Gilleain Torrance
¹jviksna@cclu.lv, Institute of Mathematics and Computer Science, University of Latvia; ²drg@brc.dcs.gla.ac.uk, Bioinformatics Research Centre, Department of Computing Science, University of Glasgow Abstract: We present a new approach to protein structure comparison using the existing, on graph representations based, TOPS database. Instead of comparisons based on single patterns, we use profiles of patterns, which allows in an indirect way to capture \"negative\" information. This leads to a significant increase in prediction accuracy. File: drgATbrc.dcs.gla.ac.uk_175.html ************************************************* Wed Apr 30 02:55:37 2003 Number: 176 Name: Pierrat, Benoit Affiliation: Novartis Institute of Biomedical Research Address: WKL-125.8.02 City: Basel State/Provice: Postal/Zip Code: 4002 Country: Switzerland Email: benoit.pierrat@pharma.novartis.com Phone: + 41 61 696 74 72 Fax: + 41 61 696 81 32 Category: Data Mining Poster Title: Novel members of the C12/C19 cysteine proteases identified through human genome mining efforts: primary characterization of selected genes Poster Authors and organization: Pierrat Benoit¹, Bruengger Adrian², Cai Richard, Gerhartz Bernd, Kossida Sophia, Nirmala Nanguniri, Worpenberg Susanne
¹benoit.pierrat@pharma.novartis.com, Novartis Institute of Biomedical Research; ²adrian.bruengger@pharma.novartis.com, Novartis Institute of Biomedical Research Abstract: DUBs are cysteine proteases controlling the ubiquitination status of target proteins. Using genome mining tools, we have conducted searches for new human DUB members leading to the identification of 11 new sequences. Here we report on their in silico annotation and discuss the primary functional characterization of selected members. File: benoit.pierratATpharma.novartis.com_176.html ************************************************* Wed Apr 30 04:55:08 2003 Number: 177 Name: HYDE, LAVINIA C Affiliation: WALTER AND ELIZA HALL INSTITUTE Address: 1G ROYAL PARADE City: MELBOURNE State/Provice: VICTORIA Postal/Zip Code: 3050 Country: AUSTRALIA Email: hyde@wehi.edu.au Phone: 0393452324 Fax: 0393479852 Category: Databases Poster Title: Melbourne Brain Genome Project Poster Authors and organization: Seong-Seng Tan¹, Lavinia Hyde², Masters C, Gunnersen J, Kenshole B, Job C, Augustine C, Boon W-M, Brown M, Scott HS
¹s.tan@hfi.unimelb.edu.au, Howard Florey Institute of Experimental Medicine and Physiology; ²hyde@wehi.edu.au, Walter and Eliza Hall Institute Abstract: The Melbourne Brain Genome Project is an Internet resource for studying gene expression as measured by serial analysis of gene expression, in both normal mice and specific mouse models. These models mimic neurodegenerative human diseases. The resource includes tools developed to analyse this data and is available at http://www.mbgproject.org. File: hydeATwehi.edu.au_177.html ************************************************* Wed Apr 30 06:28:14 2003 Number: 178 Name: Niu, Yanwei Affiliation: . Department of ECE, University of Delaware, USA Address: 310 Evans Hall, University of Delaware City: Newark State/Provice: DE Postal/Zip Code: 19716 Country: U.S.A Email: niu@capsl.udel.edu Phone: 1-302-831-3406 Fax: 1-302-831-4316 Category: Data Mining Poster Title: Mapping and Visual Exploration of GPCR Classification Hierarchy in Interpro and GPCRDB System Poster Authors and organization: Yanwei Niu¹, Xiangyun Wang², Yockey, Anastasia Christianson, Guang R. Gao
¹niu@capsl.udel.edu, . Department of ECE, University of Delaware, USA; ²Xiangyun.Wang@astrazeneca.com, EST Informatics Wilmington, Astra Zeneca PLC Abstract:

Interpro and GPCRDB are two GPCR classification systems. Using data mining technique, we compared the two systems family by family at each level of the classification hierarchy and established mapping relation between them. We introduced a novel visualization tool that allows us to directly and easily compare them.

File: niuATcapsl.udel.edu_178.html ************************************************* Wed Apr 30 07:05:01 2003 Number: 179 Name: Prompramote, Supawan Affiliation: Queensland University of Technology Address: 126 Magaret St City: brisbane State/Provice: Queenlands Postal/Zip Code: 4001 Country: Australia Email: s.prompramote@student.qut.edu.au Phone: 3864 9354 Fax: 3864 9390 Category: Microarrays Poster Title: Integrated Storage For Microarray Experimental Data Poster Authors and organization: Supawan Prompramote¹, Yi-Ping Phoebe Chen², Frederic Maire
¹s.prompramote@student.qut.edu.au, Centre for Information Technology Innovation, Faculty of Information Technology, Queensland University of Technology; ²p.chen@qut.edu.au, Centre for Information Technology Innovation, Faculty of Information Technology, Queensland University of Technology Abstract:
The use of different terminologies and structures in microarray databases is limiting the sharing of data and the collating of results between laboratories. We have proposed an integrated information management architecture for microarray experimental data that will focus on addressing these problems.
File: s.prompramoteATstudent.qut.edu.au_179.html ************************************************* Wed Apr 30 07:06:50 2003 Number: 180 Name: Pascual-Montano, Alberto D. Affiliation: National Center of Biotechnology Address: Campus Universidad Autonoma de Madrid. Cantoblanco City: Madrid State/Provice: Madrid Postal/Zip Code: 28049 Country: Spain Email: pascual@cnb.uam.es Phone: +34-915854543 Fax: +34-915854506 Category: Data Mining Poster Title: Discovering biological knowledge from gene expression using association rules Poster Authors and organization: P. Carmona-Saez¹, M. Chagoyen², A. Rodriguez, O. Trelles, J.M. Carazo and A. Pascual-Montano
¹pcarmona@cnb.uam.es, National Center of Biotechnology. Madrid; ²monica@cnb.uam.es, National Center of Biotechnology. Madrid Abstract: We describe the application of association rule discovery technique to find relevant relations between different genes attributes and experimental conditions in microarrays expression dataset. This method can be used to extract interesting and very diverse biological information. The method is implemented in EngeneTM software package that it is freely available upon request at http://www.engene.cnb.uam.es File: pascualATcnb.uam.es_180.html ************************************************* Wed Apr 30 07:29:55 2003 Number: 181 Name: BenKahla, Alia Affiliation: Max Planck Institute for Molecular Genetics Address: Ihnestrasse 63-73 City: Berlin State/Provice: Postal/Zip Code: 14195 Country: Germany Email: kahla@molgen.mpg.de Phone: +49-30-8413-1658 Fax: +49-30-8413-1128 Category: Data Mining Poster Title: Human and Mouse expression maps from in silico expression profiles Poster Authors and organization: Alia BenKahla¹, Ralf Herwig², Yaspo Lehrach
¹kahla@molgen.mpg.de, Max Planck Institute for Molecular Genetics; ²herwig@molgen.mpg.de, Max Planck Institute for Molecular Genetics Abstract: We present the strategy used to extract the \"in silico expression profiles\" of the human and mouse genes (EST mining approache) and the data describing differentially expressed genes, disease related genes, and cluster of genes potentially involved in a common cellular function. Orthology gene expression comparison will also be presented. File: kahlaATmolgen.mpg.de_181.html ************************************************* Wed Apr 30 09:07:19 2003 Number: 182 Name: Herrmann, Alexander Affiliation: MDC Berlin Address: Robert-Roessle-Str. 10 City: Berlin State/Provice: Postal/Zip Code: 13125 Country: Germany Email: alexander.herrmann@mdc-berlin.de Phone: ++49 30 9406 2831 Fax: ++49 30 9406 2834 Category: Databases Poster Title: EASED: A Database on Alternative Splice Forms Poster Authors and organization: Heike Pospisil¹, Alexander Herrmann², Ralf Bortfeldt, Andreas Kuntzagk
¹pospisil@mdc-berlin.de, MDC Berlin; ²alexander.herrmann@mdc-berlin.de, MDC Berlin Abstract: EASED (Extended Alternatively Spliced EST Database) represents alternative splice forms for 9 organisms. We included exon-intron information, tissue information, and a so called alternative splice profile that indicates the number of alternatively and constitutively spliced ESTs as well as the number of alternative splice sites. File: alexander.herrmannATmdc-berlin.de_182.html ************************************************* Wed Apr 30 09:16:39 2003 Number: 183 Name: Finnerty, Caroline S Affiliation: Bioinformatics and Pharmacogenomics Laboratory Address: National University of Ireland City: Maynooth State/Provice: Co. Kildare Postal/Zip Code: N/A Country: Ireland Email: caroline.s.finnerty@may.ie Phone: 00353-1-7086211 Fax: 00353-1-7083845 Category: Functional Genomics Poster Title: A Whole-genome Analysis of Transcription Factor Binding Site Data. Poster Authors and organization: Caroline Finnerty¹, Dr. James McInerney²
¹caroline.s.finnerty@may.ie, Bioinformatics and Pharmacogenomics Laboratory; ²james.o.mcinerney@may.ie, Bioinformatics and Pharmacogenomics Laboratory Abstract:
It is widely accepted that our complexity as a species results from the regulation of our genes. Our approach is to analyse, on a genome-wide scale the upstream regions of human genes with particular emphasis on transcription factor binding sites. The ultimate goal is to infer expression pattern from sequence.
File: caroline.s.finnertyATmay.ie_183.html ************************************************* Wed Apr 30 09:43:58 2003 Number: 184 Name: Theron, Daniel F Affiliation: University of Pretoria Address: Room 6-25 Agriculture Building, Lunnon Road City: Pretoria State/Provice: Gauteng Postal/Zip Code: 0002 Country: South Africa Email: danie.theron@fabi.up.ac.za Phone: +27 12 420 4239 Fax: +27 12 362 5327 Category: Microarrays Poster Title: Implementation of BASE for microarray data analysis at ACGT Microarray facility, Pretoria, South Africa Poster Authors and organization: Daniel F. Theron¹, David K. Berger², Sanushka Naidoo, Fourie Joubert
¹danie.theron@fabi.up.ac.za, University of Pretoria; ²dberger@postino.up.ac.za, University of Pretoria Abstract:
This concise guide demonstrates the implementation of BASE as a microarray data analysis pipeline. BioArray Software Environment is an open-source platform for archiving, analysis and visualizing of microarray data. Data for this demonstration compares gene expression between a wild-type and mutant Arabidopsis plants that identified 86 differentially expressed genes.
File: danie.theronATfabi.up.ac.za_184.html ************************************************* Wed Apr 30 10:00:26 2003 Number: 185 Name: Pawlowski, Krzysztof Affiliation: AstraZeneca Address: AstraZeneca RD Lund City: Lund State/Provice: Postal/Zip Code: 221 87 Country: Sweden Email: Krzysztof.Pawlowski@astrazeneca.com Phone: 46 46 33 71 64 Fax: 46 46 33 80 19 I plan to use my laptop computer as part of my poster Category: Functional Genomics Poster Title: In the search of genomic clusters of human co-expressed genes using microarray gene expression data. Poster Authors and organization: Johannes Olson¹, Per Broberg², Krzysztof Pawlowski
¹Johannes.EXT.Olson@astrazeneca.com, AstraZeneca; ²Per.Broberg@astrazeneca.com, AstraZeneca Abstract: Adjacent human gene co-expression was investigated using GeneLogic library. We analyzed average and maximum expression profile correlation for gene pairs within sliding genomic windows for normal or diseased tissue samples. Significance estimates used randomized gene sets. Co-expressed clusters were analyzed for gene duplication, subcellular localization, functional themes, inter-species conservation. File: Krzysztof.PawlowskiATastrazeneca.com_185.html ************************************************* Wed Apr 30 15:38:58 2003 Number: 186 Name: Gardy, Jennifer L. Affiliation: Department of Molecular Biology and Biochemistry, Simon Fraser University Address: 8888 University Drive City: Burnaby State/Provice: British Columbia Postal/Zip Code: V5A 1S6 Country: Canada Email: jlgardy@sfu.ca Phone: 1-604-291-5414 Fax: 1-604-291-5583 Category: Predictive Methods Poster Title: Identifying Bacterial Outer Membrane Proteins using Frequent Subsequences - A Data Mining Approach Poster Authors and organization: Rong She¹, Fei Chen², Ke Wang, Martin Ester, Jennifer L. Gardy, Fiona S.L. Brinkman
¹rshe@cs.sfu.ca, School of Computing Science, Simon Fraser University; ²fchena@cs.sfu.ca, School of Computing Science, Simon Fraser University Abstract: Outer membrane proteins (OMPs) of bacteria are medically important as drug targets. We developed two OMP predictors based on frequent subsequences studied in data mining. Both significantly outperformed the state-of-the-art method and one also produced explicit patterns of OMPs that can be used for further biological analysis. File: jlgardyATsfu.ca_186.html ************************************************* Wed Apr 30 16:51:28 2003 Number: 187 Name: Gondro, Cedric Affiliation: University of New England Address: Animal Science - UNE City: Armidale State/Provice: NSW Postal/Zip Code: 2351 Country: Australia Email: genetics@sigex.com.br Phone: 61 2 6773 5135 Fax: 61 2 6773 3922 Category: Systems Biology Poster Title: Models and Simulations in Systems Biology Poster Authors and organization: Joao Carlos Marques Magalhaes¹, Cedric Gondro²
¹jcmm@bio.ufpr.br, Federal University of Parana; ²cgondro@pobox.une.edu.au, University of New England Abstract: Computational models that simulate complex adaptive systems offer an alternative where analytical handling is untenable. A relatively small set of objects and simple rules, computationally implemented via techniques as genetic algorithms or genetic programming can replicate such complexity. An example of this approach is available for download from http://www.sigex.com.br/genetics. File: geneticsATsigex.com.br_187.html ************************************************* Wed Apr 30 18:00:53 2003 Number: 188 Name: Tian, Tianhai Affiliation: Advanced Computational Modelling Center Address: University of Queensland City: Brisbane State/Provice: Queensland Postal/Zip Code: 4072 Country: Australia Email: tian@maths.uq.edu.au Phone: +61-7-33656137 Fax: +61-7-33651477 Category: Systems Biology Poster Title: Stochastic Neural Network Models for Gene Regulatory Networks Poster Authors and organization: Tianhai Tian¹, Kevin Burrage²
¹tian@maths.uq.edu.au, ACMC, University of Queensland; ²kb@maths.uq.edu.au, ACMC University of Queensland Abstract: Stochastic models are presented by introducing stochastic processes into neural network models for studying the genome dynamics. Poisson random variables are used to represent chance events in the processes of synthesis and degradation. Using an example network, we show how to study robustness and stability properties of gene expression patterns. File: tianATmaths.uq.edu.au_188.html ************************************************* Wed Apr 30 18:05:48 2003 Number: 189 Name: Hou, Jingtong Affiliation: UC Berkeley Address: 1059 Monroe St. Apt7D City: Albany State/Provice: CA Postal/Zip Code: 94706 Country: USA Email: JTHOU@LBL.GOV Phone: 15104864338 Fax: 15104866059 Category: Structural Biology Poster Title: Into protein universe - a global representation of the protein fold space Poster Authors and organization: Jingtong Hou¹, Gregory E. Sims², Chao Zhang, Sung-Hou Kim
¹JTHou@lbl.gov, UC Berkeley; ²gsims1997@yahoo.com, UC Berkeley Abstract: A global view of the �protein structure universe� was constructed. Such a representation reveals a high-level organization of the fold space that is intuitively interpretable, offering an interesting perspective on both the demography and the evolution of protein structures. The protein fold space is available at http://pro.lbl.gov/~jingtong/foldspace. File: JTHOUATLBL.GOV_189.html ************************************************* Wed Apr 30 18:07:08 2003 Number: 190 Name: Jung, Ho-Youl Affiliation: National Genome Research Institute Address: 5 Nokbun-dong, Eunpyeng-gu City: Seoul State/Provice: Postal/Zip Code: 122-701 Country: Republic of Korea Email: hyjung@ngri.re.kr Phone: +82-2-354-1068 Fax: +82-2-354-1063 Category: Predictive Methods Poster Title: A New Hybrid Haplotype Inference Method based-on Maximum Likelihood Estimation Poster Authors and organization: Ho-Youl Jung¹, Gil-Mi Ryu², Jee-Yeon Heo, Ju-Young Lee, Hyo-Mi Kim, Jong-Keuk Lee, Chan Park, Bermseok Oh, and Kuchan Kimm
¹hyjung@ngri.re.kr, National Genome Research Institute; ²gmryu@ngri.re.kr, National Genome Research Institute Abstract: This article presents a hybrid method that can identify the individual\'s haplotype from the given genotypes. Our method combines statistical and computational approaches in order to increase the accuracy. The individuals\' haplotypes are resolved by considering the MLE (maximum likelihood estimation) in the process of computing the frequencies of the common haplotypes. File: hyjungATngri.re.kr_190.html ************************************************* Wed Apr 30 18:07:45 2003 Number: 191 Name: Jung, Ho-Youl Affiliation: National Genome Research Institute Address: 5 Nokbun-dong, Eunpyeng-gu City: Seoul State/Provice: Seoul Postal/Zip Code: 122-701 Country: Republic of Korea Email: hyjung@ngri.re.kr Phone: +82-2-354-1068 Fax: +82-2-354-1063 Category: Predictive Methods Poster Title: A New Hybrid Haplotype Inference Method based-on Maximum Likelihood Estimation Poster Authors and organization: Ho-Youl Jung¹, Gil-Mi Ryu², Jee-Yeon Heo, Ju-Young Lee, Hyo-Mi Kim, Jong-Keuk Lee, Chan Park, Bermseok Oh, and Kuchan Kimm
¹hyjung@ngri.re.kr, National Genome Research Institute; ²gmryu@ngri.re.kr, National Genome Research Institute Abstract: This article presents a hybrid method that can identify the individual\'s haplotype from the given genotypes. Our method combines statistical and computational approaches in order to increase the accuracy. The individuals\' haplotypes are resolved by considering the MLE (maximum likelihood estimation) in the process of computing the frequencies of the common haplotypes. File: hyjungATngri.re.kr_191.html ************************************************* Wed Apr 30 18:08:05 2003 Number: 192 Name: Jung, Ho-Youl Affiliation: National Genome Research Institute Address: 5 Nokbun-dong, Eunpyeng-gu City: Seoul State/Provice: Seoul Postal/Zip Code: 122-701 Country: Republic of Korea Email: hyjung@ngri.re.kr Phone: +82-2-354-1068 Fax: +82-2-354-1063 Category: Predictive Methods Poster Title: A New Hybrid Haplotype Inference Method based-on Maximum Likelihood Estimation Poster Authors and organization: Ho-Youl Jung¹, Gil-Mi Ryu², Jee-Yeon Heo, Ju-Young Lee, Hyo-Mi Kim, Jong-Keuk Lee, Chan Park, Bermseok Oh, and Kuchan Kimm
¹hyjung@ngri.re.kr, National Genome Research Institute; ²gmryu@ngri.re.kr, National Genome Research Institute Abstract: This article presents a hybrid method that can identify the individual\'s haplotype from the given genotypes. Our method combines statistical and computational approaches in order to increase the accuracy. The individuals\' haplotypes are resolved by considering the MLE (maximum likelihood estimation) in the process of computing the frequencies of the common haplotypes. File: hyjungATngri.re.kr_192.html ************************************************* Wed Apr 30 18:08:17 2003 Number: 193 Name: Jung, Ho-Youl Affiliation: National Genome Research Institute Address: 5 Nokbun-dong, Eunpyeng-gu City: Seoul State/Provice: Seoul Postal/Zip Code: 122-701 Country: Republic of Korea Email: hyjung@ngri.re.kr Phone: +82-2-354-1068 Fax: +82-2-354-1063 Category: Predictive Methods Poster Title: A New Hybrid Haplotype Inference Method based-on Maximum Likelihood Estimation Poster Authors and organization: Ho-Youl Jung¹, Gil-Mi Ryu², Jee-Yeon Heo, Ju-Young Lee, Hyo-Mi Kim, Jong-Keuk Lee, Chan Park, Bermseok Oh, and Kuchan Kimm
¹hyjung@ngri.re.kr, National Genome Research Institute; ²gmryu@ngri.re.kr, National Genome Research Institute Abstract: This article presents a hybrid method that can identify the individual\'s haplotype from the given genotypes. Our method combines statistical and computational approaches in order to increase the accuracy. The individuals\' haplotypes are resolved by considering the MLE (maximum likelihood estimation) in the process of computing the frequencies of the common haplotypes. File: hyjungATngri.re.kr_193.html ************************************************* Wed Apr 30 18:08:30 2003 Number: 194 Name: Jung, Ho-Youl Affiliation: National Genome Research Institute Address: 5 Nokbun-dong, Eunpyeng-gu City: Seoul State/Provice: Seoul Postal/Zip Code: 122-701 Country: Republic of Korea Email: hyjung@ngri.re.kr Phone: +82-2-354-1068 Fax: +82-2-354-1063 Category: Predictive Methods Poster Title: A New Hybrid Haplotype Inference Method based-on Maximum Likelihood Estimation Poster Authors and organization: Ho-Youl Jung¹, Gil-Mi Ryu², Jee-Yeon Heo, Ju-Young Lee, Hyo-Mi Kim, Jong-Keuk Lee, Chan Park, Bermseok Oh, and Kuchan Kimm
¹hyjung@ngri.re.kr, National Genome Research Institute; ²gmryu@ngri.re.kr, National Genome Research Institute Abstract: This article presents a hybrid method that can identify the individual\'s haplotype from the given genotypes. Our method combines statistical and computational approaches in order to increase the accuracy. The individuals\' haplotypes are resolved by considering the MLE (maximum likelihood estimation) in the process of computing the frequencies of the common haplotypes. File: hyjungATngri.re.kr_194.html ************************************************* Wed Apr 30 18:26:03 2003 Number: 195 Name: Jung, Ho-Youl Affiliation: National Genome Research Institute Address: 5 Nokbun-dong, Eunpyeng-gu City: Seoul State/Provice: Seoul Postal/Zip Code: 122-701 Country: South Korea Email: hyjung@ngri.re.kr Phone: +82-2-354-1068 Fax: +82-2-354-1063 Category: Predictive Methods Poster Title: A New Hybrid Haplotype Inference Method based-on Maximum Likelihood Estimation Poster Authors and organization: Ho-Youl Jung¹, Gil-Mi Ryu², Jee-Yeon Heo, Ju-Young Lee, Hyo-Mi Kim, Jong-Keuk Lee, Chan Park, Bermseok Oh, and Kuchan Kimm
¹hyjung@ngri.re.kr, National Genome Research Institute; ²gmryu@ngri.re.kr, National Genome Research Institute Abstract: This article presents a hybrid method that can identify the individual\'s haplotype from the given genotypes. Our method combines statistical and computational approaches in order to increase the accuracy. The individuals\' haplotypes are resolved by considering the MLE (maximum likelihood estimation) in the process of computing the frequencies of the common haplotypes. File: hyjungATngri.re.kr_195.html ************************************************* Wed Apr 30 18:26:39 2003 Number: 196 Name: Jung, Ho-Youl Affiliation: National Genome Research Institute Address: 5 Nokbun-dong, Eunpyeng-gu City: Seoul State/Provice: Seoul Postal/Zip Code: 122-701 Country: South Korea Email: hyjung@ngri.re.kr Phone: +82-2-354-1068 Fax: +82-2-354-1063 Category: Predictive Methods Poster Title: A New Hybrid Haplotype Inference Method based-on Maximum Likelihood Estimation Poster Authors and organization: Ho-Youl Jung¹, Gil-Mi Ryu², Jee-Yeon Heo, Ju-Young Lee, Hyo-Mi Kim, Jong-Keuk Lee, Chan Park, Bermseok Oh, and Kuchan Kimm
¹hyjung@ngri.re.kr, National Genome Research Institute; ²gmryu@ngri.re.kr, National Genome Research Institute Abstract: This article presents a hybrid method that can identify the individual\'s haplotype from the given genotypes. Our method combines statistical and computational approaches in order to increase the accuracy. The individuals\' haplotypes are resolved by considering the MLE in the process of computing the frequencies of the common haplotypes. File: hyjungATngri.re.kr_196.html ************************************************* Wed Apr 30 18:27:04 2003 Number: 197 Name: Jung, Ho-Youl Affiliation: National Genome Research Institute Address: 5 Nokbun-dong, Eunpyeng-gu City: Seoul State/Provice: Seoul Postal/Zip Code: 122-701 Country: South Korea Email: hyjung@ngri.re.kr Phone: +82-2-354-1068 Fax: +82-2-354-1063 Category: Predictive Methods Poster Title: A New Hybrid Haplotype Inference Method based-on Maximum Likelihood Estimation Poster Authors and organization: Ho-Youl Jung¹, Gil-Mi Ryu², Jee-Yeon Heo, Ju-Young Lee, Hyo-Mi Kim, Jong-Keuk Lee, Chan Park, Bermseok Oh, and Kuchan Kimm
¹hyjung@ngri.re.kr, National Genome Research Institute; ²gmryu@ngri.re.kr, National Genome Research Institute Abstract: This article presents a hybrid method that can identify the individual\'s haplotype from the given genotypes. Our method combines statistical and computational approaches in order to increase the accuracy. The individuals\' haplotypes are resolved by considering the MLE in the process of computing the frequencies of the common haplotypes. File: hyjungATngri.re.kr_197.html ************************************************* Wed Apr 30 18:31:48 2003 Number: 198 Name: Jung, Ho-Youl Affiliation: National Genome Research Institute Address: 5 Nokbun-dong, Eunpyeng-gu City: Seoul State/Provice: Seoul Postal/Zip Code: 122-701 Country: South Korea Email: hyjung@ngri.re.kr Phone: +82-2-354-1068 Fax: +82-2-354-1063 Category: Predictive Methods Poster Title: A New Hybrid Haplotype Inference Method based-on Maximum Likelihood Estimation Poster Authors and organization: Ho-Youl Jung¹, Gil-Mi Ryu², Jee-Yeon Heo, Ju-Young Lee, Hyo-Mi Kim, Jong-Keuk Lee, Chan Park, Bermseok Oh, and Kuchan Kimm
¹hyjung@ngri.re.kr, National Genome Research Institute; ²gmryu@ngri.re.kr, National Genome Research Institute Abstract: This article presents a hybrid method that can identify the individual\'s haplotype from the given genotypes. Our method combines statistical and computational approaches in order to increase the accuracy. The individuals\' haplotypes are resolved by considering the MLE in the process of computing the frequencies of the common haplotypes. File: hyjungATngri.re.kr_198.html ************************************************* Wed Apr 30 18:32:40 2003 Number: 199 Name: Jung, Ho-Youl Affiliation: National Genome Research Institute Address: 5 Nokbun-dong, Eunpyeng-gu City: Seoul State/Provice: Seoul Postal/Zip Code: 122-701 Country: South Korea Email: hyjung@ngri.re.kr Phone: +82-2-354-1068 Fax: +82-2-354-1063 Category: Predictive Methods Poster Title: A New Hybrid Haplotype Inference Method based-on Maximum Likelihood Estimation Poster Authors and organization: Ho-Youl Jung¹, Gil-Mi Ryu², Jee-Yeon Heo, Ju-Young Lee, Hyo-Mi Kim, Jong-Keuk Lee, Chan Park, Bermseok Oh, and Kuchan Kimm
¹hyjung@ngri.re.kr, National Genome Research Institute; ²gmryu@ngri.re.kr, National Genome Research Institute Abstract: This article presents a hybrid method that can identify the individual\'s haplotype from the given genotypes. Our method combines statistical and computational approaches in order to increase the accuracy. The individuals\' haplotypes are resolved by considering the MLE in the process of computing the frequencies of the common haplotypes. File: hyjungATngri.re.kr_199.html ************************************************* Wed Apr 30 18:34:02 2003 Number: 200 Name: Jung, Ho-Youl Affiliation: National Genome Research Institute Address: 5 Nokbun-dong, Eunpyeng-gu City: Seoul State/Provice: Seoul Postal/Zip Code: 122-701 Country: South Korea Email: hyjung@ngri.re.kr Phone: +82-2-354-1068 Fax: +82-2-354-1063 Category: Predictive Methods Poster Title: A New Hybrid Haplotype Inference Method based-on Maximum Likelihood Estimation Poster Authors and organization: Ho-Youl Jung¹, Gil-Mi Ryu², Jee-Yeon Heo, Ju-Young Lee, Hyo-Mi Kim, Jong-Keuk Lee, Chan Park, Bermseok Oh, and Kuchan Kimm
¹hyjung@ngri.re.kr, National Genome Research Institute; ²gmryu@ngri.re.kr, National Genome Research Institute Abstract: This article presents a hybrid method that can identify the individual\'s haplotype from the given genotypes. Our method combines statistical and computational approaches in order to increase the accuracy. The individuals\' haplotypes are resolved by considering the MLE in the process of computing the frequencies of the common haplotypes. File: hyjungATngri.re.kr_200.html ************************************************* Wed Apr 30 18:34:28 2003 Number: 201 Name: Jung, Ho-Youl Affiliation: National Genome Research Institute Address: 5 Nokbun-dong, Eunpyeng-gu City: Seoul State/Provice: Seoul Postal/Zip Code: 122-701 Country: South Korea Email: hyjung@ngri.re.kr Phone: +82-2-354-1068 Fax: +82-2-354-1063 Category: Phylogeny and Evolution Poster Title: A New Hybrid Haplotype Inference Method based-on Maximum Likelihood Estimation Poster Authors and organization: Ho-Youl Jung¹, Gil-Mi Ryu², Jee-Yeon Heo, Ju-Young Lee, Hyo-Mi Kim, Jong-Keuk Lee, Chan Park, Bermseok Oh, and Kuchan Kimm
¹hyjung@ngri.re.kr, National Genome Research Institute; ²gmryu@ngri.re.kr, National Genome Research Institute Abstract: This article presents a hybrid method that can identify the individual\'s haplotype from the given genotypes. Our method combines statistical and computational approaches in order to increase the accuracy. The individuals\' haplotypes are resolved by considering the MLE in the process of computing the frequencies of the common haplotypes. File: hyjungATngri.re.kr_201.html ************************************************* Wed Apr 30 18:37:26 2003 Number: 202 Name: Jung, Ho-Youl Affiliation: National Genome Research Institute Address: 5 Nokbun-dong, Eunpyeng-gu City: Seoul State/Provice: Seoul Postal/Zip Code: 122-701 Country: South Korea Email: hyjung@ngri.re.kr Phone: +82-2-354-1068 Fax: +82-2-354-1063 Category: Predictive Methods Poster Title: A New Hybrid Haplotype Inference Method based-on Maximum Likelihood Estimation Poster Authors and organization: Ho-Youl Jung¹, Gil-Mi Ryu², Jee-Yeon Heo, Ju-Young Lee, Hyo-Mi Kim, Jong-Keuk Lee, Chan Park, Bermseok Oh, and Kuchan Kimm
¹hyjung@ngri.re.kr, National Genome Research Institute; ²gmryu@ngri.re.kr, National Genome Research Institute Abstract: This article presents a hybrid method that can identify the individual\'s haplotype from the given genotypes. Our method combines statistical and computational approaches in order to increase the accuracy. The individuals\' haplotypes are resolved by considering the MLE in the process of computing the frequencies of the common haplotypes. File: hyjungATngri.re.kr_202.html ************************************************* Wed Apr 30 18:45:52 2003 Number: 203 Name: Martins dos Santos, Vitor A Affiliation: National Centre for Biotechnology Research Address: Division Microbiology City: Braunschweig State/Provice: Postal/Zip Code: 38124 Country: Germany Email: vds@gbf.de Phone: 49 531 6181 422 Fax: Category: Systems Biology Poster Title: Metabolic comparison of the in-silico phenotype-genotype relationship of Pseudomonas putida and Pseudomonas aeruginosa Poster Authors and organization: Vitor A.P. Martins dos Santos ¹, Miguel Godinho de Almeida ²
¹vds@gbf.de, National Centre for Biotechnology Research; ², University of Delaware Abstract: We report on an in-silico representation of Pseudomonas putida and Pseudomonas aeruginosa that describes their metabolic capacities within the scope of their environmental constraints. Using annotated genome sequence data, biochemical information and strain-specific knowledge, we analysed the cellular behaviour of this micro-organism under a wide range of conditions relevant for both human health. File: vdsATgbf.de_203.html ************************************************* Wed Apr 30 18:48:31 2003 UPDATE ----- Number: 203 Name: Martins dos Santos, Vitor A Affiliation: National Centre for Biotechnology Research Address: Division Microbiology City: Braunschweig State/Provice: Postal/Zip Code: 38124 Country: Germany Email: vds@gbf.de Phone: 49 531 6181 422 Fax: Category: Systems Biology Poster Title: Metabolic comparison of the in-silico phenotype-genotype relationship of Pseudomonas putida and Pseudomonas aeruginosa Poster Authors and organization: Vitor A.P. Martins dos Santos ¹, Miguel Godinho de Almeida ², Jeremy S. Edwards2, Kenneth N. Timmis1
¹vds@gbf.de, National Centre for Biotechnology Research; ², University of Delaware Jeremy S. Edwards2, Kenneth N. Timmis1 Abstract: We report on an in-silico representation of Pseudomonas putida and Pseudomonas aeruginosa that describes their metabolic capacities within the scope of their environmental constraints. Using annotated genome sequence data, biochemical information and strain-specific knowledge, we analysed the cellular behaviour of this micro-organism under a wide range of conditions relevant for both human health. File: vdsATgbf.de_203 ************************************************* Wed Apr 30 19:08:35 2003 Number: 204 Name: Zmasek, Christian M. Affiliation: Genomics Institute of the Novartis Research Foundation Address: 10675 John Jay Hopkins Drive City: San Diego State/Provice: CA Postal/Zip Code: 92121 Country: USA Email: czmasek@gnf.org Phone: 858 812 1983 Fax: 858 812 1502 Category: Databases Poster Title: Assembly as part of a DNA sequence management system Poster Authors and organization: Zmasek, C. M.¹, Lapp, H.², Ching, K.; Wiltshire, T.; Fletcher, C.; Orth, A.
¹czmasek@gnf.org, Genomics Institute of the Novartis Research Foundation; ²hlapp@gnf.org, Genomics Institute of the Novartis Research Foundation Abstract: We describe a tool to manage assembly processes. Two main advantages of this system are: [i] Based on \"assembly projects\" which contain all the relevant data of an assembly. This allows for re-assembly at a later point with (e.g.) additional input sequences. [ii] All user interaction is through a GUI. File: czmasekATgnf.org_204.html ************************************************* Wed Apr 30 19:21:29 2003 Number: 205 Name: Lin, Chung-Yen Affiliation: National Health Research Institutes Address: 128 Yen-Chiu-Yuan Road, Sec.2 City: Taipei State/Provice: Postal/Zip Code: 115 Country: Taiwan Email: cylin@nhri.org.tw Phone: 886-2-26534401-7511 Fax: 886-2-27890253 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: Yeast Protein Interactomes: The Novel Platform and Value-Added Database Poster Authors and organization: Chung-Yen Lin¹, Chi-Shang Cho², Chen-Zen Lo, Chao A. Hsiung
¹cylin@nhri.org.tw, National Health Research Institutes; ²vecstar@nhri.org.tw, National Health Research Institutes Abstract: Based on the composing of php, Mysql, Linux, we construct the S. cerevisiae (15,000 entries) and putative C. elegans protein interactions database. This database can help to annotate novel proteins by the interacting partners; also can provide proper candidates to narrow down the scale of further high-throughput screening experiments. File: cylinATnhri.org.tw_205.html ************************************************* Wed Apr 30 20:51:38 2003 Number: 206 Name: Goode, Matthew G Affiliation: University of Auckland Address: Private Bag 92019 City: AUCKLAND State/Provice: Postal/Zip Code: Country: New Zealand Email: m.goode@auckland.ac.nz Phone: +6493737599ext83777 Fax: Category: Phylogeny and Evolution Poster Title: Modelling change in codon substituion, using serially sampled sequence data. Poster Authors and organization: Matthew Goode¹, Allen Rodrigo²
¹m.goode@auckland.ac.nz, University of Auckland; ²a.rodrigo@auckland.ac.nz, University of Auckland Abstract: We describe a method for modeling changes in codon substitution in populations where evolution can be measured, e.g. rapidly evolving viral populations. Our model extends Neilsen and Yang\'s codon model to allow parameters associated with selection and proportion of selected sites to vary over time. File: m.goodeATauckland.ac.nz_206.html ************************************************* Wed Apr 30 21:57:55 2003 Number: 207 Name: Yoon, Jeong H Affiliation: IDRTech. Inc Address: 461-6, Jeonmin Dong, Yusung Gu City: Daejeong State/Provice: Postal/Zip Code: 305-390 Country: Korea Email: yoon@idrtech.com Phone: 82-42-861-6551 Fax: 82-42-861-6558 Category: Structural Biology Poster Title: IDPharmo: A Virtual High Throughput Screening System Based on Stuctural Bio and Cheminformaics. Poster Authors and organization: Jeong Hyeok Yoon¹, Jee Young Lee ², Won Seok Oh, Doo Ho Cho, Jae Min Shin
¹yoon@idrtech.com, IDRTech. Inc; ²jyoung@idrtech.com, IDRTech. Inc Abstract: IDPharmoTM is the integrated programs that can discover the potential lead compounds using protein structures and 3D chemicals database in silico. This tool was evaluated for discovery of potential lead compound of various disease targets such as HIV-RT, PDE5, HCV pol and DPP IV. We could get new chemical entities whose biological activities are from IC50 50uM to 1uM File: yoonATidrtech.com_207.html ************************************************* Wed Apr 30 22:07:14 2003 Number: 208 Name: Motono, Chie Affiliation: Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology Address: 2-43 Aomi City: Koto-ku State/Provice: Tokyo Postal/Zip Code: 135-0064 Country: Japan Email: c-motono@aist.go.jp Phone: +81-3-3599-8067 Fax: +81-3-3599-8081 Category: Structural Biology Poster Title: Differences in dynamics of dimeric and monomeric human prion protein revealed by molecular dynamics simulations Poster Authors and organization: Chie Motono¹, Masakazu Sekijima², Satoshi Yamasaki,Kiyotoshi Kaneko,and Yutaka Akiyama
¹c-motono@aist.go.jp, Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology; ²sekijima@cbrc.jp, Computational Biology Research Center , National Institute of Advanced Industrial Science and Technology Abstract: We performed molecular dynamics simulations on monomeric and dimeric forms of human prion protein at various conditions (at 300K, 500K, acidic pH, or with a mutation D178N) for 10 ns to investigate the differences in the dynamics of each form. Most differences resulted from additional inter-subunit interactions of dimeric HuPrP. File: c-motonoATaist.go.jp_208.html ************************************************* Wed Apr 30 22:34:10 2003 Number: 209 Name: Kotani, Shuji Affiliation: RIKEN Genomic Sciences Center Address: Suehirocho 1-7-22, Tsurumiku City: Yokohama State/Provice: Kanagawa Postal/Zip Code: 230-0045 Country: JAPAN Email: shuji.kotani@nifty.ne.jp Phone: 81-45-503-9111 Fax: 81-45-503-9158 Category: Systems Biology Poster Title: Functional Analysis of Mammalian Cell Cycle using A Computational Model of Hybrid Petri Net. Poster Authors and organization: Shuji Kotani¹, Takashi Yoshioka², Kaoru Takahashi, Akihiko Konagaya
¹shuji.kotani@nifty.ne.jp, RIKEN Genomic Sciences Center ; ²yoshiokatks@nttdata.co.jp, NTT Data Corp Abstract: To describe the molecular mechanism of the mammalian cell cycle, we developed a new computational model by using Hybrid Petri Nets. Using the model, we presume how the change of gene product influences the cell cycle progression. This model maybe useful for exploring the relationship between gene functions and diseases. File: shuji.kotaniATnifty.ne.jp_209.html ************************************************* Wed Apr 30 23:01:22 2003 Number: 210 Name: McGrath, Annette Affiliation: Australian Genome Research Facility Address: Level 5 Gehrmann Laboratories, University of Queensland, City: St Lucia State/Provice: QLD Postal/Zip Code: 4072 Country: Australia Email: annette@agrf.org.au Phone: + 61 7 33469201 Fax: + 61 7 33651823 Category: Genome Annotation Poster Title: ASSEMBLY AND ANNOTATION OF THE Leptospira borgpetersenii SEROVAR Hardjobovis GENOME SEQUENCE Poster Authors and organization: Annette McGrath¹, John Davis², Peter J Wilson, Dieter Bulach, Torsten Seemann, John Davies, Ross Coppel, Ben Adler, Elizabeth S Kuczek
¹annette@agrf.org.au, Australian Genome Research Facility; ²john@agrf.org.au, Australian Genome Research Facility Abstract: We have completed the assembly of the Leptospira borgpetersenii serovar hardjobovis genome, which contains a large chromosome (CI) of 3,614,529 base pairs and a smaller chromosome (CII) of 317,585 base pairs. The annotation of CII is complete and is currently in progress for CI. File: annetteATagrf.org.au_210.html ************************************************* Wed Apr 30 23:17:13 2003 Number: 211 Name: McWilliam, Sean M Affiliation: CSIRO Livestock Industries Address: 306 Carmody Road St Lucia City: Brisbane State/Provice: QLD Postal/Zip Code: 4067 Country: Australia Email: sean.mcwilliam@csiro.au Phone: 07 3214 2504 Fax: 07 3214 2480 Category: Genome Annotation Poster Title: Towards the Bovine Ensembl Poster Authors and organization: Sean M. McWilliam¹, Wes Barris², Brian P. Dalrymple
¹sean.mcwilliam@csiro.au, CSIRO Livestock Industries, Brisbane, Australia; ²wes.barris@csiro.ai, CSIRO Livestock Industries, Brisbane, Australia Abstract: We have implemented the Ensembl genome sequence database and interface for handling the annotation of the bovine genome. Initial efforts have focussed on display of the annotation of small and micro RNAs and linking to the SNP database, IBISS. File: sean.mcwilliamATcsiro.au_211.html ************************************************* Thu May 1 00:55:28 2003 Number: 212 Name: Imoto, Seiya Affiliation: Institute of Medical Science, University of Tokyo Address: 4-6-1 Shirokanetai, Minato-ku City: Tokyo State/Provice: Postal/Zip Code: 108-8639 Country: Japan Email: imoto@ims.u-tokyo.ac.jp Phone: +81-3-5449-5615 Fax: +81-3-5449-5442 Category: Microarrays Poster Title: Estimating Gene Networks by Bayesian Networks from Microarrays and Biological Knowledge Poster Authors and organization: Seiya Imoto¹, Tomoyuki Higuchi², Takao Goto, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano
¹imoto@ims.u-tokyo.ac.jp, University of Tokyo; ²higuchi@ism.ac.jp, The Institute of Statistical Mathematics Abstract: We propose a statistical method for estimating a gene network based on Bayesian networks from microarray data together with biological knowledge including protein-protein interactions, protein-DNA interactions, binding site information, existing literature and so on. Our method can optimize the balance between microarray and biological knowledge automatically. File: imotoATims.u-tokyo.ac.jp_212.html ************************************************* Thu May 1 01:12:47 2003 Number: 213 Name: SAGARA, Jun-Ichi Affiliation: CBRC Address: Aomi F Build. 17F, 2-43 Aomi, City: Koto-ku, State/Provice: Tokyo, Postal/Zip Code: 135-0064 Country: JAPAN Email: jun@ni.aist.go.jp Phone: +81-3-3599-8066 Fax: +81-3-3599-8081 I plan to use my laptop computer as part of my poster Category: Predictive Methods Poster Title: Prediction of snoRNAs in Human Genome Poster Authors and organization: SAGARA Jun-Ichi¹, ASAI Kiyoshi², Nakamura Shugo, KENMOCHI Naoya
¹jun@ni.aist.go.jp, CBRC; ², CBRC Abstract: we predict snoRNAs in human genome using several methods for sequence analysis. We also develop a Predicted Human Intron database produced from exons predicted by Gene Decoder which is a gene finding technology based on HMMs. We show the results of prediction of snoRNAs and the databases of human intron in ismb2003 poster session. File: junATni.aist.go.jp_213.html ************************************************* Thu May 1 01:36:05 2003 Number: 214 Name: Harte, Nicola A Affiliation: EMBL-EBI Address: Wellcome Trust genome Campus, Hinxton City: Cambridge State/Provice: Cambrigeshire Postal/Zip Code: CB10 1SD Country: United Kingdom Email: nharte@ebi.ac.uk Phone: 0044-1223-494442 Fax: 0044-1223-494468 Category: Databases Poster Title: Free public services from the European Bioinformatics Institute, the European Molecular Biology Laboratory outstation. Poster Authors and organization: Nicola Harte¹, Rodrigo Lopez², Karyn Duggan, Rob Harper, Asif Kibria, Adam Lowe, Gulam Patel, Sharmila Pillai, Emmanuel Quevillon, Stephen Robinson, Ville Silventoinen
¹nharte@ebi.ac.uk, EMBL-EBI; ²rls@ebi.ac.uk, EMBL-EBI Abstract: The EBI provides free, publicly available bioinformatics services for the scientific community. These can be divided up into the following categories: data submissions processing, biological database production, access to query, analysis and retrieval systems, ftp downloads, training and education and user support. These services are available at: http://www.ebi.ac.uk/services. File: nharteATebi.ac.uk_214.html ************************************************* Thu May 1 02:17:19 2003 Number: 215 Name: Chang, Yu-Jung Affiliation: Institute of Information Science, Academia Sinica Address: 128 Sec.2,Yen-Chiu-Yuan Rd.,Nangkang District City: Taipei State/Provice: Taiwan Postal/Zip Code: 115 Country: Taiwan, R.O.C. Email: yjchang@iis.sinica.edu.tw Phone: 886-2-2788-3799 ext. 1619 Fax: 886-2-2782-4814 I plan to use my laptop computer as part of my poster Category: Sequence Comparison Poster Title: Human and Mouse Genome Comparison Using Genome-Wide Unique Sequences Poster Authors and organization: Ben-Yang Liao¹, Yu-Jung Chang², Jan-Ming Ho and Ming-Jing Hwang
¹liaoby@gate.sinica.edu.tw, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan; ²yjchang@iis.sinica.edu.tw, Institute of Information Science, Academia Sinica, Taipei, Taiwan Abstract: We used coexistent genome-wide unique sequences in human and mouse genomes to recognize their homologous regions. The resulting syntenic map revealed more than 400 conserved segments and covering more than 90% of both genomes. This alignment-free method is capable of comparing two mammalian genomes within hours on one personal computer. File: yjchangATiis.sinica.edu.tw_215.html ************************************************* Thu May 1 02:18:37 2003 Number: 216 Name: Chang, Yu-Jung Affiliation: Institute of Information Science, Academia Sinica Address: 128 Sec.2,Yen-Chiu-Yuan Rd.,Nangkang District City: Taipei State/Provice: Taiwan Postal/Zip Code: 115 Country: Taiwan, R.O.C. Email: yjchang@iis.sinica.edu.tw Phone: 886-2-2788-3799 ext. 1619 Fax: 886-2-2782-4814 I plan to use my laptop computer as part of my poster Category: Sequence Comparison Poster Title: Human and Mouse Genome Comparison Using Genome-Wide Unique Sequences Poster Authors and organization: Ben-Yang Liao¹, Yu-Jung Chang², Jan-Ming Ho and Ming-Jing Hwang
¹liaoby@gate.sinica.edu.tw, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan; ²yjchang@iis.sinica.edu.tw, Institute of Information Science, Academia Sinica, Taipei, Taiwan Abstract: We used coexistent genome-wide unique sequences in human and mouse genomes to recognize their homologous regions. The resulting syntenic map revealed more than 400 conserved segments and covering more than 90% of both genomes. This alignment-free method is capable of comparing two mammalian genomes within hours on one personal computer. File: yjchangATiis.sinica.edu.tw_216.html ************************************************* Thu May 1 02:35:59 2003 Number: 217 Name: Shida, Kazuhito Affiliation: Center for Interdisciplinary Research, Tohoku University Address: Aramaki, Aoba-ku City: Sendai State/Provice: Miyaghi Postal/Zip Code: 980-8578 Country: JAPAN Email: shida@cir.tohoku.ac.jp Phone: +81-22-217-5764 Fax: +81-22-217-7810 Category: Sequence Comparison Poster Title: Long-range correlation in protein sequences and its implication Poster Authors and organization: Kazuhito Shida¹, Makoto Ikeda², Atsuo Kasuya
¹shida@cir.tohoku.ac.jp, CIR Tohoku University; ²ikeda@imr.edu, CIR Tohoku University Abstract: Long-range correlations in the amino-acid sequences of natural proteins are extracted from GanBank sequences. Some of bigrams with more than one letter of gaps turned out to be clearly over-represented. This data may improve the assessment of alignment quality, phylogeny analyses, and perhaps database searches. File: shidaATcir.tohoku.ac.jp_217.html ************************************************* Thu May 1 03:27:33 2003 Number: 218 Name: Kawashima, Shuichi Affiliation: Bioinformatics Center, Institute for Chemical Research, Kyoto University Address: Gokasho City: Uji State/Provice: Kyoto Postal/Zip Code: 611-0011 Country: Japan Email: shuichi@kuicr.kyoto-u.ac.jp Phone: +81-774-38-3273 Fax: +81-774-38-3269 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: KEGG API: A new web service for accessing the KEGG database Poster Authors and organization: Shuichi Kawashima¹, Toshiaki Katayama², Yoko Sato, Minoru Kanehisa
¹shuichi@kuicr.kyoto-u.ac.jp, Bioinformatics Center, Institute for Chemical Research, Kyoto University; ²k@bioruby.org, Bioinformatics Center, Institute for Chemical Research, Kyoto University Abstract:
KEGG API is a new web service for accessing the KEGG database. Using the APIs in the local program, the user can retrieve various information about genes, pathways, chemical compounds etc. stored in the latest versions of the KEGG database. KEGG API is available at http://www.genome.ad.jp/kegg/soap/.
File: shuichiATkuicr.kyoto-u.ac.jp_218.html ************************************************* Thu May 1 03:55:01 2003 Number: 219 Name: Samsonova, Maria GG Affiliation: St.Petersburg State Polytechnical University Address: 29 Polytechnicheskaya ul. City: St.Petersburg State/Provice: Postal/Zip Code: 195251 Country: Russia Email: samson@spbcas.ru Phone: 7-812-556-2230 Fax: 7-812-555-2762 Category: Databases Poster Title: A technology for integration of databases with common subject domains Poster Authors and organization: Maria Samsonova¹, Andrei Pisarev², Maxim Blagov
¹samson@spbcas.ru, SPbSPU; ²pisarev@spbcas.ru, SPbSPU Abstract: We present a novel approach to the integration of distributed molecular biology information resources, which consists in a design of adaptive natural language interface and application of multiagent technology. Our approach permits to integrate any databases, which have a common subject domain. The implemented prototype is available at http://urchin.spbcas.ru/NLP/NLP.htm. File: samsonATspbcas.ru_219.html ************************************************* Thu May 1 04:51:09 2003 Number: 220 Name: Kurata, Hiroyuki Affiliation: Kyushu Institute of Technology Address: 680-4 Kawazu City: Iizuka State/Provice: Fukuoka Postal/Zip Code: 820-8502 Country: Japan Email: kurata@bse.kyutech.ac.jp Phone: 81-948-29-7828 Fax: 81-948-29-7828 I plan to use my laptop computer as part of my poster Category: Systems Biology Poster Title: CADLIVE for constructing a yeast cell cycle network Poster Authors and organization: Hiroyuki Kurata¹
¹kurata@bse.kyutech.ac.jp, Kyushu Institute of Technology Abstract: CADLIVE is a powerful software suit with GUI for constructing a large-scale map of complicated biochemical reaction networks. We constructed a biochemical map of the budding yeast cell cycle, which consists of 184 molecules and 152 reactions, and integrated postgenomic data into the map to predict novel pathways. File: kurataATbse.kyutech.ac.jp_220.html ************************************************* Thu May 1 05:16:43 2003 Number: 221 Name: Kim, Ki-Bong Affiliation: SmallSoft Co., Ltd. Address: Daeduk BioCommunity, Jonmin-Dong 461-6, Yusung-Gu City: Daejeon State/Provice: Postal/Zip Code: 305-811 Country: South Korea Email: kbkim@bioinfo.smallsoft.co.kr Phone: +82-42-864-2524 Fax: +82-42-866-9241 Category: Predictive Methods Poster Title: PIVS: Protein-protein interaction inference and visualization system using sequence-based homology search with DIP and BIND Poster Authors and organization: Ki-Bong Kim¹, Mi-Kyung Lee²
¹kbkim@bioinfo.smallsoft.co.kr, SmallSoft Co., Ltd.; ²mklee@bioinfo.smallsoft.co.kr, SmallSoft Co., Ltd. Abstract: We developed the system, PIVS, which is very useful for predicting the function and interaction of unknown protein sequence as well as for visualizing its protein-protein interaction map. In addition, it offers integral genomic and motif/domain-related information concerning unknown input protein sequence. File: kbkimATbioinfo.smallsoft.co.kr_221.html ************************************************* Thu May 1 05:24:41 2003 Number: 222 Name: Garcia, Alex Affiliation: Institute for Molecular Bioscience Address: Research Rd. City: Brisbane State/Provice: QLD Postal/Zip Code: 4072 Country: Australia Email: a.garcia@imb.uq.edu.au Phone: 61733462606 Fax: 6173365 4388 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: JPIPE, A pipeline module for JEMBOSS Poster Authors and organization: Alex Garcia¹, Leyla J. Garcia², Mark A. Ragan, Institute for Molecular Bioscience
¹a.Garcia@imb.uq.edu.au, Institute for Molecular Bioscience; ²leyla.garcia@unisabana.edu.co, U. de la Sabana Abstract: We present a module (JPIPE) that allows EMBOSS users to build analysis pipelines under the JEMBOSS GUI. JPIPE is a flexible workflow system that complements JEMBOSS. A tracking system is a part of JPIPE so the user is able to recreate pipelines, compare results at a particular point of the workflow and administer ongoing jobs. File: a.garciaATimb.uq.edu.au_222.html ************************************************* Thu May 1 05:31:44 2003 Number: 223 Name: Bergheim, Anton S Affiliation: University of the Witwatersrand Address: 1 Jan Smuts Avenue City: Johannesburg State/Provice: Gauteng Postal/Zip Code: 2000 Country: South Africa Email: anton@cs.wits.ac.za Phone: +27 11 717 6178 Fax: +27 11 717 6199 Category: Data Mining Poster Title: An architecture for a modularized gene information retrieval and summarization tool: Bioretrieve Poster Authors and organization: Anton Bergheim¹, Sheila Rock²
¹anton@cs.wits.ac.za, University of the Witwatersrand; ²sheila@cs.wits.ac.za, University of the Witwatersrand Abstract: The ability to process natural language based information computationally is becoming a necessity for the geneticist. We present here an architecture for Bioretrieve, a computational tool for the management of the extremely large body of knowledge that exists about genes. Designed in a modular fashion and employing an open-source approach, it has advantages over existing monolithic systems. File: antonATcs.wits.ac.za_223.html ************************************************* Thu May 1 05:35:56 2003 Number: 224 Name: Park, Ji-Yoon Affiliation: Dept. of Biochemistry and Moleluar Biology, Hanyang University Address: 1271 Sa-Dong City: Ansan State/Provice: Kyunggi-do Postal/Zip Code: 425-791 Country: Korea Email: scolaswhite@hotmail.com Phone: 82-31-400-5513 Fax: 82-31-406-6316 Category: New Frontiers Poster Title: A DNA-based Theorem Proving by Resolution Refutation Poster Authors and organization: Ji-Yoon Park¹, In-Hee Lee², Young-Gyu Chai, Byoung-Tak Zhang
¹scolaswhite@hotmail.com, Dept. of Biochemistry and Moleluar Biology, Hanyang University; ²ihlee@bi.snu.ac.kr, Biointelligence Laboratory School of Computer Science and Engineering, Seoul National University Abstract: Theorem proving is a method involving logical reasoning and has a variety of applications, including diagnosis and decision-making. Resolution refutation is a general technique of proving the validity of a theorem given a set of axioms and rules. To prove theorem proving, DNA molecular reaction is implemented by resolution refutation. File: scolaswhiteAThotmail.com_224.html ************************************************* Thu May 1 05:43:11 2003 Number: 225 Name: Garcia, Alex Affiliation: Institute for Molecular Bioscience Address: Research Rd. City: Brisbane State/Provice: QLD Postal/Zip Code: 4072 Country: Australia Email: a.garcia@imb.uq.edu.au Phone: 61733462606 Fax: 6173365 4388 I plan to use my laptop computer as part of my poster Category: Data Mining Poster Title: SEMA, A semantic literature annotator Poster Authors and organization: Alex Garcia¹, Cleary John², Mark A. Ragan, Institute for Molecular Bioscience
¹a.Garcia@imb.uq.edu.au, Institute for Molecular Bioscience; ²jcleary@reeltwo.com, Reel Two Abstract: We are using a machine-learning algorithm implemented in GO-KDS to complement SwissProt literature citation fields for each database entry. SEMA organizes this new relevant information, then builds a conceptual navigable map that is presented to the user as a flat or hyperbolic tree. This map allows redefining queries over the same database or over other information sources. File: a.garciaATimb.uq.edu.au_225.html ************************************************* Thu May 1 06:05:10 2003 Number: 226 Name: Pascual-Montano, Alberto D. Affiliation: National Center of Biotechnology Address: Campus Universidad Autonoma de Madrid. Cantoblanco City: Madrid State/Provice: Madrid Postal/Zip Code: 28049 Country: Spain Email: pascual@cnb.uam.es Phone: +34-915854543 Fax: +34-915854506 Category: Data Mining Poster Title: Non-negative matrix factorization for gene expression and scientific texts analysis Poster Authors and organization: A. D. Pascual-Montano¹, P. Carmona-Saez², M. Chagoyen and J.M. Carazo
¹pascual@cnb.uam.es, National Center of Biotechnology. Madrid. Spain; ²pcarmona@cnb.uam.es, National Center of Biotechnology. Madrid. Spain Abstract: We describe the application of Non-negative Matrix Factorization (NMF) technique to reduce dimensionality and to find local patterns hidden in gene expression data sets and in the scientific literature. Results show the potential of this new machine learning technique to find relevant biological information. Contact: pascual@cnb.uam.es File: pascualATcnb.uam.es_226.html ************************************************* Thu May 1 06:08:24 2003 Number: 227 Name: Pascual-Montano, Alberto D. Affiliation: National Center of Biotechnology Address: Campus Universidad Autonoma de Madrid. Cantoblanco City: Madrid State/Provice: Madrid Postal/Zip Code: 28049 Country: Spain Email: pascual@cnb.uam.es Phone: +34-915854543 Fax: +34-915854506 Category: Data Mining Poster Title: Non-negative matrix factorization for gene expression and scientific texts analysis Poster Authors and organization: A. D. Pascual-Montano¹, P. Carmona-Saez², M. Chagoyen and J.M. Carazo
¹pascual@cnb.uam.es, National Center of Biotechnology. Madrid. Spain; ²pcarmona@cnb.uam.es, National Center of Biotechnology. Madrid. Spain Abstract: We describe the application of Non-negative Matrix Factorization (NMF) technique to reduce dimensionality and to find local patterns hidden in gene expression data sets and in the scientific literature. Results show the potential of this new machine learning technique to find relevant biological information. Contact: pascual@cnb.uam.es File: pascualATcnb.uam.es_227.html ************************************************* Thu May 1 07:04:10 2003 Number: 228 Name: Gioiosa, Gianpaolo Affiliation: University of South Australia Address: Unit 4, 130 Lestrange Street, GLENUNGA City: Adelaide State/Provice: South Australia Postal/Zip Code: 5064 Country: Australia Email: GIOGY001@students.unisa.edu.au Phone: 83791660 Fax: I plan to use my laptop computer as part of my poster Category: Sequence Comparison Poster Title: Implementing the Smith-Waterman Algorithm on a Reconfigurable Computer Poster Authors and organization: Gianpaolo Gioiosa¹, David Kearney²
¹GIOGY001@students.unisa.edu.au, University of South Australia; ²David.Kearney@unisa.edu.au, University of South Australia Abstract: The Smith-Waterman algorithm is a dynamic-programming algorithm that finds the optimal alignment between two biological sequences. The algorithm was implemented on a field programmable gate array (FPGA) in order to investigate the advantages and disadvantages of using reconfigurable computers and associated tools for computationally intensive sequence analysis applications. File: GIOGY001ATstudents.unisa.edu.au_228.html ************************************************* Thu May 1 07:25:05 2003 Number: 229 Name: Muju, Sumeet Affiliation: NIH-NINDS Address: 36 Convent Drive MSC 4123 City: Bethesda State/Provice: MD Postal/Zip Code: 20892 Country: USA Email: mujus@ninds.nih.gov Phone: 301-402-1790 Fax: 301-496-9946 Category: Databases Poster Title: An integrative searchable database for Bioinformatics tools, algorithms and software: pBIRD Poster Authors and organization: Sumeet Muju¹, Catherine Campbell², KaiIng Chow Yang Fann
¹mujus@ninds.nih.gov, NIH-NINDS; ²campbelc@ninds.nih.gov, NIH-NINDS Abstract: pBIRD is a fully-searchable web based system designed to identify, catalog and describe a broad range of available bioinformatics software. The system is designed to upload, store, track and retrieve information associated with and about bioinformatics software products deposited in the database from both internal and external sources. File: mujusATninds.nih.gov_229.html ************************************************* Thu May 1 07:31:20 2003 Number: 230 Name: Campbell, Catherine E Affiliation: NIH-NINDS Address: 36 Convent Drive MSC 4123 City: Bethesda State/Provice: MD Postal/Zip Code: 20892 Country: USA Email: campbelc@ninds.nih.gov Phone: 301-402-1956 Fax: 301-496-9946 I plan to use my laptop computer as part of my poster Category: Data Visualisation Poster Title: Comparing Patterns in Gene Expression in Longitudinal Array Experiments Using a Novel Algorithm, TAPiR: Time-course Algorithm for Pattern Recognition Poster Authors and organization: Catherine Campbell¹, Raj Lingam², Yang Fann
¹campbelc@ninds.nih.gov, NIH-NINDS; ²lingamr@ninds.nih.gov, NIH-NINDS Abstract: TAPiR is a novel algorithm for identifying, clustering and visualizing time-course microarray experiments based on either fold change or t-test p-value thresholds. TAPiR assigns letters to specific patterns of change that can be oriented along the time-course to form �words� that can then be sorted alphabetically to identify similar clusters. File: campbelcATninds.nih.gov_230.html ************************************************* Thu May 1 07:31:36 2003 Number: 231 Name: Kim, Pan-Gyu Affiliation: Dept. of Computer Science, Pusan National Univ. Address: san 30, Jang-jeon Dong, Gum-jeong Gu City: Pusan State/Provice: Postal/Zip Code: 609735 Country: KOREA Email: pgkim@pearl.cs.pusan.ac.kr Phone: +82-51-510-2871 Fax: +82-51-515-2208 Category: Data Mining Poster Title: GENAW: GEnetic Network Analysis Workbench for microarray raw data Poster Authors and organization: Pan-Gyu Kim¹, Kyung Shin Lee², Seon- Hee Park, Mi Young Shin, Hwan-Gue Cho
¹pgkim@pearl.cs.pusan.ac.kr, Department of computer science, Pusan national university; ²kslee@pearl.cs.pusan.ac.kr, Department of computer engineering, Pusan national university Abstract: We develop GENAW (GEnetic Network Analysis Workbench for microarray raw data) system that produces automatically the network from raw expression data. GENAW accepts various data formats of commercial tools and provides various visualization tools. We experimented with Yeast cell cycle data from Stanford university, our experiment was sufficiently reasonable. File: pgkimATpearl.cs.pusan.ac.kr_231.html ************************************************* Thu May 1 07:31:55 2003 Number: 232 Name: Kim, Pan-Gyu Affiliation: Dept. of Computer Science, Pusan National Univ. Address: san 30, Jang-jeon Dong, Gum-jeong Gu City: Pusan State/Provice: Postal/Zip Code: 609735 Country: KOREA Email: pgkim@pearl.cs.pusan.ac.kr Phone: +82-51-510-2871 Fax: +82-51-515-2208 Category: Data Mining Poster Title: GENAW: GEnetic Network Analysis Workbench for microarray raw data Poster Authors and organization: Pan-Gyu Kim¹, Kyung Shin Lee², Seon- Hee Park, Mi Young Shin, Hwan-Gue Cho
¹pgkim@pearl.cs.pusan.ac.kr, Department of computer science, Pusan national university; ²kslee@pearl.cs.pusan.ac.kr, Department of computer engineering, Pusan national university Abstract: We develop GENAW (GEnetic Network Analysis Workbench for microarray raw data) system that produces automatically the network from raw expression data. GENAW accepts various data formats of commercial tools and provides various visualization tools. We experimented with Yeast cell cycle data from Stanford university, our experiment was sufficiently reasonable. File: pgkimATpearl.cs.pusan.ac.kr_232.html ************************************************* Thu May 1 07:36:51 2003 Number: 233 Name: van Enckevort, Frank H.J. Affiliation: NIZO food research Address: Kernhemseweg 2 City: Ede State/Provice: Gelderland Postal/Zip Code: 6718ZB Country: The Netherlands Email: Frank.van.Enckevort@nizo.nl Phone: +31318659511 Fax: +31318650400 Category: Functional Genomics Poster Title: LacplantCyc: a Pathway / Genome Database for Lactobacillus plantarum as the model PGDB for Lactic Acid Bacteria. Poster Authors and organization: Frank H.J. van Enckevort¹, Bas Teusink², Roland J. Siezen
¹Frank.van.Enckevort@nizo.nl, Centre for Molecular and Biomolecular Informatics, University of Nijmegen, The Netherlands; ²Bas.Teusink@nizo.nl, NIZO food research, Ede, The Netherlands Abstract: Lactobacillus plantarum is a versatile lactic acid bacterium that is encountered in various niches. LacplantCyc is a newly created pathway/genome database predicted from the annotated complete genome sequence of L. plantarum WCFS1 (PNAS 2003;100:1990), using the PathoLogic software from PathwayTools (Peter Karp). Manual editing and experimental verification is in progress. File: Frank.van.EnckevortATnizo.nl_233.html ************************************************* Thu May 1 08:01:59 2003 Number: 234 Name: OSullivan , Orla J Affiliation: University College Cork Address: Western Road City: Cork State/Provice: Postal/Zip Code: Country: Ireland Email: ojos@student.ucc.ie Phone: +353-21-4901307 Fax: Category: Sequence Comparison Poster Title: Multiple alignments of sequences and structures using T-Coffee Poster Authors and organization: Orla OSullivan ¹
¹ojos@student.ucc.ie, Univesity College Cork Abstract: T-Coffee is a novel method for multiple sequence alignment that allows you to combine heterogeneous sources of data to produce very accurate alignments. In this poster we look at the effects of mixing sequence and structural information using two structural alignment programs, SAP and FUGUE, in combination with T-Coffee. File: ojosATstudent.ucc.ie_234.html ************************************************* Thu May 1 09:29:42 2003 Number: 235 Name: Schwacke, John H Affiliation: Medical University of South Carolina Address: 135 Cannon Street, Suite 303 City: Charleston State/Provice: South Carolina Postal/Zip Code: 29425 Country: USA Email: schwacke@musc.edu Phone: 843-876-1100 Fax: 843-876-1126 I plan to use my laptop computer as part of my poster Category: Systems Biology Poster Title: BSTLab: A Matlab Toolbox for Biochemical Systems Theory Poster Authors and organization: John Schwacke¹, Eberhard O. Voit²
¹schwacke@musc.edu, Medical University of South Carolina; ²voiteo@musc.edu, Medical University of South Carolina Abstract: To facilitate application of Biochemical Systems Theory (BST), we have begun development of BSTLab, a Matlab-based toolbox implementing functions common to BST-based studies. The toolbox automates common computations, permits expansion and customization, and includes functions needed to reformulate and transport models between Matlab and the Systems Biology Markup Language (SBML). File: schwackeATmusc.edu_235.html ************************************************* Thu May 1 09:38:28 2003 Number: 236 Name: Bowman, Christopher S Affiliation: Institute for Biodiganostics Address: 435 Ellice Avenue City: Winnipeg State/Provice: Manitoba Postal/Zip Code: R3B 1Y6 Country: Canada Email: Christopher.Bowman@nrc-cnrc.gc.ca Phone: 204 984 6573 Fax: 204 984 5472 Category: Data Visualisation Poster Title: Correlation analysis as a preprocessing tool in clustering of time-course gene expression timecourse data Poster Authors and organization: Christopher Bowman¹, Richard Baumgartner², Ray Somorjai
¹Christppher.Bowman@nrc-cnrc.gc.ca, Institute for Biodiagnostics; ²Richard.Baumgartner@nrc-cnrc.gc.ca, Institute for Biodiagnostics Abstract: We apply correlation analysis, a tool developed for analysis of functional magnetic resonance images to microarray timecourse experiments. Although fMRI and microarray timecourses share little in common physically, the data analysis tasks are quite similar, and correlation analysis is shown to be a useful preprocessing tool to apply prior to clustering gene expression timecourses. File: Christopher.BowmanATnrc-cnrc.gc.ca_236.html ************************************************* Thu May 1 09:44:39 2003 Number: 237 Name: Bowman, Christopher S Affiliation: Institute for Biodiganostics Address: 435 Ellice Avenue City: Winnipeg State/Provice: Manitoba Postal/Zip Code: R3B 1Y6 Country: Canada Email: Christopher.Bowman@nrc-cnrc.gc.ca Phone: 204 984 6573 Fax: 204 984 5472 Category: Predictive Methods Poster Title: Correlated Feature Extraction for Classification of Microarray and Mass Spectroscopy Data Poster Authors and organization: Christopher Bowman¹, Richard Baumgartner², Stephanie Booth
¹Christppher.Bowman@nrc-cnrc.gc.ca, Institute for Biodiagnostics; ²Richard.Baumgartner@nrc-cnrc.gc.ca, Institute for Biodiagnostics Abstract: We present a novel correlation based technique for unsupervised feature extraction in large datasets. The algorithm selects features based on their redundancy and unlike PCA, preserves the spatial information in the data, allowing one to easily interpret the extracted features. We demonstrate that classification accuracy on the reduced feature data is comparable to that on the original data. File: Christopher.BowmanATnrc-cnrc.gc.ca_237.html ************************************************* Thu May 1 09:56:39 2003 Number: 238 Name: Lee, Dong-Yup Affiliation: KAIST Address: 373-1 Guseong-dong, Yuseong-gu City: Daejeon State/Provice: Daejeon Postal/Zip Code: 305-701 Country: Korea Email: dylee@pse.kaist.ac.kr Phone: 82-42-869-3960 Fax: 82-42-862-5961 Category: Systems Biology Poster Title: Comparative Metabolic Flux Analysis by MetaFluxNet Poster Authors and organization: Dong-Yup Lee¹, Hongsoek Yun², Sang-Yup Lee and Sunwon Park
¹dylee@pse.kaist.ac.kr, KAIST; ²hsyun@pse.kaist.ac.kr, KAIST Abstract: MetaFluxNet is a program package for managing information on the metabolic reaction network and for quantitatively analyzing metabolic fluxes in an interactive and customized way. Using the feature of the comparative metabolic flux analysis supported in MetaFluxNet, one can design and evaluate various metabolically engineered in silico strains interactively. MetaFluxNet is available at http://mbel.kaist.ac.kr. File: dyleeATpse.kaist.ac.kr_238.html ************************************************* Thu May 1 10:19:07 2003 Number: 239 Name: Grant, Gregory R Affiliation: University of Pennsylvania Address: 1429 Blockley Hall, 423 Guardian Drive City: Philadelphia State/Provice: PA Postal/Zip Code: 19104-6021 Country: USA Email: ggrant@pcbi.upenn.edu Phone: 215-573-3117 Fax: 215-573-3111 Category: Microarrays Poster Title: A new FDR algorithm for differential expression analysis of microarray data Poster Authors and organization: Gregory Grant¹, Elisabetta Manduchi², Christian Stoeckert
¹ggrant@pcbi.upenn.edu, CBIL; ²manduchi@pcbi.upenn.edu, CBIL Abstract: PaGE is an algorithm we have developed at CBIL which uses statistical methods to assign discrete patterns to gene expression data. This poster will highlight the new implementation (version 5.0) with improved novel FDR alrogithm based on the Westfall and Young minP stepdown distributions, and new interface. File: ggrantATpcbi.upenn.edu_239.html ************************************************* Thu May 1 10:19:51 2003 Number: 240 Name: Liao, Li Affiliation: University of Delaware Address: 103 Smith Hall City: Newark State/Provice: Delaware Postal/Zip Code: 19716 Country: USA Email: lliao@cis.udel.edu Phone: 302-831-3500 Fax: 302-831-4091 Category: Sequence Comparison Poster Title: Correlation between antisense activity and RNA secondary structure Poster Authors and organization: Li Liao¹, Zhongwei Li²
¹lliao@cis.udel.edu, University of Delaware; ²zli@fau.edu, Florida Atlantic University Abstract: Correlation between activity of antisense oligonucleotides and local structural features of target RNAs is studied. Statistical analysis showed that high activity of antisense oligonucleotides is more likely to occur in regions of target RNA having hairpin or multi-branched loops with flanking stems. File: lliaoATcis.udel.edu_240.html ************************************************* Thu May 1 10:43:04 2003 Number: 241 Name: TAN, AIK CHOON Affiliation: BIOINFORMATICS RESEARCH CENTRE, DEPARTMENT OF COMPUTING SCIENCE, UNIVERSITY OF GLASGOW Address: 17 LILYBANK GARDENS City: GLASGOW State/Provice: SCOTLAND Postal/Zip Code: G12 8QQ Country: UNITED KINGDOM Email: actan@brc.dcs.gla.ac.uk Phone: 00 44 141 330 2421 Fax: 00 44 141 330 3690 Category: Data Mining Poster Title: Multi-class protein fold classification using an integrative machine learning approach Poster Authors and organization: Aik Choon TAN¹, David GILBERT²
¹actan@brc.dcs.gla.ac.uk, Bioinformatics Research Centre, Department of Computing Science, University of Glasgow; ²drg@brc.dcs.gla.ac.uk, Bioinformatics Research Centre, Department of Computing Science, University of Glasgow Abstract: We devised a novel approach to integrate rules induced from multi-class and unbalanced data sets; and to demonstrate its usefulness to multi-class protein fold classification which contains 700 examples for 27 SCOP folds. We showed that this approach increases the sensitivity of the classifiers and yielding more useful classifiers. File: actanATbrc.dcs.gla.ac.uk_241.html ************************************************* Thu May 1 11:15:01 2003 Number: 242 Name: Dahlquist, Kam D Affiliation: Department of Biology, Vassar College Address: 124 Raymond Avenue City: Poughkeepsie State/Provice: NY Postal/Zip Code: 12604 Country: USA Email: kadahlquist@vassar.edu Phone: 1-845-437-7000 Fax: 1-845-437-7315 I plan to use my laptop computer as part of my poster Category: Microarrays Poster Title: GenMAPP and MAPPFinder 2.0: Tools for Viewing and Analyzing Genomic and Proteomic Data Using Gene Ontology and Biological Pathways Poster Authors and organization: Kam D. Dahlquist¹, Scott W. Doniger², Nathan Salomonis, Karen Vranizan, Steven C. Lawlor, and Bruce R. Conklin
¹kadahlquist@vassar.edu, Department of Biology, Vassar College; ²sdoniger@gladstone.ucsf.edu, Gladstone Institute of Cardiovascular Disease Abstract: GenMAPP is designed for viewing expression data on biological pathways. GenMAPP automatically color-codes the genes according to criteria supplied by the user. MAPPFinder matches expression data to the Gene Ontology and indicates whether there is a significant over-representation of genes meeting the user�s criterion for each GO term. http://www.GenMAPP.org. File: kadahlquistATvassar.edu_242.html ************************************************* Thu May 1 12:24:18 2003 Number: 243 Name: Leslin, Chesley M Affiliation: NEU Address: 360 Huntington Ave City: Boston State/Provice: MA Postal/Zip Code: 02115 Country: United States Email: chesley.leslin@verizon.net Phone: 617-437-1646 Fax: 617-373-3724 I plan to use my laptop computer as part of my poster Category: Structural Biology Poster Title: Database of Three-Dimensional Exon Structures, SEDB Poster Authors and organization: Chesley Leslin¹, Valentin Ilyin², Alex Abyzov, Grigory Makarevich
¹chesley.leslin@verizon.net, Theoretical Molecular Biology and Bioinformatics Lab, Northeastern University, Boston, Massachusetts; ²valentin.ilyin@verizon.net, Theoretical Molecular Biology and Bioinformatics Lab, Northeastern University, Boston, Massachusetts Abstract: Expeditious mapping of exon borders and intron phase data onto structurally similar proteins presents a novel approach to studying protein structure evolution. We present SEDB, which allows researchers to examine and quickly identify where exon/intron boundaries are located and how these borders have possibly shaped current protein structure. http://glinka.bio.neu.edu/~cleslin/SEDB/SEDB.html File: chesley.leslinATverizon.net_243.html ************************************************* Thu May 1 13:35:58 2003 Number: 244 Name: Perumal, Narayanan Affiliation: School of Informatics, Indiana University Purdue University Indianapolis Address: 306 Walker Plaza, 719 Indiana Avenue City: Indianapolis State/Provice: Indiana Postal/Zip Code: 46202 Country: USA Email: nperumal@iupui.edu Phone: 317-278-4147 Fax: 317-278-7669 I plan to use my laptop computer as part of my poster Category: Phylogeny and Evolution Poster Title: Evolution of Toll genes from the perspective of transcriptional regulatory regions Poster Authors and organization: Rajakumar Sankula¹, Narayanan Perumal², Lang Li
¹rsankula@iupui.edu, School of Informatics, Indiana University Purdue University Indianapolis ; ²nperumal@iupui.edu, School of Informatics, Indiana University Purdue University Indianapolis Abstract: Phylogenetic analysis of Toll gene evolution across insects, plants, and mammals using their transcriptional regulatory regions has been performed. This analysis is based on a unique approach employing the frequency of �evolutionarily� informative transcription factor binding sites. Interestingly, the resultant phylogeny produced results similar to that of protein-based phylogeny. File: nperumalATiupui.edu_244.html ************************************************* Thu May 1 13:58:36 2003 Number: 245 Name: Taylor, Ronald C Affiliation: University of Colorado, Center for Computational Pharmacology Address: 4200 E. Ninth Ave, SOM room 2633 City: Denver State/Provice: CO Postal/Zip Code: 80262 Country: USA Email: ronald.taylor@uchsc.edu Phone: 303-315-1091 Fax: 303-315-1089 Category: Functional Genomics Poster Title: Reconstruction of Genetic Networks from Gene Expression Perturbation Data Using a Boolean Model Poster Authors and organization: Ronald Taylor¹
¹ronald.taylor@uchsc.edu, U of Colorado Abstract: The use of Boolean models is explored in reconstruction of the topology of genetic transcriptional networks, employing gene expression data from simulated perturbations. The construction and employment of a software suite for such exploration is described. Results are compared for different simulated topologies, inference methods, and amount of noise. File: ronald.taylorATuchsc.edu_245.html ************************************************* Thu May 1 14:25:56 2003 Number: 246 Name: Ma, Changqing Affiliation: Center for Pathology Informatics, University of Pittsburgh Address: Center for Pathology Informatics, UPMC Cancer Pavilion, Third Floor, 5230 Center Avenue City: Pittsburgh State/Provice: PA Postal/Zip Code: 15232 Country: USA Email: chmst40@pitt.edu Phone: 412-623-5951 Fax: 412-647-9588 Category: Microarrays Poster Title: Decision-tree approach to the classification of prostate tissue samples using microarray gene expression data Poster Authors and organization: Changqing Ma¹, John Gilbertson², Dhir, Jianhua Luo, George Michalopoulos, Michael Becich
¹chmst40@pitt.edu, University of Pittsburgh; ²GilbertsonJR@MSX.UPMC.EDU, University of Pittsburgh Abstract: A decision-tree learning approach was applied to classify three types of prostate tumor tissue samples using microarray gene-expression data. In LOOCV, results were comparable to those obtained from applying SVMs or weighted voting method to this dataset. Furthermore, human-understandable models from decision-tree learning correctly predicted sample classes in previously published prostate tumor datasets. File: chmst40ATpitt.edu_246.html ************************************************* Thu May 1 15:12:01 2003 Number: 247 Name: Liongosari, Edy S Affiliation: Accenture Technology Labs Address: 161 N. Clark Street City: Chicago State/Provice: Illinois Postal/Zip Code: 60601 Country: United States of America Email: edy.s.liongosari@accenture.com Phone: +1-312-693-6744 Fax: +1-312-652-6744 I plan to use my laptop computer as part of my poster Category: Data Visualisation Poster Title: Uncovering Hidden Linkages among Disparate Information Sources Poster Authors and organization: Edy S. Liongosari¹, Mitu Singh²
¹edy.s.liongosari@accenture.com, Accenture Technology Labs; ²mitu.singh@accenture.com, Accenture Technology Labs Abstract: The Knowledge Discovery Tool or KDT is a tool that utilizes a knowledge modeling approach to intelligently extract and integrate a large set of disconnected bio-medical information. Its unique user interface allows it users to see how the entities are linked together, uncovers hidden linkages and highlights certain unusual links that might be worth exploring. File: edy.s.liongosariATaccenture.com_247.html ************************************************* Thu May 1 15:14:35 2003 Number: 248 Name: Tillier, Elisabeth R Affiliation: Ontario Cancer Institute and University of Toronto Address: 620 University Ave, Suite 703 City: Toronto State/Provice: Ontario Postal/Zip Code: M5G 2M9 Country: Canada Email: e.tillier@utoronto.ca Phone: 416 946 4501 x 3978 Fax: Category: Phylogeny and Evolution Poster Title: An empirical model of substitutions in RNA of sequence and structure Poster Authors and organization: Andrew D. Smith¹, Elisabeth R. M. Tillier ², Thomas H . Lui
¹asmith@uhnres.utoronto.ca, University Health Network; ²e.tillier@utoronto.ca, Ontario Cancer Institute and Dept Medical Biophysics, University of Toronto Abstract: An empirical model of substitution for evolution of RNA sequence and structure is derived using a method we have previously developed for proteins. Sequences are recoded into a 20 letter code before analysis. Models derived for SSU and LSU rRNA give accurate phylogenies in computer simulations and actual rRNA alignments. File: e.tillierATutoronto.ca_248.html ************************************************* Thu May 1 15:18:58 2003 Number: 249 Name: Tillier, Elisabeth R Affiliation: Ontario Cancer Institute and University of Toronto Address: 620 University Ave, Suite 703 City: Toronto State/Provice: Ontario Postal/Zip Code: M5G 2M9 Country: Canada Email: e.tillier@utoronto.ca Phone: 416 946 4501 x 3978 Fax: Category: Phylogeny and Evolution Poster Title: Confirming orthologue identification with gene order information Poster Authors and organization: Ingrid Burgetz¹, Elisabeth R. M. Tillier ²
¹iburgetz@uhnres.utoronto.ca, University Health Network; ²e.tillier@utoronto.ca, Ontario Cancer Institute and Dept Medical Biophysics, University of Toronto Abstract: In closely related bacterial genomes, conservation of gene position and gene order can be used to confirm the identification or detect the mis-identification of orthologous genes. We investigated the specificity and sensitivity of orthologous pair identification using different E-value cutoffs in BLAST and FASTA. File: e.tillierATutoronto.ca_249.html ************************************************* Thu May 1 15:24:31 2003 Number: 250 Name: Lancaster, Alex K Affiliation: Dept. of Integrative Biology, UC Berkeley Address: 3060 Valley Life Sciences Building City: Berkeley State/Provice: CA Postal/Zip Code: 94720-3140 Country: USA Email: alexl@socrates.berkeley.edu Phone: 510 642-1233 Fax: 510 643-5144 I plan to use my laptop computer as part of my poster Category: Phylogeny and Evolution Poster Title: PyPop: A framework for large-scale population genomics analysis Poster Authors and organization: Alex Lancaster¹, Mark P. Nelson², Richard M. Single; Diogo Meyer; Glenys Thomson
¹alexl@socrates.berkeley.edu, UC Berkeley; ², UC Berkeley Abstract: PyPop (Python for Population Genetics) is a suite of programs for the analysis of multi-locus population genetic data, outputs are stored in XML and can be transformed into other data formats. PyPop will be made freely available under the GNU GPL at: http://allele5.biol.berkeley.edu/pypop/ File: alexlATsocrates.berkeley.edu_250.html ************************************************* Thu May 1 15:41:49 2003 Number: 251 Name: Black, Michael Affiliation: Centre for Human Genetics Address: Edith Cowan University City: Perth State/Provice: Western Australia Postal/Zip Code: 6027 Country: Australia Email: m.black@ecu.edu.au Phone: 61 8 0422948162 Fax: Category: Phylogeny and Evolution Poster Title: Bayesian Population Genetics and the Human History of China Poster Authors and organization: Michael Black ¹, Wei Wang ², Cheryl Wise and Alan Bittles
¹m.black@ecu.edu.au, Centre for Human Genetics, Edith Cowan University, Perth, Western Australia; ², Department of Research and Development, Medical Centre, Peking University � Hong Kong University of Sciences and Technology, Shenzhen, P.R. China Abstract: The history of China is a record of migration, population admixture and community endogamy. While comparing current Bayesian and \"Classical\" methodologies, these factors were prevalent in the genetic structure of eight Chinese ethnic populations. It�s concluded that Bayesian models comprising multiple-system data and historical factors are required for future studies. File: m.blackATecu.edu.au_251.html ************************************************* Thu May 1 15:48:55 2003 Number: 252 Name: Dalrymple, Brian P Affiliation: CSIRO Livestock Industries Address: Queensland Bioscience Precinct, 306 Carmody Road City: St Lucia State/Provice: QLD Postal/Zip Code: 4067 Country: Australia Email: Brian.Dalrymple@csiro.au Phone: 07 3214 2503 Fax: Category: Genome Annotation Poster Title: Annotation of non-coding RNA molecules in cattle genomic sequences Poster Authors and organization: Brian Dalrymple¹, Sean McWilliam², Wes Barris, Pradeep Tokachichu
¹Brian.Dalrymple@csiro.au, CSIRO Livestock Industries; ²Sean.McWilliam@csiro.au, CSIRO Livestock Industries Abstract: To identify members of known families of RNAs a combination of BLAST and INFERNAL is used with the RNA covariance models in Rfam. To identify potential new RNAs a combination of genome specific BLAST and QRNA is used. The results of analysis of bovine BAC-end sequences will be shown. File: Brian.DalrympleATcsiro.au_252.html ************************************************* Thu May 1 16:02:32 2003 Number: 253 Name: Nielsen, Poul F Affiliation: University of Auckland Address: Bioengineering Institute, Private Bag 92019 City: Auckland State/Provice: Postal/Zip Code: 1000 Country: New Zealand Email: p.nielsen@auckland.ac.nz Phone: +64 9 3737599 88391 Fax: +64 9 3677157 Category: Systems Biology Poster Title: Ontologies in CellML: A Versatile Method to Describe Cellular Models Poster Authors and organization: Poul Nielsen¹, Matt Halstead², Autumn Cuellar, Michael Dunstan, David Bullivant, Peter Hunter
¹p.nielsen@auckland.ac.nz, University of Auckland; ²matt.halstead@auckland.ac.nz, University of Auckland Abstract: CellML is an XML-based exchange language used to describe the underlying mathematics and topology of a wide variety of biological models. Knowledge implicitly associated with a model, however, is not normally included in the CellML representation. In order to address this problem facilities to include ontologies have been added to CellML. File: p.nielsenATauckland.ac.nz_253.html ************************************************* Thu May 1 16:03:53 2003 UPDATE ----- Number: 233 Name: van Enckevort, Frank H Affiliation: NIZO food research Address: Kernhemseweg 2 City: Ede State/Provice: Gelderland Postal/Zip Code: 6718ZB Country: The Netherlands Email: Frank.van.Enckevort@nizo.nl Phone: +31318659511 Fax: +31318650400 Category: Functional Genomics Poster Title: LacplantCyc: a Pathway / Genome Database for Lactobacillus plantarum as the model PGDB for Lactic Acid Bacteria. Poster Authors and organization: Frank H.J. van Enckevort¹, Bas Teusink², Roland J. Siezen
¹Frank.van.Enckevort@nizo.nl, Centre for Molecular and Biomolecular Informatics, University of Nijmegen, The Netherlands; ²Bas.Teusink@nizo.nl, NIZO food research, Ede, The Netherlands Abstract: Lactobacillus plantarum is a versatile lactic acid bacterium that is encountered in various niches. LacplantCyc is a newly created pathway/genome database predicted from the annotated complete genome sequence of L. plantarum WCFS1 (PNAS 2003;100:1990), using the PathoLogic software from PathwayTools (Peter Karp). Manual editing and experimental verification is in progress. File: Frank.van.EnckevortATnizo.nl_233 ************************************************* Thu May 1 16:09:46 2003 UPDATE ----- Number: 236 Name: Bowman, Christopher S Affiliation: Institute for Biodiganostics Address: 435 Ellice Avenue City: Winnipeg State/Provice: Manitoba Postal/Zip Code: R3B 1Y6 Country: Canada Email: Christopher.Bowman@nrc-cnrc.gc.ca Phone: 204 984 6573 Fax: 204 984 5472 Category: Data Visualisation Poster Title: Correlation analysis as a preprocessing tool in clustering of time-course gene expression timecourse data Poster Authors and organization: Christopher Bowman¹, Richard Baumgartner², Stephanie Booth
¹Christppher.Bowman@nrc-cnrc.gc.ca, Institute for Biodiagnostics; ²Richard.Baumgartner@nrc-cnrc.gc.ca, Institute for Biodiagnostics Abstract: We apply correlation analysis, a tool developed for analysis of functional magnetic resonance images to microarray timecourse experiments. Although fMRI and microarray timecourses share little in common physically, the data analysis tasks are quite similar, and correlation analysis is shown to be a useful preprocessing tool to apply prior to clustering gene expression timecourses. File: Christopher.BowmanATnrc-cnrc.gc.ca_236 ************************************************* Thu May 1 16:13:01 2003 UPDATE ----- Number: 237 Name: Bowman, Christopher S Affiliation: Institute for Biodiganostics Address: 435 Ellice Avenue City: Winnipeg State/Provice: Manitoba Postal/Zip Code: R3B 1Y6 Country: Canada Email: Christopher.Bowman@nrc-cnrc.gc.ca Phone: 204 984 6573 Fax: 204 984 5472 Category: Predictive Methods Poster Title: Correlated Feature Extraction for Classification of Microarray and Mass Spectroscopy Data Poster Authors and organization: Christopher Bowman¹, Richard Baumgartner², Ray Somorjai
¹Christppher.Bowman@nrc-cnrc.gc.ca, Institute for Biodiagnostics; ²Richard.Baumgartner@nrc-cnrc.gc.ca, Institute for Biodiagnostics Abstract: We present a novel correlation based technique for unsupervised feature extraction in large datasets. The algorithm selects features based on their redundancy and unlike PCA, preserves the spatial information in the data, allowing one to easily interpret the extracted features. We demonstrate that classification accuracy on the reduced feature data is comparable to that on the original data. File: Christopher.BowmanATnrc-cnrc.gc.ca_237 ************************************************* Thu May 1 16:18:24 2003 UPDATE ----- Number: 54 Name: Wong, Sharyl L Affiliation: Harvard Medical School Address: 1353 Beacon St. Apt. 4 City: Brookline State/Provice: MA Postal/Zip Code: 02446 Country: USA Email: sharyl_wong@student.hms.harvard.edu Phone: 617-893-0490 Fax: 617-432-3557 Category: Predictive Methods Poster Title: Predicting Synthetic Lethality Poster Authors and organization: Sharyl L. Wong¹, Lan O. Zhang², Amy H. Tong, Debra S. Goldberg, Oliver D. King, Guillaume Lesage, Marc Vidal, Brenda Andrews, Howard Bussey, Charles Boone, Frederick P. Roth
¹sharyl_wong@student.hms.harvard.edu, Harvard Medical School; ²lan_zhang@student.hms.harvard.edu, Harvard Medical School Abstract: We successfully predicted synthetic lethal genes in Saccharomyces cerevisiae by integrating multiple data types including co-localization, correlated mRNA expression, physical interaction, protein function, and sequence homology. Our predictions may help identify redundant genes and pathways. Furthermore, gene pair characteristics important in generating predictions may better our understanding of genetic robustness. File: sharyl_wongATstudent.hms.harvard.edu_54 ************************************************* Thu May 1 16:46:51 2003 Number: 254 Name: Yan, Changhui Affiliation: Iowa State University Address: 226 Atanasoff, Iowa State University City: Ames State/Provice: IA Postal/Zip Code: 50010 Country: USA Email: chhyan@iastate.edu Phone: 1-515-572-4879 Fax: 1-515-294-0258 Category: Predictive Methods Poster Title: Approaches for Predicting Protein-Protein Interaction Residues from Amino Acid Sequences Poster Authors and organization: Changhui Yan¹, Vasant Honavar², Drena Dobbs
¹chhyan@iastate.edu, Iowa State University, IA, USA; ²honavar@cs.iastate.edu, Iowa State University, IA, USA Abstract: We have used support vector machines and Naive Bayes methods to classify protein surface residues into interface residues and non-interface residues based on the sequence neighbors of target residues. The results showed that both methods are able to successfully discover and use sequence neighbor features predictive of functional properties to identify interface residues. File: chhyanATiastate.edu_254.html ************************************************* Thu May 1 16:59:37 2003 Number: 255 Name: Miranda, Kevin C Affiliation: University of Queensland, Institute for Molecular Bioscience Address: QBP Building, University of Queensland City: Brisbane State/Provice: Queensland Postal/Zip Code: 4072 Country: Australia Email: k.miranda@imb.uq.edu.au Phone: 61-7-3346-2347 Fax: Category: Predictive Methods Poster Title: Determination of sub-cellular localization of membrane proteins Poster Authors and organization: Kevin C Miranda¹, Rajith Aturaliya², Melissa Davis, Zheng Yuan, Cameron Flegg and Rohan Teasdale
¹k.miranda@imb.uq.edu.au, University of Queensland; ²r.aturaliya@imb.uq.edu.au, Univerity of Queensland Abstract: The RIKEN Representative Protein Set was subdivided into groups based on signal peptide and transmembrane domain combination. Functional analysis using InterPro and SCOP was performed on three sub-groups: type I and II transmembrane and secreted proteins. The sub-cellular localization of type II proteins were computationally predicted and tested in vivo. File: k.mirandaATimb.uq.edu.au_255.html ************************************************* Thu May 1 17:08:22 2003 Number: 256 Name: Reiss, David J Affiliation: Institute for Systems Biology Address: 1441 N. 34th St. City: Seattle State/Provice: WA Postal/Zip Code: 98103 Country: USA Email: dreiss@systemsbiology.org Phone: 206-732-1391 Fax: Category: Predictive Methods Poster Title: A Statistical Model of Protein Sequences in Interaction Networks and Its Solution via Gibbs Sampling Poster Authors and organization: David J. Reiss¹, Benno Schwikowski², Andrew F. Siegel, Stanley Fields
¹dreiss@systemsbiology.org, Institute for Systems Biology; ²benno@systemsbiology.org, Institute for Systems Biology Abstract: We describe a novel statistical model of protein sequences and interaction networks that utilizes discriminative and informed priors, and apply it via a Gibbs sampling algorithm to the experimental SH3 domain-peptide interaction network of Tong et al (2001). Our results reveal that such interaction networks can, to a large degree, be modelled by this technique. File: dreissATsystemsbiology.org_256.html ************************************************* Thu May 1 17:15:23 2003 Number: 257 Name: Ptitsyn, Andrey Affiliation: Pennington Biomedical Research Center Address: 6400 Perkins Rd City: Baton Rouge State/Provice: LA Postal/Zip Code: 70808 Country: USA Email: ptitsyaa@pbrc.edu Phone: 225 763 2621 Fax: 225 763 2525 I plan to use my laptop computer as part of my poster Category: Functional Genomics Poster Title: Scalable multi-processor application for gene expression profile clustering Poster Authors and organization: Andrey Ptitsyn¹
¹ptitsyaa@pbrc.edu, Pennington Biomedical Research Center Abstract: We would like to report a scalable multi-processor application for clustering of gene expression profiles. The program implements the flexible clustering algorithms developed at PBRC. The program is written in MPI standard and tested on IBM AIX Parallel Environment. File: ptitsyaaATpbrc.edu_257.html ************************************************* Thu May 1 17:45:47 2003 Number: 258 Name: Bellido, Mar Affiliation: Fred Hutchinson Cancer Research Center Address: 1100 Fairview Ave City: Seattle State/Provice: Washington Postal/Zip Code: 98109 Country: USA Email: mbellido@fhcrc.org Phone: 206-667-5309 Fax: 206-667-2917 Category: Microarrays Poster Title: Common transcription factor binding sites in the regulatory regions of a cluster of genes statistically linked to the hox gene HB24 Poster Authors and organization: Mar Bellido ¹, Whipple Neely², Fan W, Beppu L, Zhao LP, Radich JP
¹mbellido@fhcrc.org, Fred Hutchinson Cancer Research Center; ²whipple@fhcrc.org, Fred Hutchinson Cancer Research Center Abstract: The hox gene HB24 encodes a protein expressed in CD34 cells which plays a role in T-cell activation. Using a statistical approach based on regression analysis we identified 29 genes co-regulated with the HB24 gene. The analysis of the regulatory regions of these genes revealed common transcription factor binding sites. File: mbellidoATfhcrc.org_258.html ************************************************* Thu May 1 18:19:43 2003 Number: 259 Name: Ragan, Mark A. Affiliation: Institute for Molecular Bioscience, The University of Queensland Address: Building 80, UQ St Lucia Campus City: Brisbane State/Provice: Queensland Postal/Zip Code: 4069 Country: Australia Email: m.ragan@imb.uq.edu.au Phone: +61-7-3346-2616 Fax: +61-7-3346-2101 Category: Phylogeny and Evolution Poster Title: A hybrid clustering approach to genome-scale recognition of protein families Poster Authors and organization: Timothy J. Harlow¹, J. Peter Gogarten², Mark A. Ragan
¹t.harlow@imb.uq.edu.au, Institute for Molecular Bioscience, University of Queensland; ²gogarten@uconn.edu, University of Connecticut Abstract: We develop a hybrid approach to recognizing protein families among multi-genomic datasets based on Markov and single-linkage clustering of normalised pairwise BLASTP bit scores. We present results for all proteins from 114 microbial genomes, and illustrate its utility by recognizing orthologs and paralogs of rotary motor ATP synthetase F1 subunits. File: m.raganATimb.uq.edu.au_259.html ************************************************* Thu May 1 18:47:40 2003 Number: 260 Name: Taguchi, Y-h. Affiliation: Department of Physics, Chuo University Address: 1-13-27 Kasuga City: Bunkyo-ku State/Provice: Tokyo Postal/Zip Code: 112-8551 Country: Japan Email: tag@granular.com Phone: +81-3-3817-1791 Fax: +81-3-3817-1792 I plan to use my laptop computer as part of my poster Category: Data Mining Poster Title: C. elegans microarray data seen through a novel nonmetric multidimensional scaling method Poster Authors and organization: Y-h. Taguchi¹, Y. Oono²
¹tag@granular.com, Department of Physics, Chuo University; ²y-oono@uiuc.ed, Department of Physics, UIUC Abstract: C.elegans microarray data is analysed by a novel nonmetric multidimensional scaling method that is maximally nonmetric. The genes are embeddable in 3D. Their annotations are consistent with their positions in this space. A method to compute the 3D coordinates directly from the microarray data is also developed. File: tagATgranular.com_260.html ************************************************* Thu May 1 18:51:21 2003 Number: 261 Name: Taguchi, Y-h. Affiliation: Department of Physics, Chuo Universit Address: 1-13-27 Kasuga City: Bunkyo-ku State/Provice: Tokyo Postal/Zip Code: 112-8551 Country: Japan Email: tag@granular.com Phone: +81-3-3817-1791 Fax: +81-3-3817-1792 I plan to use my laptop computer as part of my poster Category: Data Mining Poster Title: Non-metric analysis of temporal patterns captured in microarray data Poster Authors and organization: Y-h. Taguchi¹, Y. Oono²
¹tag@granular.com, Department of Physics, Chuo Universit; ²y-oono@uiuc.edu, Department of Physics, UIUC Abstract: A nonmetric multidimensional scaling analysis of the gene activity response of cell cycle-synchronized human fibroblasts to serum [Lyer et al. Science 283, 83-87 (1999)] automatically gives a ring-like gene arrangement along which the expression level peak rotates. This unambiguously demonstrates the power of a nonlinear data mining method. File: tagATgranular.com_261.html ************************************************* Thu May 1 19:08:37 2003 Number: 262 Name: Park, Mihwa Affiliation: POSDATA co. Address: 276-2 City: SungNam-City State/Provice: Gyuggi-DO Postal/Zip Code: 463-775 Country: Korea Email: bfpark@posdata.co.kr Phone: 82-031-779-2707 Fax: 82-031-779-2709 I plan to use my laptop computer as part of my poster Category: Systems Biology Poster Title: SPACE-BLAST: Linux Cluster based Biological Sequence Parallel Processing system Summarized by Gene Ontology Poster Authors and organization: Mihwa Park¹, Jaewoo Kim², Hyungsuk Won, Seungsik Yoo
¹bfpark@posdata.co.kr, POSDATA; ²jaewoo@posdata.co.kr, POSDATA Abstract:

50-word abstract:
SPACE-BLAST (Super PArallel Computer Engine for BLAST) is a high performance bioinformatics system that implements the NCBI�s BLAST system with low cost Linux cluster based parallel processing to search DNA sequencing at high speed. Also, Gene Ontology is applied to summarize massive amount of the BLAST search results. SPACE-BLAST is available at at http://space-blast.posdata.co.kr.

File: bfparkATposdata.co.kr_262.html ************************************************* Thu May 1 19:13:09 2003 Number: 263 Name: Pandey, Ritu Affiliation: Bioinformatics, Arizona Cancer Center, University of Arizona Address: 1515 N Campbell Ave. City: Tucson State/Provice: Arizona Postal/Zip Code: 85724 Country: USA Email: ritu@u.arizona.edu Phone: 520-621-0391 Fax: Category: Microarrays Poster Title: BioRag - Bio Resource for Array Genes: An Online Resource for Analyzing and interpreting Microarray data Poster Authors and organization: Ritu Pandey¹, Raghavendra K Guru ², David W Mount
¹ritu@u.arizona.edu, Bioinformatics, Arizona Cancer Center, University of Arizona; ²graghave@cs.arizona.edu, Bioinformatics, Arizona Cancer Center, University of Arizona Abstract: 50-word abstract:
BioRag (Bio Resource for Array Genes at http://www.biorag.org) is an interactive platform for analyzing and developing a biological interpretation of the microarray results. Differential gene expression patterns can be interpreted using tools that mine and extract variety of biological relationships captured in this integrative resource. File: rituATu.arizona.edu_263.html ************************************************* Thu May 1 19:16:47 2003 Number: 264 Name: Samish, Ilan Affiliation: Weizmann Institute of Science Address: - City: Rehovot State/Provice: - Postal/Zip Code: 76100 Country: Israel Email: ilan.samish@weizmann.ac.il Phone: 972-8-9344300 Fax: 972-8-9344181 Category: Structural Biology Poster Title: Contribution of Interhelical Weak Interactions to the Regulation of Protein-Gated Electron Transfer in the Membrane Milieu Poster Authors and organization: Ilan Samish¹, Haim J. Wolfson², Avigdor Scherz
¹ilan.samish@weizmann.ac.il, Weizmann Institute of Science; ², Tel Aviv University Abstract: The mechanism of protein-gated electron transfer between two quinones of photosystem II was investigated. Sequence and structural conservation of a high-packing motif including an intersubunit H-bond, combined with in-silico and in-vivo combinatorial mutagenesis and biophysical characterization of the H-bond donor suggests that reversible dissociation of the bond regulates the gating. File: ilan.samishATweizmann.ac.il_264.html ************************************************* Thu May 1 19:17:02 2003 Number: 265 Name: Light, Marc N Affiliation: University of Iowa Address: 3072 Main Library City: Iowa City State/Provice: Iowa Postal/Zip Code: 52242-1420 Country: USA Email: marc-light@uiowa.edu Phone: 1-319-335-5712 Fax: 1-319-335-5374 Category: Data Mining Poster Title: Extracting Transcription Factor Interactions from Medline Abstracts Poster Authors and organization: Marc Light¹, Robert Arens, Vladimir Leontiev, Meredith Patterson, Xinying Qiu, Hudong Wang
¹marc-light@uiowa.edu, University of Iowa Abstract: Staying abreast of research on transcription factors (TFs) is currently a difficult task for biologists. We are building a system that will extract TF interactions from Medline abstracts automatically. To date, we have annotated a corpus for TF interactions and evaluated a number of component technologies. File: marc-lightATuiowa.edu_265.html ************************************************* Thu May 1 19:21:05 2003 Number: 266 Name: Chung, Tae-Hoon Affiliation: KRIBB Address: 52 Eoeun-dong, Yuseong-gu City: Daejeon State/Provice: Postal/Zip Code: 305-333 Country: Korea Email: thcng@kribb.re.kr Phone: 82-42-879-8561 Fax: 82-42-879-8569 Category: Microarrays Poster Title: QUINTET: An R-based unified cDNA microarray data analysis system with graphical user interface Poster Authors and organization: Tae-Hoon Chung¹, Cheol-Goo Hur², Sun Yong Park, Hyo Soo Lee
¹thcng@kribb.re.kr, KRIBB; ²hurlee@kribb.re.kr, KRIBB Abstract: We present QUINTET: an R-based unified cDNA microarray data analysis system with graphical user interface. It can seamlessly perform five principal categories of the data analysis: data quality assessment, faulty spot filtering and normalization, identification of differentially expressed genes, clustering of gene expression profiles and classification of samples. File: thcngATkribb.re.kr_266.html ************************************************* Thu May 1 19:31:26 2003 Number: 267 Name: Zhang, Miao Affiliation: Department of Genetics and Department of Biomedical Engineering, Washington University Address: 4444 Forest Park Ave City: St. Louis State/Provice: MO Postal/Zip Code: 63108 Country: USA Email: mzhang@sapiens.wustl.edu Phone: 1-314-286-1845 Fax: Category: Sequence Comparison Poster Title: Alexa: an improved EST and genomic sequence alignment tool Poster Authors and organization: Miao Zhang¹, Warren Gish²
¹mzhang@sapiens.wustl.edu, Department of Genetics and Department of Biomedical Engineering, Washington University; ²gish@watson.wustl.edu, Department of Genetics , Washington University Abstract: To better align EST and genomic sequence, we developed a tool named Alexa, which incorporates a splice site model into the recursive dynamic programming equation. For reduced memory consumption and increased speed, Alexa can be guided by an input file produced by WU-BLASTN. Alexa is available at http://sapiens.wustl.edu/alexa. File: mzhangATsapiens.wustl.edu_267.html ************************************************* Thu May 1 19:46:24 2003 Number: 268 Name: Noh, Seung-Jae Affiliation: Korea Research Institute of Bioscience and Biotechnology Address: 52 Eoeun-dong Yusong-gu City: Taejon State/Provice: Postal/Zip Code: 305-333 Country: South Korea Email: sjnoh@kribb.re.kr Phone: 82-42-879-8563 Fax: 82-42-879-8569 Category: Data Mining Poster Title: Construction of the plant gene index system based on tissue-categorized EST sets Poster Authors and organization: Seung-Jae Noh¹, Cheol-Goo Hur², Sung-Ho Goh, Ho-Jin Chung, Kyoung-Oak Choi
¹sjnoh@kribb.re.kr, Korea Research Institute of Bioscience and Biotechnology; ²hurlee@kribb.re.kr, Korea Research Institute of Bioscience and Biotechnology Abstract: Our plant gene index system based on stackPACK EST clustering with tissue categorization contains valuable information about 150,000 consensus sequences obtained from 9 principal plant model organisms. The information can be browsable, searchable, and downloadable with user-friendly web-interface at http://plant.pdrc.re.kr/new_korea/genepool/Plant/index.html File: sjnohATkribb.re.kr_268.html ************************************************* Thu May 1 19:53:24 2003 Number: 269 Name: Batalov, Serge Affiliation: GNF Address: 10675 JJ Hopkins Dr City: San Diego State/Provice: CA Postal/Zip Code: 92121 Country: USA Email: batalov@gnf.org Phone: +1-858-8121569 Fax: +1-858-8121502 I plan to use my laptop computer as part of my poster Category: Data Visualisation Poster Title: GENOME-WIDE HAPLOTYPE STRUCTURE VISUALIZATION AND ANALYSIS IN MOUSE Poster Authors and organization: Serge Batalov¹, Mathew Pletcher², R.J.Mural, M.D.Adams, C.F.Fletcher, T.Wiltshire
¹batalov@gnf.org, GNF; ²mpletche@gnf.org, TSRI Abstract: SNPview, the interactive navigator for the individual SNPs, SSLPs, alleles and haplotypes projected to the genomic axis is available on-line at http://www.gnf.org/SNP/ . Large, but discrete regions of the genome are not very polymorphic between particular strain pairs, and thus cannot easily be interrogated for natural genetic variations influencing QTLs. File: batalovATgnf.org_269.html ************************************************* Thu May 1 20:03:30 2003 UPDATE ----- Number: 262 Name: Park, Mihwa Affiliation: POSDATA co. Address: 276-2 City: SungNam-City State/Provice: Gyuggi-DO Postal/Zip Code: 463-775 Country: Korea Email: bfpark@posdata.co.kr Phone: 82-031-779-2707 Fax: 82-031-779-2709 I plan to use my laptop computer as part of my poster Category: Systems Biology Poster Title: SPACE-BLAST: Linux Cluster based Biological Sequence Parallel Processing system Summarized by Gene Ontology Poster Authors and organization: Mihwa Park¹, Jaewoo Kim², Hyungsuk Won, Seungsik Yoo
¹bfpark@posdata.co.kr, POSDATA; ²jaewoo@posdata.co.kr, POSDATA Abstract: SPACE-BLAST (Super PArallel Computer Engine for BLAST) is a high performance bioinformatics system that implements the NCBI�s BLAST system with low cost Linux cluster based parallel processing to search DNA sequencing at high speed. Also, Gene Ontology is applied to summarize massive amount of the BLAST search results. SPACE-BLAST is available at http://space-blast.posdata.co.kr File: bfparkATposdata.co.kr_262 ************************************************* Thu May 1 20:18:12 2003 UPDATE ----- Number: 260 Name: Taguchi, Y-h. Affiliation: Department of Physics, Chuo University Address: 1-13-27 Kasuga City: Bunkyo-ku State/Provice: Tokyo Postal/Zip Code: 112-8551 Country: Japan Email: tag@granular.com Phone: +81-3-3817-1791 Fax: +81-3-3817-1792 I plan to use my laptop computer as part of my poster Category: Data Mining Poster Title: C. elegans microarray data seen through a novel nonmetric multidimensional scaling method Poster Authors and organization: Y-h. Taguchi¹, Y. Oono²
¹tag@granular.com, Department of Physics, Chuo University; ²y-oono@uiuc.edu, Department of Physics, UIUC Abstract: C.elegans microarray data is analysed by a novel nonmetric multidimensional scaling method that is maximally nonmetric. The genes are embeddable in 3D. Their annotations are consistent with their positions in this space. A method to compute the 3D coordinates directly from the microarray data is also developed. File: tagATgranular.com_260 ************************************************* Thu May 1 20:22:43 2003 UPDATE ----- Number: 221 Name: Kim, Ki-Bong Affiliation: SmallSoft Co., Ltd. Address: Daeduk BioCommunity, Jonmin-Dong 461-6, Yusung-Gu City: Daejeon State/Provice: Postal/Zip Code: 305-811 Country: South Korea Email: kbkim@bioinfo.smallsoft.co.kr Phone: +82-42-864-2524 Fax: +82-42-866-9241 Category: Predictive Methods Poster Title: PIVS: Protein-protein interaction inference and visualization system using sequence-based homology search with DIP and BIND Poster Authors and organization: Ki-Bong Kim¹, Mi-Kyung Lee², Seo, Hwajung
¹kbkim@bioinfo.smallsoft.co.kr, SmallSoft Co., Ltd.; ²mklee@bioinfo.smallsoft.co.kr, SmallSoft Co., Ltd. Abstract: We developed the system, PIVS, which is very useful for predicting the function and interaction of unknown protein sequence as well as for visualizing its protein-protein interaction map. In addition, it offers integral genomic and motif/domain-related information concerning unknown input protein sequence. File: kbkimATbioinfo.smallsoft.co.kr_221 ************************************************* Thu May 1 20:28:35 2003 Number: 270 Name: lefevre, christophe Affiliation: Victorian Bioinformatics Consortium Address: Monash Universiry, PO box 53 City: Clayton State/Provice: Victoria Postal/Zip Code: 3800 Country: Australia Email: chris.lefevre@med.monash.edu.au Phone: 61 3 9905 9338 Fax: 61 3 9905 9773 Category: Data Visualisation Poster Title: Linguistic profiling of genome sequences. The Sequence identifier position end set cardinal: an estimate of linear sequence complexity: algorithms and genome profiling applications. Linguistic profiling of genome sequences. The Sequence identifier position end set cardinal: an estimate of linear sequence complexity: algorithms and genome profiling applications. Linguistic profiling of genome sequences. Linguistic profiling of genome sequences. The Sequence identifier position end set cardinal: an estimate of linear sequence complexity: algorithms and genome profiling applications. Poster Authors and organization: christophe lefevre¹
¹chris.lefevre@med.monash.edu.au, Victorian Bioinformatics Consortium Abstract: The sequence identifier end set cardinal is proposed as a new estimator of linear sequence linguistic complexity. A scanning window algorithm to compute this value is presented and profiles obtained with genomic sequences are discussed. File: chris.lefevreATmed.monash.edu.au_270.html ************************************************* Thu May 1 20:33:03 2003 Number: 271 Name: Tamada, Yoshinori Affiliation: Laboratory of Biological Information Network, Bioinformatics Center, Institute for Chemical Research, Kyoto University Address: Gokasho City: Uji State/Provice: Kyoto Postal/Zip Code: 611-0011 Country: Japan Email: tamada@kuicr.kyoto-u.ac.jp Phone: +81-774-38-3018 Fax: Category: Microarrays Poster Title: Combining Bayesian Network Model with Promoter Element Detection for Estimating Gene Networks from Gene Expression Data Poster Authors and organization: Yoshinori Tamada¹, SunYong Kim², Hideo Bannai, Seiya Imoto, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano
¹tamada@kuicr.kyoto-u.ac.jp, Laboratory of Biological Information Network, Bioinformatics Center, Institute for Chemical Research, Kyoto University; ²sunk@ims.u-tokyo.ac.jp, Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo Abstract: We developed a statistical method for estimating gene networks and detecting promoter elements simultaneously. The estimation of gene network from cDNA microarray data alone is likely to cause misdirected edges. Our method overcomes this problem by integrating microarray data and the DNA sequence information into a Bayesian network estimation. File: tamadaATkuicr.kyoto-u.ac.jp_271.html ************************************************* Thu May 1 20:48:41 2003 Number: 272 Name: Chen, Yan Affiliation: Queensland University of Technology Address: 126 Margaret Street City: Brisbane State/Provice: Queensland Postal/Zip Code: QLD 4001 Country: Australia Email: y52.chen@student.qut.edu.au Phone: 38649447 Fax: Category: Data Mining Poster Title: BioInfoCallboratory: Towards an Agent- Assisted Web-Based Collaboration Environment for Bioinformatics Poster Authors and organization: Yan Chen¹, Yi-Ping Phoebe Chen²
¹y52.chen@student.qut.edu.au, Queensland University of Technology; ²p.chen@qut.edu.au, Queensland University of Technology Abstract: Collaborations in web based bioinformatics environment require intelligent supports to assist human computer interaction. BioInfoCallboratory is an agent assisted web based environment for supporting bioinformatics research. It facilitates sophisticated interactions such as: matchmaking based on common interests; internet spanning data mining for bioinformatics data; and event alert for interested parties. File: y52.chenATstudent.qut.edu.au_272.html ************************************************* Thu May 1 20:54:35 2003 Number: 273 Name: Tang, Jijun Affiliation: University of New Mexico Address: CS Department, University of New Mexico City: Albuquerque State/Provice: NM Postal/Zip Code: 87131 Country: USA Email: jtang@cs.unm.edu Phone: 1-505-2776185 Fax: 1-505-2776927 I plan to use my laptop computer as part of my poster Category: Phylogeny and Evolution Poster Title: Computing accurate phylogenies from gene-order data Poster Authors and organization: Jijun Tang¹, Bernard M.E. Moret²
¹jtang@cs.unm.edu, University of New Mexico; ²moret@cs.unm.edu, University of New Mexico Abstract: DCM-GRAPPA is a method for phylogeny recontruction based on gene-order data; it scales gracefully to one thousand genomes, using a day or two of computation and producing highly accurate results (within 1%). GRAPPA and DCM-GRAPPA are available in source form at http://www.cs.unm.edu/~moret/GRAPPA/ File: jtangATcs.unm.edu_273.html ************************************************* Thu May 1 21:10:15 2003 Number: 274 Name: Sarai, Akinori Affiliation: Department of Biochemical Engineering and Science Address: Kyushu Institute of Technology City: Iizuka State/Provice: Fukuoka Postal/Zip Code: 8208502 Country: Japan Email: sarai@bse.kyutech.ac.jp Phone: +81-948-29-7811 Fax: +81-948-29-7801 Category: Predictive Methods Poster Title: Ligand specificity of proteases and Kinases: an applicationto IC50 prediction on a large scale Poster Authors and organization: Shandar Ahmad¹, Koji Kitajima², Akinori Sarai
¹shandar@bse.kyutech.ac.jp, Department of Biochemical Enigineering and Science, Kyushu Institute of Technology, Japan; ², Abstract: We have attempted neural-network-based predictions of inhibition coefficient (IC50) from the SMILES of ligands for kinases and proteases in the protein-ligand interaction database, ProLINT. Our method is useful for a large scale filtering of ligands in drug-design. We have also attempted to develop ligand fragment-signature for proteins in ProLINT. File: saraiATbse.kyutech.ac.jp_274.html ************************************************* Thu May 1 21:10:36 2003 Number: 275 Name: Kim, Namshin Affiliation: School of Chemistry, Seoul National University Address: Shilim9-dong City: Seoul State/Provice: Kwanak-gu Postal/Zip Code: 151-747 Country: KOREA Email: deepreds@hanmail.net Phone: +82-2-879-2721 Fax: +82-2-889-1568 Category: Genome Annotation Poster Title: ASmodeler: Gene modeling of alternative splicing events from genomic alignment of mRNA and ESTs Poster Authors and organization: Namshin Kim¹, Seokmin Shin², Sanghyuk Lee
¹deepreds@hanmail.net, School of Chemistry, Seoul National University; ²sshin@snu.ac.kr, School of Chemistry, Seoul National University Abstract:
ASmodeler is a novel web-based utility to find gene models of alternative splicing events from genomic alignment of mRNA and ESTs. It can be used as a transcript assembly program, an EST clustering utility, and a method of comparative gene modeling. ASmodeler is available at http://genome.ewha.ac.kr/ASmodeler/.
File: deepredsAThanmail.net_275.html ************************************************* Thu May 1 21:16:25 2003 Number: 276 Name: Batalov, Serge Affiliation: GNF Address: 10675 JJ Hopkins Dr City: San Diego State/Provice: CA Postal/Zip Code: 92121 Country: USA Email: batalov@gnf.org Phone: +1-858-8121569 Fax: +1-858-8121502 Category: Microarrays Poster Title: Design of the custom whole-genome malaria oligonucleotide array Poster Authors and organization: Serge Batalov¹, Elizabeth A. Winzeler²
¹batalov@gnf.org, GNF; ²winzeler@scripps.edu, TSRI/GNF Abstract: To study the transcriptome of the malaria parasite, we designed a custom no-mismatch oligonucleotide array containing 260,596 25mer single stranded probes from predicted coding sequence (including mitochondrion and plastid genome sequences) and 106,630 probes from non-coding sequence. In addition 124,957 probes from Plasmodium yoelli contigs are include on the array. File: batalovATgnf.org_276.html ************************************************* Thu May 1 21:37:17 2003 Number: 277 Name: Huttley, Gavin A Affiliation: Australian National University Address: Centre for Bioinformation Science, JCSMR City: ANU State/Provice: ACT Postal/Zip Code: 0200 Country: Australia Email: gavin.huttley@anu.edu.au Phone: 61-2-6125-0730 Fax: 61-2-6125-4712 Category: Phylogeny and Evolution Poster Title: EVOLVE: a toolkit for statistical molecular evolutionary analysis of genomes Poster Authors and organization: Gavin Huttley¹, Alex Isaev², Andrew Butterfield, Edward lang, Cath Lawrence
¹gavin.huttley@anu.edu.au, ANU; ²Alexander.Isaev@maths.anu.edu.au, ANU Abstract: The number of genes and species for which data are now available present an opportunity for statistically powerful examinations of molecular evolutionary processes. We will present a description of the functionality and performance of EVOLVE (cbis.anu.edu.au/software), a high performance computing package for phylogeny-based maximum likelihood modeling and hypothesis testing. File: gavin.huttleyATanu.edu.au_277.html ************************************************* Thu May 1 22:11:07 2003 Number: 278 Name: Reimers, Mark A Affiliation: Karolinska Institute Address: Berzeliusv. 35 City: Stockholm State/Provice: Postal/Zip Code: 171 77 Country: Sweden Email: mark.reimers@cgb.ki.se Phone: +46-8-728-7826 Fax: Category: Microarrays Poster Title: Better Affymetrix Estimates Poster Authors and organization: Mark Reimers¹
¹mark.reimers@cgb.ki.se, Karolinska Abstract: This shows improvements on the best current estimates for gene abundance using Affymetrix raw data, by compensating for spatial heterogeneity, and by assessing individual probe quality and background, prior to using a robust method for fit. File: mark.reimersATcgb.ki.se_278.html ************************************************* Thu May 1 22:20:57 2003 Number: 279 Name: Satterley, Keith R Affiliation: The Walter and Eliza Hall Institute of Medical Research Address: 1G Royal Pd. City: Melbourne State/Provice: Victoria Postal/Zip Code: 3050 Country: Australia Email: keith@wehi.edu.au Phone: +61 4 2570 0 419 Fax: +61 3 9347 0852 Category: Sequence Comparison Poster Title: ASAD-A Sequence Attribute Display tool Poster Authors and organization: Keith Satterley¹
¹keith@wehi.edu.au, The Walter and Eliza Hall Institute of Medical Research Abstract: ISMB 2003 ASAD Poster

50-word abstract:
ASAD is A Sequence Attribute Display tool. It is written as a set of Excel macros. It builds on the familiar Excel interface to allow for flexible and efficient display of attributes (hydrophobicity etc.) using similar colours and styles for one sequence or multiple aligned sequences. ASAD is available at ftp://ftp.wehi.edu.au/pub/biology/ASAD.

File: keithATwehi.edu.au_279.html ************************************************* Thu May 1 22:21:58 2003 Number: 280 Name: Long, Stephen M Affiliation: School of Physical Sciences and Institute for Molecular Bioscience Address: The University of Queensland City: Brisbane State/Provice: Queensland Postal/Zip Code: 4072 Country: Australia Email: sml@maths.uq.edu.au Phone: +61 7 3346 1429 Fax: +61 7 3365 1477 Category: Structural Biology Poster Title: Towards modulating protein-protein interactions: Clustering protein surfaces to identify biologically-relevant structural space to focus molecular design Poster Authors and organization: Stephen Long¹, Mark Smythe², Peter Adams, Darryn Bryant and Tran Trung Tran
¹sml@maths.uq.edu.au, School of Physical Sciences, Institute for Molecular Biosciences, The University of Queensland; ²M.Smythe@protagonist.com.au, Institute for Molecular Bioscience, The University of Queensland and Protagonist Pty. Ltd. Abstract: Identifying small molecules that modulate protein-protein interactions continues to be a major challenge for drug discovery. From a database of homologous protein-protein interactions, datasets were extracted representing the interaction region of pairs of proteins of these complexes. The aim of this research is to cluster features of each of these datasets. File: smlATmaths.uq.edu.au_280.html ************************************************* Thu May 1 22:22:46 2003 Number: 281 Name: Hartig, Gerald R Affiliation: Institute for Molecular Bioscience, University of Queensland Address: Queensland Bioscience Precinct, St Lucia City: Brisbane State/Provice: QLD Postal/Zip Code: 4072 Country: Australia Email: g.hartig@imb.uq.edu.au Phone: 3346-2975 Fax: Category: Data Mining Poster Title: Comparison of intra-molecular disulphide bonding arrangements between disulphide-rich and -poor proteins in the Protein Data Bank Poster Authors and organization: Gerald Hartig¹, Mark Smythe²
¹g.hartig@imb.uq.edu.au, Institute for Molecular Bioscience; ²m.smythe@imb.uq.edu.au, Institute for Molecular Bioscience Abstract: Intra-molecular disulphide bonds (IDSB) are an important determinant of a protein?s 3D conformation. This work described the differences in IDSB arrangements between disulphide-rich and -poor proteins. A naturally occurring partition of 25.2 residues / IDSB was used, revealing differences in PDB headers, SCOP folds, IDSB bonding patterns and loop lengths. File: g.hartigATimb.uq.edu.au_281.html ************************************************* Thu May 1 22:25:34 2003 Number: 282 Name: Reimers, Mark A Affiliation: Karolinska Institute Address: Berzeliusv. 35 City: Stockholm State/Provice: Postal/Zip Code: 171 77 Country: Sweden Email: mark.reimers@cgb.ki.se Phone: +46-8-728-7826 Fax: Category: Systems Biology Poster Title: Is Segmentation a Robust Gene Network Poster Authors and organization: Mark Reimers¹
¹mark.reimers@cgb.ki.se, Karolinska Abstract: A major question in evo-devo is whether conserved developmental networks are robust. We address this with a simulation study and an evolutionary comparison of gene networks. File: mark.reimersATcgb.ki.se_282.html ************************************************* Thu May 1 22:35:16 2003 Number: 283 Name: Gondro, Cedric Affiliation: University of New England Address: Animal Science - UNE City: Armidale State/Provice: NSW Postal/Zip Code: 2351 Country: Australia Email: genetics@sigex.com.br Phone: 61 2 6773 5135 Fax: 61 2 6773 3922 Category: Systems Biology Poster Title: On Metabolic Pathway Reconstruction from Gene Expression Data Poster Authors and organization: Cedric Gondro¹, Brian P. Kinghorn²
¹genetics@sigex.com.br, University of New England; ²bkinghor@une.edu.au, University of New England Abstract: This work aims to infer metabolic pathways and other biological processes from data generated in kinetically simulated microarray experiments using evolutionary algorithms. A preliminary test has shown correct reconstruction of lac operon model parameters derived from simulated expression data collected following a perturbation in the level of lactose. File: geneticsATsigex.com.br_283.html ************************************************* Thu May 1 22:37:52 2003 Number: 284 Name: Saunders, Neil FW Affiliation: School of Biotechnology and Biomolecular Sciences, The University of New South Wales Address: UNSW City: Sydney State/Provice: NSW Postal/Zip Code: 2052 Country: Australia Email: neil.saunders@unsw.edu.au Phone: +61 2 9385 2092 Fax: +61 2 9385 1591 Category: Data Mining Poster Title: Pathogenic archaea-do they exist Poster Authors and organization: Neil Saunders¹, Ricardo Cavicchioli², Paul M.G. Curmi, Torsten Thomas
¹neil.saunders@unsw.edu.au, The University of New South Wales; ²r.cavicchioli@unsw.edu.au, The University of New South Wales Abstract: We have developed a rapid, automated search strategy for the detection of contaminating sequence from putative novel pathogenic archaea in human EST sequence data. The system has general application to the detection of microbial pathogens and will be available at http://psychro.bioinformatics.unsw.edu.au. File: neil.saundersATunsw.edu.au_284.html ************************************************* Thu May 1 22:39:17 2003 UPDATE ----- Number: 270 Name: lefevre, christophe Affiliation: Victorian Bioinformatics Consortium Address: Monash Universiry, PO box 53 City: Clayton State/Provice: Victoria Postal/Zip Code: 3800 Country: Australia Email: chris.lefevre@med.monash.edu.au Phone: 61 3 9905 9338 Fax: 61 3 9905 9773 Category: Data Visualisation Poster Title: Poster Title: Linguistic profiling of genome sequences. The Sequence identifier position end set cardinal: an estimate of linear sequence complexity: algorithms and genome profiling applications. Poster Authors and organization: christophe lefevre¹
¹chris.lefevre@med.monash.edu.au, Victorian Bioinformatics Consortium Abstract: The sequence identifier end set cardinal is proposed as a new estimator of linear sequence linguistic complexity. A scanning window algorithm to compute this value is presented and profiles obtained with genomic sequences are discussed. File: chris.lefevreATmed.monash.edu.au_270 ************************************************* Thu May 1 22:40:17 2003 Number: 285 Name: Yoo, Si-Ho Affiliation: Yonsei University Address: 134 Shinchon-dong, Sudaemoon-ku City: Seoul State/Provice: Postal/Zip Code: 120749 Country: Korea, Republic of Korea Email: bonanza@candy.yonsei.ac.kr Phone: +82221234803 Fax: +8223652579 Category: Data Mining Poster Title: Regression analysis in optimal gene selection for DNA microarray analysis Poster Authors and organization: Si-Ho Yoo¹, Sung-Bae Cho²
¹bonanza@candy.yonsei.ac.kr, Yonsei University; ²sbcho@cs.yonsei.ac.kr, Yonsei University Abstract: We propose a new gene selection method based on forward selection method in regression analysis. This method reduces redundant information about cancer that could be in the subset of selected genes. The result shows high accuracy of 90.3% for colon cancer data. File: bonanzaATcandy.yonsei.ac.kr_285.html ************************************************* Thu May 1 22:40:47 2003 Number: 286 Name: Wakefield, Matthew J Affiliation: CBiS The Australian National University Address: JCSMR City: Canberra State/Provice: ACT Postal/Zip Code: 0200 Country: Australia Email: matthew.wakefield@kangaroo.genome.org.au Phone: +61 2 6125 5093 Fax: +61 2 6125 4891 Category: Phylogeny and Evolution Poster Title: Analyses using novel Markov models of substitution support a significant role for germline methylation in male biased evolution. Poster Authors and organization: Matthew J Wakefield¹, Gavin A Huttley², Alexander Isaev, Andrew Butterfield, Edward Lang & Cath Lawrence
¹Matthew.Wakefield@kangaroo.genome.org.au, Centre for Bioinformation Science, The Australian National University; ²Gavin.Huttley@anu.edu.au, Centre for Bioinformation Science, The Australian National University Abstract:
We have constructed a novel Markov model of dinucleotide substitution including parameters for methylation and strand using the EVOLVE toolkit. Our analysis supports a significant contribution of differential methylation in the germline elevating male mutation rates: clearly demonstrating the utility of EVOLVE (http://cbis.anu.edu.au/software/) in developing new sequence evolution models.
File: matthew.wakefieldATkangaroo.genome.org.au_286.html ************************************************* Thu May 1 22:44:44 2003 Number: 287 Name: Joslyn, Cliff AA Affiliation: Los Alamos National Laboratory Address: MS B265 LANL City: Los Alamos State/Provice: New Mexico Postal/Zip Code: 87501 Country: USA Email: joslyn@lanl.gov Phone: +1-505-667-9096 Fax: +1-505-665-5220 Category: Data Mining Poster Title: Structural Classification in the Gene Ontology Poster Authors and organization: Cliff Joslyn¹, Susan Mniszewski², Andy Fulmer, Gary Heaton
¹joslyn@lanl.gov, Los Alamos National Laboratory; ²smm@lanl.gov, Los Alamos National Laboratory Abstract: We present the Gene Ontology Clusterer (GOC), which structurally classifies the GO based on pseudo-distances between comparable nodes in posets, in conjunction with scoring algorithms, to rank-order the GO nodes with respect to a set of requested genes. We will also share lessons we\'ve learned about working with the GO. File: joslynATlanl.gov_287.html ************************************************* Thu May 1 22:47:43 2003 Number: 288 Name: Faux, Noel G Affiliation: Department of Biochemistry and Molecular Biology. Monash University Address: Wellington Rd City: Clayton State/Provice: Victoria Postal/Zip Code: 3800 Country: Australia Email: noel.faux@med.monash.edu.au Phone: 03 9905 1418 Fax: Category: Sequence Comparison Poster Title: Detection of false positive results from PSI-BLAST Poster Authors and organization: N. Faux¹, M. Cameron², M. Garcia de la Banda, J.C. Whisstock
¹noel.faux@med.monash.edu.au, Department of Biochemistry and Molecular Biology. Monash University; ²mcam@csse.monash.edu.au, School of Computer Science and Software Engineering. Monash University Abstract: PSI-BLAST is a sensitive and fast database search algorithm, however false positive results can taint the final results. We are currently investigating ways of detecting when the matrix generated by PSI-BLAST no longer describes the original query sequence or family. File: noel.fauxATmed.monash.edu.au_288.html ************************************************* Thu May 1 22:57:50 2003 Number: 289 Name: Won, Hong-Hee Affiliation: Yonsei University Address: 134 Shinchon-dong, Sudaemoon-ku City: Seoul State/Provice: Postal/Zip Code: 120749 Country: Korea, Republic Of Korea Email: cool@candy.yonsei.ac.kr Phone: +82221234803 Fax: +8223652579 Category: Data Mining Poster Title: Extracting informative genes with negative correlation for accurate cancer classification Poster Authors and organization: Hong-Hee Won¹, Sung-Bae Cho²
¹cool@candy.yonsei.ac.kr, Yonsei University; ²sbcho@cs.yonsei.ac.kr, Yonsei University Abstract: We define two negatively correlated ideal gene vectors which represent the patterns of classes well and extracted two significant gene subsets (SGSs) based on the similarity to two ideal genes. We train the neural network classifiers with SGSs and combine them. The ensemble classifier produces the best recognition rate-97.1% in Leukemia, 87.1% in Colon, and 92.0% in Lymphoma. File: coolATcandy.yonsei.ac.kr_289.html ************************************************* Thu May 1 22:58:05 2003 Number: 290 Name: Jin, Hee-Jeong Affiliation: School of Comp. Sci. and Eng., Pusan National University Address: San-30, Jangjeon-dong, Keumjeong-gu City: Busan State/Provice: Postal/Zip Code: 609-735 Country: Korea Email: hjjin@pearl.cs.pusan.ac.kr Phone: +82-51-582-5009 Fax: +82-51-515-2208 Category: Microarrays Poster Title: A New Method of Block/Spot Indexing with Maximal epsilon-Regularity Point Set for Microarray Image Analysis Poster Authors and organization: Hee-Jeing Jin¹, Ho-Youl Jung², Hyun-Kyung Lee, Choon-Hwan Lee, Hwan-Gue Cho
¹hjjin@pearl.cs.pusan.ac.kr, Pusan National University; ²hyjung@ngri.re.kr, National Genome Research Institute Abstract: It is very difficult to automatically analyze microarray images due to several problems such as spot position variation. We propose a novel block and spot indexing algorithm with the use of maximal epsilon-regularity. The time complexity of our algorithm is O(n²) where n is the number of cells. File: hjjinATpearl.cs.pusan.ac.kr_290.html ************************************************* Thu May 1 22:59:17 2003 Number: 291 Name: Won, Hong-Hee Affiliation: Yonsei University Address: 134 Shinchon-dong, Sudaemoon-ku City: Seoul State/Provice: Postal/Zip Code: 120749 Country: Korea, Republic Of Korea Email: cool@candy.yonsei.ac.kr Phone: +82221234803 Fax: +8223652579 Category: Data Mining Poster Title: Extracting informative genes with negative correlation for accurate cancer classification Poster Authors and organization: Hong-Hee Won¹, Sung-Bae Cho²
¹cool@candy.yonsei.ac.kr, Yonsei University; ²sbcho@cs.yonsei.ac.kr, Yonsei University Abstract: We define two negatively correlated ideal gene vectors which represent the patterns of classes well and extracted two significant gene subsets (SGSs) based on the similarity to two ideal genes. We train the neural network classifiers with SGSs and combine them. The ensemble classifier produces the best recognition rate-97.1% in Leukemia, 87.1% in Colon, and 92.0% in Lymphoma. File: coolATcandy.yonsei.ac.kr_291.html ************************************************* Thu May 1 23:02:05 2003 Number: 292 Name: Goh, Liang K Affiliation: Knowledge Engineering and Discovery Research Institute, Auckland University of Technology Address: 581-585, Great South Road, Ronald Trotter House, Penrose City: City State/Provice: Postal/Zip Code: Country: New Zealand Email: liang.goh@aut.ac.nz Phone: 6499179556 Fax: 6499179501 I plan to use my laptop computer as part of my poster Category: Microarrays Poster Title: A Novel Feature Selection Method using Evolving Supervised Clustering and Applications for Gene Expression Data Modeling Poster Authors and organization: Nikola Kasabov¹, Liang Goh²
¹nkasabov@aut.ac.nz, KEDRI; ²liang.goh@aut.ac.nz, KEDRI Abstract: The method combines the tasks of classification and feature selection by using the obtained clusters in ECOS to further extract specific features for each of the clusters. The method overcomes the problem of the signal to noise ratio method when data of the same class are spread in several clusters. File: liang.gohATaut.ac.nz_292.html ************************************************* Thu May 1 23:06:34 2003 Number: 293 Name: Yeo, Sang-Soo Affiliation: Chung-Ang University Address: 221 Huk-Suk City: Dong-Jak-Gu State/Provice: Seoul Postal/Zip Code: 156-756 Country: Republic of Korea Email: ssyeo@alg.cse.cau.ac.kr Phone: +82-2-825-6997 Fax: +82-2-820-5301 Category: Predictive Methods Poster Title: EPP: Eukaryotic Promoter Prediction system using an efficient training approach Poster Authors and organization: Sang-Soo Yeo¹, Sung-Kwon Kim², Jung-Won Rhee, Kyoung-Rak Na
¹ssyeo@alg.cse.cau.ac.kr, Chung-Ang University, Seoul, Republic of Korea; ²skkim@cau.ac.kr, Chung-Ang University, Seoul, Republic of Korea Abstract:
EPP is a eukaryotic promoter prediction system. In EPP, after training set is divided into many clusters, each cluster is separately trained to make a decision model. This approach enhances the sensitivity and specificity of EPP. EPP is available at http://epp.cau.ac.kr
File: ssyeoATalg.cse.cau.ac.kr_293.html ************************************************* Thu May 1 23:13:07 2003 Number: 294 Name: Chalifa-Caspi, Vered Affiliation: Weizmann Institute of Science Address: P.O. Box 26 City: Rehovot State/Provice: Postal/Zip Code: 76100 Country: Israel Email: vered.caspi@weizmann.ac.il Phone: 972-8-9343188 Fax: 972-8-9344113 Category: Microarrays Poster Title: GeneAnnot: Annotation of high-density oligunocleotide arrays and their linking with GeneCards. Poster Authors and organization: Vered Chalifa-Caspi¹, Itai Yanai², Ron Ophir, Michael Shmoish, Hila Benjamin-Rodrig, Naomi Rosen, Pavel Kats, Marilyn Safran, Orit Shmueli and Doron Lancet.
¹vered.caspi@weizmann.ac.il, Weizmann Insitute of Science; ²Iyanai@wisemail.weizmann.ac.il, Weizmann Insitute of Science Abstract: The availability of entire genomic sequences enables matching the short probe sequences of oligonucleotide arrays to their annotated gene representations. Here, we present a framework for estimating the sensitivity and specificity of gene-representing probe sets, and for integrating this information with the comprehensive genome and transcriptome repositories of the GeneCards databases suite. File: vered.caspiATweizmann.ac.il_294.html ************************************************* Thu May 1 23:16:39 2003 Number: 295 Name: Yun, HwaSeob Affiliation: Rutgers University Address: Hill Center, Computer Science City: New Brunswick State/Provice: NJ Postal/Zip Code: 08903 Country: USA Email: seabee@cs.rutgers.edu Phone: 732-445-2122 Fax: 732-445-0537 Category: Genome Annotation Poster Title: Protein domain extraction by quasi-convex set functions Poster Authors and organization: HwaSeob Yun¹, Casimir Kulikowski², Ilya Muchnik
¹seabee@cs.rutgers.edu, Rutgers University; ²kulikows@cs.rutgers.edu, Rutgers University Abstract: We present a fast, fully automatic procedure for protein domain extraction from single query sequences without pre-calculation of domain statistics. Combinatorial clustering of domains from BLAST hits using quasi-convex set functions, followed by domain parsing and pattern discovery permits highly efficient (polynomial time) whole genome functional annotation. File: seabeeATcs.rutgers.edu_295.html ************************************************* Thu May 1 23:29:23 2003 Number: 296 Name: Tyrelle, Greg D Affiliation: UNSW Address: UNSW City: Sydney State/Provice: NSW Postal/Zip Code: 2052 Country: Australia Email: greg@kinglab.unsw.edu.au Phone: 9385 2036 Fax: 9385 1483 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: A genetic polymorphism object model and XML implementation: Biological Variation Markup Language. Poster Authors and organization: anGreg Tyrelle¹, Garry C. King²
¹greg@kinglab.unsw.edu.au, UNSW; ²garry@kinglab.unsw.edu.au, UNSW Abstract: As molecular genotyping technologies accelerate there is an increasing need to communicate precise information on polymorphism data in machine-readable format. We have developed a hierarchical object model and XML implementation called Biological Variation Markup Language (BVML) to facilitate exchange between genotyping laboratories and distributed databases. File: gregATkinglab.unsw.edu.au_296.html ************************************************* Thu May 1 23:30:48 2003 Number: 297 Name: Geard, Nicholas L Affiliation: The University of Queensland Address: School of ITEE, The University of Queensland City: Brisbane State/Provice: Queensland Postal/Zip Code: 4072 Country: Australia Email: nic@itee.uq.edu.au Phone: 3365 8302 Fax: Category: Systems Biology Poster Title: Modelling the Role of Small RNAs in Gene Regulation Poster Authors and organization: Nicholas Geard¹, Janet Wiles²
¹nic@itee.uq.edu.au, The University of Queensland; ²j.wiles@itee.uq.edu.au, The University of Queensland Abstract: Small functional RNA molecules have been discovered to play an important role in the regulation of gene transcription. The abstract model presented here uses a sequence-matching paradigm to generate regulatory networks that utilise multiple levels of transcriptional control to increase their computational power. File: nicATitee.uq.edu.au_297.html ************************************************* Thu May 1 23:31:03 2003 Number: 298 Name: Di Giusto, Daniel Affiliation: UNSW Address: UNSW City: Sydney State/Provice: NSW Postal/Zip Code: 2052 Country: Australia Email: daniel@kinglab.unsw.edu.au Phone: 9385 2036 Fax: 9385 1483 I plan to use my laptop computer as part of my poster Category: Predictive Methods Poster Title: Multiplexed SBE primer design for highly polymorphic loci. Poster Authors and organization: Greg Tyrelle¹, Daniel Di Giusto², Garry C. King
¹greg@kinglab.unsw.edu.au, UNSW; ²daniel@kinglab.unsw.edu.au, UNSW Abstract: Single base extension (SBE) is the most widely used SNP genotyping method. When multiplex SBE (MSBE) is applied to highly polymorphic regions, hybridisation to variable DNA may occur. We have developed an MSBE primer design algorithm that increases the coverage of MSBE for these regions by up to 20%. File: danielATkinglab.unsw.edu.au_298.html ************************************************* Thu May 1 23:33:27 2003 Number: 299 Name: Lai, Yuching Affiliation: UNSW Address: UNSW City: Sydney State/Provice: NSW Postal/Zip Code: 2052 Country: Australia Email: yuching@kinglab.unsw.edu.au Phone: 9385 2036 Fax: 9385 1483 I plan to use my laptop computer as part of my poster Category: Microarrays Poster Title: Reliable feature extraction from mechanically spotted two-color microarrays. What is a poor girl to do Poster Authors and organization: Yuching Lai¹, Greg Tyrelle², Daniel Di Giusto, Garry C. King
¹yuching@kinglab.unsw.edu.au, UNSW; ²greg@kinglab.unsw.edu.au, UNSW Abstract: Spotted DNA microarrays allow skinny girls to play with the big bully boys. An intrinsic weakness � spot inhomogeneity � can be turned into a strength by using pixel correlation methods to reliably extract red/green ratios, identify dye-selective quenching and cull spots by data quality. We compare our methods to established approaches. File: yuchingATkinglab.unsw.edu.au_299.html ************************************************* Thu May 1 23:34:43 2003 Number: 300 Name: Willadsen, Kai Affiliation: Univeristy of Queensland Address: Unit 2 18 Ada St., Taringa City: Brisbane State/Provice: QLD Postal/Zip Code: 4066 Country: Australia Email: kaiw@itee.uq.edu.au Phone: 33658302 Fax: Category: Systems Biology Poster Title: High level properties of genetic regulatory network Poster Authors and organization: Kai Willadsen¹, Janet Wiles²
¹kaiw@itee.uq.edu.au, University of Queensland; ², University of Queensland Abstract: Abstract models of gene regulation date back to the development of the Random Boolean Network model in 1969. This class of models aims to investigate emergent properties of genetic regulatory networks with a view to better understanding high-level characteristics of the behaviours that these systems display. File: kaiwATitee.uq.edu.au_300.html ************************************************* Thu May 1 23:36:08 2003 Number: 301 Name: Upadhyaya, Minesh Affiliation: UCHSC Address: 4200 East 9th Avenue, C-245 City: Denver State/Provice: Colorado Postal/Zip Code: 80262 Country: USA Email: minesh.upadhyaya@uchsc.edu Phone: 3033156876 Fax: Category: Predictive Methods Poster Title: Metabolic Pathway Analysis, Prediction and Visualization Poster Authors and organization: Minesh Upadhyaya¹, Daniel McShan², Imran Shah
¹minesh.upadhyaya@uchsc.edu, UCHSC; ²daniel.mcshan@uchsc.edu, UCHSC Abstract: Elucidating the metabolic network of a living system is an important requirement for modeling its physiological behavior and for engineering its pathways. We have developed an artificial intelligence (AI) approach for the prediction of metabolic pathways and their interactive visualization. File: minesh.upadhyayaATuchsc.edu_301.html ************************************************* Thu May 1 23:45:37 2003 Number: 302 Name: Clark, Francis Affiliation: Advanced Computational Modelling Centre, University of Queensland, Australia. Address: University of Queensland City: Brisbane State/Provice: Queensland Postal/Zip Code: 4067 Country: Australia Email: fc@maths.uq.edu.au Phone: 33658586 Fax: Category: Data Mining Poster Title: Issues and principles in the analysis of large genomic datasets. Poster Authors and organization: Francis Clark¹, Susan Lilley²
¹fc@maths.uq.edu.au, Advanced Computational Modelling Centre, University of Queensland, Australia.; ²s364202@student.uq.edu.au, School of Information Technology & Electrical Engineering, University of Queensland, Australia. Abstract: Development of research analysis pipelines often involves working with poorly understood data to answer questions that are, initially, simplistic. This poster overviews some strategies and best practices that may be employed in such work, including; handling & appraisal of the data, choice of appropriate thresholds, extrapolation, and checking for reasonableness. File: fcATmaths.uq.edu.au_302.html ************************************************* Thu May 1 23:50:00 2003 Number: 303 Name: Batalov, Serge Affiliation: GNF Address: 10675 JJ Hopkins Dr City: San Diego State/Provice: CA Postal/Zip Code: 92121 Country: USA Email: batalov@gnf.org Phone: +1-858-8121569 Fax: +1-858-8121502 Category: Microarrays Poster Title: Target selection for the custom oligonucleotide array by clustering experimentally determined and computationally predicted transcript sets in mouse Poster Authors and organization: Serge Batalov¹
¹batalov@gnf.org, GNF Abstract: Custom oligonucleotide array design is aimed at effectively interrogating a largest possible non-redundant set of transcripts under a physical size constraint. 200,000+ publicly available and proprietary mouse transcript sequences were clustered. The custom chip was subsequently extensively used to profile the expression in 70+ different tissues. File: batalovATgnf.org_303.html ************************************************* Thu May 1 23:50:20 2003 Number: 304 Name: Matthews, Paul L Affiliation: Australian Genome Research Facility Address: Gehrmann Labs, Research Road, University of Queensland City: Brisbane State/Provice: QLD Postal/Zip Code: 4072 Country: Australia Email: paul@agrf.org.au Phone: 33469204 Fax: 33651823 I plan to use my laptop computer as part of my poster Category: Predictive Methods Poster Title: Genefiler: High throughput genetic analysis. Raw data to analysed results with one click Poster Authors and organization: Paul Matthews¹, I Findlay², D Mouradov, BK Mulcahy
¹paul@agrf.org.au, AGRF; ²Ian@agrf.org.au, AGRF Abstract: Current genotyping analysis packages provide basic genetic marker interpretation. However, many applications often require further manual specialised analysis, which is labour intensive and expensive. We developed Genefiler, software providing massive genotyping capability, giving diagnostic results from raw data, comprehensive project management, intuitive GUI and a flexible modular format. File: paulATagrf.org.au_304.html ************************************************* Thu May 1 23:58:45 2003 Number: 305 Name: Lee, Su-Hyun Affiliation: Changwon National University Address: 9 Sarim-Dong City: Changwon State/Provice: Kyung-Nam Postal/Zip Code: 641-773 Country: South Korea Email: suhyun@sarim.changwon.ac.kr Phone: +82-55-279-7426 Fax: +82-55-279-7420 Category: Structural Biology Poster Title: Comparing Protein Structures with Constraints Poster Authors and organization: Su-Hyun Lee¹, Jin-Hong Kim², Geon-Tae Ahn, and Myung-Joon Lee
¹suhyun@sarim.changwon.ac.kr, Changwon National University, South Korea; ²avenue@ulsan.ac.kr, University of Ulsan, South Korea Abstract:
S4E, a protein structure comparison system using constraint technology, searches common substructures of secondary structure elements between two proteins given in PDB format. For fast comparison, we developed an efficient algorithm for constructing the compatibility graphs and applying constraint programming to finding maximal common subgraphs.
File: suhyunATsarim.changwon.ac.kr_305.html ************************************************* Fri May 2 00:03:00 2003 Number: 306 Name: Sarai, Akinori Affiliation: Kyushu Institute of Technology Address: 680-4 Kawazu City: Iizuka State/Provice: Fukuoka Postal/Zip Code: 820-8502 Country: Japan Email: sarai@bse.kyutech.ac.jp Phone: 81-948-29-7811 Fax: 81-948-29-7801 Category: Predictive Methods Poster Title: QSAR Analysis of Transcription Factors Poster Authors and organization: Akinori Sarai¹, Samuel Selvaraj², Michael M. Gromiha, Hidetoshi Kono
¹sarai@bse.kyutech.ac.jp, KIT; ²sel_emi@yahoo.co.uk, Bharathidasan University Abstract: We have analyzed relationship between structure and function (activity) of transcription factors, based on two approaches: a knowledge-based approach, utilizing structural data of protein-DNA complexes, and computer simulations. We have examined the roles of structural deformation of DNA and cooperativity in target recognition, and predicted targets in yeast genome. File: saraiATbse.kyutech.ac.jp_306.html ************************************************* Fri May 2 00:04:21 2003 Number: 307 Name: Kim, Bumjin Affiliation: Division of Molecular Life Sciences, Ewha Womans University Address: 11-1 Daehyun-dong, Seodaemun-gu City: Seoul State/Provice: Postal/Zip Code: 120-750 Country: KOREA Email: uandikbj@hotmail.com Phone: +82-2-3277-2288 Fax: Category: Data Mining Poster Title: Hierarchical classification of cDNA libraries for gene expression analysis Poster Authors and organization: Bumjin Kim¹, Sanghyuk Lee², Hyunjung Lee, Young-Ah Shin, Euiju Jung, Pora Kim
¹unikbj@ewha.ac.kr, Division of Molecular Life Sciences, Ewha Womans University, Seoul 120-750, KOREA; ²sanghyuk@ewha.ac.kr, Division of Molecular Life Sciences, Ewha Womans University, Seoul 120-750, KOREA Abstract: Approximately 8,200 human cDNA libraries in dbEST were hierarchically classified in a hierarchical fashion in four gene expression categories � tissue, pathology, developmental stage, and sex. Web-based application for profiling gene expression using the resulting database is available at http://genome.ewha.ac.kr/EODB/. File: uandikbjAThotmail.com_307.html ************************************************* Fri May 2 00:04:57 2003 Number: 308 Name: Flegg, Robert H Affiliation: Victorian Bioinformatics Consortium Address: Monash University City: Clayton State/Provice: Vic Postal/Zip Code: 3800 Country: Australia Email: robert.flegg@med.monash.edu.au Phone: 61 3 9905 9866 Fax: 61 3 9905 9773 Category: Phylogeny and Evolution Poster Title: BOSS: Boxes of Sequence Similarity Poster Authors and organization: Robert Flegg¹, Malcolm Simons²
¹robert.flegg@med.monash.edu.au, VBC; ²mjsimons@optusnet.com.au, Abstract: Alignments display a mosaic pattern due to recombination. Existing programs use a broad window to find major events. This leads to not recognising the finer detail where multiple events occur at different points in different lineages. BOSS uses pairwise comparison and a short sliding window to analyse this mosaic structure. File: robert.fleggATmed.monash.edu.au_308.html ************************************************* Fri May 2 00:11:53 2003 Number: 309 Name: Yamada, Yohei S Affiliation: Department of Environmental Information, Keio University Address: 5322 Endo City: Fujisawa State/Provice: Kanagawa Postal/Zip Code: 252-0807 Country: Japan Email: skipper@g-language.org Phone: 0466475099 Fax: 0466475099 I plan to use my laptop computer as part of my poster Category: New Frontiers Poster Title: G-language Genome Analysis Environment Version 2 Poster Authors and organization: Yohei Yamada¹, Kazuharu Arakawa², Ryo Hattori, Yusuke Kobayashi, Hayataro Kouchi, Atsuko Kishi, Masaru Tomita
¹skipper@g-language.org, Keio University, Department of Environmental Information; ²gaou@g-language.org, Keio Institute for Advanced Biosciences Abstract: Version 2 of the G-language Genome Analysis Environment is developed to gain further speed and integrity through the object-oriented architecture. Powered by the front-end \"inspire\" based on Flash/HTML and the database system \"bluebird\", the new environment aims to achieve greater flexibility and integrity. File: skipperATg-language.org_309.html ************************************************* Fri May 2 00:15:34 2003 Number: 310 Name: Stolk, Henk Affiliation: University of Queensland Address: St Lucia Campus City: Brisbane State/Provice: QLD Postal/Zip Code: 4072 Country: Australia Email: hjs@maths.uq.edu.au Phone: 07 3378 3173 Fax: Category: Systems Biology Poster Title: Emergent Models in Complex System Simulations of Genetic and Biochemical Networks Poster Authors and organization: Henk Stolk¹, Kevin Gates², Jim Hanan
¹hjs@maths.uq.edu.au, University of Queensland; ²keg@maths.uq.edu.au, University of Queensland Abstract: Complex systems are simulated by interacting software agents at various hierarchical levels. Emergent macro-level models are derived from micro-level properties and behavior, for example by genetic programming algorithms. Micro-level models are also derived from macro-level behavior. The methodology can relate micro-level genetic and biochemical networks to macro-level gene expression patterns. File: hjsATmaths.uq.edu.au_310.html ************************************************* Fri May 2 00:23:21 2003 Number: 311 Name: Kim, Chan-Wha Affiliation: Graduate School of Life Sciences and Biotechnology Address: 5-1 ga, Anam-dong City: Seoul State/Provice: Postal/Zip Code: 136-701 Country: South Korea Email: cwkim@korea.ac.kr Phone: 82-2-3290-3439 Fax: 82-2-3290-3957 Category: Predictive Methods Poster Title: Improved Approach on Protein Identification Using Poster Authors and organization: Won-A Joo¹, Kap-Soon Noh², Chan-Wha Kimm
¹wajoo0824@hanmail.net, Graduate School of Life Sciences and Biotechnology; ², Graduate School of Life Sciences and Biotechnology Abstract: Peptide mass fingerprint (PMF) has been a useful method for rapid and high-throughput protein identification. In our study, we compared softwares used frequently to identify the proteins of Homo sapience and Halobacterium salinarum. These attempts could provide more effective algorithm for the protein identification as each species using PMF. File: cwkimATkorea.ac.kr_311.html ************************************************* Fri May 2 00:32:46 2003 Number: 312 Name: Izumitani, Tomonori Affiliation: NTT Communication Science Laboratories Address: 2-4, Hikaridai City: Seika-cho, Soraku-gun State/Provice: Kyoto Postal/Zip Code: 619-0237 Country: JAPAN Email: izumi@cslab.kecl.ntt.co.jp Phone: +81-774-93-5354 Fax: +81-774-93-5385 Category: Data Mining Poster Title: Detection of implicit protein-protein interactions from literature Poster Authors and organization: Tomonori Izumitani¹, Frederic Tingaud², Hirotoshi Taira, Eisaku Maeda
¹izumi@cslab.kecl.ntt.co.jp, NTT Communication Science Laboratories; ²tingaud@cslab.kecl.ntt.co.jp, NTT Communication Science Laboratories Abstract: In this study, we propose a method to detect explicit or implicit protein-protein interactions from text data. It was applied to the detection of interactions between yeast proteins. The result indicates that the putative interactions detected by the method can contain true and experimentally unidentified interactions. File: izumiATcslab.kecl.ntt.co.jp_312.html ************************************************* Fri May 2 00:36:35 2003 Number: 313 Name: Brown, Chris M Affiliation: University of Otago Address: 710 Cumberland Street City: Dunedin State/Provice: Otago Postal/Zip Code: 9000 Country: New Zealand Email: chris.brown@otago.ac.nz Phone: 643 4795201 Fax: 643 4797866 Category: Functional Genomics Poster Title: Detection of Global and Gene Specific Translational Control Signals in mRNAs Poster Authors and organization: Chris M Brown¹, Grant Jacobs², Mark Dalphin and Peter Stockwell
¹chris.brown@otago.ac.nz, University of Otago; ²gjacobs@bioinfotools.com, Bioinfotools Abstract: We wish to detect signals in mRNAs that influence their translation. These include signals that modulate translation efficiency, mRNA stability or its localisation. To do this we have developed the TransTerm database (transterm.otago.ac.nz) of mRNA regions and regulatory elements. We have detected novel elements and are testing them in vivo. File: chris.brownATotago.ac.nz_313.html ************************************************* Fri May 2 00:35:35 2003 Number: 314 Name: Hartig, Gerald R Affiliation: Institute for Molecular Bioscience, University of Queensland Address: St Lucia, Queensland Bioscience Precinct City: Brisbane State/Provice: QLD Postal/Zip Code: 4072 Country: Australia Email: g.hartig@imb.uq.edu.au Phone: 3346-2975 Fax: Category: Data Mining Poster Title: Comparison of intra-molecular disulphide bonding arrangements between disulphide-rich and -poor proteins in the Protein Data Bank Poster Authors and organization: Gerald Hartig¹, Tran Trung Tran², Mark Smythe
¹g.hartig@imb.uq.edu.au, Institute for Molecular Bioscience; ²tran@doctor.com, Protagonist Pty Ltd Abstract: Intra-molecular disulphide bonds (IDSB) are an important determinant of a protein�s 3D conformation. This work describes the differences in IDSB arrangements between disulphide-rich and -poor proteins. A naturally occurring partition of 25.2 residues / IDSB was used, revealing differences in PDB headers, SCOP folds, IDSB bonding patterns and loop lengths. File: g.hartigATimb.uq.edu.au_314.html ************************************************* Fri May 2 00:38:17 2003 Number: 315 Name: Chae, Sujin Affiliation: Bioinfomatix, Inc. Address: Seocho 1-dong City: SEOUL State/Provice: Seocho-gu Postal/Zip Code: 137-864 Country: KOREA Email: sujin@bioinfomatix.com Phone: 82-2-3445-4533 Fax: 82-2-514-1977 Category: Databases Poster Title: updateBASE : Real-time automatic updating system of biological databases under the client-server environment. Poster Authors and organization: Sujin Chae¹, Mira Roh², Ji-Hoon Jun, Geunwoo Lee, Yong-ho In
¹sujin@bioinfomatix.com, Bioinfomatix Inc.; ²mrroh@bioinfomatix.com, Bioinfomatix Inc. Abstract: We developed the updateBASE system which provides real-time, automatic updating of biological databases under the client-server architecture. Using this system, an annotator can get up-to-date database sources and get more confident annotation results. The updateBASE will do effective supporting role in predicting functions and relationships of unknown sequences. File: sujinATbioinfomatix.com_315.html ************************************************* Fri May 2 00:55:42 2003 Number: 316 Name: Kim, Sang Cheol Affiliation: Brain Korea 21 Project for Medical Science, Cancer Metastasis Research Center, Yonsei University College of Medicine Address: 134, Shinchon-Dong Seodaemun-ku, C.P.O.BOX 8044 City: Seoul State/Provice: Postal/Zip Code: Country: S. Korea Email: kimsc77@yonsei.ac.kr Phone: 82-2-2123-4471 Fax: 82-2-362-5592 Category: Microarrays Poster Title: Normalization of cDNA Microarray Data Using R-Language Poster Authors and organization: Sang Cheol Kim¹, In Uk Hwang², In Young Kim�, Sunho Lee�, Hyun Cheol Chung�, Sun Young Rha� Byung Soo Kim�
¹kimsc77@yonsei.ac.kr, Brain Korea 21 Project for Medical Science, Cancer Metastasis Research Center, Yonsei University College of Medicine; ²mzhwang@yonsei.ac.kr, Applied Statistics, Yonsei University Abstract: The user-friendly R-based software program NOM-R, implemented Yang et al�s normalization procedures is developed. This program is not only convenient for the biologists to use in microarray data normalization, but also can handle the repeated intensity values and dye-swap experiments, simultaneously. File: kimsc77ATyonsei.ac.kr_316.html ************************************************* Fri May 2 01:09:06 2003 Number: 317 Name: Rubin, Eitan Affiliation: Bioinformatics and Biological Computing, Weizmann Institute of Science Address: PO Box 26 City: Rehovot State/Provice: Postal/Zip Code: 76100 Country: Israel Email: Eitan.Rubin@weizmann.ac.il Phone: 972-8-9343456 Fax: 972-8-9346006 Category: Databases Poster Title: CleanBank: a database of sequence artifacts Poster Authors and organization: Hanne Volpin¹, Eitan Rubin²
¹hanne@agri.gov.il, Bioinformatics, Agricultural Research Organization, Bet Dagan, Israel; ²Eitan.Rubin@weizmann.ac.il, Bioinformatics and Biological Computing, Weizmann Institute of Science, Rehovot, Israel Abstract:
CleanBank is a database that documents suspected artifacts found in sequences and/or their annotation in the international sequence databases. The artifacts are either reported by researchers, or identified by curated algorithms. Current algorithms detect E. coli and vector contamination. For a detailed description and a preview, see http://bip.weizmann.ac.il/MIW/CleanBank/index.html
File: Eitan.RubinATweizmann.ac.il_317.html ************************************************* Fri May 2 01:16:45 2003 Number: 318 Name: Zadissa, Amonida Affiliation: Biochemistry Department, Otago University Address: 710 Cumberland Street City: Dunedin State/Provice: NA Postal/Zip Code: 9015 Country: New Zealand Email: amonida@sanger.otago.ac.nz Phone: +64 3 479 78 75 Fax: +64 3 479 78 66 Category: Sequence Comparison Poster Title: Use of motif analysis programs to identify putative regulatory elements in the orthologous human promoters of co-regulated bovine genes Poster Authors and organization: Amonida Zadissa¹, John McEwan², Chris Brown
¹amonida@sanger.otago.ac.nz, Biochemistry Department, Otago University; ²john.mcewan@agresearch.co.nz, AgResearch Abstract: We aim to identify putative regulatory elements in the orthologous human promoters of co-regulated bovine genes. Promoters were extracted and Motif prediction was performed by MEME. The MatInspector Professional software and BioPerl programs were used to assess the results. Novel putative elements were identified in the human promoters. File: amonidaATsanger.otago.ac.nz_318.html ************************************************* Fri May 2 01:20:00 2003 Number: 319 Name: Shin, Dong-Mi Affiliation: Hanyang University Address: Haengdang-dong City: Seoul State/Provice: . Postal/Zip Code: 133-792 Country: Korea Email: dongmishin@yahoo.com Phone: 82-2-2291-8396 Fax: 82-2-2291-8397 Category: Microarrays Poster Title: Expression profiling and analysis of transcription factors for neuronal differentiation from stem cells Poster Authors and organization: Dong Mi Shin¹, Joon Ik Ahn², Ki Hwan Lee, Young Seek Lee, Yong Sung Lee
¹dongmishin@yahoo.com, Hanyang University; ²joonic@gaiagene.com, Hanyang University Abstract: To identify transcription factors that may play an important role in the differentiation of stem cells to neurons, high throughput gene expression experiment and computational analysis were performed. Our result suggest many transcription factors- novel transcription factors as well as those previously known to be involved in differentiation signaling. File: dongmishinATyahoo.com_319.html ************************************************* Fri May 2 01:28:35 2003 Number: 320 Name: Dogrusoz, Ugur Affiliation: Bilkent Center for Bioinformatics Address: Bilkent University City: Ankara State/Provice: Postal/Zip Code: 06800 Country: Turkey Email: ugur@cs.bilkent.edu.tr Phone: 90 312 290 1612 Fax: 90 312 266 4047 I plan to use my laptop computer as part of my poster Category: Functional Genomics Poster Title: PATIKA: Pathway Analysis Tool for Integration and Knowledge Acquisition Poster Authors and organization: Emek¹, Ozgun², Ugur Dogrusoz, Attila Gursoy, Asli Ayaz, Gurcan Gulesir, Gurkan Nisanci, Rengul Cetin-Atalay, and Mehmet Ozturk
¹emek@cs.bilkent.edu.tr, BCBI; ²babur@cs.bilkent.edu.tr, BCBI Abstract: PATIKA is an ongoing research and development project for collaborative construction and analysis of cellular pathways. Our software tool provides an integrated, multi-user environment for visualizing and manipulating network of cellular events. PATIKA is available at http://www.patika.org. File: ugurATcs.bilkent.edu.tr_320.html ************************************************* Fri May 2 01:32:15 2003 Number: 321 Name: Hwang, Young S. Affiliation: Dept of CSE, Korea Univ. Address: 5ga Anam-dong SungBuk-gu City: Seoul State/Provice: NA Postal/Zip Code: 136-701 Country: KOREA Email: yshwang@nlp.korea.ac.kr Phone: 82-2-924-2054 Fax: 82-2-929-7914 Category: Data Mining Poster Title: Intimately Incorporated NLP System Adapted for Bio-Text Mining Poster Authors and organization: Young-Sook Hwang¹, Hae-Chang Rim², Kyoung-MePark, Ki-Joong Lee, Hong-Woo Chun
¹yshwang@nlp.korea.ac.kr, Korea Univ.; ²rim@nlp.korea.ac.kr, Korea Univ. Abstract: BioNLPro is a system for providing the base for a robust bio-text mining system. It is an intimately integrated NLP system consisting of the adapted core NLP modules reflecting the peculiarities of bio-text including a POS tagger, a biological term recognizer, a grammatical relation tagger based on chunking and a biological event extractor. File: yshwangATnlp.korea.ac.kr_321.html ************************************************* Fri May 2 01:37:58 2003 Number: 322 Name: Jeong, Kwang Su Affiliation: Chungbuk National University Address: 48 Gaeshin-dong City: Cheongju State/Provice: Chungbuk Postal/Zip Code: 361-763 Country: Republic of Korea Email: ksjeong@dblab.chungbuk.ac.kr Phone: 82-43-267-2250 Fax: 82-43-275-2254 I plan to use my laptop computer as part of my poster Category: New Frontiers Poster Title: Integrated data Modeling of Protein Structures by using a fact constellation model based on a XML Mediated Warehouse System Poster Authors and organization: RongHua Li¹, Sung-Hee Park², Kwang Su Jeong, Keun Ho Ryu
¹lrh@dblab.chungbuk.ac.kr, Chungbuk University; ²shpark@dblab.chungbuk.ac.kr, Chungbuk University Abstract: This paper describes integrated protein structure modeling by using a fact constellation model and represents this modeling to XML in order to store and query highly complex protein data based on a XML mediated warehouse system. It performs complex queries employed during analyzing process by using XML query processing. File: ksjeongATdblab.chungbuk.ac.kr_322.html ************************************************* Fri May 2 01:49:59 2003 Number: 323 Name: Hamano, Tetsutaro Affiliation: Division of Biostatistics, Kitasato University Graduate School Address: 5-9-1 City: Shirokane, Minato-ku State/Provice: Tokyo Postal/Zip Code: 108-8641 Country: Japan Email: hamanot@pharm.kitasato-u.ac.jp Phone: +81-3-5791-6322 Fax: +81-3-3444-2546 Category: Microarrays Poster Title: Latin Square Design to Gene Expression Experiments Poster Authors and organization: Tetsutaro Hamano¹, Akira Ohide², Masaru Sekijima, Kazuto Nishio, Masahiro Takeuchi, Yasuhiro Fujiwara
¹hamanot@pharm.kitasato-u.ac.jp, Division of Biostatistics, Kitasato University Graduate School, Japan; ²a-ohide@ankaken.co.jp, Applied Biology Division, Kashima Laboratory, Mitsubishi Chemical Safety Institute, Japan Abstract: We used a randomized Latin square design for blocking experimental variations and for estimating tamoxifen effect in human breast cancer cell lines assay. Orthogonal decomposition of a gene expression map based on the experimental design is expected to elucidate treatment effects as well as systematic error components. File: hamanotATpharm.kitasato-u.ac.jp_323.html ************************************************* Fri May 2 01:59:41 2003 Number: 324 Name: von Langen, Johannes R.G. Affiliation: IMB-Jena Address: Beutenbergstr. 11 City: Jena State/Provice: Thueringen Postal/Zip Code: 07743 Country: Germany Email: langen@imb-jena.de Phone: +49-3641-656213 Fax: +49-3641-656210 Category: Structural Biology Poster Title: Molecular basis of ligand recognition in the human glucocorticoid receptor Poster Authors and organization: Johannes R.G. von Langen¹, Stephan Diekmann², Alexander Hillisch
¹langen@imb-jena.de, IMB-Jena; ²diekmann@imb-jena.de, IMB-Jena Abstract: The glucocorticoid receptor selectively recognises cortisol with high affinity. We build a homology model of this receptor on the basis of the progesterone receptor x-ray structure and simulated binding of different steroids (estradiol, progesterone, testosterone, aldosterone and cortisol). Using molecular dynamics simulations and free energy calculations we were able reveal the molecular basis of ligand recognition. File: langenATimb-jena.de_324.html ************************************************* Fri May 2 02:00:16 2003 Number: 325 Name: Kim, Yong Wook Affiliation: Bioinfomatix, Inc. Address: Sung Woo Bldg., 1424-2, Seocho 1-dong City: Seoul State/Provice: Postal/Zip Code: 137-864 Country: Korea Email: yongari@bioinfomatix.com Phone: 82-2-3445-4533 Fax: 82-2-514-1977 Category: New Frontiers Poster Title: Using XML-RPC for Distributed BLAST -Desterilizing idle resources- Poster Authors and organization: Yong Wook Kim¹
¹yongari@bioinfomatix.com, Bioinfomatix, Inc. Abstract: Usually, personal computers are operated on the MS Window. But the computing power is used for simple works. We try to use these available resources for a member of the clustering system. XML-RPC provides the straight way for distributed BLAST and heterogeneous operating systems can be used as a member of the distributed system for BLAST. File: yongariATbioinfomatix.com_325.html ************************************************* Fri May 2 02:05:07 2003 Number: 326 Name: Lapp, Hilmar Affiliation: Genomics Institute of the Novartis Research Institute Address: 10675 John J Hopkins Dr City: San Diego State/Provice: CA Postal/Zip Code: 92121 Country: USA Email: hlapp@gnf.org Phone: +1-858-812-1757 Fax: Category: Databases Poster Title: Optimizing Genome Interval Overlap Queries Using an R-Tree Index Poster Authors and organization: Hilmar Lapp¹, Chris Mungall², Scott Cain, Lincoln Stein
¹hlapp@gnf.org, GNF; ²cjm@fruitfly.org, University of California, Berkely Abstract: We present a solution to the huge variance problem that has plagued B-tree supported genome interval overlap queries. Our approach is based on translating the overlap query into a two-dimensional point-in-box geometric query supported by an R-tree index. File: hlappATgnf.org_326.html ************************************************* Fri May 2 02:10:44 2003 Number: 327 Name: Chung, Myungguen Affiliation: Hanyang University Address: Sa-1dong Sangnok-Gu City: Ansan State/Provice: Kyunggido Postal/Zip Code: 426-791 Country: Korea Email: aobo@chollian.net Phone: +82 16 776 3726 Fax: +82 31 419 0940 Category: Functional Genomics Poster Title: Prediction of a full length gene from partial sequence Poster Authors and organization: Chung, Myungguen¹, Cho, Sooyoung², Ban, hyojeong ; Kim, hyun and Lee Youngseek
¹aobo@ihanyang.ac.kr, Hanyang University; ²singylu@hanmail.net, Hanyang University Abstract: We obtained 3’ end partial sequence of cDNA which do not have homologous of ‘nr’ by using BLAST. We predicted full length genes from partial sequence and cloned full length genes by using a predicted sequence File: aoboATchollian.net_327.html ************************************************* Fri May 2 02:19:52 2003 Number: 328 Name: Do, Chuong B Affiliation: Stanford University Address: P.O. Box 17454 City: Stanford State/Provice: CA Postal/Zip Code: 94309 Country: USA Email: chuong.do@stanford.edu Phone: 650-497-4227 Fax: Category: Sequence Comparison Poster Title: LAGAN2: Probabilistic Global Alignment of DNA Under Multiple Conservation Models Poster Authors and organization: Chuong B. Do¹, Michael Brudno², Serafim Batzoglou
¹chuong.do@stanford.edu, Stanford University; ²brudno@cs.stanford.edu, Stanford University Abstract: LAGAN2 is a probabilistic method for limited area global nucleotide alignment of distantly related species. The algorithm incorporates multiple conservation models for protein-coding, non-coding, and unconstrained alignments, approximate logarithmic gap penalties, and Hidden Markov Model based training of alignment parameters through expectation-maximization. Additional information is available at http://lagan.stanford.edu. File: chuong.doATstanford.edu_328.html ************************************************* Fri May 2 02:23:29 2003 Number: 329 Name: Upadhyaya, Minesh Affiliation: UCHSC Address: 4200 East 9th Avenue, C-245 City: Denver State/Provice: Colorado Postal/Zip Code: 80262 Country: USA Email: minesh.upadhyaya@uchsc.edu Phone: 3033156876 Fax: Category: Predictive Methods Poster Title: Metabolic Pathway Analysis, Prediction and Visualization Poster Authors and organization: Minesh Upadhyaya¹, Daniel McShan², Imran Shah
¹minesh.upadhyaya@uchsc.edu, UCHSC; ²daniel.mcshan@uchsc.edu, UCHSC Abstract: Elucidating the metabolic network of a living system is an important requirement for modeling its physiological behavior and for engineering its pathways. We have developed an artificial intelligence (AI) approach for the prediction of metabolic pathways and their interactive visualization. File: minesh.upadhyayaATuchsc.edu_329.html ************************************************* Fri May 2 02:29:24 2003 Number: 330 Name: Chalk, Alistair M Affiliation: Center for Genomics and Bioinformatics, Karolinksa Institute Address: Berzelius vag 35 City: Stockholm State/Provice: Stockholm Postal/Zip Code: 171 77 Country: Sweden Email: alistair.chalk@cgb.ki.se Phone: +46739824296 Fax: +468337983 Category: Functional Genomics Poster Title: Design of Antisense Oligonucleotides Poster Authors and organization: Alistair M. Chalk¹, Erik L.L. Sonnhammer²
¹alistair.chalk@cgb.ki.se, CGB, Karolinska Institute; ²esr@algol.cgb.ki.se, CGB, Karolinska Institute Abstract: Antisense oligonucelotides are an important tool for gene-knockdown approaches in functional genomics. We assess the usefulness of current approaches predicting accessibility and/or efficacy using a database of known results. A set of utilities developed for AO and siRNA design (control design, specificity, site selection) is available at http://sonnhammer.cgb.ki.se. File: alistair.chalkATcgb.ki.se_330.html ************************************************* Fri May 2 02:37:20 2003 Number: 331 Name: Eriksson, Tore Affiliation: Taisho Pharmaceuticals, Co., Ltd. Address: Yoshino-cho 1-403 City: Saitama-shi State/Provice: Saitama-ken Postal/Zip Code: 330-8530 Country: Japan Email: tore.eriksson@po.rd.taisho.co.jp Phone: +81-48-669-3026 Fax: +81-48-652-7254 Category: Data Mining Poster Title: A dimensional data warehouse for biological data Poster Authors and organization: Tore Eriksson¹, Katsuki Tsuritani²
¹tore.eriksson@po.rd.taisho.co.jp, Taisho Pharmaceuticals, Co., Ltd.; ²k.tsuritani@po.rd.taisho.co.jp, Taisho Pharmaceuticals, Co., Ltd. Abstract:
Data warehousing using dimensional modeling and star schema data marts was applied to biological information. The data marts capture biological relationships like gene--protein, as well as numerical data in the intersection between dimensions for example expression data.

Focus was also on building a automatized extraction and transformation of a wide range of public data sources.
File: tore.erikssonATpo.rd.taisho.co.jp_331.html ************************************************* Fri May 2 02:44:31 2003 Number: 332 Name: Kang, Eun-Mi Affiliation: Pusan National University Address: Jangjeon-dong, Geumjeong-gu City: Busan State/Provice: Postal/Zip Code: 609-735 Country: Rep. of KOREA Email: emkang@pearl.cs.pusan.ac.kr Phone: +82-51-582-5009 Fax: +82-51-515-2208 Category: Data Mining Poster Title: Detection of Program Source Code Plagiarism Using Genomic Sequence Alignments Methodology Poster Authors and organization: Eun-Mi Kang¹, Hwan-Gue Cho², Young-Min Kang
¹emkang@pearl.cs.pusan.ac.kr, Pusan National University; ²hgcho@pusan.ac.kr, Pusan National University Abstract: We propose a new method for detecting the plagiarism by exploiting the genomic sequence alignment. The system extracts linear sequences of keywords from the source code flow, and computes the local alignments to detect local similarity of original sources. The experimental results show this approach is more powerful than fingerprinting-matching. File: emkangATpearl.cs.pusan.ac.kr_332.html ************************************************* Fri May 2 02:48:45 2003 UPDATE ----- Number: 289 Name: Won, Hong-Hee Affiliation: Yonsei University Address: 134 Shinchon-dong, Sudaemoon-ku City: Seoul State/Provice: Postal/Zip Code: 120749 Country: Korea, Republic Of Korea Email: cool@candy.yonsei.ac.kr Phone: +82221234803 Fax: +8223652579 Category: Data Mining Poster Title: Extracting informative genes with negative correlation for accurate cancer classification Poster Authors and organization: Hong-Hee Won¹, Sung-Bae Cho²
¹cool@candy.yonsei.ac.kr, Yonsei University; ²sbcho@cs.yonsei.ac.kr, Yonsei University Abstract: We define two negatively correlated ideal gene vectors which represent the patterns of classes well and extract two significant gene subsets (SGSs) based on the similarity to two ideal genes. We train the neural network classifiers with SGSs and combine them. The ensemble classifier produces the best recognition rate-97.1% in Leukemia, 87.1% in Colon, and 92.0% in Lymphoma. File: coolATcandy.yonsei.ac.kr_289 ************************************************* Fri May 2 03:01:59 2003 Number: 333 Name: Tae, Hongseok Affiliation: Dept. of Microbiology, Kyungpook National University Address: Pook-Gu Sankyuk-Dong City: Daegu State/Provice: Postal/Zip Code: 702-701 Country: South Korea Email: hstae@smallsoft.co.kr Phone: +82-42-864-2524 Fax: +82-42-866-9241 Category: Systems Biology Poster Title: ISAWB : a Windows-based Integrated Workbench for Managing Sequence Information in Small Scale Poster Authors and organization: Hongseok Tae¹, Hyeweon Nam², Daesang Lee, Kiejung Park
¹hstae@smallsoft.co.kr, Dept. of Microbiology, Kyungpook National University; ²hwnam@smallsoft.co.kr, Information Technology Institute, SmallSoft Co., Ltd. Abstract: ISAWB is a small workbench for managing sequence data and analyzing them to get processed information with Windows GUI. It contains data management features and eleven analysis module tools suggested by a Korean MOST project while each module is composed of a few objects in C++ classes, for reusability. File: hstaeATsmallsoft.co.kr_333.html ************************************************* Fri May 2 03:02:38 2003 UPDATE ----- Number: 269 Name: Wiltshire, T Affiliation: GNF Address: 10675 JJ Hopkins Dr City: San Diego State/Provice: CA Postal/Zip Code: 92121 Country: USA Email: batalov@gnf.org Phone: +1-858-8121569 Fax: +1-858-8121502 I plan to use my laptop computer as part of my poster Category: Data Visualisation Poster Title: GENOME-WIDE HAPLOTYPE STRUCTURE VISUALIZATION AND ANALYSIS IN MOUSE Poster Authors and organization: T.Wiltshire¹, Serge Batalov ², Mathew Pletcher, R.J.Mural, M.D.Adams, C.F.Fletcher
¹batalov@gnf.org, GNF; ²mpletche@gnf.org, TSRI Abstract: SNPview, the interactive navigator for the individual SNPs, SSLPs, alleles and haplotypes projected to the genomic axis is available on-line at http://www.gnf.org/SNP/ . Large, but discrete regions of the genome are not very polymorphic between particular strain pairs, and thus cannot easily be interrogated for natural genetic variations influencing QTLs. File: batalovATgnf.org_269 ************************************************* Fri May 2 03:06:33 2003 UPDATE ----- Number: 308 Name: Flegg, Robert H Affiliation: Victorian Bioinformatics Consortium Address: Monash University City: Clayton State/Provice: Vic Postal/Zip Code: 3800 Country: Australia Email: robert.flegg@med.monash.edu.au Phone: 61 3 9905 9866 Fax: 61 3 9905 9773 Category: Phylogeny and Evolution Poster Title: BOSS: Boxes of Sequence Similarity Poster Authors and organization: Robert Flegg¹, Malcolm Simons²
¹robert.flegg@med.monash.edu.au, GeneType Pty. Ltd., Fitzroy Vic 3065, Australia and Victorian Bioinformatics Consortium, PO Box 53, Monash University, Clayton Vic 3800, Australia; ²mjsimons@optusnet.com.au, Abstract: Alignments display a mosaic pattern due to recombination. Existing programs use a broad window to find major events. This leads to not recognising the finer detail where multiple events occur at different points in different lineages. BOSS uses pairwise comparison and a short sliding window to analyse this mosaic structure. File: robert.fleggATmed.monash.edu.au_308 ************************************************* Fri May 2 03:06:40 2003 Number: 334 Name: Tae, Hongseok Affiliation: Dept. of Microbiology, Kyungpook National University Address: Pook-Gu Sankyuk-Dong City: Daegu State/Provice: Postal/Zip Code: 702-701 Country: South Korea Email: hstae@smallsoft.co.kr Phone: +82-42-864-2524 Fax: +82-42-866-9241 Category: Genome Annotation Poster Title: Development of a Web-based Genome Annotation System and Two Analysis Tools Poster Authors and organization: Hongseok Tae¹, Hyeweon Nam², Daesang Lee, Kiejung Park
¹hstae@smallsoft.co.kr, Dept. of Microbiology, Kyungpook National University; ²hwnam@smallsoft.co.kr, Information Technology Institute, SmallSoft Co., Ltd. Abstract: Our web-based genome annotation system has major modules such as gene prediction, homology search, promoter analysis, motif analysis, gene ontology analysis, annotation databases, and a genome browser which shows the entire information of a genome. We have also developed a motif analysis and a gene prediction programs based on HMM. File: hstaeATsmallsoft.co.kr_334.html ************************************************* Fri May 2 03:10:54 2003 Number: 335 Name: Fariselli, Piero Affiliation: University of Bologna Address: via Irnerio 42 City: Bologna State/Provice: Postal/Zip Code: 40126 Country: Italy Email: piero.fariselli@unibo.it Phone: +390512094005 Fax: +39051242576 Category: Structural Biology Poster Title: Optimizing the location and the number of the maximal scoring subsequences with constrained segment lengths with MaxSubSeq Poster Authors and organization: Piero Fariselli¹, Pier Luigi Martelli², Ivan Rossi and Rita Casadio
¹gigi@biocomp.unibo.it, Uinversity of Bologna; ²gigi@biocomp.unibo.it, Uinversity of Bologna Abstract: We describe a general dynamic programming-like algorithm (MaxSubSeq) specifically designed to optimise the number and length of segments with constrained length in a protein sequence. Our algorithm is independent of the underling predictive method and is available through the web interface at http://gpcr.biocomp.unibo.it/predictor File: piero.fariselliATunibo.it_335.html ************************************************* Fri May 2 03:14:00 2003 UPDATE ----- Number: 320 Name: Dogrusoz, Ugur Affiliation: Bilkent Center for Bioinformatics Address: Bilkent University City: Ankara State/Provice: Postal/Zip Code: 06800 Country: Turkey Email: ugur@cs.bilkent.edu.tr Phone: 90 312 290 1612 Fax: 90 312 266 4047 I plan to use my laptop computer as part of my poster Category: Functional Genomics Poster Title: PATIKA: Pathway Analysis Tool for Integration and Knowledge Acquisition Poster Authors and organization: Emek Demir¹, Ozgun Babur², Ugur Dogrusoz, Attila Gursoy, Asli Ayaz, Gurcan Gulesir, Gurkan Nisanci, Rengul Cetin-Atalay, and Mehmet Ozturk
¹emek@cs.bilkent.edu.tr, BCBI; ²babur@cs.bilkent.edu.tr, BCBI Abstract: PATIKA is an ongoing research and development project for collaborative construction and analysis of cellular pathways. Our software tool provides an integrated, multi-user environment for visualizing and manipulating network of cellular events. PATIKA is available at http://www.patika.org. File: ugurATcs.bilkent.edu.tr_320 ************************************************* Fri May 2 03:20:30 2003 Number: 336 Name: Engstrom, Par Affiliation: Center for Genomics and Bioinformatics, Karolinska Institutet Address: Berzelius vag 35 City: Stockholm State/Provice: - Postal/Zip Code: 171 77 Country: Sweden Email: par.engstrom@cgb.ki.se Phone: +46-8-7286132 Fax: +46-8-324826 I plan to use my laptop computer as part of my poster Category: Functional Genomics Poster Title: Detection of natural antisense transcripts conserved between human and mouse Poster Authors and organization: Par Engstrom¹, Hidenori Kiyosawa², Claes Wahlestedt, Yoshihide Hayashizaki, Boris Lenhard
¹par.engstrom@cgb.ki.se, Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden; ²kiyosawa@rtc.riken.go.jp, RIKEN Bio Resource Center, RIKEN Tsukuba Institute, Tsukuba, Japan Abstract: We devised an automated computational procedure to detect pairs of overlapping and oppositely directed human transcriptional units (sense-antisense pairs) equivalent to a large set of putative mouse sense-antisense pairs previously predicted by cDNA mapping. We found support in the human transcriptome for a significant proportion of mouse sense-antisense pairs. File: par.engstromATcgb.ki.se_336.html ************************************************* Fri May 2 03:23:31 2003 Number: 337 Name: Fariselli, Piero Affiliation: Department of Biology CIRB, University of Bologna Address: via Irnerio 42 City: Bologna State/Provice: Postal/Zip Code: 40126 Country: Italy Email: piero@lipid.biocomp.unibo.it Phone: +39-51-2094005 Fax: +39-51-242576 Category: Predictive Methods Poster Title: Optimizing the location and the number of the maximal scoring Poster Authors and organization: Piero Fariselli¹, Pier Luigi Martelli², Ivan Rossi and Rita Casadio
¹piero@lipid.biocomp.unibo.it, Department of Biology CIRB, University of Bologna; ², Department of Biology CIRB, University of Bologna Abstract: We describe a general dynamic programming-like algorithm (MaxSubSeq) specifically designed to optimise the number and length of segments with constrained length in a protein sequence. Our algorithm is independent of the underling predictive method and is available through the web interface at http://gpcr.biocomp.unibo.it File: pieroATlipid.biocomp.unibo.it_337.html ************************************************* Fri May 2 03:31:32 2003 Number: 338 Name: Bellgard, Matthew I Affiliation: Centre for Bioinformatics and Biological Computing, Murdoch University Address: Murdoch South Street City: Perth State/Provice: Western Australia Postal/Zip Code: 6150 Country: Australia Email: m.bellgard@murdoch.edu.au Phone: +61-8-93606088 Fax: +61-8-93607238 I plan to use my laptop computer as part of my poster Category: Data Mining Poster Title: Computational comparative analysis framework at the Centre for Bioinformatics and Biological Computing. Poster Authors and organization: M Bellgard¹, A Hunter², D Schibeci
¹m.bellgard@murdoch.edu.au, CBBC, Murdoch University; ²a.hunter@cbbc.murdoch.edu.au, CBBC, Murdoch University Abstract: The CBBC conducts research in computational biology ranging from comparative genomic sequence analysis, microarray and proteomic data analysis, and novel algorithms and software. The CBBC is developing a comparative analysis framework incorporating audit trailing of analysis, open source activities and distributed resource management. We present an overview of this framework. File: m.bellgardATmurdoch.edu.au_338.html ************************************************* Fri May 2 03:35:50 2003 Number: 339 Name: Ahrens, Christian H Affiliation: MDS Denmark Address: Staermosegaardsvej 6 City: Odense M State/Provice: Fyn Postal/Zip Code: DK-5230 Country: Denmark Email: cahrens@mdsdenmark.com Phone: +45-6557-2119 Fax: +45-6557-2001 I plan to use my laptop computer as part of my poster Category: Functional Genomics Poster Title: A modular software platform integrating the processing and bioinformatic analysis of proteomics data Poster Authors and organization: Soeren Schandorff¹, Hans Jespersen², C. H. Ahrens, M. Damsbo, S. Larsen, B. K. Ramsgaard, E. T. Nielsen, G. Thorvil, J. P. Kristensen, K. P. Budin, J. Matthiesen, P. Ven�, J. C. Br�nd, T. Topaloglou, P. T. Ruhoff
¹schandorff@mdsdenmark.com, MDS Denmark; ²hjespersen@mdsdenmark.com, MDS Denmark Abstract: We have developed an integrated software platform that addresses data generation and handling, data verification/quality control and bioinformatic analysis steps of large scale proteomics projects. Experimental data is integrated with computationally enriched data from public and proprietary databases enabling protein isoform distinction, protein-protein interactions analysis, pathway analysis and text mining. File: cahrensATmdsdenmark.com_339.html ************************************************* Fri May 2 03:38:27 2003 Number: 340 Name: Huh, Jeoungho Affiliation: Division of Molecular Life Sciences, Pohang University of Science and Technology Address: San 31, Hyojadong, Namgu City: Pohang State/Provice: Kyungbuk Postal/Zip Code: 790-784 Country: Korea Email: artist3@postech.ac.kr Phone: 82-54-279-8194 Fax: 82-54-279-5540 Category: Data Mining Poster Title: Extraction of patterns in each domain of G-protein-coupled receptors Poster Authors and organization: Jeongho Huh¹, Chungoo Park², Dong Soo Jung, Hong Gil Nam, Jiin Choi, Young Bock Lee
¹artist3@postech.ac.kr, Division of Molecular Life Sciences, Pohang University of Science and Technology; ²madreach@bric.postech.ac.kr, Biological Research Information Center(BRIC), Pohang University of Science and Technology Abstract: Detecting local functional sequence patterns is suitable in GPCR sequence analyses. We attempted to extract patterns that are specific in GPCR subtypes. For extracting patterns, we applied different rules to each domain of three GPCR domains. Consequently, we obtained specific patterns of GPCR clans with high frequency and high specificity. File: artist3ATpostech.ac.kr_340.html ************************************************* Fri May 2 03:38:54 2003 Number: 341 Name: Fukuda, Ken I Affiliation: CBRC, AIST Address: Aomi Frontier Bldg. 17F, 2-43 Aomi City: Koto-ku State/Provice: TOKYO Postal/Zip Code: 135-0064 Country: JAPAN Email: fukuda-cbrc@aist.go.jp Phone: +81-3-3599-8049 Fax: +81-3-3599-8081 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: A Pathway DB: Annotating Signal Transduction Pathways with bio-processes using hierarchical multi-layered structures. Poster Authors and organization: Ken Ichiro Fukuda¹, Yuki Yamagata², Toshihisa Takagi
¹fukuda-cbrc@aist.go.jp, CBRC, AIST; ²snowfox@hgc.jp, BIRD, JST Abstract: A database formalizes Signal Transduction Pathway knowledge in scientific literatures is presented. The database focuses on annotating pathways or sub-pathways according to their related biological processes. Every process and element in a pathway has a pointer to ontologies, such as GO, and one can search (sub-)pathways, molecules by using them. File: fukuda-cbrcATaist.go.jp_341.html ************************************************* Fri May 2 03:44:07 2003 Number: 342 Name: Kao, Cheng-Yan Affiliation: Bioinfo Lab., Department of CSIE, National Taiwan University Address: No.1, Sec. 4, Roosevelt Road City: Taipei State/Provice: Taiwan Postal/Zip Code: 106 Country: R.O.C. Email: cykao@csie.ntu.edu.tw Phone: 886-2-23625336 Fax: 886-2-23658741 Category: Microarrays Poster Title: An automatic and unbiased GA for finding the most discriminant gene sets on Microarray Poster Authors and organization: Han-Yu Chuang¹, Hwa-Sheng Chiu², Huai-Kuang Tsai, Cheng-Yan Kao
¹r90002@csie.ntu.edu.tw, Bioinfo Lab., Department of CSIE, National Taiwan University; ²r91031@csie.ntu.edu.tw, Bioinfo Lab., Department of CSIE, National Taiwan University Abstract: A multi-objective genetic algorithm based approach, combining univariate and multivariate techniques, was proposed to find optimal gene sets for sample classification on gene expression data automatically and unbiased. Eight genes with 93% LOOCV accuracy of KNN were selected to be the optimal predictive gene sets for Colon cancer dataset. File: cykaoATcsie.ntu.edu.tw_342.html ************************************************* Fri May 2 03:52:59 2003 Number: 343 Name: Park, Chungoo Affiliation: Biological Research Information Center, Pohang University of Science and Technology Address: San 31, Hyojadong, Namgu City: Pohang State/Provice: Kyungbuk Postal/Zip Code: 790-784 Country: South Korea Email: madreach@bric.postech.ac.kr Phone: +82-54-279-8195 Fax: +82-54-279-5540 Category: Genome Annotation Poster Title: New approach to build models for predicting prokaryotic genes Poster Authors and organization: Chungoo Park¹, Mihwa Park², Jongwon Chang, Jeongho Huh, Dong Soo Jung, Hong Gil Nam, Young Bock Lee, Jiin Choi, Seungsik Yoo, Jaewoo Kim
¹madreach@bric.postech.ac.kr, Biological Research Information Center, Pohang University of Science and Technology; ²bfpark@posdata.co.kr, Solution Development Research Institute,POSDATA Abstract: we propose a new method for increasing the gene prediction accuracy without using information of known genes. To increase the gene prediction accuracy we used the additional learning data through the phylogenetic concept. Tests on 3 complete prokaryotic genomes performed with the GLIMMER program demonstrate the ability of the new approach to detect additional genes. File: madreachATbric.postech.ac.kr_343.html ************************************************* Fri May 2 04:00:00 2003 Number: 344 Name: Brahmachary, Manisha Affiliation: Institute of Infocomm Research Address: 21, heng Mui keng Terrace City: Singapore State/Provice: Singapore Postal/Zip Code: 119613 Country: Singapore Email: manisha@lit.org.sg Phone: 65-68748233, 65-68748237 Fax: 65-67748056 Category: Databases Poster Title: ANTIMIC: A database of antimicrobial peptides Poster Authors and organization: Manisha Brahmachary¹, Judice L.Y.Koh, Mohammad Asif Khan,Seah Seng Hong Tin Wee Tan, Vladimir Bajic
¹manisha@lit.org.sg, Institute of Infocomm Research Abstract: ANTIMIC is a specialized database dedicated to antimicrobial peptides. It contains useful analysis tools that can aid wet-lab scientists to determine the family and function of a putative new anti-microbial peptide and also in design of artificial anti-microbial peptides. File: manishaATlit.org.sg_344.html ************************************************* Fri May 2 04:04:39 2003 Number: 345 Name: Zheng, Wei-Mou Affiliation: Inst. Theor. Phys., Academia Sinica Address: PO Box 2735 City: Beijing State/Provice: Postal/Zip Code: 100080 Country: China Email: zheng@itp.ac.cn Phone: 86-10-62541820 Fax: 86-10-62562587 I plan to use my laptop computer as part of my poster Category: Genome Annotation Poster Title: A flexible model for promoter motifs Poster Authors and organization: Wei-Mou Zheng¹
¹zheng@itp.ac.cn, Inst. Theor. Phys., Academia Sinica Abstract: A general and flexible multi-motif model is proposed for promoter motif analysis based on dynamic programming. By extending the Gibbs sampler to the dynamic programming and introducing temperature, an efficient algorithm is developed for searching motifs in promoters. The algorithm is tested with plant promoters. File: zhengATitp.ac.cn_345.html ************************************************* Fri May 2 04:11:12 2003 Number: 346 Name: Takenaka, Yoichi Affiliation: Department of Bioinformatic Engineering, Osaka University Address: Machikaneyama 1-3 City: Toyonaka State/Provice: Osaka Postal/Zip Code: 5608531 Country: Japan Email: takenaka@ist.osaka-u.ac.jp Phone: +81-6-6850-6601 Fax: +81-6-6850-6602 Category: Sequence Comparison Poster Title: Frequency enumeration of DNA subsequences from large-scale sequences using linear codes Poster Authors and organization: Yoichi Takenaka¹, Hideo Matsuda²
¹takenaka@ist.osaka-u.ac.jp, Department of Bioinformatic Engineering, Osaka Univ. Japan; ²matsuda@ist.osaka-u.ac.jp, Department of Bioinformatic Engineering, Osaka Univ. Japan Abstract: Frequency enumeration of the DNA subsequence is one of the important techniques. The algorithm is simple, but it takes enormous memory space. We propose an enumerate method that uses linear codes to reduce the memory space. The method with 2-ary (31,26) Hamming code requires 1/60 of the usual memory space. File: takenakaATist.osaka-u.ac.jp_346.html ************************************************* Fri May 2 04:16:04 2003 Number: 347 Name: O Brien, Kevin P Affiliation: Karolinska Institutet Address: CGB Karolinska Institutet City: Stockholm State/Provice: Postal/Zip Code: 17177 Country: Sweden Email: kevobr@mbox.ki.se Phone: +4687286688 Fax: +468337983 Category: Databases Poster Title: OrthoDisease: A Human Disease Ortholog Database Poster Authors and organization: Kevin O Brien¹, Isabelle Westerlund², Erik Sonnhammer
¹kevobr@mbox.ki.se, Karolinska Institutet; ², Abstract: We report the construction of a novel database termed OrthoDisease, which was constructed using the Inparanoid program to analyze a list of disease genes derived from the Mendelian Inheritance in Man database. Our database is accessible online at orthodisease.cgb.ki.se and can be searched according to disease/gene/protein name or EC/MIM number. File: kevobrATmbox.ki.se_347.html ************************************************* Fri May 2 04:29:05 2003 Number: 348 Name: Syeda-Mahmood, Tanveer F Affiliation: IBM Almaden Research Address: 650 Harry Road City: San Jose State/Provice: CA Postal/Zip Code: 95120 Country: USA Email: stf@almaden.ibm.com Phone: 408-927-1883 Fax: 408-927-3030 Category: New Frontiers Poster Title: MineLink: A novel information integration framework for Life Sciences Poster Authors and organization: Tanveer Syeda-Mahmood¹, Bhooshan Kelkar²
¹stf@almaden.ibm.com, IBM Almaden Research; ²bkelkar@us.ibm.com, IBM Life Sciences Abstract: MineLink is a novel information integration framework that can pull together life sciences data and analytic applications from disparate sources. It specifies a design methodology for automatically integrating individual components, be they data sources, processors, data miners or visualization components without the need for explicit programming. It addresses both syntactic and semantic aspects of information integration. File: stfATalmaden.ibm.com_348.html ************************************************* Fri May 2 04:30:00 2003 Number: 349 Name: Kao, Cheng-Yan Affiliation: Bioinfo Lab., Department of CSIE, National Taiwan University Address: No.1, Sec. 4, Roosevelt Road City: Taipei State/Provice: Taiwan Postal/Zip Code: 106 Country: R.O.C. Email: cykao@csie.ntu.edu.tw Phone: 886-2-23625336 Fax: 886-2-23658741 Category: Structural Biology Poster Title: Prediction of disulfide connectivity patterns in proteins Poster Authors and organization: Shih-Chieh Chen¹, Chi-Hung Tsai², Huai-Kuang Tsai, Cheng-Yan Kao
¹r90039@csie.ntu.edu.tw, Bioinfo Lab., Department of CSIE, National Taiwan University; ²d90008@csie.ntu.edu.tw, Bioinfo Lab., Department of CSIE, National Taiwan University Abstract: We propose an approach to predict the protein disulfide connectivity directly from the sequence. The proposed approach trained a SVR model and predicted the disulfide connectivity by Gabow�s algorithm. The experiments showed the proposed method has an accuracy of 62%, which is promising to locate the disulfide bridges in proteins. File: cykaoATcsie.ntu.edu.tw_349.html ************************************************* Fri May 2 04:33:30 2003 Number: 350 Name: Maeda, Eisaku Affiliation: NTT Communication Science Laboratories Address: 2-4, Hikari-dai City: Seika-cho State/Provice: Kyoto-fu Postal/Zip Code: 619-0237 Country: JAPAN Email: maeda@cslab.kecl.ntt.co.jp Phone: +81-774-93-5370 Fax: +81-774-93-5385 Category: Microarrays Poster Title: Statistical Characterization of Spervised Learning and Gene Selection Algorithms for Gene Expression Analysis Poster Authors and organization: Eisaku Maeda¹, Ichiro Takemasa², Tomonori Izumitani, Hirotoshi Taira, Kenichi Matsubara, Morito Monden
¹maeda@cslab.kecl.ntt.co.jp, NTT Communication Science Laboratories; ²alfa-t@sf6.so-net.ne.jp, Graduate School of Medicine, Osaka University Abstract: We focused on histopathological phenotype prediction in colorectal carcinoma from microarray expression data, and investigated statistically their prediction performance of various combinations of classification techniques and gene selection methods. The results demonstrated detected marker genes and prediction accuracy strongly depends on the employed combination. File: maedaATcslab.kecl.ntt.co.jp_350.html ************************************************* Fri May 2 04:40:29 2003 Number: 351 Name: Zou, Yanming Affiliation: University of Melbourne Address: Sneydes Road City: Melbourne State/Provice: Victoria Postal/Zip Code: 3030 Country: Australia Email: y.zou@pgrad.unimelb.edu.au Phone: 61 3 97313391 Fax: 61 3 97313254 Category: Structural Biology Poster Title: Prediction of RNA Secondary Structures with XNAfold Poster Authors and organization: Yanming Zou¹, Alan J. Hillier², P. Scott Chandry
¹y.zou@pgrad.unimelb.edu.au, University of Melbourne; ²Alan.Hillier@foodscience.afisc.csiro.au, University of Melbourne Abstract: XNAfold is a JAVA-C hybrid program that takes an RNA sequence as input and predicts RNA secondary structure. The minimum free energy structure predicted by XNAfold matched the experimentally determined structure for 77 out of 133 different RNA molecules. XNAfold is freely available at http://www.student.unimelb.edu.au/~yanmz/index.html File: y.zouATpgrad.unimelb.edu.au_351.html ************************************************* Fri May 2 04:44:54 2003 Number: 352 Name: Wang, Yu-Tai Affiliation: Institute of Biochemistry, NYMU, Taiwan Address: No. 155, Li-Non St. Peitou City: Taipei State/Provice: Taipei Postal/Zip Code: 112 Country: Taiwan Email: ytwang@ym.edu.tw Phone: +886-2-28267000 Ext 5666 Fax: +886-2-28264843 Category: Data Mining Poster Title: Pathway data mining: tissue specificity and potential cross talks between pathways Poster Authors and organization: Yu-Tai Wang¹, Ueng-Cheng Yang², Yung-Wen Deng, Cheng-Min Wei, Kai-Lung Tang, Der-Ming Liou.
¹ytwang@ym.edu.tw, Institute of Biochemistry, National Yang-Ming University, Taiwan; ²yang@ym.edu.tw, Bioinformatics Research Center, National Yang-Ming University, Taiwan Abstract: Pathway is a way to present the mechanism behind a biological phenomenon. We have developed methods to integrate pathway-related information. By querying this integrated database, users will be able to look up tissue specific pathways and discover possible cross talk between pathways. The query results can output in graphic form. File: ytwangATym.edu.tw_352.html ************************************************* Fri May 2 04:51:00 2003 Number: 353 Name: Troein, Carl _ Affiliation: Dept. of Theor. Phys., Lund University Address: Solvegatan 14A City: Lund State/Provice: NONE Postal/Zip Code: 223 62 Country: Sweden Email: carl@thep.lu.se Phone: +46 46 2223496 Fax: +46 46 2229686 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: BASE - a free microarray database system Poster Authors and organization: Carl Troein¹, Johan Vallon-Christersson², Lao Saal, Jari H�kkinen
¹carl@thep.lu.se, Dept. of Theor. Phys., Lund University; ²johan.vallon-christersson@onk.lu.se, Dept. of Oncology, Lund University Abstract: BASE is a free microarray database system with a clean and intuitive web interface. It manages biomaterials, array production and raw data with images. Analysis tools are included, and users can provide new tools through a plugin interface. The BASE web site is http://base.thep.lu.se/. File: carlATthep.lu.se_353.html ************************************************* Fri May 2 04:51:54 2003 Number: 354 Name: Schliep, Alexander Affiliation: Dept. of Comp. Biology, Max Planck Institute for Molecular Genetics Address: Ihnestrasse 73 City: Berlin State/Provice: Postal/Zip Code: 14195 Country: Germany Email: schliep@molgen.mpg.de Phone: 49-30 8413 - 1166 Fax: 49-30 8413 - 1152 Category: Data Mining Poster Title: GHMM and HMMEd: A toolkit for Hidden Markov Models Poster Authors and organization: Wasinee Rungsarityotin¹, Alexander Schliep²
¹rungsari@molgen.mpg.de, Max Planck Institute for Molecular Genetics; ²schliep@molgen.mpg.de, Max Planck Institute for Molecular Genetics Abstract:
We have developed and implemented a library for a general Hidden Markov Model (GHMM) to assist in designing a topology and visualizing parameters for a HMM. The tool has been used in solving problems such as identification of circular permutation with Profile HMMs. GHMM and HMMEd is freely availabel at http://sourceforge.net/projects/ghmm/.
File: schliepATmolgen.mpg.de_354.html ************************************************* Fri May 2 05:02:21 2003 Number: 355 Name: Liao, Li Affiliation: University of Delaware Address: 77 E. Delaware Avenue City: Newark State/Provice: DE Postal/Zip Code: 19716 Country: U.S.A. Email: lliao@cis.udel.edu Phone: 302-831-3500 Fax: 302-831-8458 Category: Sequence Comparison Poster Title: SeqFreq: A Statistical Repetitive Motif Discovery Tool Poster Authors and organization: Roger Craig¹, Li Liao², Javier Garcia-Frias, Adam Marsh
¹rcraig@eecis.udel.edu, University of Delaware; ²lliao@cis.udel.edu, University of Delaware Abstract: SeqFreq is a repetitive motif discovery tool for finding repeats in both intragenomic and intergenomic sequences. SeqFreq uses a numerical suffix tree method to enumerate repetitive n-mers. Currently, intragenomic n-mer repeats of multiple bacterial genomes and their statistical distributions have been analyzed. File: lliaoATcis.udel.edu_355.html ************************************************* Fri May 2 05:08:24 2003 Number: 356 Name: Mizushima, Hiroshi Affiliation: National Cancer Center Research Institute Address: 5-1-1 Tsukiji City: Chuo-ku State/Provice: Tokyo Postal/Zip Code: 104-0045 Country: Japan Email: hmizushi@ncc.go.jp Phone: +81-3-5550-2020 Fax: +81-5550-2027 Category: Predictive Methods Poster Title: Finding transcription regulatory elements, using transcription factor data base and genome comparison. Poster Authors and organization: Hiroshi Mizushima¹, Kozo Kawahara², Mitsuru Takatsu, Teruhiko Yoshida
¹hmizushi@ncc.go.jp, National Cancer Center Research Institute; ²kkawahara@w-fusion.co.jp, World Fusion Co. Abstract: We have developed a Web based system for searching transcriptional regulatory elements in Human Genome Sequences using Transcription Factor Database (TFDB: which we have been maintaining) and Genome comparison. Combined with Microarray data, we will give some common regulatory elements between similar expression genes. File: hmizushiATncc.go.jp_356.html ************************************************* Fri May 2 05:12:00 2003 Number: 357 Name: Yamada, Yohei Affiliation: Institute for Advanced Biosciences, Keio University Address: 5322 Endo City: Fujisawa State/Provice: Kanagawa Postal/Zip Code: 252-8520 Country: Japan Email: yoyo@sfc.keio.ac.jp Phone: 0466-45-4286 Fax: 0466-45-4286 I plan to use my laptop computer as part of my poster Category: Systems Biology Poster Title: Multi-algorithm, multi-timescale cell simulation using E-Cell3 Poster Authors and organization: Kouichi Takahashi¹, Kazunari Kaizu², Bin Hu, Yohei Yamada, Masaru Tomita
¹shafi@sfc.keio.ac.jp, Institute for Advanced Biosciences, Keio University; ²t00220kk@sfc.keio.ac.jp, Institute for Advanced Biosciences, Keio University Abstract: The integration of sub-cellular models running on different types of algorithms poses a significant computational challenge. A heat-shock response model combining the Gillespie-Gibson stochastic algorithm and deterministic equations, and a multi-timescale model with multiple ODE components have been constructed. An implementation of the method is available at http://www.e-cell.org/. File: yoyoATsfc.keio.ac.jp_357.html ************************************************* Fri May 2 05:16:42 2003 Number: 358 Name: Huang, Yu Cheng Affiliation: National Taiwan University Address: No.1, Sec. 4, Roosevelt Road City: Taipei State/Provice: Computer Science and Information Engineering Department, R401 Postal/Zip Code: 106 Country: Taiwan Email: r91021@csie.ntu.edu.tw Phone: 886-0910919172 Fax: 886-0223036111 Category: Sequence Comparison Poster Title: DSC : Efficient Primer design algorithm with partial order graphs Poster Authors and organization: Yu-Cheng Huang¹, Cheng-Yan Kao²
¹r91021@csie.ntu.edu.tw, NTU. Computer Science and Information Engineering Department; ²cykao@csie.ntu.edu.tw, NTU. Computer Science and Information Engineering Department Abstract: DSC is a new method to reduce the search space and speed up the process when we have to find primer from extremely large amount of sequences. The DSC method presents a partially ordered graph of DNA sequences and also reserves all information of sequences. File: r91021ATcsie.ntu.edu.tw_358.html ************************************************* Fri May 2 05:22:43 2003 Number: 359 Name: Upadhyaya, Minesh Affiliation: School of Medicine, University of Colorado Address: 4200 E 9th Ave, B-119 City: Denver State/Provice: Co Postal/Zip Code: 80262 Country: USA Email: minesh.upadhyaya@uchsc.edu Phone: +1 303 315 7222 Fax: +1 303 315 3183 I plan to use my laptop computer as part of my poster Category: New Frontiers Poster Title: TransMiner: Biotransformation Prediction Poster Authors and organization: Minesh Upadhyaya¹, Imran Shah², Daniel McShan, Weiming Zhang
¹minesh.upadhyaya@uchsc.edu, UCHSC; ²imran.shah@uchsc.edu, UCHSC Abstract: We developed TransMiner, a symbolic computational approach for inferring novel biochemical functions. We have developed a novel sub-graph isomorphism-based algorithm to search the detailed representations of known biotransformations to induce biocatalytic \"rules\". These symbolic biocatalytic rules represent the simplified functions of enzymes and can be used to infer novel biochemistry. File: minesh.upadhyayaATuchsc.edu_359.html ************************************************* Fri May 2 05:23:57 2003 Number: 360 Name: Park, Mihwa Affiliation: POSDATA co. Address: 276-2 City: SungNam-City State/Provice: Gyuggi-DO Postal/Zip Code: 463-775 Country: Korea Email: bfpark@posdata.co.kr Phone: 82-031-779-2707 Fax: 82-031-779-2709 I plan to use my laptop computer as part of my poster Category: Systems Biology Poster Title: SPACE-BLAST: Linux Cluster based Biological Sequence Parallel Processing system Summarized by Gene Ontology Poster Authors and organization: Mihwa Park¹, Jaewoo Kim², Hyungsuk Won, Seungsik Yoo
¹bfpark@posdata.co.kr, POSDATA; ²jaewoo@posdata.co.kr, POSDATA Abstract:

50-word abstract:
SPACE-BLAST (Super PArallel Computer Engine for BLAST) is a high performance bioinformatics system that implements the NCBI�s BLAST system with low cost Linux cluster based parallel processing to search DNA sequencing at high speed. Also, Gene Ontology is applied to summarize massive amount of the BLAST search results. SPACE-BLAST is available at at http://space-blast.posdata.co.kr.

File: bfparkATposdata.co.kr_360.html ************************************************* Fri May 2 05:29:45 2003 Number: 361 Name: Mizushima, Hiroshi Affiliation: National Cancer Center Research Institute Address: 5-1-1 Tsukiji City: Chuo-ku State/Provice: Tokyo Postal/Zip Code: 104-0045 Country: Japan Email: hmizushi@ncc.go.jp Phone: +81-3-5550-2020 Fax: +81-5550-2027 Category: Data Visualisation Poster Title: Molecular Modeling using Virtual Reality with Force Feed Back Poster Authors and organization: Hiroshi Mizushima¹, Hiroshi Tanaka², Masaaki Hatsuta, Daisuke Arai, Hiroshi Nagata
¹hmizushi@ncc.go.jp, National Cancer Center Research Institute; ²tanaka@tmd.ac.jp, Tokyo Medical Dental University Abstract: We developed computer aided molecular modeling system using virtual reality technologies. Although it is still a prototype, the most characteristic function of the system is enabling its user to �touch� and �feel� the electrostatic potential field of a protein or a drug molecule. File: hmizushiATncc.go.jp_361.html ************************************************* Fri May 2 05:30:07 2003 Number: 362 Name: McShan, Daniel C Affiliation: University of Colorado School of Medicine Address: 4200 East Ninth Avenue, B119 City: Denver State/Provice: CO Postal/Zip Code: 80262 Country: USA Email: Daniel.McShan@uchsc.edu Phone: 303-315-2963 Fax: 303-314-3183 I plan to use my laptop computer as part of my poster Category: Predictive Methods Poster Title: PathMiner: de novo Synthesis Poster Authors and organization: McShan, D.¹, Upadhyaya, M.², Imran Shah
¹Daniel.McShan@uchsc.edu, UCHSC; ²Minesh.Upadhayaya@uchsc.edu, UCHSC Abstract: This poster presents PathMiner, a computational framework for exploring metabolic pathways. To make inferences about pathways we abstract metabolism as a state-space in which compounds are points and biotransformations are state-transitions. In this poster, we discuss applications of PathMiner to two quite different biological problems. File: Daniel.McShanATuchsc.edu_362.html ************************************************* Fri May 2 05:30:55 2003 Number: 363 Name: McShan, Daniel Affiliation: School of Medicine, University of Colorado Address: 4200 E 9th Ave, B-119 City: Denver State/Provice: Co Postal/Zip Code: 80262 Country: USA Email: daniel.mcshan@uchsc.edu Phone: 303 315 7222 Fax: 303 315 3183 I plan to use my laptop computer as part of my poster Category: Systems Biology Poster Title: PathMiner: de novo Pathway Synthesis Poster Authors and organization: Daniel McShan¹, Imran Shah²
¹daniel.mcshan@uchsc.edu, UCHSC; ²imran.shah@uchsc.edu, UCHSC Abstract: We developed PathMiner, a computational framework for inferring metabolic pathways using biochemical and genomic information. We abstract metabolism as a state-space in which compounds are points and biotransformations are state-transitions, and we infer pathways through heuristic search. PathMiner is being used to explore the metabolism of microbial and synthetic systems. File: daniel.mcshanATuchsc.edu_363.html ************************************************* Fri May 2 05:34:40 2003 Number: 364 Name: Bannai, Hideo Affiliation: Human Genome Center, Institute of Medical Science, University of Tokyo Address: 4-6-1 Shirokanedai City: Minato-ku State/Provice: Tokyo Postal/Zip Code: 108-8639 Country: Japan Email: bannai@ims.u-tokyo.ac.jp Phone: +81-3-5449-5615 Fax: +81-3-5449-5442 Category: Data Mining Poster Title: Efficiently finding regulatory elements using correlation with gene expression Poster Authors and organization: Hideo Bannai¹, Shunsuke Inenaga², Ayumi Shinohara, Masayuki Takeda, Satoru Miyano
¹bannai@ims.u-tokyo.ac.jp, Human Genome Center, Institute of Medical Science, University of Tokyo; ²s-ine@i.kyushu-u.ac.jp, Department of Informatics, Kyushu University Abstract: We present an efficient algorithm for detecting putative regulatory elements in the upstream sequences of genes, using expression data obtained from microarrays. We are able to find the optimal pattern, most correlated with the expression levels of the genes, in time linear in the total length of the upstream sequences. File: bannaiATims.u-tokyo.ac.jp_364.html ************************************************* Fri May 2 05:41:20 2003 Number: 365 Name: de Hoon, Michiel JL Affiliation: University of Tokyo, Human Genome Center Address: 4-6-1 Shirokanedai, Minato-ku City: Tokyo State/Provice: Postal/Zip Code: 108-8639 Country: Japan Email: mdehoon@ims.u-tokyo.ac.jp Phone: +81-3-54495615 Fax: +81-3-54495442 I plan to use my laptop computer as part of my poster Category: Systems Biology Poster Title: Transcription factor prediction in Bacillus subtilis using stochastic differential equations Poster Authors and organization: Michiel de Hoon¹, Sascha Ott², SunYong Kim, Seiya Imoto, Satoru Miyano
¹mdehoon@ims.u-tokyo.ac.jp, University of Tokyo; ²ott@ims.u-tokyo.ac.jp, university of Tokyo Abstract: We model gene regulation in Bacillus subtilis using stochastic differential equations, including both linear and nonlinear interactions. Using synthetic data, we found that about fifty time points are needed to determine a gene network reliably. Combining several time-course experiments yielded a highly significant prediction for the sigW transcription factor. File: mdehoonATims.u-tokyo.ac.jp_365.html ************************************************* Fri May 2 05:41:40 2003 Number: 366 Name: Kang, Byeong-Chul Affiliation: Pusan National University Address: 1401, College of Medicine, Pusan National University10, 1-Ga Ami-dong Seo-ku City: Busan State/Provice: Postal/Zip Code: 602-739 Country: South Korea Email: bckang@pusan.ac.kr Phone: +82-51-246-4828 Fax: +82-51-242-6935 Category: Databases Poster Title: MARS: Mutation Analysis Reporting System for Human Genetic Disease Poster Authors and organization: Byeong-Chul Kang¹, Jun-Hyung Park², In-Joo Kim, Hyo-Myung Kim, Hee-Kyung Park, and Cheol-Min Kim
¹bckang@pusan.ac.kr, Pusan National University; ²jhaprk98@pusan.ac.kr, Pusan National University Abstract: MARS is an intelligent diagnosis system for human genetic disease. The MARS consists of databases of human genetic disease information and mutation detection system. The first release of MARS contains genetic information of MECP2 gene and its website is available at http://www.genome.re.kr/mars/ File: bckangATpusan.ac.kr_366.html ************************************************* Fri May 2 05:58:08 2003 Number: 367 Name: Shin, Chang-Jin Affiliation: Busan Genome Center Address: 10, Amidong 1-Ga, Seoku City: Busan State/Provice: Postal/Zip Code: 602-739 Country: South Korea Email: teragene@pusan.ac.kr Phone: +82-51-242-4828 Fax: +82-51-240-1118 Category: Genome Annotation Poster Title: Analysis of human herpesvirus genomes based on COGs and Phylogenomics Poster Authors and organization: ChangJin Shin¹, CheolMin Kim², Byeong-Chul Kang, Jun-Hyung Par, Dong-Hoon Shin, Ok-Kyung Ham, Choon-Hwan Lee
¹teragene@pusan.ac.kr, Busan Genome Center; ²kimcm@pusan.ac.kr, Busan National University Abstract: The aim of this study is to predict the function of genes from 9 species of human herpesvirus group (HHV) by using COGs technique and phylogenomics to overcome conventional similarity search and computational prediction methods. It will provide a more precise method to predict the function of new genes. File: terageneATpusan.ac.kr_367.html ************************************************* Fri May 2 06:04:16 2003 Number: 368 Name: Saarikko, Ilana E Affiliation: Univ of Turku, Turku Centre for Biotechnology Address: PO Box 123 City: Turku State/Provice: Postal/Zip Code: FIN-20521 Country: Finland Email: ilana.saarikko@btk.utu.fi Phone: +358 2 333 8002 Fax: +358 2 333 8000 Category: Systems Biology Poster Title: Preliminary Simulation Studies for Prediction of Regulatory Networks Poster Authors and organization: Ilana Saarikko¹, Tero Aittokallio, Mikko Katajamaa
¹ilana.saarikko@btk.utu.fi, Univ of Turku, Turku Centre for Biotechnology Abstract: Methods such as Bayesain networks have been proposed to predict gene regulatory networks from expression data. The aim of this study is to simulate data corresponding the expression levels of genes in IL-4 signalling pathway and thus asses the amount of material needed to infer the initial network structure. File: ilana.saarikkoATbtk.utu.fi_368.html ************************************************* Fri May 2 06:08:50 2003 Number: 369 Name: Shin, Chang-Jin Affiliation: Busan Genome Center Address: 10, Amidong 1-Ga, Seoku City: Busan State/Provice: Postal/Zip Code: 602-739 Country: South Korea Email: teragene@pusan.ac.kr Phone: +82-51-242-4828 Fax: +82-51-240-1118 Category: Genome Annotation Poster Title: Analysis of human herpesvirus genomes based on COGs and Phylogenomics Poster Authors and organization: ChangJin Shin¹, CheolMin Kim², Byeong-Chul Kang, Jun-Hyung Par, Dong-Hoon Shin, Ok-Kyung Ham, Choon-Hwan Lee
¹teragene@pusan.ac.kr, Busan Genome Center; ²kimcm@pusan.ac.kr, Busan National University Abstract: The aim of this study is to predict the function of genes from 9 species of human herpesvirus group (HHV) by using COGs technique and phylogenomics to overcome conventional similarity search and computational prediction methods. It will provide a more precise method to predict the function of new genes. File: terageneATpusan.ac.kr_369.html ************************************************* Fri May 2 06:21:32 2003 Number: 370 Name: ODonoghue, Sean I Affiliation: LION Bioscience AG Address: Waldhoferstr. 98 City: Heidelberg State/Provice: Postal/Zip Code: 69123 Country: Germany Email: sean.odonoghue@lionbioscience.com Phone: +49 6221 40 38 363 Fax: +49 6221 40 38 480 I plan to use my laptop computer as part of my poster Category: Functional Genomics Poster Title: LION Target Engine 1.0: an Enterprise Platform for Target Identification and Validation Poster Authors and organization: Sean I ODonoghue¹, S. Bernauer, Z. Bilkic, N. Bojunga, T. Brostrom, D. Croft, N. Delhomme, A. Denagbe, L. Ehrlich, K. Fries, C. Girardot, M. Goeschl, M. Gumbel, J. Hermans, C. Kassner, C. Katz, U. Keck, H.-P. Keck, R. Kern, G. Kurapkat, P. Lederer, D. Leon, S. Marcel, S. Markel, B. Markus, J.E.M. Meyer, E. Minch, J. Mistry, C. Muench, S.I. O�Donoghue, C. Ohr, S. Richter, H.-J. Roemming, R. Russ, S. Schaefer, A. Schafferhans, T. Schlegl, T. Schlueter, A. Schmidt, O. Schmidt, D. Schulz, A. Sooky, A. Sergienko, F. Spangenberg, J. Suckow, B. Sulzer, C. Suter-Crazzolara, A. Tarasenko, E. Vatcheva, H. Voss, M. Weindel, G. Zhang
¹sean.odonoghue@lionbioscience.com, LION bioscience AG, Waldhoferstr. 98, 69123 Germany Abstract: LION Target Engine is a user-friendly system designed to streamline the identification and validation of targets in an enterprise environment. The system components for: sequence registration and curation; sequence analysis; gene and protein index; text mining; pathways and interaction networks; 3D structures; TaqMan and microarray data handling, and target tracking. File: sean.odonoghueATlionbioscience.com_370.html ************************************************* Fri May 2 06:25:33 2003 Number: 371 Name: Kim, Ju Han Affiliation: Seoul National University Human Genome Research Institute Address: 28 Yongon-dong Chongno-gu City: Seoul State/Provice: Postal/Zip Code: 110-799 Country: Korea, Republic Of Email: juhan@snu.ac.kr Phone: +82-2-740-8320 Fax: +82-2-747-4830 Category: Data Mining Poster Title: Discovering useful patterns from DNA microarray experiment with large-scale multifactor design by genetic algorithm and permutation test Poster Authors and organization: Ju Han Kim¹, Tae Su Chung², Jihun Kim, Ji Yeon Park, Hye Won Lee, Jihoon Kim, Mingoo Kim
¹juhan@snu.ac.kr, Seoul National University Human Genome Research Institute; ²epiai@korea.com, Seoul National University Human Genome Research Institute Abstract: We present a method of discovering useful patterns from DNA microarray experiment with large-scale multifactor design with no replication using genetic algorithm. Permutation test for the distance measures between observation and the pattern discovered statistically significant multifactor gene expression patterns with simple biological interpretations. File: juhanATsnu.ac.kr_371.html ************************************************* Fri May 2 06:32:01 2003 Number: 372 Name: Kim, Jin Hyuk Affiliation: Hanyang University College of Medicine Address: 17, Hengdang-dong, Sungdong-ku City: Seoul State/Provice: Postal/Zip Code: 133-791 Country: Korea Email: jhkim1@hanyang.ac.kr Phone: +82-2-2290-0614 Fax: +82-2-2281-3603 I plan to use my laptop computer as part of my poster Category: Microarrays Poster Title: Automation of cDNA microarray image analysis Poster Authors and organization: Jin Hyuk Kim¹, Hye Young Kim², Tae Sung Park, Ki Woong Kim, Young Seek Lee, and Yong Sung Lee
¹jhkim1@hanyang.ac.kr, Hanyang Univeirsity College of Medicine; ²hykim121@hanyang.ac.kr, Hanyang University College of Medicine Abstract: To automate the microarray image analysis, several processes were developed for detecting spots, filtering bad spots, and generating HTML reports. It can analyze a lot of microarray images without user�s attention. Therefore, it can be a connection in high throughput pipeline. File: jhkim1AThanyang.ac.kr_372.html ************************************************* Fri May 2 06:34:45 2003 Number: 373 Name: Kim, Hye Young Affiliation: Hanyang University College of Medicine Address: 17, Hengdang-dong, Sungdong-ku City: Seoul State/Provice: Postal/Zip Code: 133-791 Country: Korea Email: hykim121@hanyang.ac.kr Phone: +82-2-2290-0614 Fax: +82-2-2281-3603 Category: Microarrays Poster Title: Compensation of scanner before robust M regression normalization in cDNA microarray Poster Authors and organization: Hye Young Kim¹, Jin Hyuk Kim², Yong Sung Lee, Young Seek Lee, Tae Sung Park, Ki Woong Kim, and Hyun Ju Chang
¹hykim121@hanyang.ac.kr, Hanyang Univeirsity College of Medicine; ²jhkim1@hanyang.ac.kr, Hanyang University College of Medicine Abstract: In cDNA microarray, the conversion of the amount of fluorescence to the image intensity with the scanning process must be carefully handed to find gene expression ratio. We developed a reverse scanning method for the microarray image and applied robust M regression to normalize the data from the compensated image. File: hykim121AThanyang.ac.kr_373.html ************************************************* Fri May 2 06:42:18 2003 Number: 374 Name: Nakamichi, Reiichiro Affiliation: Human Genome Center, Institute of Medical Science, the University of Tokyo Address: Shirokanedai 4-6-1 City: Minato-ku State/Provice: Tokyo Postal/Zip Code: 108-8639 Country: JAPAN Email: rei-naka@ims.u-tokyo.ac.jp Phone: +81-3-5449-5615 Fax: +81-3-5449-5442 Category: Data Mining Poster Title: QTL analysis for outcrossing family data using genetic algorithm and simulated EM algorithm Poster Authors and organization: Reiichiro Nakamichi¹, Satoru Miyano²
¹rei-naka@ims.u-tokyo.ac.jp, Human Genome Center, Institute of Medical Science, the University of Tokyo; ²miyano@ims.u-tokyo.ac.jp, Human Genome Center, Institute of Medical Science, the University of Tokyo Abstract: We propose a new method of quantitative trait loci (QTL) mapping using genetic algorithm (GA) with simulated EM algorithm. It detects QTL without highly organized experimental cross and is applicable to human genetics. Simulation studies showed high performance of our method in the cases not supported by traditional gene mappings. File: rei-nakaATims.u-tokyo.ac.jp_374.html ************************************************* Fri May 2 06:42:21 2003 Number: 375 Name: Tolstrup, Niels Affiliation: Exiqon Address: Bygstubben 9 City: Vedbaek State/Provice: Postal/Zip Code: DK-2950 Country: Denmark Email: tolstrup@exiqon.com Phone: +45 45 65 04 44 Fax: +45 45 66 18 88 Category: Microarrays Poster Title: OligoDesign: Design of LNA oligonucleotides for gene expression arrays Poster Authors and organization: Niels Tolstrup¹, Peter S. Nielsen and Sakari Kauppinen
¹tolstrup@exiqon.com, Exiqon Abstract: OligoDesign is a webservice for the design of DNA/LNA mixmer oligonucleotides. The OligoDesign software features recognition and filtering of the target sequence by genome-wide BLAST analysis. It includes routines for prediction of melting temperature, self-annealing and secondary structure for LNA substituted oligonucleotides. The OligoDesign program is freely accesible at http://lnatools.com/ File: tolstrupATexiqon.com_375.html ************************************************* Fri May 2 06:52:42 2003 Number: 376 Name: Arakawa, Kazuharu Affiliation: Institute for Advanced Biosciences, Keio University Address: Endo 5322 City: Fujisawa State/Provice: Kanagawa Postal/Zip Code: 252-8520 Country: Japan Email: gaou@sfc.keio.ac.jp Phone: 0466-47-5099 Fax: 0466-47-5099 I plan to use my laptop computer as part of my poster Category: Systems Biology Poster Title: Automatic generation of cell-wide pathway model from complete genome Poster Authors and organization: Kazuharu Arakawa¹, Yohei Yamada², Hiromi Komai, Kosaku Shinoda, Yoichi Nakayama, Masaru Tomita
¹gaou@g-language.org, Institute for Advanced Biosciences, Keio University; ²skipper@g-language.org, Keio University Abstract: Genome-based E-Cell Modeling System realizes a fully automatically conversion of the genome sequence data into a qualitative virtual cell model, linking information from major public database such as GenBank, EMBL, SWISS-PROT, KEGG, ARM, Brend, and WIT, by a combined method of annotation, homology, and orthology. File: gaouATsfc.keio.ac.jp_376.html ************************************************* Fri May 2 06:54:30 2003 Number: 377 Name: Liew, Alan Wee-Chung Affiliation: Dept of Computer Engineering and Information Technology, City University of Hong Kong Address: 83 Tat Chee Avenue, Kowloon Tong City: Hong Kong SAR State/Provice: Postal/Zip Code: Country: HKSAR, China Email: itwcliew@cityu.edu.hk Phone: +852 27887522 Fax: +852 2788-292 Category: Data Mining Poster Title: A Binary Hierarchical Clustering and Visualization Algorithm for Gene Expression Data Poster Authors and organization: Alan Wee-Chung Liew¹, Hong Yan², Lap Keung Szeto
¹itwcliew@cityu.edu.hk, Dept of Computer Engineering and Information Technology, City University of Hong Kong; ²ityan@cityu.edu.hk, Dept of Computer Engineering and Information Technology, City University of Hong Kong Abstract: We recently introduce a novel binary hierarchical clustering algorithm, which combines both features of hierarchical clustering and partitioning-based clustering. Our algorithm performs a successive binary subdivision of the data into smaller and smaller partitions hierarchically, until no further splitting of a (parent) partition into two smaller (children) partitions is possible. A tree structure visualization of the result is also implemented. File: itwcliewATcityu.edu.hk_377.html ************************************************* Fri May 2 06:55:22 2003 Number: 378 Name: Rux, John J. Affiliation: The Wistar Institute Address: 3601 Spruce Street City: Philadelphia State/Provice: PA Postal/Zip Code: 19104 Country: USA Email: rux@wistar.upenn.edu Phone: 1-215-898-0126 Fax: 1-215-898-3868 Category: Functional Genomics Poster Title: siRNA Design Tool: A Functional Genomics Accelerator Poster Authors and organization: Natasha Levenkova¹, Qingjuan Gu², John J. Rux
¹nlevenkov@wistar.upenn.edu, The Wistar Institute; ²qingjuan@wistar.upenn.edu, The Wistar Institute Abstract: Small interfering RNA (siRNA) is used in functional genomics applications to produce �knock-down� cells. The siRNA design tool scans a target gene for candidate siRNA sequences that satisfy user-adjustable rules. Selected candidates are then screened to identify those siRNA sequences that match only the gene of interest. File: ruxATwistar.upenn.edu_378.html ************************************************* Fri May 2 06:55:57 2003 Number: 379 Name: Philip, Gayle K Affiliation: Bioinformatics laboratory Address: National University of ireland City: Maynooth State/Provice: Co. Kildare Postal/Zip Code: N/A Country: Ireland Email: gayle.k.philip@may.ie Phone: 353 1 708 6211 Fax: 353 1 708 3845 Category: Phylogeny and Evolution Poster Title: Determining the Eukaryote Phylogeny Poster Authors and organization: Gayle Philip¹, James McInerney²
¹gayle.k.philip@may.ie, National University of Ireland, Maynooth; ²james.o.mcinerney@may.ie, National University of Ireland, Maynooth Abstract: The relationship of nematodes to arthropods and vertebrates can be described by the Coelomata and Ecdysozoa hypotheses. Our aim was to test these hypotheses by finding the supertree that best described the relationship of orthologous, single gene family trees from ten eukaryotic taxa. Our results support the traditional Coelomata hypothesis. File: gayle.k.philipATmay.ie_379.html ************************************************* Fri May 2 07:00:15 2003 Number: 380 Name: Luo, Jingchu Affiliation: Centre of Bioinformatics, Peking University Address: Haidian City: Beijing State/Provice: Postal/Zip Code: 100871 Country: PR China Email: luojc@pku.edu.cn Phone: 86-10-6275-7281 Fax: 86-10-6275-9001 Category: Sequence Comparison Poster Title: Analysis of corona virus genome sequences Poster Authors and organization: Jingchu Luo¹
¹luojc@pku.edu.cn, Centre of Bioinformatics, Peking University Abstract: ClustalW analysis of 27 corona virus genome sequences reveals that 9 SARS virus sequences are identical. Multiple sequence alignment was also performed to the different groups of corona virus genome sequence and coding product to find conservative and divergent regions. All the analysis results are available at ftp://ftp.cbi.pku.edu.cn/pub/sars/analysis/. File: luojcATpku.edu.cn_380.html ************************************************* Fri May 2 07:02:16 2003 Number: 381 Name: Seno, Shigeto Affiliation: Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University Address: 1-3 Machikaneyama City: Toyonaka State/Provice: Osaka Postal/Zip Code: 560-8531 Country: JAPAN Email: s-senoo@ist.osaka-u.ac.jp Phone: +81-6-6850-6603 Fax: +81-6-6850-6602 Category: Data Mining Poster Title: P-quasi complete linkage clustering method for gene-expression profiles based on distribution analysis Poster Authors and organization: Shigeto Seno¹, Reiji Teramoto², Yoichi Takenaka, Hideo Matsuda
¹s-senoo@ist.osaka-u.ac.jp, Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University; ²teramoto@sumitomopharm.co.jp, Genomic Science Laboratories, Research Division, Sumitomo Pharmaceuticals Abstract: We propose a new clustering method with the following two features. First, this method exploits a new similarity measure based on distribution of gene expressions. Second, this method leverages the P-quasi complete linkage algorithm for describing clusters. The synergy of the two features provides more informative clustering than traditional ones. File: s-senooATist.osaka-u.ac.jp_381.html ************************************************* Fri May 2 07:13:27 2003 Number: 382 Name: Baldo, Angela M Affiliation: USDA ARS PGRU Address: 4974 Collier Drive City: Geneva State/Provice: New York Postal/Zip Code: 14456-0462 Country: USA Email: abaldo@pgru.ars.usda.gov Phone: 315 787 2413 Fax: 315 787 2339 Category: Predictive Methods Poster Title: Polymorphism Prediction Poster Authors and organization: Baldo¹, Labate²
¹abaldo@pgru.ars.usda.gov, USDA ARS PGRU; ²jl265@cornell.edu, USDA ARS PGRU Abstract: Single nucleotide polymorphism (SNP) distribution has been demonstrated as nonrandom in the genomes of animals and plants. While genetic variation is traditionallyexpected in noncoding regions, additional genetic feature have been correlated with SNPs. We investigate whether this information might be used to predict regions of polymorphism. File: abaldoATpgru.ars.usda.gov_382.html ************************************************* Fri May 2 07:20:37 2003 Number: 383 Name: Kim, Mingoo Affiliation: SNUBI Seoul National University Biomedical Informatics Address: 28 Yongon-dong, Chongno-gu City: Seoul State/Provice: kyunggi Postal/Zip Code: 110799 Country: South Korea Email: satyrs1@snu.ac.kr Phone: 8227408320 Fax: 8227474830 Category: Systems Biology Poster Title: Social Network Analysis of DNA Microarray Data Poster Authors and organization: Jung Hun Ohn¹, Tae Su Chung², Jihoon Kim, Mingoo Kim, Jihun Kim, Hye Won Lee, Ji Yeon Park, Ju Han Kim
¹jhohn2@snu.ac.kr, SNUBI Seoul National University Biomedical Informatics; ²epiai@korea.com, SNUBI Seoul National University Biomedical Informatics Abstract: Genomic interactions are quite complicated that special skills are needed to understand the network. Application of social affiliation network analysis on the yeast gene expression compendium dataset of hundreds of systematic perturbations shows the core-peripheral and the significant intermediary genes by network density and centrality indices. File: satyrs1ATsnu.ac.kr_383.html ************************************************* Fri May 2 07:27:49 2003 Number: 384 Name: Choe, Sunghwa Affiliation: Seoul National University Address: School of biological sciences, College of natural science City: Seoul State/Provice: S. Korea Postal/Zip Code: 151-747 Country: S. Korea Email: shchoe@snu.ac.kr Phone: 82-2-880-6691 Fax: 82-2-872-1993 Category: Functional Genomics Poster Title: Statistical Analysis of Arabidopsis T-DNA-flanking sequences Poster Authors and organization: Hyung Seok Choi¹
¹gnie@lycos.co.kr, Seoul National University Abstract: T-DNA use in plant functional genomics is based on a hypothesis that the T-DNA randomly inserts plant genomes. To test this, we analyzed 120,000 T-DNA flanking sequences iof the SIGnAl database. Of the total 29,084 Arabidopsis genes, approximately 70% have >1insert, whereas 8760 (30%) genes are still left without any. File: shchoeATsnu.ac.kr_384.html ************************************************* Fri May 2 07:42:43 2003 Number: 385 Name: Zauhar, Randy J Affiliation: Dept. of Chemistry and Biochemistry, University of the Sciences in Philadelphia Address: 600 S. 43rd Street City: Philadelphia State/Provice: PA Postal/Zip Code: 19104 Country: USA Email: r.zauhar@usip.edu Phone: 215-596-8691 Fax: 215-596-8543 I plan to use my laptop computer as part of my poster Category: New Frontiers Poster Title: Shape Signatures, a New Approach for Ligand- and Receptor-Based Molecular Design Poster Authors and organization: Randy J. Zauhar¹, Karthi Nagarajan², Izabela Gierach, Mukesh Kumar, ZhiJian Li, LiFeng Tian, William J. Welsh
¹r.zauhar@usip.edu, University of the Sciences in Philadelphia; ²nagaraka@umdnj.edu, University of Medicine and Dentistry of New Jersey Abstract: We present several applications of \"Shape Signatures\", a new method for compactly encoding and rapidly comparing the shapes of ligand molecules and receptors. Our approach uses a technique much like ray-tracing to explore the volumes of both drug molecules and the protein actve sites they target. File: r.zauharATusip.edu_385.html ************************************************* Fri May 2 07:49:08 2003 Number: 386 Name: Naito, Yasuhiro Affiliation: Inst. Adv. Biosci., Keio Univ. Address: 14-1 Babacho City: Tsuruoka State/Provice: Yamagata Postal/Zip Code: 997-0035 Country: Japan Email: ynaito@sfc.keio.ac.jp Phone: +81-235-29-0828 Fax: +81-235-29-0525 Category: Systems Biology Poster Title: in silico Knockout Experiment of Myocardial Cell Using E-CELL System Poster Authors and organization: Yasuhiro Naito¹, Motohiro Yoneda², Sayaka Ishinabe, Shoko Miyamoto, Katsuya Kawai, Masaru Tomita
¹ynaito@sfc.keio.ac.jp, Inst. Adv. Biosci., Keio Univ.; ²moto@sfc.keio.ac.jp, Inst. Adv. Biosci., Keio Univ. Abstract: The Kyoto model of the myocardial cell was implemented into E-CELL. The simulation results accurately represented the electrophysiological behavior of intact guinea pig myocardial cells. We tried in silico knockout of Kir2.1 channel. When the conductance of Kir2.1 was suppressed approximately 80%, the simulation showed behavior roughly consistent with the antecedent experimental results. File: ynaitoATsfc.keio.ac.jp_386.html ************************************************* Fri May 2 07:51:17 2003 Number: 387 Name: Kao, Cheng-Yan Affiliation: Bioinfo Lab., Department of CSIE, National Taiwan University Address: No.1, Sec. 4, Roosevelt Road City: Taipei State/Provice: Taiwan Postal/Zip Code: 106 Country: R.O.C. Email: cykao@csie.ntu.edu.tw Phone: 886-2-23625336 Fax: 886-2-23628167 Category: Microarrays Poster Title: An automatic and unbiased GA for finding the most discriminant gene sets on Microarray Poster Authors and organization: Han-Yu Chuang¹, Hwa-Sheng Chiu², Huai-Kuang Tsai, Cheng-Yan Kao
¹r90002@csie.ntu.edu.tw, Bioinfo Lab., Department of CSIE, National Taiwan University; ²r91031@csie.ntu.edu.tw, Bioinfo Lab., Department of CSIE, National Taiwan University Abstract: A multi-objective genetic algorithm based approach, combining univariate and multivariate techniques, was proposed to find optimal gene sets for sample classification on gene expression data automatically and unbiased. Eight genes with 93% LOOCV accuracy of KNN were selected to be the optimal predictive gene sets for Colon cancer dataset. File: cykaoATcsie.ntu.edu.tw_387.html ************************************************* Fri May 2 07:51:52 2003 Number: 388 Name: Kong, Lesheng Affiliation: National University of Singapore Address: Block MD7, 02-07, Biochemistry Department City: Singapore State/Provice: Postal/Zip Code: 119260 Country: Singapore Email: lesheng@bic.nus.edu.sg Phone: 65-6874-4459 Fax: 65-6778-2466 Category: Databases Poster Title: SDPS: Small Disulphide-bonded Proteins Structural database Poster Authors and organization: Lesheng Kong¹, Shoba Ranganathan²
¹lesheng@bic.nus.edu.sg, National University of Singapore; ²shoba@bic.nus.edu.sg, National University of Singapore Abstract: SDPS database is a comprehensive structural database of small disulphide-bonded proteins. This database is enriched with a number of new features which cannot be easily accessed through public databases. The database aims to facilitate the research on small disulphide-bonded proteins especially on disulphide connectivity features. SDPS database can be accessed freely at http://origin.bic.nus.edu.sg/sdps. File: leshengATbic.nus.edu.sg_388.html ************************************************* Fri May 2 07:57:48 2003 Number: 389 Name: Stanley, Stefan M Affiliation: Institute for Molecular Bioscience Address: University of Queensland City: Brisbane State/Provice: Qld Postal/Zip Code: 4312 Country: Australia Email: S.Stanley@imb.uq.edu.au Phone: 33651571 Fax: Category: Data Mining Poster Title: New tools for exploring noncoding RNA-mediated regulatory networks Poster Authors and organization: S.Stanley¹
¹S.Stanley@imb.uq.edu.au, IMB Abstract: We present a method for the extraction of minimal complete sets of exactly repeated sequences from genomes, and then extracting subsets with the potential for producing primary sequence-dependent RNA regulatory signals and regulatory networks, initially focused on intronic sequences, wherein we can examine clustering of matched sequences by functional groups. Results are presented for S.cerevisiae. File: S.StanleyATimb.uq.edu.au_389.html ************************************************* Fri May 2 08:09:20 2003 Number: 390 Name: Faith, Jeremiah J Affiliation: Cold Spring Harbor Laboratory Address: PO Box 100, 1 Bungtown Rd City: Cold Spring Harbor State/Provice: NY Postal/Zip Code: 11724 Country: USA Email: faith@cshl.org Phone: 516-367-6976 Fax: 516-367-8461 Category: Functional Genomics Poster Title: The Yeast Interactome -- analysis and evaluation of diverse sources of information. Poster Authors and organization: Jeremiah J Faith¹, Ravi Sachidanandam²
¹faith@cshl.org, Cold Spring Harbor Laboratory; ²sachidan@cshl.org, Cold Spring Harbor Laboratory Abstract: A network analysis of the protein-protein interactions in yeast reveals distinct clusters. Some of the clusters are due to functional groups, while most are due to methods of detection; interactions detected by yeast two-hybrid tend to cluster proteins into groups that are different from the clusters due to mass spectrometry. We quantify these differences and discuss implications. File: faithATcshl.org_390.html ************************************************* Fri May 2 08:17:40 2003 Number: 391 Name: Fristensky, Brian Affiliation: University of Manitoba Address: Department of Plant Science City: Winnipeg State/Provice: MB Postal/Zip Code: R3T 2N2 Country: CANADA Email: frist@cc.umanitoba.ca Phone: 204-474-6085 Fax: 204-474-7528 Category: Data Visualisation Poster Title: BIRCH - A portable and comprehensive bioinformatics platform Poster Authors and organization: Brian Fristensky¹
¹frist@cc.umanitoba.ca, University of Manitoba Abstract: BIRCH is a resource of integrated programs and databases for molecular biology, unified through the GDE graphic interface. The BIRCH framework is designed for semi-automated installation and customization on Unix systems, and integration of locally-installed software and databases into BIRCH. http://home.cc.umanitoba.ca/~psgendb
File: fristATcc.umanitoba.ca_391.html ************************************************* Fri May 2 08:46:43 2003 Number: 392 Name: Culhane, Aedin C. Affiliation: University College Cork Address: 5.28 Bioscience Institute City: Cork State/Provice: Cork Postal/Zip Code: Ireland Country: Ireland Email: A.Culhane@ucc.ie Phone: 353214901306 Fax: 353214904259 I plan to use my laptop computer as part of my poster Category: Microarrays Poster Title: A multivariate method for comparison of microarray data from different platforms Poster Authors and organization: Aedin C Culhane¹, Guy Perri�re², Desmond G. Higgins
¹A.Culhane@ucc.ie, University College Cork; ²perriere@biomserv.univ-lyon.fr, Universite Claude Bernard Abstract: We describe a powerful method for comparison and visualisation of gene expression data from different microarray platforms. Co-inertia analysis (CIA) is a multivariate method that identifies co-relationships in multiple datasets. The genes from each dataset, which define these trends, can be identified. Further details: http://bioinfo.ucc.ie. File: A.CulhaneATucc.ie_392.html ************************************************* Fri May 2 09:55:41 2003 Number: 393 Name: Deane, Charlotte M Affiliation: Department of Statistics, Oxford University Address: 1 South Parks Road City: Oxford State/Provice: Postal/Zip Code: OX1 3TG Country: UK Email: deane@stats.ox.ac.uk Phone: +44 1865 281301 Fax: +44 1865 272595 I plan to use my laptop computer as part of my poster Category: Structural Biology Poster Title: Inside the beta sheet Poster Authors and organization: Charlotte Deane¹
¹deane@stats.ox.ac.uk, Oxford University Abstract: Beta sheets are one of the two common repeating elements found in protein structures. Despite their importance in structure they are not well or fully understood. Here we investigate the properties of beta sheets in order to better predict protein structure/folding and understand amyloid (and general aggregate) formation. File: deaneATstats.ox.ac.uk_393.html ************************************************* Fri May 2 10:18:18 2003 Number: 394 Name: Chapman, Brad A Affiliation: University of Georgia Address: 240 Segrest Circle City: Athens State/Provice: GA Postal/Zip Code: 30605 Country: USA Email: chapmanb@uga.edu Phone: 706-372-6705 Fax: Category: Phylogeny and Evolution Poster Title: Evolutionary analysis of single nucleotide polymorphism distribution in duplicated gene pairs of Arabidopsis thaliana Poster Authors and organization: Brad Chapman¹, Andrew Paterson²
¹chapmanb@uga.edu, University of Georgia; ²paterson@uga.edu, University of Georgia Abstract: Whole genome duplication has played a major role in the structuring of the Arabidopsis thaliana genome. We examined single nucleotide polymorphism (SNP) variation in duplicate genes retained after these duplication events. We compare SNP accumulation in duplicates and singletons with respect to their effect on protein evolution. File: chapmanbATuga.edu_394.html ************************************************* Fri May 2 10:34:28 2003 Number: 395 Name: Yandava, Chandri N Affiliation: Ceres Inc Address: 3007 Malibu Canyon Road City: Malibu State/Provice: California Postal/Zip Code: 90325 Country: USA Email: cyandava@ceres-inc.com Phone: 310-317-8916 Fax: 310-317-8998 Category: Phylogeny and Evolution Poster Title: MICROSATELLITE REPEATS IN PLANTS Poster Authors and organization: Chandri N Yandava¹, Roger Pennell², Kenneth Feldmann, Peter Mascia, Richard Flavell, William Kimmerly
¹cyandava@ceres-inc.com, Ceres Inc; ²rpennell@ceres-inc.com, Ceres Inc Abstract: The classes AAC, AAG present in higher number in Arabidopsis, whereas AAT AGG and CCG are more abundant in rice. Repeats with A and T bases (except AAT) are more frequent in Arabidopsis, repeats with G and C bases are more in rice, as rice is high in GC composition. File: cyandavaATceres-inc.com_395.html ************************************************* Fri May 2 11:41:45 2003 Number: 396 Name: Luciano, Joanne S Affiliation: BioPAX Address: 45 Orchard Street City: Belmont State/Provice: MA Postal/Zip Code: 02478-3008 Country: USA Email: jluciano@biopathways.org Phone: 617 993-9994 Fax: 208-728-1133 Category: Systems Biology Poster Title: BioPAX Data Exchange Ontology for Biological Pathway Databases Poster Authors and organization: BioPAX Group¹
¹pax@cbio.mskcc.org, BioPAX Abstract: BioPAX (http://biopax.org) is a new community-based effort to develop a data exchange format for biological pathway data. The ontology will be able to represent data from diverse sources such as aMAZE, BIND, BioCyc, and WIT. Initial implementations of BioPAX will be available in both OWL and XML Schema.
File: jlucianoATbiopathways.org_396.html ************************************************* Fri May 2 11:47:22 2003 Number: 397 Name: Luciano, Joanne S Affiliation: BioPAX Address: 45 Orchard Street City: Belmont State/Provice: MA Postal/Zip Code: 02478-3008 Country: USA Email: jluciano@biopathways.org Phone: 617 993-9994 Fax: 208.728.1133 Category: Databases Poster Title: BioPAX - Biological Pathway Data Exchange Format Poster Authors and organization: BioPAX Group¹
¹pax@cbio.mskcc.org, BioPAX Abstract:
BioPAX (http://biopax.org) is a new community-based initiative to address the growing need for a unified framework for sharing pathway information. Several groups are participating in BioPAX to develop a data exchange format that will allow communication between existing pathway databases and facilitate deposition of data into a common public repository.
File: jlucianoATbiopathways.org_397.html ************************************************* Fri May 2 11:51:32 2003 Number: 398 Name: Blake, Judith A Affiliation: The Jackson Laboratory Address: 600 Main St. City: Bar Harbor State/Provice: ME Postal/Zip Code: 04609 Country: USA Email: jblake@informatics.jax.org Phone: 1-207-288-6248 Fax: 1-207-288-6132 Category: Databases Poster Title: Mouse Genome Informatics: Integration Nexus for Mammalian Biology Poster Authors and organization: JA Blake¹, M Ringwald², CJ Bult, JA Kadin, JE Richardson, JT Eppig, Mouse Genome Informatics Group
¹jblake@informatics.jax.org, Jackson Laboratory; ²ringwlad @informatics.jax.org, Jackson Laboratory Abstract: The Mouse Genome Informatics (MGI) databases provide access to comprehensive, integrated, experimental data for the laboratory mouse in the domains of sequence, expression, gene function (GO), molecular variation, phenotype, inbred strain characterization, homology, and tumor biology. MGI provides the definitive mouse gene index. MGI can be accessed at www.informatics.jax.org . File: jblakeATinformatics.jax.org_398.html ************************************************* Fri May 2 11:54:55 2003 Number: 399 Name: Gewehr, Jan E Affiliation: Institute for Computer Science, Ludwig-Maximilians-University Munich Address: Theresienstr. 39 City: Munich State/Provice: Postal/Zip Code: D-80333 Country: Germany Email: gewehr@bio.informatik.uni-muenchen.de Phone: +49 89 2180 4048 Fax: +49 89 2180 4054 Category: Predictive Methods Poster Title: On the Correspondence between Scoring Matrices and Binding Site Sequence Distributions Poster Authors and organization: Jan E. Gewehr¹, Jan T. Kim², Thomas Martinetz
¹gewehr@bio.informatik.uni-muenchen.de, Institute for Computer Science, Ludwig-Maximilians-University Munich, Theresienstr. 39, D-80333 Munich, Germany; ²kim@inb.uni-luebeck.de, Institute for Neuro- and Bioinformatics, University of Luebeck, Seelandstr. 1a, D-23569, Germany Abstract: Using maximum likelihood estimation, we analyze the correspondence between popular scoring matrix classifiers for binding site prediction and specific probability distributions of binding site sequences. For unknown distributions, the binding matrix is a good choice since it achieves maximal specificity under the constraint that all known sequences are classified correctly. File: gewehrATbio.informatik.uni-muenchen.de_399.html ************************************************* Fri May 2 12:23:10 2003 Number: 400 Name: Rombauts, Stephane M Affiliation: University of Gent, dep. Plant Systems Biology Address: Ledeganckstraat 35 City: Gent State/Provice: Oost-Vlaanderen Postal/Zip Code: 9000 Country: Belgium Email: strom@gengenp.rug.ac.be Phone: +3292648721 Fax: +3292645008 Category: Predictive Methods Poster Title: In silico detection of CpG-island in plants Poster Authors and organization: Stephane Rombauts¹, Kobe Florquin², Rouze Pierre and Yves Van de Peer
¹strom@gengenp.rug.ac.be, University of Gent, dep. Plant Systems Biology; ²koflo@gengenp.rug.ac.be, University of Gent, dep. Plant Systems Biology Abstract: CpG-islands are considered evolutionary remnants linked to the regulation of genes. Compared to animal systems, plants have a higher number of genes encoding DNA-methyltransferases that show a broader specificity. In this work we explored the compositional landscape surrounding promoters that would enable the identification of distinct CpG or CpNpG-islands. File: stromATgengenp.rug.ac.be_400.html ************************************************* Fri May 2 12:45:20 2003 Number: 401 Name: Morgan, Richard D Affiliation: New England Biolabs Address: 32 Tozer Road City: Beverly State/Provice: MA Postal/Zip Code: 01915 Country: USA Email: morgan@neb.com Phone: 978-927-5054 Fax: 978-921-1350 Category: Phylogeny and Evolution Poster Title: Phylogeny of DNA Methyltransferases recognizing GATC and related DNA sequences. Poster Authors and organization: Richard D. Morgan¹
¹morgan@neb.com, New England Bioloabs Abstract: DNA modification plays important roles in nucleic acid metabolism. Methyltransferases modifying the related DNA sequences GATC and GANTC are close homologs. We present a phylogeny of these enzymes as an example of how DNA sequence recognition has evolved, and predict how to evolve further specificities in vitro File: morganATneb.com_401.html ************************************************* Fri May 2 13:44:05 2003 UPDATE ----- Number: 353 Name: Troein, Carl Affiliation: Dept. of Theor. Phys., Lund University Address: Solvegatan 14A City: Lund State/Provice: NONE Postal/Zip Code: 223 62 Country: Sweden Email: carl@thep.lu.se Phone: +46 46 2223496 Fax: +46 46 2229686 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: BASE - a free microarray database system Poster Authors and organization: Carl Troein¹, Johan Vallon-Christersson², Lao Saal, Jari H�kkinen
¹carl@thep.lu.se, Dept. of Theor. Phys., Lund University; ²johan.vallon-christersson@onk.lu.se, Dept. of Oncology, Lund University Abstract: BASE is a free microarray database system with a clean and intuitive web interface. It manages biomaterials, array production and raw data with images. Analysis tools are included, and users can provide new tools through a plugin interface. The BASE web site is http://base.thep.lu.se/. File: carlATthep.lu.se_353 ************************************************* Fri May 2 13:46:26 2003 UPDATE ----- Number: 269 Name: Wiltshire, Tim Affiliation: GNF Address: 10675 JJ Hopkins Dr City: San Diego State/Provice: CA Postal/Zip Code: 92121 Country: USA Email: timw@gnf.org Phone: +1-858-8121569 Fax: +1-858-8121502 I plan to use my laptop computer as part of my poster Category: Data Visualisation Poster Title: GENOME-WIDE HAPLOTYPE STRUCTURE VISUALIZATION AND ANALYSIS IN MOUSE Poster Authors and organization: Tim Wiltshire¹, Serge Batalov ², Mathew Pletcher, R.J.Mural, M.D.Adams, C.F.Fletcher
¹timw@gnf.org, GNF; ²batalov@gnf.org, GNF Abstract: SNPview, the interactive navigator for the individual SNPs, SSLPs, alleles and haplotypes projected to the genomic axis is available on-line at http://www.gnf.org/SNP/ . Large, but discrete regions of the genome are not very polymorphic between particular strain pairs, and thus cannot easily be interrogated for natural genetic variations influencing QTLs. File: timwATgnf.org_269 ************************************************* Fri May 2 13:58:32 2003 Number: 402 Name: Hunter, Lawrence Affiliation: U. Colorado School of Medicine Address: 4200 E. 9th Ave., Campus Box C236 City: Denver State/Provice: CO Postal/Zip Code: 80262 Country: USA Email: Larry.Hunter@uchsc.edu Phone: 1-303-315-1094 Fax: 1-303-315-1098 Category: Microarrays Poster Title: Exact Power Under Independence for the False Discovery Rate in Gene Expression Array Experiments Poster Authors and organization: Lawrence Hunter¹, Deborah H. Glueck², Anis Karimpour-Fard and Keith E. Muller
¹Larry.Hunter@uchsc.edu, U. Colorado School of Medicine; ², U. Colorado School of Medicine Abstract: The false discovery rate (Benjamini & Hochberg, 1995) is widely used for multiple comparison problems, including gene expression array studies. For independent, but not necessarily identically distributed test statistics, we derive the joint probability distribution of the number of total and false rejections, and thereby provide methods for exact small sample power and sample size. File: Larry.HunterATuchsc.edu_402.html ************************************************* Fri May 2 14:11:21 2003 Number: 403 Name: Sabripour, Mahyar Affiliation: The University of Texas M. D. Anderson Cancer Center Address: 1515 Holcombe Blvd. City: Houston State/Provice: Texas Postal/Zip Code: 77030 Country: USA Email: msabripo@mdanderson.org Phone: 713-745-1127 Fax: 713-792-8261 Category: Microarrays Poster Title: Application of Stellar Photometry To The Analysis of Microarray Images Poster Authors and organization: Mahyar Sabripour¹, Christopher I. Amos², Kevin Coombes
¹msabripo@mdanderson.org, Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center; ²camos@request.mdacc.tmc.edu, Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center Abstract:
Improvements in quantifying spots can directly impact the identification of genes critical to the development and progression of cancer. We utilize a stellar photometric model, the Moffat function, to analyze cDNA membrane microarray images. In the current setting, we fit the Moffat function to cDNA spots on the array.
File: msabripoATmdanderson.org_403.html ************************************************* Fri May 2 15:16:13 2003 Number: 404 Name: San Gil, Inigo Affiliation: Yale University Address: 333 cedar st. City: new haven State/Provice: ct Postal/Zip Code: 06511 Country: usa Email: inigo.sangil@yale.edu Phone: 203-737-5011 Fax: 203-785-4035 Category: New Frontiers Poster Title: Gene-Protein networks in Drosophila Melanogaster Poster Authors and organization: Inigo San Gil ¹, Kevin White², Joel Bader
¹inigo.sangil@yale.edu, Yale University; ²kevin.white@yale.edu, Yale University Abstract: We present a gene network or map of interactions between proteins and genes for the Drosophila melanogaster organism. The map info is based on cross-correlations of the genome-wide timecourses of gene expression profile and yeast to hybrid interactions. Results show rich networks of genes and proteins ready to be explored. File: inigo.sangilATyale.edu_404.html ************************************************* Fri May 2 17:03:05 2003 Number: 405 Name: Lewis, Christopher T Affiliation: Agriculture and Agri-food Canada Address: 107 Science Place City: Saskatoon State/Provice: Sk Postal/Zip Code: S7N 0X2 Country: Canada Email: LewisCT@agr.gc.ca Phone: 01.306.956.7693 Fax: 01.306.956.7247 Category: Functional Genomics Poster Title: cSAGE and the Serial Analysis of Gene Expression in Arabidopsis thaliana Poster Authors and organization: Chritopher T Lewis¹, Steve Robinson², Tony Kusalik, Isobel Parkin
¹LewisCT@agr.gc.ca, Agriculture and Agri-food Canada; ²robinsons@agr.gc.ca, Agriculture and Agri-food Canada Abstract:
cSAGE is an open-source application written in C to provide an efficient mechanism for extracting SAGE tags and assigning matches to DNA sequences. It has been used for a cold tolerance experiment in A. thaliana involving 3 librarys with more than 180,000 tags. See http://homepage.usask.ca/ctl271/csage for more information. File: LewisCTATagr.gc.ca_405.html ************************************************* Fri May 2 17:16:30 2003 Number: 406 Name: Lewis, Christopher T Affiliation: Ariculture and Agri-food Canada Address: 107 Science Place City: Saskatoon State/Provice: SK Postal/Zip Code: S7N 0X2 Country: Canada Email: LewisCT@agr.gc.ca Phone: 01.306.956.7693 Fax: 01.306.956.7247 Category: Data Visualisation Poster Title: BioViz: Brassica Arabidopsis Comparative Genome Browser - The application of Scalable Vector Graphics to comparative genomics Poster Authors and organization: Christopher T Lewis¹, Andrew Sharpe², Steve Karcz, Isobel AP Parkin, Derek Lydiate
¹LewisCT@agr.gc.ca, Agriculture and Agri-food Canada; ²sharpea@agr.gc.ca, Agriculture and Agri-food Canada Abstract:
SVG has enabled a visually appealing application for the visual comparison of Brassica napus and Arabidopsis thaliana. SVG overcomes two key drawbacks of current web-based genome browsers: fixed displays and frequent page reloads. The Brassica Araboidopsis Comparative Genome Browser is available online at www.brassica.ca.
File: LewisCTATagr.gc.ca_406.html ************************************************* Fri May 2 17:36:10 2003 Number: 407 Name: Hennig, Steffen Affiliation: MPI for Molecular Genetics Address: Ihnestrasse 73 City: Berlin State/Provice: Berlin Postal/Zip Code: D-14195 Country: Germany Email: hennig@molgen.mpg.de Phone: +49-30-8413-1612 Fax: +49-30-8413-1380 I plan to use my laptop computer as part of my poster Category: Genome Annotation Poster Title: Automated Gene Ontology annotation for anonymous sequence data Poster Authors and organization: Steffen Hennig¹, Detlef Groth², Hans Lehrach
¹hennig@molgen.mpg.de, MPI for Molecular Genetics, Berlin; ²dgroth@molgen.mpg.de, MPI for Molecular Genetics, Berlin Abstract: The unified vocabulary of terms provided by the Gene Ontology consortium has become a standard tool in annotation of genes and their products. We present a web-service available at http://goblet.molgen.mpg.de, which allows annotation of anonymous cDNA or protein sequences by GO terms. File: hennigATmolgen.mpg.de_407.html ************************************************* Fri May 2 17:59:26 2003 Number: 408 Name: Raphael, Ben J Affiliation: University of California, San Diego Address: 9500 Gilman Drive City: La Jolla State/Provice: CA Postal/Zip Code: 92093 Country: United States of America Email: braphael@ucsd.edu Phone: 858-822-5004 Fax: 858-534-7029 Category: Functional Genomics Poster Title: Reconstructing Genome Architectures by End Sequence Profiling: Applications to Tumor Genomes Poster Authors and organization: Ben Raphael¹, Pavel Pevzner², Stas Volik, Colin Collins
¹braphael@ucsd.edu, University of Californa, San Diego; ²ppevzner@cs.ucsd.edu, Univeristy of Californa, San Diego Abstract: We describe a computational approach to the reconstruction of the architecture of a rearranged genome based on data from end sequence profiling experiments. We apply our techniques to the reconstruction of the genome of a human MCF7 tumor cell. File: braphaelATucsd.edu_408.html ************************************************* Fri May 2 18:00:10 2003 UPDATE ----- Number: 403 Name: Sabripour, Mahyar Affiliation: The University of Texas M. D. Anderson Cancer Center Address: 1515 Holcombe Blvd. City: Houston State/Provice: Texas Postal/Zip Code: 77030 Country: USA Email: msabripo@mdanderson.org Phone: 713-745-1127 Fax: 713-792-8261 Category: Microarrays Poster Title: Application of Stellar Photometry To The Analysis of Microarray Images Poster Authors and organization: Mahyar Sabripour¹, Christopher I. Amos², Kevin Coombes
¹msabripo@mdanderson.org, Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center; ²camos@request.mdacc.tmc.edu, Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center Abstract: Improvements in quantifying spots can directly impact the identification of genes critical to the development and progression of cancer. We utilize a stellar photometric model, the Moffat function, to analyze cDNA membrane microarray images. In the current setting, we fit the Moffat function to cDNA spots on the array.
File: msabripoATmdanderson.org_403 ************************************************* Fri May 2 18:24:35 2003 Number: 409 Name: Kim, Tae Yong Affiliation: Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology Address: 373-1 Guseong-dong, Yuseong-gu City: Daejeon State/Provice: Postal/Zip Code: 305-701 Country: Korea Email: kimty@webmail.kaist.ac.kr Phone: 82-42-869-5970 Fax: 82-42-869-3910 I plan to use my laptop computer as part of my poster Category: Systems Biology Poster Title: Identification of metabolic characteristics through metabolic flux analysis using MetaFluxNet Poster Authors and organization: Tae Yong Kim¹, Soon Ho Hong², Sang Yup Lee
¹kimty@webmail.kaist.ac.kr, Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology; ²totenkof@mail.kaist.ac.kr, Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology Abstract: The variation of intracellular metabolic flux distributions of E. coli was estimated by MetaFluxNet under various conditions, and the response of metabolic fluxes were evaluated. MFA results were applied to identify the metabolic characteristics of E. coli. File: kimtyATwebmail.kaist.ac.kr_409.html ************************************************* Fri May 2 18:52:43 2003 Number: 410 Name: Bristol, Douglas W. Affiliation: NIH-NIEHS Address: P. O. Box 12233 City: Research Triangle Park State/Provice: NC Postal/Zip Code: 27709 Country: USA Email: bristol@niehs.nih.gov Phone: 919-541-2756 Fax: 919-541-3867 I plan to use my laptop computer as part of my poster Category: Predictive Methods Poster Title: Predicting Chemical Carcinogenesis: Problem Representation Governs Model Performance Poster Authors and organization: Douglas W. Bristol¹
¹bristol@niehs.nih.gov, NIH-NIEHS Abstract: The predictive performance and comprehensibility of 54 chemical-carcinogenicity models, generated by three Predictive-Toxicology Challenges, was evaluated using ROC convex-hull analysis. Models from problem representations that used a mix of attributes, reflecting interactions between chemical and biological features, clearly outperformed those derived using only attributes of chemical structure or biological features. File: bristolATniehs.nih.gov_410.html ************************************************* Fri May 2 20:13:18 2003 Number: 411 Name: Hucka, Michael Affiliation: Caltech Address: 1200 E. California Blvd. City: Pasadena State/Provice: CA Postal/Zip Code: 91125 Country: USA Email: mhucka@caltech.edu Phone: 626-395-6911 Fax: 626-796-8914 Category: Systems Biology Poster Title: Recent Developments in the Systems Biology Markup Language Poster Authors and organization: Michael Hucka¹, Andrew Finney², Benjamin Bornstein, Bruce Shapiro, John Doyle, Hiroaki Kitano
¹mhucka@caltech.edu, Caltech; ²a.finney@herts.ac.uk, University of Hertfordshire Abstract: SBML (http://www.sbml.org) is an XML-based format for representing biochemical network models and is intended to serve as a common exchange language for computational models in systems biology. This poster will summarize recent developments in SBML, including the new SBML Level 2. File: mhuckaATcaltech.edu_411.html ************************************************* Fri May 2 20:59:58 2003 Number: 412 Name: Pavlovic, Vladimir Affiliation: Rutgers University Address: 110 Frelinghuysen Rd City: Piscataway State/Provice: NJ Postal/Zip Code: 08854 Country: USA Email: vladimir@cs.rutgers.edu Phone: 732-445-2654 Fax: 732-445-2654 I plan to use my laptop computer as part of my poster Category: Predictive Methods Poster Title: Predicting accuracy of comparative gene finders using evolutionary models Poster Authors and organization: Vladimir Pavlovic ¹
¹vladimir@cs.rutgers.edu, Rutgers University Abstract: Comparative computational analysis can lead to improved identification of genes, while relying on a given pair of genomes, such as human and mouse. We propose a formal way to select an optimal pair of genomes by linking Markov models of molecular evolution to comparative HMMs and studying their prediction accuracy. File: vladimirATcs.rutgers.edu_412.html ************************************************* Fri May 2 22:46:22 2003 Number: 413 Name: Forrest, Alistair RR Affiliation: Institute for molecular Bioscience Address: Queensland Bioscience Precint Building, University of Queensland City: Brisbane State/Provice: QLD Postal/Zip Code: 4072 Country: Australia Email: a.forrest@imb.uq.edu.au Phone: 61-7-33462609 Fax: Category: Functional Genomics Poster Title: Phosphoregulators: Protein kinases and Protein phosphatases of mouse Poster Authors and organization: Alistair RR Forrest¹, Timothy Ravasi², Darrin Taylor, Rohan Teasdale, RIKEN GER Group Members ,and Sean Grimmond
¹a.forrest@imb.uq.edu.au, IMB; ²t.ravasi@imb.uq.edu.au, IMB Abstract: We describe the identification and classification of the complement of protein kinases and phosphatases in mouse. We also present preliminary results from a functional screen of these proteins, coupling sequence based classification with high throughput functional screens. File: a.forrestATimb.uq.edu.au_413.html ************************************************* Sat May 3 00:27:52 2003 Number: 414 Name: Hsu, William H. Affiliation: Kansas State University Address: 234 Nichols Hall City: Manhattan State/Provice: KS Postal/Zip Code: 66506-2302 Country: USA Email: bhsu@cis.ksu.edu Phone: 785-532-6350 Fax: 785-532-7353 I plan to use my laptop computer as part of my poster Category: Data Mining Poster Title: DESCRIBER: Graphical Relational Models for Collaborative Filtering in Microarray Data Mining Poster Authors and organization: William H. Hsu¹, Roby Joehanes², Prashanth Boddhireddy
¹bhsu@cis.ksu.edu, Kansas State University; ²robbyjo@cis.ksu.edu, Kansas State University Abstract: This poster presents DESCRIBER, a system that uses graphical models to represent relational data in computational genomics portals cf. myGrid, integrating descriptive data models for microarray data mining and extending the information retrieval capabilities of indices such as ResearchIndex. The objective is to provid collaborative filtering (CF) over data, metadata, source code (cf. OpenBio), and experimental documentation. File: bhsuATcis.ksu.edu_414.html ************************************************* Sat May 3 01:03:14 2003 Number: 415 Name: Hsu, William H Affiliation: Kansas State University Address: 234 Nichols Hall City: Manhattan State/Provice: KS Postal/Zip Code: 66506-2302 Country: USA Email: bhsu@cis.ksu.edu Phone: 785-532-6350 Fax: 785-532-7353 I plan to use my laptop computer as part of my poster Category: Data Mining Poster Title: A Software Toolkit for Learning Dynamic Graphical Models of Gene Regulatory Structure from Microarray Data Poster Authors and organization: William H. Hsu¹, Youping Deng², Judith L. Roe
¹bhsu@cis.ksu.edu, Kansas State University; ²ypdeng@ksu.edu, Kansas State University Abstract: We present BNJ, an experimental Java-based software toolkit for learning network models of gene regulation from microarray data. We survey current research issues in learning the structure of graphical models, outline the components of BNJ used in modeling regulatory dynamics of S. cerevisiae, and present preliminary results and current research directions. File: bhsuATcis.ksu.edu_415.html ************************************************* Sat May 3 14:18:25 2003 UPDATE ----- Number: 412 Name: Pavlovic, Vladimir Affiliation: Rutgers University Address: 110 Frelinghuysen Rd City: Piscataway State/Provice: NJ Postal/Zip Code: 08854 Country: USA Email: vladimir@cs.rutgers.edu Phone: 732-445-2654 Fax: 732-445-2654 I plan to use my laptop computer as part of my poster Category: Predictive Methods Poster Title: Predicting accuracy of comparative gene finders using evolutionary models Poster Authors and organization: Vladimir Pavlovic ¹
¹vladimir@cs.rutgers.edu, Rutgers University Abstract: Comparative computational analysis can lead to improved identification of genes, while relying on a given pair of genomes, such as human and mouse. We propose a formal way to select an optimal pair of genomes by linking Markov models of molecular evolution to comparative HMMs and studying their prediction accuracy. File: vladimirATcs.rutgers.edu_412 ************************************************* Sat May 3 14:40:26 2003 UPDATE ----- Number: 148 Name: Verspoor, Cornelia M Affiliation: Los Alamos National Laboratory Address: PO Box 1663, MS B256 City: Los Alamos State/Provice: NM Postal/Zip Code: 87545 Country: USA Email: verspoor@lanl.gov Phone: 1-505-667-5086 Fax: 1-505-667-1126 Category: Data Mining Poster Title: A Constructional Approach to Extraction Poster Authors and organization: Cornelia M. Verspoor¹, George J. Papcun², Kari Sentz
¹verspoor@lanl.gov, Los Alamos National Laboratory; ²gjp@lanl.gov, Los Alamos National Laboratory Abstract: We present a prototype implementation of a system for extracting protein/gene interactions from biological literature which is motivated by the theory of Construction Grammar. CG provides a powerful framework for combining domain-specific terminology management with patterns incorporating generic linguistic structural constraints. File: verspoorATlanl.gov_148 ************************************************* Sat May 3 14:53:05 2003 UPDATE ----- Number: 174 Name: Sklyar, Nataliya Affiliation: University of Leipzig Address: Feldstr. 88 City: Greifswald State/Provice: na Postal/Zip Code: 17489 Country: Germany Email: sklyar@informatik.uni-leipzig.de Phone: +491752116289 Fax: +493834515239 Category: New Frontiers Poster Title: Using Web Services as part of the 2D gel analysis workflow Poster Authors and organization: Nataliya Sklyar¹, Matthias Berth ², Dirk Lewerentz
¹sklyar@informatik.uni-leipzig.de, University of Leipzig; ²berth@decodon.com , DECODON GmbH Abstract: We present the integration of web services into Delta2D, an end-user 2D gel analysis application. With Delta2D's web services plugins, users can access data from external sources and display it alongside the image analysis results in a uniform way. We describe the plugin architecture and first experiences in its use. File: sklyarATinformatik.uni-leipzig.de_174 ************************************************* Sat May 3 15:02:11 2003 UPDATE ----- Number: 174 Name: Sklyar, Nataliya Affiliation: University of Leipzig Address: Feldstr. 88 City: Greifswald State/Provice: na Postal/Zip Code: 17489 Country: Germany Email: sklyar@informatik.uni-leipzig.de Phone: +491752116289 Fax: +493834515239 Category: New Frontiers Poster Title: Using Web Services as part of the 2D gel analysis workflow Poster Authors and organization: Nataliya Sklyar¹, Matthias Berth ², Dirk Lewerentz
¹sklyar@informatik.uni-leipzig.de, University of Leipzig; ²berth@decodon.com , DECODON GmbH Abstract: We present the integration of web services into Delta2D, an end-user 2D gel analysis application. With Delta2D's web services plugins, users can access data from external sources and display it alongside the image analysis results in a uniform way. We describe the plugin architecture and first experiences in its use. File: sklyarATinformatik.uni-leipzig.de_174 ************************************************* Sat May 3 15:06:03 2003 UPDATE ----- Number: 178 Name: Niu, Yanwei Affiliation: . Department of ECE, University of Delaware, USA Address: 310 Evans Hall, University of Delaware City: Newark State/Provice: DE Postal/Zip Code: 19716 Country: U.S.A Email: niu@capsl.udel.edu Phone: 1-302-831-3406 Fax: 1-302-831-4316 Category: Data Mining Poster Title: Mapping and Visual Exploration of GPCR Classification Hierarchy in Interpro and GPCRDB System Poster Authors and organization: Yanwei Niu¹, Xiangyun Wang², Yockey, Anastasia Christianson, Guang R. Gao
¹niu@capsl.udel.edu, . Department of ECE, University of Delaware, USA; ²Xiangyun.Wang@astrazeneca.com, EST Informatics Wilmington, Astra Zeneca PLC Abstract:
Interpro and GPCRDB are two GPCR classification systems. Using data mining technique, we compared the two systems family by family at each level of the classification hierarchy and established mapping relation between them. We introduced a novel visualization tool that allows us to directly and easily compare them.
File: niuATcapsl.udel.edu_178 ************************************************* Sat May 3 15:06:57 2003 UPDATE ----- Number: 178 Name: Niu, Yanwei Affiliation: . Department of ECE, University of Delaware, USA Address: 310 Evans Hall, University of Delaware City: Newark State/Provice: DE Postal/Zip Code: 19716 Country: U.S.A Email: niu@capsl.udel.edu Phone: 1-302-831-3406 Fax: 1-302-831-4316 Category: Data Mining Poster Title: Mapping and Visual Exploration of GPCR Classification Hierarchy in Interpro and GPCRDB System Poster Authors and organization: Yanwei Niu¹, Xiangyun Wang², Yockey, Anastasia Christianson, Guang R. Gao
¹niu@capsl.udel.edu, . Department of ECE, University of Delaware, USA; ²Xiangyun.Wang@astrazeneca.com, EST Informatics Wilmington, Astra Zeneca PLC Abstract:
Interpro and GPCRDB are two GPCR classification systems. Using data mining technique, we compared the two systems family by family at each level of the classification hierarchy and established mapping relation between them. We introduced a novel visualization tool that allows us to directly and easily compare them.
File: niuATcapsl.udel.edu_178 ************************************************* Sat May 3 15:08:34 2003 UPDATE ----- Number: 177 Name: HYDE, LAVINIA C Affiliation: WALTER AND ELIZA HALL INSTITUTE Address: 1G ROYAL PARADE City: MELBOURNE State/Provice: VICTORIA Postal/Zip Code: 3050 Country: AUSTRALIA Email: hyde@wehi.edu.au Phone: 0393452324 Fax: 0393479852 Category: Databases Poster Title: Melbourne Brain Genome Project Poster Authors and organization: Seong-Seng Tan¹, Lavinia Hyde², Masters C, Gunnersen J, Kenshole B, Job C, Augustine C, Boon W-M, Brown M, Scott HS
¹s.tan@hfi.unimelb.edu.au, Howard Florey Institute of Experimental Medicine and Physiology; ²hyde@wehi.edu.au, Walter and Eliza Hall Institute Abstract: The Melbourne Brain Genome Project is an Internet resource for studying gene expression as measured by serial analysis of gene expression, in both normal mice and specific mouse models. These models mimic neurodegenerative human diseases. The resource includes tools developed to analyse this data and is available at http://www.mbgproject.org. File: hydeATwehi.edu.au_177 ************************************************* Sat May 3 15:13:59 2003 UPDATE ----- Number: 180 Name: Pascual-Montano, Alberto D Affiliation: National Center of Biotechnology Address: Campus Universidad Autonoma de Madrid. Cantoblanco City: Madrid State/Provice: Madrid Postal/Zip Code: 28049 Country: Spain Email: pascual@cnb.uam.es Phone: +34-915854543 Fax: +34-915854506 Category: Data Mining Poster Title: Discovering biological knowledge from gene expression using association rules Poster Authors and organization: P. Carmona-Saez¹, M. Chagoyen², A. Rodriguez, O. Trelles, J.M. Carazo and A. Pascual-Montano
¹pcarmona@cnb.uam.es, National Center of Biotechnology. Madrid; ²monica@cnb.uam.es, National Center of Biotechnology. Madrid Abstract: We describe the application of association rule discovery technique to find relevant relations between different genes attributes and experimental conditions in microarrays expression dataset. This method can be used to extract interesting and very diverse biological information. The method is implemented in EngeneTM software package that it is freely available upon request at http://www.engene.cnb.uam.es File: pascualATcnb.uam.es_180 ************************************************* Sat May 3 15:20:24 2003 UPDATE ----- Number: 183 Name: Finnerty, Caroline S Affiliation: Bioinformatics and Pharmacogenomics Laboratory Address: National University of Ireland City: Maynooth State/Provice: Co. Kildare Postal/Zip Code: N/A Country: Ireland Email: caroline.s.finnerty@may.ie Phone: 00353-1-7086211 Fax: 00353-1-7083845 Category: Functional Genomics Poster Title: A Whole-genome Analysis of Transcription Factor Binding Site Data. Poster Authors and organization: Caroline Finnerty¹, Dr. James McInerney²
¹caroline.s.finnerty@may.ie, Bioinformatics and Pharmacogenomics Laboratory; ²james.o.mcinerney@may.ie, Bioinformatics and Pharmacogenomics Laboratory Abstract:
It is widely accepted that our complexity as a species results from the regulation of our genes. Our approach is to analyse, on a genome-wide scale the upstream regions of human genes with particular emphasis on transcription factor binding sites. The ultimate goal is to infer expression pattern from sequence.
File: caroline.s.finnertyATmay.ie_183 ************************************************* Sat May 3 15:21:01 2003 UPDATE ----- Number: 183 Name: Finnerty, Caroline S Affiliation: Bioinformatics and Pharmacogenomics Laboratory Address: National University of Ireland City: Maynooth State/Provice: Co. Kildare Postal/Zip Code: N/A Country: Ireland Email: caroline.s.finnerty@may.ie Phone: 00353-1-7086211 Fax: 00353-1-7083845 Category: Functional Genomics Poster Title: A Whole-genome Analysis of Transcription Factor Binding Site Data. Poster Authors and organization: Caroline Finnerty¹, Dr. James McInerney²
¹caroline.s.finnerty@may.ie, Bioinformatics and Pharmacogenomics Laboratory; ²james.o.mcinerney@may.ie, Bioinformatics and Pharmacogenomics Laboratory Abstract: It is widely accepted that our complexity as a species results from the regulation of our genes. Our approach is to analyse, on a genome-wide scale the upstream regions of human genes with particular emphasis on transcription factor binding sites. The ultimate goal is to infer expression pattern from sequence. File: caroline.s.finnertyATmay.ie_183 ************************************************* Sat May 3 15:22:19 2003 UPDATE ----- Number: 184 Name: Theron, Daniel F Affiliation: University of Pretoria Address: Room 6-25 Agriculture Building, Lunnon Road City: Pretoria State/Provice: Gauteng Postal/Zip Code: 0002 Country: South Africa Email: danie.theron@fabi.up.ac.za Phone: +27 12 420 4239 Fax: +27 12 362 5327 Category: Microarrays Poster Title: Implementation of BASE for microarray data analysis at ACGT Microarray facility, Pretoria, South Africa Poster Authors and organization: Daniel F. Theron¹, David K. Berger², Sanushka Naidoo, Fourie Joubert
¹danie.theron@fabi.up.ac.za, University of Pretoria; ²dberger@postino.up.ac.za, University of Pretoria Abstract:
This concise guide demonstrates the implementation of BASE as a microarray data analysis pipeline. BioArray Software Environment is an open-source platform for archiving, analysis and visualizing of microarray data. Data for this demonstration compares gene expression between a wild-type and mutant Arabidopsis plants that identified 86 differentially expressed genes.
File: danie.theronATfabi.up.ac.za_184 ************************************************* Sat May 3 15:27:24 2003 UPDATE ----- Number: 190 Name: Jung, Ho-Youl Affiliation: National Genome Research Institute Address: 5 Nokbun-dong, Eunpyeng-gu City: Seoul State/Provice: na Postal/Zip Code: 122-701 Country: Republic of Korea Email: hyjung@ngri.re.kr Phone: +82-2-354-1068 Fax: +82-2-354-1063 Category: Predictive Methods Poster Title: A New Hybrid Haplotype Inference Method based-on Maximum Likelihood Estimation Poster Authors and organization: Ho-Youl Jung¹, Gil-Mi Ryu², Jee-Yeon Heo, Ju-Young Lee, Hyo-Mi Kim, Jong-Keuk Lee, Chan Park, Bermseok Oh, and Kuchan Kimm
¹hyjung@ngri.re.kr, National Genome Research Institute; ²gmryu@ngri.re.kr, National Genome Research Institute Abstract: This article presents a hybrid method that can identify the individual's haplotype from the given genotypes. Our method combines statistical and computational approaches in order to increase the accuracy. The individuals' haplotypes are resolved by considering the MLE (maximum likelihood estimation) in the process of computing the frequencies of the common haplotypes. File: hyjungATngri.re.kr_190 ************************************************* Sat May 3 15:31:29 2003 UPDATE ----- Number: 184 Name: Theron, Daniel F Affiliation: University of Pretoria Address: Room 6-25 Agriculture Building, Lunnon Road City: Pretoria State/Provice: Gauteng Postal/Zip Code: 0002 Country: South Africa Email: danie.theron@fabi.up.ac.za Phone: +27 12 420 4239 Fax: +27 12 362 5327 Category: Microarrays Poster Title: Implementation of BASE for microarray data analysis at ACGT Microarray facility, Pretoria, South Africa Poster Authors and organization: Daniel F. Theron¹, David K. Berger², Sanushka Naidoo, Fourie Joubert
¹danie.theron@fabi.up.ac.za, University of Pretoria; ²dberger@postino.up.ac.za, University of Pretoria Abstract:
This concise guide demonstrates the implementation of BASE as a microarray data analysis pipeline. BioArray Software Environment is an open-source platform for archiving, analysis and visualizing of microarray data. Data for this demonstration compares gene expression between a wild-type and mutant Arabidopsis plants that identified 86 differentially expressed genes.
File: danie.theronATfabi.up.ac.za_184 ************************************************* Sat May 3 15:34:14 2003 UPDATE ----- Number: 210 Name: McGrath, Annette Affiliation: Australian Genome Research Facility Address: Level 5 Gehrmann Laboratories, University of Queensland, City: St Lucia State/Provice: QLD Postal/Zip Code: 4072 Country: Australia Email: annette@agrf.org.au Phone: + 61 7 33469201 Fax: + 61 7 33651823 Category: Genome Annotation Poster Title: Assembly and Annotation of the Leptospira borgpetersenii serovar Hardjobovis Genome Sequence. Poster Authors and organization: Annette McGrath¹, John Davis², Peter J Wilson, Dieter Bulach, Torsten Seemann, John Davies, Ross Coppel, Ben Adler, Elizabeth S Kuczek
¹annette@agrf.org.au, Australian Genome Research Facility; ²john@agrf.org.au, Australian Genome Research Facility Abstract: We have completed the assembly of the Leptospira borgpetersenii serovar hardjobovis genome, which contains a large chromosome (CI) of 3,614,529 base pairs and a smaller chromosome (CII) of 317,585 base pairs. The annotation of CII is complete and is currently in progress for CI. File: annetteATagrf.org.au_210 ************************************************* Sat May 3 15:37:03 2003 UPDATE ----- Number: 212 Name: Imoto, Seiya Affiliation: Institute of Medical Science, University of Tokyo Address: 4-6-1 Shirokanetai, Minato-ku City: Tokyo State/Provice: na Postal/Zip Code: 108-8639 Country: Japan Email: imoto@ims.u-tokyo.ac.jp Phone: +81-3-5449-5615 Fax: +81-3-5449-5442 Category: Microarrays Poster Title: Estimating Gene Networks by Bayesian Networks from Microarrays and Biological Knowledge Poster Authors and organization: Seiya Imoto¹, Tomoyuki Higuchi², Takao Goto, Kousuke Tashiro, Satoru Kuhara, Satoru Miyano
¹imoto@ims.u-tokyo.ac.jp, University of Tokyo; ²higuchi@ism.ac.jp, The Institute of Statistical Mathematics Abstract: We propose a statistical method for estimating a gene network based on Bayesian networks from microarray data together with biological knowledge including protein-protein interactions, protein-DNA interactions, binding site information, existing literature and so on. Our method can optimize the balance between microarray and biological knowledge automatically. File: imotoATims.u-tokyo.ac.jp_212 ************************************************* Sat May 3 15:40:17 2003 UPDATE ----- Number: 214 Name: Harte, Nicola A Affiliation: EMBL-EBI Address: Wellcome Trust genome Campus, Hinxton City: Cambridge State/Provice: Cambrigeshire Postal/Zip Code: CB10 1SD Country: United Kingdom Email: nharte@ebi.ac.uk Phone: 0044-1223-494442 Fax: 0044-1223-494468 Category: Databases Poster Title: Free public services from the European Bioinformatics Institute, the European Molecular Biology Laboratory outstation. Poster Authors and organization: Nicola Harte¹, Rodrigo Lopez², Karyn Duggan, Rob Harper, Asif Kibria, Adam Lowe, Gulam Patel, Sharmila Pillai, Emmanuel Quevillon, Stephen Robinson, Ville Silventoinen
¹nharte@ebi.ac.uk, EMBL-EBI; ²rls@ebi.ac.uk, EMBL-EBI Abstract: The EBI provides free, publicly available bioinformatics services for the scientific community. These can be divided up into the following categories: data submissions processing, biological database production, access to query, analysis and retrieval systems, ftp downloads, training and education and user support. These services are available at: http://www.ebi.ac.uk/services. File: nharteATebi.ac.uk_214 ************************************************* Sat May 3 15:45:03 2003 UPDATE ----- Number: 214 Name: Harte, Nicola A Affiliation: EMBL-EBI Address: Wellcome Trust genome Campus, Hinxton City: Cambridge State/Provice: Cambrigeshire Postal/Zip Code: CB10 1SD Country: United Kingdom Email: nharte@ebi.ac.uk Phone: 0044-1223-494442 Fax: 0044-1223-494468 Category: Databases Poster Title: Free public services from the European Bioinformatics Institute, the European Molecular Biology Laboratory outstation. Poster Authors and organization: Nicola Harte¹, Rodrigo Lopez², Karyn Duggan, Rob Harper, Asif Kibria, Adam Lowe, Gulam Patel, Sharmila Pillai, Emmanuel Quevillon, Stephen Robinson, Ville Silventoinen
¹nharte@ebi.ac.uk, EMBL-EBI; ²rls@ebi.ac.uk, EMBL-EBI Abstract: The EBI provides free, publicly available bioinformatics services for the scientific community. These can be divided up into the following categories: data submissions processing, biological database production, access to query, analysis and retrieval systems, ftp downloads, training and education and user support. These services are available at: http://www.ebi.ac.uk/services. File: nharteATebi.ac.uk_214 ************************************************* Sat May 3 16:18:40 2003 UPDATE ----- Number: 218 Name: Kawashima, Shuichi Affiliation: Bioinformatics Center, Institute for Chemical Research, Kyoto University Address: Gokasho City: Uji State/Provice: Kyoto Postal/Zip Code: 611-0011 Country: Japan Email: shuichi@kuicr.kyoto-u.ac.jp Phone: +81-774-38-3273 Fax: +81-774-38-3269 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: KEGG API: A new web service for accessing the KEGG database Poster Authors and organization: Shuichi Kawashima¹, Toshiaki Katayama², Yoko Sato, Minoru Kanehisa
¹shuichi@kuicr.kyoto-u.ac.jp, Bioinformatics Center, Institute for Chemical Research, Kyoto University; ²k@bioruby.org, Bioinformatics Center, Institute for Chemical Research, Kyoto University Abstract:
KEGG API is a new web service for accessing the KEGG database. Using the APIs in the local program, the user can retrieve various information about genes, pathways, chemical compounds etc. stored in the latest versions of the KEGG database. KEGG API is available at http://www.genome.ad.jp/kegg/soap/.
File: shuichiATkuicr.kyoto-u.ac.jp_218 ************************************************* Sat May 3 16:24:22 2003 UPDATE ----- Number: 222 Name: Garcia, Alex Affiliation: Institute for Molecular Bioscience Address: Research Rd. City: Brisbane State/Provice: QLD Postal/Zip Code: 4072 Country: Australia Email: a.garcia@imb.uq.edu.au Phone: 61733462606 Fax: 6173365 4388 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: JPIPE, A pipeline module for JEMBOSS Poster Authors and organization: Alex Garcia¹, Leyla J. Garcia², Mark A. Ragan, Institute for Molecular Bioscience
¹a.Garcia@imb.uq.edu.au, Institute for Molecular Bioscience; ²leyla.garcia@unisabana.edu.co, U. de la Sabana Abstract: We present a module (JPIPE) that allows EMBOSS users to build analysis pipelines under the JEMBOSS GUI. JPIPE is a flexible workflow system that complements JEMBOSS. A tracking system is a part of JPIPE so the user is able to recreate pipelines, compare results at a particular point of the workflow and administer ongoing jobs. File: a.garciaATimb.uq.edu.au_222 ************************************************* Sat May 3 16:27:55 2003 UPDATE ----- Number: 225 Name: Garcia, Alex Affiliation: Institute for Molecular Bioscience Address: Research Rd. City: Brisbane State/Provice: QLD Postal/Zip Code: 4072 Country: Australia Email: a.garcia@imb.uq.edu.au Phone: 61733462606 Fax: 6173365 4388 I plan to use my laptop computer as part of my poster Category: Data Mining Poster Title: SEMA, A semantic literature annotator Poster Authors and organization: Alex Garcia¹, Cleary John², Mark A. Ragan, Institute for Molecular Bioscience
¹a.Garcia@imb.uq.edu.au, Institute for Molecular Bioscience; ²jcleary@reeltwo.com, Reel Two Abstract: We are using a machine-learning algorithm implemented in GO-KDS to complement SwissProt literature citation fields for each database entry. SEMA organizes this new relevant information, then builds a conceptual navigable map that is presented to the user as a flat or hyperbolic tree. This map allows redefining queries over the same database or over other information sources. File: a.garciaATimb.uq.edu.au_225 ************************************************* Sat May 3 16:29:57 2003 UPDATE ----- Number: 226 Name: Pascual-Montano, Alberto D Affiliation: National Center of Biotechnology Address: Campus Universidad Autonoma de Madrid. Cantoblanco City: Madrid State/Provice: Madrid Postal/Zip Code: 28049 Country: Spain Email: pascual@cnb.uam.es Phone: +34-915854543 Fax: +34-915854506 Category: Data Mining Poster Title: Non-negative matrix factorization for gene expression and scientific texts analysis Poster Authors and organization: A. D. Pascual-Montano¹, P. Carmona-Saez², M. Chagoyen and J.M. Carazo
¹pascual@cnb.uam.es, National Center of Biotechnology. Madrid. Spain; ²pcarmona@cnb.uam.es, National Center of Biotechnology. Madrid. Spain Abstract: We describe the application of Non-negative Matrix Factorization (NMF) technique to reduce dimensionality and to find local patterns hidden in gene expression data sets and in the scientific literature. Results show the potential of this new machine learning technique to find relevant biological information. Contact: pascual@cnb.uam.es File: pascualATcnb.uam.es_226 ************************************************* Sat May 3 16:35:10 2003 UPDATE ----- Number: 211 Name: McWilliam, Sean M Affiliation: CSIRO Livestock Industries Address: 306 Carmody Road St Lucia City: Brisbane State/Provice: QLD Postal/Zip Code: 4067 Country: Australia Email: sean.mcwilliam@csiro.au Phone: 07 3214 2504 Fax: 07 3214 2480 Category: Genome Annotation Poster Title: Towards the Bovine Ensembl Poster Authors and organization: Sean M. McWilliam¹, Wes Barris², Brian P. Dalrymple
¹sean.mcwilliam@csiro.au, CSIRO Livestock Industries, Brisbane, Australia; ²wes.barris@csiro.ai, CSIRO Livestock Industries, Brisbane, Australia Abstract: We have implemented the Ensembl genome sequence database and interface for handling the annotation of the bovine genome. Initial efforts have focussed on display of the annotation of small and micro RNAs and linking to the SNP database, IBISS. File: sean.mcwilliamATcsiro.au_211 ************************************************* Sat May 3 16:36:55 2003 UPDATE ----- Number: 218 Name: Kawashima, Shuichi Affiliation: Bioinformatics Center, Institute for Chemical Research, Kyoto University Address: Gokasho City: Uji State/Provice: Kyoto Postal/Zip Code: 611-0011 Country: Japan Email: shuichi@kuicr.kyoto-u.ac.jp Phone: +81-774-38-3273 Fax: +81-774-38-3269 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: KEGG API: A new web service for accessing the KEGG database Poster Authors and organization: Shuichi Kawashima¹, Toshiaki Katayama², Yoko Sato, Minoru Kanehisa
¹shuichi@kuicr.kyoto-u.ac.jp, Bioinformatics Center, Institute for Chemical Research, Kyoto University; ²k@bioruby.org, Bioinformatics Center, Institute for Chemical Research, Kyoto University Abstract:
KEGG API is a new web service for accessing the KEGG database. Using the APIs in the local program, the user can retrieve various information about genes, pathways, chemical compounds etc. stored in the latest versions of the KEGG database. KEGG API is available at http://www.genome.ad.jp/kegg/soap/.
File: shuichiATkuicr.kyoto-u.ac.jp_218 ************************************************* Sat May 3 16:42:25 2003 UPDATE ----- Number: 228 Name: Gioiosa, Gianpaolo Affiliation: University of South Australia Address: Unit 4, 130 Lestrange Street, GLENUNGA City: Adelaide State/Provice: South Australia Postal/Zip Code: 5064 Country: Australia Email: GIOGY001@students.unisa.edu.au Phone: 83791660 Fax: I plan to use my laptop computer as part of my poster Category: Sequence Comparison Poster Title: Implementing the Smith-Waterman Algorithm on a Reconfigurable Computer Poster Authors and organization: Gianpaolo Gioiosa¹, David Kearney²
¹GIOGY001@students.unisa.edu.au, University of South Australia; ²David.Kearney@unisa.edu.au, University of South Australia Abstract: The Smith-Waterman algorithm is a dynamic-programming algorithm that finds the optimal alignment between two biological sequences. The algorithm was implemented on a field programmable gate array (FPGA) in order to investigate the advantages and disadvantages of using reconfigurable computers and associated tools for computationally intensive sequence analysis applications. File: GIOGY001ATstudents.unisa.edu.au_228 ************************************************* Sat May 3 16:51:29 2003 UPDATE ----- Number: 234 Name: OSullivan, Orla J Affiliation: University College Cork Address: Western Road City: Cork State/Provice: na Postal/Zip Code: Country: Ireland Email: ojos@student.ucc.ie Phone: +353-21-4901307 Fax: Category: Sequence Comparison Poster Title: Multiple alignments of sequences and structures using T-Coffee Poster Authors and organization: Orla OSullivan ¹
¹ojos@student.ucc.ie, Univesity College Cork Abstract: T-Coffee is a novel method for multiple sequence alignment that allows you to combine heterogeneous sources of data to produce very accurate alignments. In this poster we look at the effects of mixing sequence and structural information using two structural alignment programs, SAP and FUGUE, in combination with T-Coffee. File: ojosATstudent.ucc.ie_234 ************************************************* Sat May 3 16:53:42 2003 UPDATE ----- Number: 239 Name: Grant, Gregory R Affiliation: University of Pennsylvania Address: 1429 Blockley Hall, 423 Guardian Drive City: Philadelphia State/Provice: PA Postal/Zip Code: 19104-6021 Country: USA Email: ggrant@pcbi.upenn.edu Phone: 215-573-3117 Fax: 215-573-3111 Category: Microarrays Poster Title: A new FDR algorithm for differential expression analysis of microarray data Poster Authors and organization: Gregory Grant¹, Elisabetta Manduchi², Christian Stoeckert
¹ggrant@pcbi.upenn.edu, CBIL; ²manduchi@pcbi.upenn.edu, CBIL Abstract: PaGE is an algorithm we have developed at CBIL which uses statistical methods to assign discrete patterns to gene expression data. This poster will highlight the new implementation (version 5.0) with improved novel FDR alrogithm based on the Westfall and Young minP stepdown distributions, and new interface. File: ggrantATpcbi.upenn.edu_239 ************************************************* Sat May 3 16:58:37 2003 UPDATE ----- Number: 242 Name: Dahlquist, Kam D Affiliation: Department of Biology, Vassar College Address: 124 Raymond Avenue City: Poughkeepsie State/Provice: NY Postal/Zip Code: 12604 Country: USA Email: kadahlquist@vassar.edu Phone: 1-845-437-7000 Fax: 1-845-437-7315 I plan to use my laptop computer as part of my poster Category: Microarrays Poster Title: GenMAPP and MAPPFinder 2.0: Tools for Viewing and Analyzing Genomic and Proteomic Data Using Gene Ontology and Biological Pathways Poster Authors and organization: Kam D. Dahlquist¹, Scott W. Doniger², Nathan Salomonis, Karen Vranizan, Steven C. Lawlor, and Bruce R. Conklin
¹kadahlquist@vassar.edu, Department of Biology, Vassar College; ²sdoniger@gladstone.ucsf.edu, Gladstone Institute of Cardiovascular Disease Abstract: GenMAPP is designed for viewing expression data on biological pathways. GenMAPP automatically color-codes the genes according to criteria supplied by the user. MAPPFinder matches expression data to the Gene Ontology and indicates whether there is a significant over-representation of genes meeting the user�s criterion for each GO term. http://www.GenMAPP.org. File: kadahlquistATvassar.edu_242 ************************************************* Sat May 3 17:00:42 2003 UPDATE ----- Number: 246 Name: Ma, Changqing Affiliation: Center for Pathology Informatics, University of Pittsburgh Address: Center for Pathology Informatics, UPMC Cancer Pavilion, Third Floor, 5230 Center Avenue City: Pittsburgh State/Provice: PA Postal/Zip Code: 15232 Country: USA Email: chmst40@pitt.edu Phone: 412-623-5951 Fax: 412-647-9588 Category: Microarrays Poster Title: Decision-tree approach to the classification of prostate tissue samples using microarray gene expression data Poster Authors and organization: Changqing Ma¹, John Gilbertson², Dhir, Jianhua Luo, George Michalopoulos, Michael Becich
¹chmst40@pitt.edu, University of Pittsburgh; ²GilbertsonJR@MSX.UPMC.EDU, University of Pittsburgh Abstract: A decision-tree learning approach was applied to classify three types of prostate tumor tissue samples using microarray gene-expression data. In LOOCV, results were comparable to those obtained from applying SVMs or weighted voting method to this dataset. Furthermore, human-understandable models from decision-tree learning correctly predicted sample classes in previously published prostate tumor datasets. File: chmst40ATpitt.edu_246 ************************************************* Sat May 3 17:04:22 2003 UPDATE ----- Number: 250 Name: Lancaster, Alex K Affiliation: Dept. of Integrative Biology, UC Berkeley Address: 3060 Valley Life Sciences Building City: Berkeley State/Provice: CA Postal/Zip Code: 94720-3140 Country: USA Email: alexl@socrates.berkeley.edu Phone: 510 642-1233 Fax: 510 643-5144 I plan to use my laptop computer as part of my poster Category: Phylogeny and Evolution Poster Title: PyPop: A framework for large-scale population genomics analysis Poster Authors and organization: Alex Lancaster¹, Mark P. Nelson², Richard M. Single; Diogo Meyer; Glenys Thomson
¹alexl@socrates.berkeley.edu, UC Berkeley; ², UC Berkeley Abstract: PyPop (Python for Population Genetics) is a suite of programs for the analysis of multi-locus population genetic data, outputs are stored in XML and can be transformed into other data formats. PyPop will be made freely available under the GNU GPL at: http://allele5.biol.berkeley.edu/pypop/ File: alexlATsocrates.berkeley.edu_250 ************************************************* Sat May 3 17:08:47 2003 UPDATE ----- Number: 260 Name: Taguchi, Y-h. Affiliation: Department of Physics, Chuo University Address: 1-13-27 Kasuga City: Bunkyo-ku State/Provice: Tokyo Postal/Zip Code: 112-8551 Country: Japan Email: tag@granular.com Phone: +81-3-3817-1791 Fax: +81-3-3817-1792 I plan to use my laptop computer as part of my poster Category: Data Mining Poster Title: C. elegans microarray data seen through a novel nonmetric multidimensional scaling method Poster Authors and organization: Y-h. Taguchi¹, Y. Oono²
¹tag@granular.com, Department of Physics, Chuo University; ²y-oono@uiuc.edu, Department of Physics, UIUC Abstract: C.elegans microarray data is analysed by a novel nonmetric multidimensional scaling method that is maximally nonmetric. The genes are embeddable in 3D. Their annotations are consistent with their positions in this space. A method to compute the 3D coordinates directly from the microarray data is also developed. File: tagATgranular.com_260 ************************************************* Sat May 3 17:10:48 2003 UPDATE ----- Number: 262 Name: Park, Mihwa Affiliation: POSDATA co. Address: 276-2 City: SungNam-City State/Provice: Gyuggi-DO Postal/Zip Code: 463-775 Country: Korea Email: bfpark@posdata.co.kr Phone: 82-031-779-2707 Fax: 82-031-779-2709 I plan to use my laptop computer as part of my poster Category: Systems Biology Poster Title: SPACE-BLAST: Linux Cluster based Biological Sequence Parallel Processing system Summarized by Gene Ontology Poster Authors and organization: Mihwa Park¹, Jaewoo Kim², Hyungsuk Won, Seungsik Yoo
¹bfpark@posdata.co.kr, POSDATA; ²jaewoo@posdata.co.kr, POSDATA Abstract: SPACE-BLAST (Super PArallel Computer Engine for BLAST) is a high performance bioinformatics system that implements the NCBI�s BLAST system with low cost Linux cluster based parallel processing to search DNA sequencing at high speed. Also, Gene Ontology is applied to summarize massive amount of the BLAST search results. SPACE-BLAST is available at http://space-blast.posdata.co.kr File: bfparkATposdata.co.kr_262 ************************************************* Sat May 3 18:40:18 2003 UPDATE ----- Number: 270 Name: lefevre, christophe Affiliation: Victorian Bioinformatics Consortium Address: Monash Universiry, PO box 53 City: Clayton State/Provice: Victoria Postal/Zip Code: 3800 Country: Australia Email: chris.lefevre@med.monash.edu.au Phone: 61 3 9905 9338 Fax: 61 3 9905 9773 Category: Data Visualisation Poster Title: Poster Title: Linguistic profiling of genome sequences. The Sequence identifier position end set cardinal: an estimate of linear sequence complexity: algorithms and genome profiling applications. Poster Authors and organization: christophe lefevre¹
¹chris.lefevre@med.monash.edu.au, Victorian Bioinformatics Consortium Abstract: The sequence identifier end set cardinal is proposed as a new estimator of linear sequence linguistic complexity. A scanning window algorithm to compute this value is presented and profiles obtained with genomic sequences are discussed. File: chris.lefevreATmed.monash.edu.au_270 ************************************************* Sat May 3 18:42:39 2003 UPDATE ----- Number: 250 Name: Lancaster, Alex K Affiliation: Dept. of Integrative Biology, UC Berkeley Address: 3060 Valley Life Sciences Building City: Berkeley State/Provice: CA Postal/Zip Code: 94720-3140 Country: USA Email: alexl@socrates.berkeley.edu Phone: 510 642-1233 Fax: 510 643-5144 I plan to use my laptop computer as part of my poster Category: Phylogeny and Evolution Poster Title: PyPop: A framework for large-scale population genomics analysis Poster Authors and organization: Alex Lancaster¹, Mark P. Nelson², Richard M. Single; Diogo Meyer; Glenys Thomson
¹alexl@socrates.berkeley.edu, UC Berkeley; ², UC Berkeley Abstract: PyPop (Python for Population Genetics) is a suite of programs for the analysis of multi-locus population genetic data, outputs are stored in XML and can be transformed into other data formats. PyPop will be made freely available under the GNU GPL at: http://allele5.biol.berkeley.edu/pypop/ File: alexlATsocrates.berkeley.edu_250 ************************************************* Sat May 3 18:47:38 2003 UPDATE ----- Number: 272 Name: Chen, Yan Affiliation: Queensland University of Technology Address: 126 Margaret Street City: Brisbane State/Provice: Queensland Postal/Zip Code: QLD 4001 Country: Australia Email: y52.chen@student.qut.edu.au Phone: 38649447 Fax: Category: Data Mining Poster Title: BioInfoCallboratory: Towards an Agent- Assisted Web-Based Collaboration Environment for Bioinformatics Poster Authors and organization: Yan Chen¹, Yi-Ping Phoebe Chen²
¹y52.chen@student.qut.edu.au, Queensland University of Technology; ²p.chen@qut.edu.au, Queensland University of Technology Abstract: Collaborations in web based bioinformatics environment require intelligent supports to assist human computer interaction. BioInfoCallboratory is an agent assisted web based environment for supporting bioinformatics research. It facilitates sophisticated interactions such as: matchmaking based on common interests; internet spanning data mining for bioinformatics data; and event alert for interested parties. File: y52.chenATstudent.qut.edu.au_272 ************************************************* Sat May 3 18:50:14 2003 UPDATE ----- Number: 274 Name: Sarai, Akinori Affiliation: Department of Biochemical Engineering and Science Address: Kyushu Institute of Technology City: Iizuka State/Provice: Fukuoka Postal/Zip Code: 8208502 Country: Japan Email: sarai@bse.kyutech.ac.jp Phone: +81-948-29-7811 Fax: +81-948-29-7801 Category: Predictive Methods Poster Title: Ligand specificity of proteases and Kinases: an applicationto IC50 prediction on a large scale Poster Authors and organization: Shandar Ahmad¹, Koji Kitajima², Akinori Sarai
¹shandar@bse.kyutech.ac.jp, Department of Biochemical Enigineering and Science, Kyushu Institute of Technology, Japan; ², Abstract: We have attempted neural-network-based predictions of inhibition coefficient (IC50) from the SMILES of ligands for kinases and proteases in the protein-ligand interaction database, ProLINT. Our method is useful for a large scale filtering of ligands in drug-design. We have also attempted to develop ligand fragment-signature for proteins in ProLINT. File: saraiATbse.kyutech.ac.jp_274 ************************************************* Sat May 3 18:51:20 2003 UPDATE ----- Number: 276 Name: Batalov, Serge Affiliation: GNF Address: 10675 JJ Hopkins Dr City: San Diego State/Provice: CA Postal/Zip Code: 92121 Country: USA Email: batalov@gnf.org Phone: +1-858-8121569 Fax: +1-858-8121502 Category: Microarrays Poster Title: Design of the custom whole-genome malaria oligonucleotide array Poster Authors and organization: Serge Batalov¹, Elizabeth A. Winzeler²
¹batalov@gnf.org, GNF; ²winzeler@scripps.edu, TSRI/GNF Abstract: To study the transcriptome of the malaria parasite, we designed a custom no-mismatch oligonucleotide array containing 260,596 25mer single stranded probes from predicted coding sequence (including mitochondrion and plastid genome sequences) and 106,630 probes from non-coding sequence. In addition 124,957 probes from Plasmodium yoelli contigs are include on the array. File: batalovATgnf.org_276 ************************************************* Sat May 3 18:54:36 2003 UPDATE ----- Number: 279 Name: Satterley, Keith R Affiliation: The Walter and Eliza Hall Institute of Medical Research Address: 1G Royal Pd. City: Melbourne State/Provice: Victoria Postal/Zip Code: 3050 Country: Australia Email: keith@wehi.edu.au Phone: +61 4 2570 0 419 Fax: +61 3 9347 0852 Category: Sequence Comparison Poster Title: ASAD-A Sequence Attribute Display tool Poster Authors and organization: Keith Satterley¹
¹keith@wehi.edu.au, The Walter and Eliza Hall Institute of Medical Research Abstract: ASAD is A Sequence Attribute Display tool. It is written as a set of Excel macros. It builds on the familiar Excel interface to allow for flexible and efficient display of attributes (hydrophobicity etc.) using similar colours and styles for one sequence or multiple aligned sequences. ASAD is available at ftp://ftp.wehi.edu.au/pub/biology/ASAD. File: keithATwehi.edu.au_279 ************************************************* Sat May 3 18:58:11 2003 UPDATE ----- Number: 284 Name: Saunders, Neil F Affiliation: School of Biotechnology and Biomolecular Sciences, The University of New South Wales Address: UNSW City: Sydney State/Provice: NSW Postal/Zip Code: 2052 Country: Australia Email: neil.saunders@unsw.edu.au Phone: +61 2 9385 2092 Fax: +61 2 9385 1591 Category: Data Mining Poster Title: Pathogenic archaea-do they exist Poster Authors and organization: Neil Saunders¹, Ricardo Cavicchioli², Paul M.G. Curmi, Torsten Thomas
¹neil.saunders@unsw.edu.au, The University of New South Wales; ²r.cavicchioli@unsw.edu.au, The University of New South Wales Abstract: We have developed a rapid, automated search strategy for the detection of contaminating sequence from putative novel pathogenic archaea in human EST sequence data. The system has general application to the detection of microbial pathogens and will be available at http://psychro.bioinformatics.unsw.edu.au. File: neil.saundersATunsw.edu.au_284 ************************************************* Sat May 3 19:03:00 2003 UPDATE ----- Number: 292 Name: Goh, Liang K Affiliation: Knowledge Engineering and Discovery Research Institute, Auckland University of Technology Address: 581-585, Great South Road, Ronald Trotter House, Penrose City: City State/Provice: na Postal/Zip Code: Country: New Zealand Email: liang.goh@aut.ac.nz Phone: 6499179556 Fax: 6499179501 I plan to use my laptop computer as part of my poster Category: Microarrays Poster Title: A Novel Feature Selection Method using Evolving Supervised Clustering and Applications for Gene Expression Data Modeling Poster Authors and organization: Nikola Kasabov¹, Liang Goh²
¹nkasabov@aut.ac.nz, KEDRI; ²liang.goh@aut.ac.nz, KEDRI Abstract: The method combines the tasks of classification and feature selection by using the obtained clusters in ECOS to further extract specific features for each of the clusters. The method overcomes the problem of the signal to noise ratio method when data of the same class are spread in several clusters. File: liang.gohATaut.ac.nz_292 ************************************************* Sat May 3 19:06:09 2003 UPDATE ----- Number: 294 Name: Chalifa-Caspi, Vered Affiliation: Weizmann Institute of Science Address: P.O. Box 26 City: Rehovot State/Provice: na Postal/Zip Code: 76100 Country: Israel Email: vered.caspi@weizmann.ac.il Phone: 972-8-9343188 Fax: 972-8-9344113 Category: Microarrays Poster Title: GeneAnnot: Annotation of high-density oligunocleotide arrays and their linking with GeneCards. Poster Authors and organization: Vered Chalifa-Caspi¹, Itai Yanai², Ron Ophir, Michael Shmoish, Hila Benjamin-Rodrig, Naomi Rosen, Pavel Kats, Marilyn Safran, Orit Shmueli and Doron Lancet.
¹vered.caspi@weizmann.ac.il, Weizmann Insitute of Science; ²Iyanai@wisemail.weizmann.ac.il, Weizmann Insitute of Science Abstract: The availability of entire genomic sequences enables matching the short probe sequences of oligonucleotide arrays to their annotated gene representations. Here, we present a framework for estimating the sensitivity and specificity of gene-representing probe sets, and for integrating this information with the comprehensive genome and transcriptome repositories of the GeneCards databases suite. File: vered.caspiATweizmann.ac.il_294 ************************************************* Sat May 3 19:07:18 2003 UPDATE ----- Number: 296 Name: Tyrelle, Greg D Affiliation: UNSW Address: UNSW City: Sydney State/Provice: NSW Postal/Zip Code: 2052 Country: Australia Email: greg@kinglab.unsw.edu.au Phone: 9385 2036 Fax: 9385 1483 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: A genetic polymorphism object model and XML implementation: Biological Variation Markup Language. Poster Authors and organization: Greg Tyrelle¹, Garry C. King²
¹greg@kinglab.unsw.edu.au, UNSW; ²garry@kinglab.unsw.edu.au, UNSW Abstract: As molecular genotyping technologies accelerate there is an increasing need to communicate precise information on polymorphism data in machine-readable format. We have developed a hierarchical object model and XML implementation called Biological Variation Markup Language (BVML) to facilitate exchange between genotyping laboratories and distributed databases. File: gregATkinglab.unsw.edu.au_296 ************************************************* Sat May 3 19:09:18 2003 UPDATE ----- Number: 284 Name: Saunders, Neil F Affiliation: School of Biotechnology and Biomolecular Sciences, The University of New South Wales Address: UNSW City: Sydney State/Provice: NSW Postal/Zip Code: 2052 Country: Australia Email: neil.saunders@unsw.edu.au Phone: +61 2 9385 2092 Fax: +61 2 9385 1591 Category: Data Mining Poster Title: Pathogenic archaea-do they exist Poster Authors and organization: Neil Saunders¹, Ricardo Cavicchioli², Paul M.G. Curmi, Torsten Thomas
¹neil.saunders@unsw.edu.au, The University of New South Wales; ²r.cavicchioli@unsw.edu.au, The University of New South Wales Abstract: We have developed a rapid, automated search strategy for the detection of contaminating sequence from putative novel pathogenic archaea in human EST sequence data. The system has general application to the detection of microbial pathogens and will be available at http://psychro.bioinformatics.unsw.edu.au. File: neil.saundersATunsw.edu.au_284 ************************************************* Sat May 3 19:11:07 2003 UPDATE ----- Number: 302 Name: Clark, Francis Affiliation: Advanced Computational Modelling Centre, University of Queensland, Australia. Address: University of Queensland City: Brisbane State/Provice: Queensland Postal/Zip Code: 4067 Country: Australia Email: fc@maths.uq.edu.au Phone: 33658586 Fax: Category: Data Mining Poster Title: Issues and principles in the analysis of large genomic datasets. Poster Authors and organization: Francis Clark¹, Susan Lilley²
¹fc@maths.uq.edu.au, Advanced Computational Modelling Centre, University of Queensland, Australia.; ²s364202@student.uq.edu.au, School of Information Technology & Electrical Engineering, University of Queensland, Australia. Abstract: Development of research analysis pipelines often involves working with poorly understood data to answer questions that are, initially, simplistic. This poster overviews some strategies and best practices that may be employed in such work, including; handling & appraisal of the data, choice of appropriate thresholds, extrapolation, and checking for reasonableness. File: fcATmaths.uq.edu.au_302 ************************************************* Sat May 3 19:15:16 2003 UPDATE ----- Number: 279 Name: Satterley, Keith R Affiliation: The Walter and Eliza Hall Institute of Medical Research Address: 1G Royal Pd. City: Melbourne State/Provice: Victoria Postal/Zip Code: 3050 Country: Australia Email: keith@wehi.edu.au Phone: +61 4 2570 0 419 Fax: +61 3 9347 0852 Category: Sequence Comparison Poster Title: ASAD-A Sequence Attribute Display tool Poster Authors and organization: Keith Satterley¹
¹keith@wehi.edu.au, The Walter and Eliza Hall Institute of Medical Research Abstract: ASAD is A Sequence Attribute Display tool. It is written as a set of Excel macros. It builds on the familiar Excel interface to allow for flexible and efficient display of attributes (hydrophobicity etc.) using similar colours and styles for one sequence or multiple aligned sequences. ASAD is available at ftp://ftp.wehi.edu.au/pub/biology/ASAD. File: keithATwehi.edu.au_279 ************************************************* Sat May 3 20:26:12 2003 UPDATE ----- Number: 404 Name: San Gil, Inigo Affiliation: Yale University Address: 333 cedar st. City: new haven State/Provice: ct Postal/Zip Code: 06511 Country: usa Email: inigo.sangil@yale.edu Phone: 203-737-5011 Fax: 203-785-4035 Category: New Frontiers Poster Title: Gene-Protein networks in Drosophila Melanogaster Poster Authors and organization: Inigo San Gil ¹, Kevin White², Joel Bader
¹inigo.sangil@yale.edu, Yale University; ²kevin.white@yale.edu, Yale University Abstract: We present a gene network or map of interactions between proteins and genes for the Drosophila melanogaster organism. The map info is based on cross-correlations of the genome-wide timecourses of gene expression profile and yeast to hybrid interactions. Results show rich networks of genes and proteins ready to be explored. File: inigo.sangilATyale.edu_404 ************************************************* Sat May 3 20:32:08 2003 UPDATE ----- Number: 398 Name: Blake, Judith A Affiliation: The Jackson Laboratory Address: 600 Main St. City: Bar Harbor State/Provice: ME Postal/Zip Code: 04609 Country: USA Email: jblake@informatics.jax.org Phone: 1-207-288-6248 Fax: 1-207-288-6132 Category: Databases Poster Title: Mouse Genome Informatics: Integration Nexus for Mammalian Biology Poster Authors and organization: JA Blake¹, M Ringwald², CJ Bult, JA Kadin, JE Richardson, JT Eppig, Mouse Genome Informatics Group
¹jblake@informatics.jax.org, Jackson Laboratory; ²ringwlad @informatics.jax.org, Jackson Laboratory Abstract: The Mouse Genome Informatics (MGI) databases provide access to comprehensive, integrated, experimental data for the laboratory mouse in the domains of sequence, expression, gene function (GO), molecular variation, phenotype, inbred strain characterization, homology, and tumor biology. MGI provides the definitive mouse gene index. MGI can be accessed at www.informatics.jax.org . File: jblakeATinformatics.jax.org_398 ************************************************* Sat May 3 20:34:11 2003 UPDATE ----- Number: 396 Name: Luciano, Joanne S Affiliation: BioPAX Address: 45 Orchard Street City: Belmont State/Provice: MA Postal/Zip Code: 02478-3008 Country: USA Email: jluciano@biopathways.org Phone: 617 993-9994 Fax: 208-728-1133 Category: Systems Biology Poster Title: BioPAX Data Exchange Ontology for Biological Pathway Databases Poster Authors and organization: BioPAX Group¹
¹pax@cbio.mskcc.org, BioPAX Abstract: BioPAX (http://biopax.org) is a new community-based effort to develop a data exchange format for biological pathway data. The ontology will be able to represent data from diverse sources such as aMAZE, BIND, BioCyc, and WIT. Initial implementations of BioPAX will be available in both OWL and XML Schema.
File: jlucianoATbiopathways.org_396 ************************************************* Sat May 3 20:41:01 2003 UPDATE ----- Number: 392 Name: Culhane, Aedin C Affiliation: University College Cork Address: 5.28 Bioscience Institute City: Cork State/Provice: Cork Postal/Zip Code: Ireland Country: Ireland Email: A.Culhane@ucc.ie Phone: 353214901306 Fax: 353214904259 I plan to use my laptop computer as part of my poster Category: Microarrays Poster Title: A multivariate method for comparison of microarray data from different platforms Poster Authors and organization: Aedin C Culhane¹, Guy Perri�re², Desmond G. Higgins
¹A.Culhane@ucc.ie, University College Cork; ²perriere@biomserv.univ-lyon.fr, Universite Claude Bernard Abstract: We describe a powerful method for comparison and visualisation of gene expression data from different microarray platforms. Co-inertia analysis (CIA) is a multivariate method that identifies co-relationships in multiple datasets. The genes from each dataset, which define these trends, can be identified. Further details: http://bioinfo.ucc.ie. File: A.CulhaneATucc.ie_392 ************************************************* Sun May 4 14:37:22 2003 UPDATE ----- Number: 396 Name: Luciano, Joanne S Affiliation: BioPAX Address: 45 Orchard Street City: Belmont State/Provice: MA Postal/Zip Code: 02478-3008 Country: USA Email: jluciano@biopathways.org Phone: 617 993-9994 Fax: 208-728-1133 Category: Systems Biology Poster Title: BioPAX Data Exchange Ontology for Biological Pathway Databases Poster Authors and organization: BioPAX Group¹
¹pax@cbio.mskcc.org, BioPAX Abstract: BioPAX (http://biopax.org) is a new community-based effort to develop a data exchange format for biological pathway data. The ontology will be able to represent data from diverse sources such as aMAZE, BIND, BioCyc, and WIT. Initial implementations of BioPAX will be available in both OWL and XML Schema.
File: jlucianoATbiopathways.org_396 ************************************************* Sun May 4 14:39:18 2003 UPDATE ----- Number: 386 Name: Naito, Yasuhiro Affiliation: Inst. Adv. Biosci., Keio Univ. Address: 14-1 Babacho City: Tsuruoka State/Provice: Yamagata Postal/Zip Code: 997-0035 Country: Japan Email: ynaito@sfc.keio.ac.jp Phone: +81-235-29-0828 Fax: +81-235-29-0525 Category: Systems Biology Poster Title: in silico Knockout Experiment of Myocardial Cell Using E-CELL System Poster Authors and organization: Yasuhiro Naito¹, Motohiro Yoneda², Sayaka Ishinabe, Shoko Miyamoto, Katsuya Kawai, Masaru Tomita
¹ynaito@sfc.keio.ac.jp, Inst. Adv. Biosci., Keio Univ.; ²moto@sfc.keio.ac.jp, Inst. Adv. Biosci., Keio Univ. Abstract: The Kyoto model of the myocardial cell was implemented into E-CELL. The simulation results accurately represented the electrophysiological behavior of intact guinea pig myocardial cells. We tried in silico knockout of Kir2.1 channel. When the conductance of Kir2.1 was suppressed approximately 80%, the simulation showed behavior roughly consistent with the antecedent experimental results. File: ynaitoATsfc.keio.ac.jp_386 ************************************************* Sun May 4 14:45:02 2003 UPDATE ----- Number: 312 Name: Izumitani, Tomonori Affiliation: NTT Communication Science Laboratories Address: 2-4, Hikaridai City: Seika-cho, Soraku-gun State/Provice: Kyoto Postal/Zip Code: 619-0237 Country: JAPAN Email: izumi@cslab.kecl.ntt.co.jp Phone: +81-774-93-5354 Fax: +81-774-93-5385 Category: Data Mining Poster Title: Detection of implicit protein-protein interactions from literature Poster Authors and organization: Tomonori Izumitani¹, Frederic Tingaud², Hirotoshi Taira, Eisaku Maeda
¹izumi@cslab.kecl.ntt.co.jp, NTT Communication Science Laboratories; ²tingaud@cslab.kecl.ntt.co.jp, NTT Communication Science Laboratories Abstract: In this study, we propose a method to detect explicit or implicit protein-protein interactions from text data. It was applied to the detection of interactions between yeast proteins. The result indicates that the putative interactions detected by the method can contain true and experimentally unidentified interactions. File: izumiATcslab.kecl.ntt.co.jp_312 ************************************************* Sun May 4 14:48:11 2003 UPDATE ----- Number: 326 Name: Lapp, Hilmar Affiliation: Genomics Institute of the Novartis Research Institute Address: 10675 John J Hopkins Dr City: San Diego State/Provice: CA Postal/Zip Code: 92121 Country: USA Email: hlapp@gnf.org Phone: +1-858-812-1757 Fax: Category: Databases Poster Title: Optimizing Genome Interval Overlap Queries Using an R-Tree Index Poster Authors and organization: Hilmar Lapp¹, Chris Mungall², Scott Cain, Lincoln Stein
¹hlapp@gnf.org, GNF; ²cjm@fruitfly.org, University of California, Berkely Abstract: We present a solution to the huge variance problem that has plagued B-tree supported genome interval overlap queries. Our approach is based on translating the overlap query into a two-dimensional point-in-box geometric query supported by an R-tree index. File: hlappATgnf.org_326 ************************************************* Sun May 4 14:52:00 2003 UPDATE ----- Number: 330 Name: Chalk, Alistair M Affiliation: Center for Genomics and Bioinformatics, Karolinksa Institute Address: Berzelius vag 35 City: Stockholm State/Provice: Stockholm Postal/Zip Code: 171 77 Country: Sweden Email: alistair.chalk@cgb.ki.se Phone: +46739824296 Fax: +468337983 Category: Functional Genomics Poster Title: Design of Antisense Oligonucleotides Poster Authors and organization: Alistair M. Chalk¹, Erik L.L. Sonnhammer²
¹alistair.chalk@cgb.ki.se, CGB, Karolinska Institute; ²esr@algol.cgb.ki.se, CGB, Karolinska Institute Abstract: Antisense oligonucelotides are an important tool for gene-knockdown approaches in functional genomics. We assess the usefulness of current approaches predicting accessibility and/or efficacy using a database of known results. A set of utilities developed for AO and siRNA design (control design, specificity, site selection) is available at http://sonnhammer.cgb.ki.se. File: alistair.chalkATcgb.ki.se_330 ************************************************* Sun May 4 14:53:21 2003 UPDATE ----- Number: 334 Name: Tae, Hongseok Affiliation: Dept. of Microbiology, Kyungpook National University Address: Pook-Gu Sankyuk-Dong City: Daegu State/Provice: na Postal/Zip Code: 702-701 Country: South Korea Email: hstae@smallsoft.co.kr Phone: +82-42-864-2524 Fax: +82-42-866-9241 Category: Genome Annotation Poster Title: Development of a Web-based Genome Annotation System and Two Analysis Tools Poster Authors and organization: Hongseok Tae¹, Hyeweon Nam², Daesang Lee, Kiejung Park
¹hstae@smallsoft.co.kr, Dept. of Microbiology, Kyungpook National University; ²hwnam@smallsoft.co.kr, Information Technology Institute, SmallSoft Co., Ltd. Abstract: Our web-based genome annotation system has major modules such as gene prediction, homology search, promoter analysis, motif analysis, gene ontology analysis, annotation databases, and a genome browser which shows the entire information of a genome. We have also developed a motif analysis and a gene prediction programs based on HMM. File: hstaeATsmallsoft.co.kr_334 ************************************************* Sun May 4 14:57:57 2003 UPDATE ----- Number: 338 Name: Bellgard, Matthew I Affiliation: Centre for Bioinformatics and Biological Computing, Murdoch University Address: Murdoch City: Perth State/Provice: Western Australia Postal/Zip Code: 6150 Country: Australia Email: m.bellgard@murdoch.edu.au Phone: +61-8-93606088 Fax: +61-8-93607238 I plan to use my laptop computer as part of my poster Category: Data Mining Poster Title: Computational comparative analysis framework at the Centre for Bioinformatics and Biological Computing. Poster Authors and organization: M Bellgard¹, A Hunter², D Schibeci
¹m.bellgard@murdoch.edu.au, CBBC, Murdoch University; ²a.hunter@cbbc.murdoch.edu.au, CBBC, Murdoch University Abstract: The CBBC conducts research in computational biology ranging from comparative genomic sequence analysis, microarray and proteomic data analysis, and novel algorithms and software. The CBBC is developing a comparative analysis framework incorporating audit trailing of analysis, open source activities and distributed resource management. We present an overview of this framework. File: m.bellgardATmurdoch.edu.au_338 ************************************************* Sun May 4 14:59:49 2003 UPDATE ----- Number: 342 Name: Kao, Cheng-Yan Affiliation: Bioinfo Lab., Department of CSIE, National Taiwan University Address: No.1, Sec. 4, Roosevelt Road City: Taipei State/Provice: Taiwan Postal/Zip Code: 106 Country: R.O.C. Email: cykao@csie.ntu.edu.tw Phone: 886-2-23625336 Fax: 886-2-23658741 Category: Microarrays Poster Title: An automatic and unbiased GA for finding the most discriminant gene sets on Microarray Poster Authors and organization: Han-Yu Chuang¹, Hwa-Sheng Chiu², Huai-Kuang Tsai, Cheng-Yan Kao
¹r90002@csie.ntu.edu.tw, Bioinfo Lab., Department of CSIE, National Taiwan University; ²r91031@csie.ntu.edu.tw, Bioinfo Lab., Department of CSIE, National Taiwan University Abstract: A multi-objective genetic algorithm based approach, combining univariate and multivariate techniques, was proposed to find optimal gene sets for sample classification on gene expression data automatically and unbiased. Eight genes with 93% LOOCV accuracy of KNN were selected to be the optimal predictive gene sets for Colon cancer dataset. File: cykaoATcsie.ntu.edu.tw_342 ************************************************* Sun May 4 15:00:47 2003 UPDATE ----- Number: 344 Name: Brahmachary, Manisha Affiliation: Institute of Infocomm Research Address: 21, heng Mui keng Terrace City: Singapore State/Provice: Singapore Postal/Zip Code: 119613 Country: Singapore Email: manisha@lit.org.sg Phone: 65-68748233, 65-68748237 Fax: 65-67748056 Category: Databases Poster Title: ANTIMIC: A database of antimicrobial peptides Poster Authors and organization: Manisha Brahmachary¹, Judice L.Y.Koh, Mohammad Asif Khan,Seah Seng Hong Tin Wee Tan, Vladimir Bajic
¹manisha@lit.org.sg, Institute of Infocomm Research Abstract: ANTIMIC is a specialized database dedicated to antimicrobial peptides. It contains useful analysis tools that can aid wet-lab scientists to determine the family and function of a putative new anti-microbial peptide and also in design of artificial anti-microbial peptides. File: manishaATlit.org.sg_344 ************************************************* Sun May 4 15:11:48 2003 UPDATE ----- Number: 348 Name: Syeda-Mahmood, Tanveer F Affiliation: IBM Almaden Research Address: 650 Harry Road City: San Jose State/Provice: CA Postal/Zip Code: 95120 Country: USA Email: stf@almaden.ibm.com Phone: 408-927-1883 Fax: 408-927-3030 Category: New Frontiers Poster Title: MineLink: A novel information integration framework for Life Sciences Poster Authors and organization: Tanveer Syeda-Mahmood¹, Bhooshan Kelkar²
¹stf@almaden.ibm.com, IBM Almaden Research; ²bkelkar@us.ibm.com, IBM Life Sciences Abstract: MineLink is a novel information integration framework that can pull together life sciences data and analytic applications from disparate sources. It specifies a design methodology for automatically integrating individual components, be they data sources, processors, data miners or visualization components without the need for explicit programming. It addresses both syntactic and semantic aspects of information integration. File: stfATalmaden.ibm.com_348 ************************************************* Sun May 4 15:16:52 2003 UPDATE ----- Number: 348 Name: Syeda-Mahmood, Tanveer F Affiliation: IBM Almaden Research Address: 650 Harry Road City: San Jose State/Provice: CA Postal/Zip Code: 95120 Country: USA Email: stf@almaden.ibm.com Phone: 408-927-1883 Fax: 408-927-3030 Category: New Frontiers Poster Title: MineLink: A novel information integration framework for Life Sciences Poster Authors and organization: Tanveer Syeda-Mahmood¹, Bhooshan Kelkar²
¹stf@almaden.ibm.com, IBM Almaden Research; ²bkelkar@us.ibm.com, IBM Life Sciences Abstract: MineLink is a novel information integration framework that can pull together life sciences data and analytic applications from disparate sources. It specifies a design methodology for automatically integrating individual components, be they data sources, processors, data miners or visualization components without the need for explicit programming. It addresses both syntactic and semantic aspects of information integration. File: stfATalmaden.ibm.com_348 ************************************************* Sun May 4 15:18:25 2003 UPDATE ----- Number: 348 Name: Syeda-Mahmood, Tanveer F Affiliation: IBM Almaden Research Address: 650 Harry Road City: San Jose State/Provice: CA Postal/Zip Code: 95120 Country: USA Email: stf@almaden.ibm.com Phone: 408-927-1883 Fax: 408-927-3030 Category: New Frontiers Poster Title: MineLink: A novel information integration framework for Life Sciences Poster Authors and organization: Tanveer Syeda-Mahmood¹, Bhooshan Kelkar²
¹stf@almaden.ibm.com, IBM Almaden Research; ²bkelkar@us.ibm.com, IBM Life Sciences Abstract: MineLink is a novel information integration framework that can pull together life sciences data and analytic applications from disparate sources. It specifies a design methodology for automatically integrating individual components, be they data sources, processors, data miners or visualization components without the need for explicit programming. It addresses both syntactic and semantic aspects of information integration. File: stfATalmaden.ibm.com_348 ************************************************* Sun May 4 15:19:48 2003 UPDATE ----- Number: 348 Name: Syeda-Mahmood, Tanveer F Affiliation: IBM Almaden Research Address: 650 Harry Road City: San Jose State/Provice: CA Postal/Zip Code: 95120 Country: USA Email: stf@almaden.ibm.com Phone: 408-927-1883 Fax: 408-927-3030 Category: New Frontiers Poster Title: MineLink: A novel information integration framework for Life Sciences Poster Authors and organization: Tanveer Syeda-Mahmood¹, Bhooshan Kelkar²
¹stf@almaden.ibm.com, IBM Almaden Research; ²bkelkar@us.ibm.com, IBM Life Sciences Abstract: MineLink is a novel information integration framework that can pull together life sciences data and analytic applications from disparate sources. It specifies a design methodology for automatically integrating individual components, be they data sources, processors, data miners or visualization components without the need for explicit programming. It addresses both syntactic and semantic aspects of information integration. File: stfATalmaden.ibm.com_348 ************************************************* Sun May 4 15:21:20 2003 UPDATE ----- Number: 348 Name: Syeda-Mahmood, Tanveer F Affiliation: IBM Almaden Research Address: 650 Harry Road City: San Jose State/Provice: CA Postal/Zip Code: 95120 Country: USA Email: stf@almaden.ibm.com Phone: 408-927-1883 Fax: 408-927-3030 Category: New Frontiers Poster Title: MineLink: A novel information integration framework for Life Sciences Poster Authors and organization: Tanveer Syeda-Mahmood¹, Bhooshan Kelkar²
¹stf@almaden.ibm.com, IBM Almaden Research; ²bkelkar@us.ibm.com, IBM Life Sciences Abstract: MineLink is a novel information integration framework that can pull together life sciences data and analytic applications from disparate sources. It specifies a design methodology for automatically integrating individual components, be they data sources, processors, data miners or visualization components without the need for explicit programming. It addresses both syntactic and semantic aspects of information integration. File: stfATalmaden.ibm.com_348 ************************************************* Sun May 4 15:42:38 2003 UPDATE ----- Number: 348 Name: Syeda-Mahmood, Tanveer F Affiliation: IBM Almaden Research Address: 650 Harry Road City: San Jose State/Provice: CA Postal/Zip Code: 95120 Country: USA Email: stf@almaden.ibm.com Phone: 408-927-1883 Fax: 408-927-3030 Category: New Frontiers Poster Title: MineLink: A novel information integration framework for Life Sciences Poster Authors and organization: Tanveer Syeda-Mahmood¹, Bhooshan Kelkar²
¹stf@almaden.ibm.com, IBM Almaden Research; ²bkelkar@us.ibm.com, IBM Life Sciences Abstract: MineLink is a novel information integration framework that can pull together life sciences data and analytic applications from disparate sources. It specifies a design methodology for automatically integrating individual components, be they data sources, processors, data miners or visualization components without the need for explicit programming. It addresses both syntactic and semantic aspects of information integration. File: stfATalmaden.ibm.com_348 ************************************************* Sun May 4 15:46:44 2003 UPDATE ----- Number: 354 Name: Schliep, Alexander Affiliation: Dept. of Comp. Biology, Max Planck Institute for Molecular Genetics Address: Ihnestrasse 73 City: Berlin State/Provice: na Postal/Zip Code: 14195 Country: Germany Email: schliep@molgen.mpg.de Phone: 49-30 8413 - 1166 Fax: 49-30 8413 - 1152 Category: Data Mining Poster Title: GHMM and HMMEd: A toolkit for Hidden Markov Models Poster Authors and organization: Wasinee Rungsarityotin¹, Alexander Schliep²
¹rungsari@molgen.mpg.de, Max Planck Institute for Molecular Genetics; ²schliep@molgen.mpg.de, Max Planck Institute for Molecular Genetics Abstract:
We have developed and implemented a library for a general Hidden Markov Model (GHMM) to assist in designing a topology and visualizing parameters for a HMM. The tool has been used in solving problems such as identification of circular permutation with Profile HMMs. GHMM and HMMEd is freely availabel at http://sourceforge.net/projects/ghmm/.
File: schliepATmolgen.mpg.de_354 ************************************************* Sun May 4 15:50:00 2003 UPDATE ----- Number: 354 Name: Schliep, Alexander Affiliation: Dept. of Comp. Biology, Max Planck Institute for Molecular Genetics Address: Ihnestrasse 73 City: Berlin State/Provice: na Postal/Zip Code: 14195 Country: Germany Email: schliep@molgen.mpg.de Phone: 49-30 8413 - 1166 Fax: 49-30 8413 - 1152 Category: Data Mining Poster Title: GHMM and HMMEd: A toolkit for Hidden Markov Models Poster Authors and organization: Wasinee Rungsarityotin¹, Alexander Schliep²
¹rungsari@molgen.mpg.de, Max Planck Institute for Molecular Genetics; ²schliep@molgen.mpg.de, Max Planck Institute for Molecular Genetics Abstract:
We have developed and implemented a library for a general Hidden Markov Model (GHMM) to assist in designing a topology and visualizing parameters for a HMM. The tool has been used in solving problems such as identification of circular permutation with Profile HMMs. GHMM and HMMEd is freely availabel at http://sourceforge.net/projects/ghmm/.
File: schliepATmolgen.mpg.de_354 ************************************************* Sun May 4 15:51:53 2003 UPDATE ----- Number: 360 Name: Park, Mihwa Affiliation: POSDATA co. Address: 276-2 City: SungNam-City State/Provice: Gyuggi-DO Postal/Zip Code: 463-775 Country: Korea Email: bfpark@posdata.co.kr Phone: 82-031-779-2707 Fax: 82-031-779-2709 I plan to use my laptop computer as part of my poster Category: Systems Biology Poster Title: SPACE-BLAST: Linux Cluster based Biological Sequence Parallel Processing system Summarized by Gene Ontology Poster Authors and organization: Mihwa Park¹, Jaewoo Kim², Hyungsuk Won, Seungsik Yoo
¹bfpark@posdata.co.kr, POSDATA; ²jaewoo@posdata.co.kr, POSDATA Abstract: SPACE-BLAST (Super PArallel Computer Engine for BLAST) is a high performance bioinformatics system that implements the NCBI�s BLAST system with low cost Linux cluster based parallel processing to search DNA sequencing at high speed. Also, Gene Ontology is applied to summarize massive amount of the BLAST search results. SPACE-BLAST is available at at http://space-blast.posdata.co.kr. File: bfparkATposdata.co.kr_360 ************************************************* Sun May 4 15:55:29 2003 UPDATE ----- Number: 362 Name: McShan, Daniel C Affiliation: University of Colorado School of Medicine Address: 4200 East Ninth Avenue, B119 City: Denver State/Provice: CO Postal/Zip Code: 80262 Country: USA Email: Daniel.McShan@uchsc.edu Phone: 303-315-2963 Fax: 303-314-3183 I plan to use my laptop computer as part of my poster Category: Predictive Methods Poster Title: PathMiner: de novo Synthesis Poster Authors and organization: McShan, D.¹, Upadhyaya, M.², Imran Shah
¹Daniel.McShan@uchsc.edu, UCHSC; ²Minesh.Upadhayaya@uchsc.edu, UCHSC Abstract: This poster presents PathMiner, a computational framework for exploring metabolic pathways. To make inferences about pathways we abstract metabolism as a state-space in which compounds are points and biotransformations are state-transitions. In this poster, we discuss applications of PathMiner to two quite different biological problems. File: Daniel.McShanATuchsc.edu_362 ************************************************* Sun May 4 16:00:40 2003 UPDATE ----- Number: 396 Name: Luciano, Joanne S Affiliation: BioPAX Address: 45 Orchard Street City: Belmont State/Provice: MA Postal/Zip Code: 02478-3008 Country: USA Email: jluciano@biopathways.org Phone: 617 993-9994 Fax: 208-728-1133 Category: Systems Biology Poster Title: BioPAX Data Exchange Ontology for Biological Pathway Databases Poster Authors and organization: BioPAX Group¹
¹pax@cbio.mskcc.org, BioPAX Abstract: BioPAX (http://biopax.org) is a new community-based effort to develop a data exchange format for biological pathway data. The ontology will be able to represent data from diverse sources such as aMAZE, BIND, BioCyc, and WIT. Initial implementations of BioPAX will be available in both OWL and XML Schema.
File: jlucianoATbiopathways.org_396 ************************************************* Sun May 4 16:02:55 2003 UPDATE ----- Number: 396 Name: Luciano, Joanne S Affiliation: BioPAX Address: 45 Orchard Street City: Belmont State/Provice: MA Postal/Zip Code: 02478-3008 Country: USA Email: jluciano@biopathways.org Phone: 617 993-9994 Fax: 208-728-1133 Category: Systems Biology Poster Title: BioPAX Data Exchange Ontology for Biological Pathway Databases Poster Authors and organization: BioPAX Group¹
¹pax@cbio.mskcc.org, BioPAX Abstract: BioPAX (http://biopax.org) is a new community-based effort to develop a data exchange format for biological pathway data. The ontology will be able to represent data from diverse sources such as aMAZE, BIND, BioCyc, and WIT. Initial implementations of BioPAX will be available in both OWL and XML Schema.
File: jlucianoATbiopathways.org_396 ************************************************* Sun May 4 16:07:55 2003 UPDATE ----- Number: 396 Name: Luciano, Joanne S Affiliation: BioPAX Address: 45 Orchard Street City: Belmont State/Provice: MA Postal/Zip Code: 02478-3008 Country: USA Email: jluciano@biopathways.org Phone: 617 993-9994 Fax: 208-728-1133 Category: Systems Biology Poster Title: BioPAX Data Exchange Ontology for Biological Pathway Databases Poster Authors and organization: BioPAX Group¹
¹pax@cbio.mskcc.org, BioPAX Abstract: BioPAX (http://biopax.org) is a new community-based effort to develop a data exchange format for biological pathway data. The ontology will be able to represent data from diverse sources such as aMAZE, BIND, BioCyc, and WIT. Initial implementations of BioPAX will be available in both OWL and XML Schema.
File: jlucianoATbiopathways.org_396 ************************************************* Sun May 4 16:11:32 2003 UPDATE ----- Number: 250 Name: Lancaster, Alex K Affiliation: Dept. of Integrative Biology, UC Berkeley Address: 3060 Valley Life Sciences Building City: Berkeley State/Provice: CA Postal/Zip Code: 94720-3140 Country: USA Email: alexl@socrates.berkeley.edu Phone: 510 642-1233 Fax: 510 643-5144 I plan to use my laptop computer as part of my poster Category: Phylogeny and Evolution Poster Title: PyPop: A framework for large-scale population genomics analysis Poster Authors and organization: Alex Lancaster¹, Mark P. Nelson², Richard M. Single; Diogo Meyer; Glenys Thomson
¹alexl@socrates.berkeley.edu, UC Berkeley; ², UC Berkeley Abstract: PyPop (Python for Population Genetics) is a suite of programs for the analysis of multi-locus population genetic data, outputs are stored in XML and can be transformed into other data formats. PyPop will be made freely available under the GNU GPL at: http://allele5.biol.berkeley.edu/pypop/ File: alexlATsocrates.berkeley.edu_250 ************************************************* Sun May 4 16:14:09 2003 UPDATE ----- Number: 279 Name: Satterley, Keith R Affiliation: The Walter and Eliza Hall Institute of Medical Research Address: 1G Royal Pd. City: Melbourne State/Provice: Victoria Postal/Zip Code: 3050 Country: Australia Email: keith@wehi.edu.au Phone: +61 4 2570 0 419 Fax: +61 3 9347 0852 Category: Sequence Comparison Poster Title: ASAD-A Sequence Attribute Display tool Poster Authors and organization: Keith Satterley¹
¹keith@wehi.edu.au, The Walter and Eliza Hall Institute of Medical Research Abstract: ASAD is A Sequence Attribute Display tool. It is written as a set of Excel macros. It builds on the familiar Excel interface to allow for flexible and efficient display of attributes (hydrophobicity etc.) using similar colours and styles for one sequence or multiple aligned sequences. ASAD is available at ftp://ftp.wehi.edu.au/pub/biology/ASAD. File: keithATwehi.edu.au_279 ************************************************* Sun May 4 16:15:16 2003 UPDATE ----- Number: 284 Name: Saunders, Neil F Affiliation: School of Biotechnology and Biomolecular Sciences, The University of New South Wales Address: UNSW City: Sydney State/Provice: NSW Postal/Zip Code: 2052 Country: Australia Email: neil.saunders@unsw.edu.au Phone: +61 2 9385 2092 Fax: +61 2 9385 1591 Category: Data Mining Poster Title: Pathogenic archaea-do they exist Poster Authors and organization: Neil Saunders¹, Ricardo Cavicchioli², Paul M.G. Curmi, Torsten Thomas
¹neil.saunders@unsw.edu.au, The University of New South Wales; ²r.cavicchioli@unsw.edu.au, The University of New South Wales Abstract: We have developed a rapid, automated search strategy for the detection of contaminating sequence from putative novel pathogenic archaea in human EST sequence data. The system has general application to the detection of microbial pathogens and will be available at http://psychro.bioinformatics.unsw.edu.au. File: neil.saundersATunsw.edu.au_284 ************************************************* Sun May 4 16:17:05 2003 UPDATE ----- Number: 330 Name: Chalk, Alistair M Affiliation: Center for Genomics and Bioinformatics, Karolinksa Institute Address: Berzelius vag 35 City: Stockholm State/Provice: Stockholm Postal/Zip Code: 171 77 Country: Sweden Email: alistair.chalk@cgb.ki.se Phone: +46739824296 Fax: +468337983 Category: Functional Genomics Poster Title: Design of Antisense Oligonucleotides Poster Authors and organization: Alistair M. Chalk¹, Erik L.L. Sonnhammer²
¹alistair.chalk@cgb.ki.se, CGB, Karolinska Institute; ²esr@algol.cgb.ki.se, CGB, Karolinska Institute Abstract: Antisense oligonucelotides are an important tool for gene-knockdown approaches in functional genomics. We assess the usefulness of current approaches predicting accessibility and/or efficacy using a database of known results. A set of utilities developed for AO and siRNA design (control design, specificity, site selection) is available at http://sonnhammer.cgb.ki.se. File: alistair.chalkATcgb.ki.se_330 ************************************************* Sun May 4 16:18:28 2003 UPDATE ----- Number: 354 Name: Schliep, Alexander Affiliation: Dept. of Comp. Biology, Max Planck Institute for Molecular Genetics Address: Ihnestrasse 73 City: Berlin State/Provice: na Postal/Zip Code: 14195 Country: Germany Email: schliep@molgen.mpg.de Phone: 49-30 8413 - 1166 Fax: 49-30 8413 - 1152 Category: Data Mining Poster Title: GHMM and HMMEd: A toolkit for Hidden Markov Models Poster Authors and organization: Wasinee Rungsarityotin¹, Alexander Schliep²
¹rungsari@molgen.mpg.de, Max Planck Institute for Molecular Genetics; ²schliep@molgen.mpg.de, Max Planck Institute for Molecular Genetics Abstract:
We have developed and implemented a library for a general Hidden Markov Model (GHMM) to assist in designing a topology and visualizing parameters for a HMM. The tool has been used in solving problems such as identification of circular permutation with Profile HMMs. GHMM and HMMEd is freely availabel at http://sourceforge.net/projects/ghmm/.
File: schliepATmolgen.mpg.de_354 ************************************************* Sun May 4 16:20:42 2003 UPDATE ----- Number: 360 Name: Park, Mihwa Affiliation: POSDATA co. Address: 276-2 City: SungNam-City State/Provice: Gyuggi-DO Postal/Zip Code: 463-775 Country: Korea Email: bfpark@posdata.co.kr Phone: 82-031-779-2707 Fax: 82-031-779-2709 I plan to use my laptop computer as part of my poster Category: Systems Biology Poster Title: SPACE-BLAST: Linux Cluster based Biological Sequence Parallel Processing system Summarized by Gene Ontology Poster Authors and organization: Mihwa Park¹, Jaewoo Kim², Hyungsuk Won, Seungsik Yoo
¹bfpark@posdata.co.kr, POSDATA; ²jaewoo@posdata.co.kr, POSDATA Abstract: SPACE-BLAST (Super PArallel Computer Engine for BLAST) is a high performance bioinformatics system that implements the NCBI�s BLAST system with low cost Linux cluster based parallel processing to search DNA sequencing at high speed. Also, Gene Ontology is applied to summarize massive amount of the BLAST search results. SPACE-BLAST is available at at http://space-blast.posdata.co.kr. File: bfparkATposdata.co.kr_360 ************************************************* Sun May 4 16:39:56 2003 Number: 416 Name: Wouters, Merridee A Affiliation: Victor Chang Cardiac Research Institute Address: 384 Victoria St Darlinghurst City: Sydney State/Provice: NSW Postal/Zip Code: 2010 Country: Australia Email: m.wouters@victorchang.unsw.edu.au Phone: 612 9295 8508 Fax: 612 9295 8501 Category: Data Mining Poster Title: New Datasets for Structural Data Mining Studies. Poster Authors and organization: Carmen K. Chu¹, Merridee A. Wouters²
¹cchu@cse.unsw.edu.au, Computational Biology and Bioinformatics Program, Victor Chang Cardiac Research Institute; ²m.wouters@victorchang.unsw.edu.au, Computational Biology and Bioinformatics Program, Victor Chang Cardiac Research Institute Abstract: We compared the sequence-derived representative dataset PDB_SELECT with the structural database SCOP. Some folds remain overrepresented in PDB_SELECT. After filtering, we obtain a subset of unique protein fold representatives: approximately � of the original PDB_SELECT 25% list. We also discuss using unique representatives of SCOP folds as a representative dataset. File: m.woutersATvictorchang.unsw.edu.au_416.html ************************************************* Mon May 5 17:18:25 2003 Number: 417 Name: Hawken, Rachel Affiliation: CSIRO Livestock Industries Address: 306 Carmody Road City: St Lucia State/Provice: Queensland Postal/Zip Code: 4067 Country: Australia Email: Rachel.Hawken@csiro.au Phone: 07 3214 2901 Fax: Category: Genome Annotation Poster Title: IBISS - the interactive bovine in Silico SNP database. Poster Authors and organization: Rachel Hawken¹, Wes Barris², Brian Dalrymple
¹Rachel.Hawken@csiro.au, CSIRO Livestock Industries; ²Wes.Barris@csiro.au, CSIRO Livestock Industries Abstract: A bovine in Silico SNP database has been constructed. Contigs of �unique bovine sequences� were established which were treated as model mRNAs. A comprehensive web interface has been developed which highlights putative identity of each contig, putative SNPs, location of predicted intron-exon boundaries, and genome mapping data for each model mRNA. File: Rachel.HawkenATcsiro.au_417.html ************************************************* Mon May 5 17:48:24 2003 UPDATE ----- Number: 241 Name: TAN, AIK CHOON Affiliation: BIOINFORMATICS RESEARCH CENTRE, DEPARTMENT OF COMPUTING SCIENCE, UNIVERSITY OF GLASGOW Address: 17 LILYBANK GARDENS City: GLASGOW State/Provice: SCOTLAND Postal/Zip Code: G12 8QQ Country: UNITED KINGDOM Email: actan@brc.dcs.gla.ac.uk Phone: 00 44 141 330 2421 Fax: 00 44 141 330 3690 Category: Data Mining Poster Title: Multi-class protein fold classification using an integrative machine learning approach Poster Authors and organization: Aik Choon TAN¹, David GILBERT²
¹actan@brc.dcs.gla.ac.uk, Bioinformatics Research Centre, Department of Computing Science, University of Glasgow; ²drg@brc.dcs.gla.ac.uk, Bioinformatics Research Centre, Department of Computing Science, University of Glasgow Abstract: We devised a novel approach to integrate rules induced from multi-class and unbalanced data sets; and to demonstrate its usefulness to multi-class protein fold classification which contains 700 examples for 27 SCOP folds. We showed that this approach increases the sensitivity of the classifiers and yielding more useful classifiers. File: actanATbrc.dcs.gla.ac.uk_241 ************************************************* Mon May 5 18:01:17 2003 UPDATE ----- Number: 379 Name: Philip, Gayle K Affiliation: Bioinformatics laboratory Address: National University of ireland City: Maynooth State/Provice: Co. Kildare Postal/Zip Code: N/A Country: Ireland Email: gayle.k.philip@may.ie Phone: 353 1 708 6211 Fax: 353 1 708 3845 Category: Phylogeny and Evolution Poster Title: Determining the Eukaryote Phylogeny Poster Authors and organization: Gayle Philip¹, James McInerney²
¹gayle.k.philip@may.ie, National University of Ireland, Maynooth; ²james.o.mcinerney@may.ie, National University of Ireland, Maynooth Abstract: The relationship of nematodes to arthropods and vertebrates can be described by the Coelomata and Ecdysozoa hypotheses. Our aim was to test these hypotheses by finding the supertree that best described the relationship of orthologous, single gene family trees from ten eukaryotic taxa. Our results support the traditional Coelomata hypothesis. File: gayle.k.philipATmay.ie_379 ************************************************* Mon May 5 18:39:23 2003 UPDATE ----- Number: 360 Name: Park, Mihwa Affiliation: POSDATA co. Address: 276-2 City: SungNam-City State/Provice: Gyuggi-DO Postal/Zip Code: 463-775 Country: Korea Email: bfpark@posdata.co.kr Phone: 82-031-779-2707 Fax: 82-031-779-2709 I plan to use my laptop computer as part of my poster Category: Systems Biology Poster Title: SPACE-BLAST: Linux Cluster based Biological Sequence Parallel Processing system Summarized by Gene Ontology Poster Authors and organization: Mihwa Park¹, Jaewoo Kim², Hyungsuk Won, Seungsik Yoo
¹bfpark@posdata.co.kr, POSDATA; ²jaewoo@posdata.co.kr, POSDATA Abstract: SPACE-BLAST (Super PArallel Computer Engine for BLAST) is a high performance bioinformatics system that implements the NCBI’s BLAST system with low cost Linux cluster based parallel processing to search DNA sequencing at high speed. Also, Gene Ontology is applied to summarize massive amount of the BLAST search results. SPACE-BLAST is available at at http://space-blast.posdata.co.kr. File: bfparkATposdata.co.kr_360 ************************************************* Tue May 6 00:33:22 2003 UPDATE ----- Number: 175 Name: Gilbert, David Affiliation: Bioinformatics Research Centre, Department of Computing Science, University of Glasgow Address: 17 Lilybank Gardens City: Glasgow State/Provice: - Postal/Zip Code: G12 8QQ Country: UK Email: drg@brc.dcs.gla.ac.uk Phone: 44 1413302563 Fax: 44 1413303690 Category: Structural Biology Poster Title: Protein structure comparison based on profiles of topological motifs Poster Authors and organization: Juris Viksna¹, David Gilbert², Gilleain Torrance
¹jviksna@cclu.lv, Institute of Mathematics and Computer Science, University of Latvia; ²drg@brc.dcs.gla.ac.uk, Bioinformatics Research Centre, Department of Computing Science, University of Glasgow Abstract: We present a new approach to protein structure comparison using the existing, on graph representations based TOPS database. Instead of comparisons based on single patterns, we use profiles of patterns, which allows, in an indirect way, capture of "negative" information. This leads to a significant increase in prediction accuracy. File: drgATbrc.dcs.gla.ac.uk_175 ************************************************* Tue May 6 00:35:01 2003 UPDATE ----- Number: 181 Name: BenKahla, Alia Affiliation: Max Planck Institute for Molecular Genetics Address: Ihnestrasse 63-73 City: Berlin State/Provice: - Postal/Zip Code: 14195 Country: Germany Email: kahla@molgen.mpg.de Phone: +49-30-8413-1658 Fax: +49-30-8413-1128 Category: Data Mining Poster Title: Human and Mouse expression maps from in silico expression profiles Poster Authors and organization: Alia BenKahla¹, Ralf Herwig², Yaspo Lehrach
¹kahla@molgen.mpg.de, Max Planck Institute for Molecular Genetics; ²herwig@molgen.mpg.de, Max Planck Institute for Molecular Genetics Abstract: We present the strategy used to extract the "in silico expression profiles" of the human and mouse genes (EST mining approach) and the data describing differentially expressed genes, disease related genes, and cluster of genes potentially involved in a common cellular function. Orthology gene expression comparison will also be presented. File: kahlaATmolgen.mpg.de_181 ************************************************* Tue May 6 00:37:57 2003 UPDATE ----- Number: 187 Name: Gondro, Cedric Affiliation: University of New England Address: Animal Science - UNE City: Armidale State/Provice: NSW Postal/Zip Code: 2351 Country: Australia Email: genetics@sigex.com.br Phone: 61 2 6773 5135 Fax: 61 2 6773 3922 Category: Systems Biology Poster Title: Models and Simulations in Systems Biology Poster Authors and organization: Joao Carlos Marques Magalhaes¹, Cedric Gondro²
¹jcmm@bio.ufpr.br, Federal University of Parana; ²cgondro@pobox.une.edu.au, University of New England Abstract: Computational models that simulate complex adaptive systems offer an alternative where analytical handling is untenable. A relatively small set of objects and simple rules, computationally implemented via techniques such as genetic algorithms or genetic programming can replicate such complexity. An example of this approach is available for download from http://www.sigex.com.br/genetics. File: geneticsATsigex.com.br_187 ************************************************* Tue May 6 00:44:59 2003 UPDATE ----- Number: 213 Name: SAGARA, Jun-Ichi Affiliation: CBRC Address: Aomi F Build. 17F, 2-43 Aomi, City: Koto-ku, State/Provice: Tokyo, Postal/Zip Code: 135-0064 Country: JAPAN Email: jun@ni.aist.go.jp Phone: +81-3-3599-8066 Fax: +81-3-3599-8081 I plan to use my laptop computer as part of my poster Category: Predictive Methods Poster Title: Prediction of snoRNAs in Human Genome Poster Authors and organization: SAGARA Jun-Ichi¹, ASAI Kiyoshi², Nakamura Shugo, KENMOCHI Naoya
¹jun@ni.aist.go.jp, CBRC; ², CBRC Abstract: We predict snoRNAs in human genome using several methods for sequence analysis. We also develop a Predicted Human Intron database produced from exons predicted by Gene Decoder which is a gene finding technology based on HMMs. We show the results of prediction of snoRNAs and the databases of human introns. File: junATni.aist.go.jp_213 ************************************************* Tue May 6 00:49:07 2003 UPDATE ----- Number: 217 Name: Shida, Kazuhito Affiliation: Center for Interdisciplinary Research, Tohoku University Address: Aramaki, Aoba-ku City: Sendai State/Provice: Miyaghi Postal/Zip Code: 980-8578 Country: JAPAN Email: shida@cir.tohoku.ac.jp Phone: +81-22-217-5764 Fax: +81-22-217-7810 Category: Sequence Comparison Poster Title: Long-range correlation in protein sequences and its implication Poster Authors and organization: Kazuhito Shida¹, Makoto Ikeda², Atsuo Kasuya
¹shida@cir.tohoku.ac.jp, CIR Tohoku University; ²ikeda@imr.edu, CIR Tohoku University Abstract: Long-range correlations in the amino-acid sequences of natural proteins are extracted from GanBank sequences. Some bigrams with more than one letter gaps turned out to be clearly over-represented. This data may improve the assessment of alignment quality, phylogeny analyses, and perhaps database searches. File: shidaATcir.tohoku.ac.jp_217 ************************************************* Tue May 6 00:52:15 2003 UPDATE ----- Number: 219 Name: Samsonova, Maria G Affiliation: St.Petersburg State Polytechnical University Address: 29 Polytechnicheskaya ul. City: St.Petersburg State/Provice: - Postal/Zip Code: 195251 Country: Russia Email: samson@spbcas.ru Phone: 7-812-556-2230 Fax: 7-812-555-2762 Category: Databases Poster Title: A technology for integration of databases with common subject domains Poster Authors and organization: Maria Samsonova¹, Andrei Pisarev², Maxim Blagov
¹samson@spbcas.ru, SPbSPU; ²pisarev@spbcas.ru, SPbSPU Abstract: We present a novel approach to the integration of distributed molecular biology information resources, which consists in a design of an adaptive natural language interface and application of multiagent technology. Our approach permits integration of any databases which have a common subject domain. The implemented prototype is available at http://urchin.spbcas.ru/NLP/NLP.htm. File: samsonATspbcas.ru_219 ************************************************* Tue May 6 00:53:40 2003 Number: 418 Name: Kao, Cheng-Yan Affiliation: Bioinfo Lab., Department of CSIE, National Taiwan University Address: No.1, Sec. 4, Roosevelt Road City: Taipei State/Provice: Taiwan Postal/Zip Code: 106 Country: R.O.C. Email: cykao@csie.ntu.edu.tw Phone: 886-2-23625336 Fax: 886-2-23658741 Category: Microarrays Poster Title: An automatic and unbiased GA for finding the most discriminant gene sets on Microarray Poster Authors and organization: Han-Yu Chuang¹, Hwa-Sheng Chiu², Huai-Kuang Tsai, Cheng-Yan Kao
¹r90002@csie.ntu.edu.tw, Bioinfo Lab., Department of CSIE, National Taiwan University; ²r91031@csie.ntu.edu.tw, Bioinfo Lab., Department of CSIE, National Taiwan University Abstract: A multi-objective genetic algorithm based approach, combining univariate and multivariate techniques, was proposed to find optimal gene sets for sample classification on gene expression data automatically and unbiased. Eight genes with 93% LOOCV accuracy of KNN were selected to be the optimal predictive gene sets for Colon cancer dataset. File: cykaoATcsie.ntu.edu.tw_418.html ************************************************* Tue May 6 01:04:32 2003 UPDATE ----- Number: 263 Name: Pandey, Ritu Affiliation: Bioinformatics, Arizona Cancer Center, University of Arizona Address: 1515 N Campbell Ave. City: Tucson State/Provice: Arizona Postal/Zip Code: 85724 Country: USA Email: ritu@u.arizona.edu Phone: 520-621-0391 Fax: Category: Microarrays Poster Title: BioRag - Bio Resource for Array Genes: An Online Resource for Analyzing and interpreting Microarray data Poster Authors and organization: Ritu Pandey¹, Raghavendra K Guru ², David W Mount
¹ritu@u.arizona.edu, Bioinformatics, Arizona Cancer Center, University of Arizona; ²graghave@cs.arizona.edu, Bioinformatics, Arizona Cancer Center, University of Arizona Abstract: BioRag (Bio Resource for Array Genes at http://www.biorag.org) is an interactive platform for analyzing and developing a biological interpretation of the microarray results. Differential gene expression patterns can be interpreted using tools that mine and extract variety of biological relationships captured in this integrative resource. File: rituATu.arizona.edu_263 ************************************************* Tue May 6 01:09:55 2003 UPDATE ----- Number: 275 Name: Kim, Namshin Affiliation: School of Chemistry, Seoul National University Address: Shilim9-dong City: Seoul State/Provice: Kwanak-gu Postal/Zip Code: 151-747 Country: KOREA Email: deepreds@hanmail.net Phone: +82-2-879-2721 Fax: +82-2-889-1568 Category: Genome Annotation Poster Title: ASmodeler: Gene modeling of alternative splicing events from genomic alignment of mRNA and ESTs Poster Authors and organization: Namshin Kim¹, Seokmin Shin², Sanghyuk Lee
¹deepreds@hanmail.net, School of Chemistry, Seoul National University; ²sshin@snu.ac.kr, School of Chemistry, Seoul National University Abstract: ASmodeler is a novel web-based utility to find gene models of alternative splicing events from genomic alignment of mRNA and ESTs. It can be used as a transcript assembly program, an EST clustering utility, and a method of comparative gene modeling. ASmodeler is available at http://genome.ewha.ac.kr/ASmodeler/.
File: deepredsAThanmail.net_275 ************************************************* Tue May 6 01:13:16 2003 UPDATE ----- Number: 275 Name: Kim, Namshin Affiliation: School of Chemistry, Seoul National University Address: Shilim9-dong City: Seoul State/Provice: Kwanak-gu Postal/Zip Code: 151-747 Country: KOREA Email: deepreds@hanmail.net Phone: +82-2-879-2721 Fax: +82-2-889-1568 Category: Genome Annotation Poster Title: ASmodeler: Gene modeling of alternative splicing events from genomic alignment of mRNA and ESTs Poster Authors and organization: Namshin Kim¹, Seokmin Shin², Sanghyuk Lee
¹deepreds@hanmail.net, School of Chemistry, Seoul National University; ²sshin@snu.ac.kr, School of Chemistry, Seoul National University Abstract: ASmodeler is a novel web-based utility to find gene models of alternative splicing events from genomic alignment of mRNA and ESTs. It can be used as a transcript assembly program, an EST clustering utility, and a method of comparative gene modeling. ASmodeler is available at http://genome.ewha.ac.kr/ASmodeler/.
File: deepredsAThanmail.net_275 ************************************************* Tue May 6 01:18:26 2003 UPDATE ----- Number: 279 Name: Satterley, Keith R Affiliation: The Walter and Eliza Hall Institute of Medical Research Address: 1G Royal Pd. City: Melbourne State/Provice: Victoria Postal/Zip Code: 3050 Country: Australia Email: keith@wehi.edu.au Phone: +61 4 2570 0 419 Fax: +61 3 9347 0852 Category: Sequence Comparison Poster Title: ASAD-A Sequence Attribute Display tool Poster Authors and organization: Keith Satterley¹
¹keith@wehi.edu.au, The Walter and Eliza Hall Institute of Medical Research Abstract: ASAD is A Sequence Attribute Display tool. It is written as a set of Excel macros. It builds on the familiar Excel interface to allow for flexible and efficient display of attributes (hydrophobicity etc.) using similar colours and styles for one sequence or multiple aligned sequences. ASAD is available at ftp://ftp.wehi.edu.au/pub/biology/ASAD. File: keithATwehi.edu.au_279 ************************************************* Tue May 6 01:19:54 2003 UPDATE ----- Number: 279 Name: Satterley, Keith R Affiliation: The Walter and Eliza Hall Institute of Medical Research Address: 1G Royal Pd. City: Melbourne State/Provice: Victoria Postal/Zip Code: 3050 Country: Australia Email: keith@wehi.edu.au Phone: +61 4 2570 0 419 Fax: +61 3 9347 0852 Category: Sequence Comparison Poster Title: ASAD-A Sequence Attribute Display tool Poster Authors and organization: Keith Satterley¹
¹keith@wehi.edu.au, The Walter and Eliza Hall Institute of Medical Research Abstract: ASAD is A Sequence Attribute Display tool. It is written as a set of Excel macros. It builds on the familiar Excel interface to allow for flexible and efficient display of attributes (hydrophobicity etc.) using similar colours and styles for one sequence or multiple aligned sequences. ASAD is available at ftp://ftp.wehi.edu.au/pub/biology/ASAD. File: keithATwehi.edu.au_279 ************************************************* Tue May 6 01:22:59 2003 UPDATE ----- Number: 287 Name: Joslyn, Cliff A Affiliation: Los Alamos National Laboratory Address: MS B265 LANL City: Los Alamos State/Provice: New Mexico Postal/Zip Code: 87501 Country: USA Email: joslyn@lanl.gov Phone: +1-505-667-9096 Fax: +1-505-665-5220 Category: Data Mining Poster Title: Structural Classification in the Gene Ontology Poster Authors and organization: Cliff Joslyn¹, Susan Mniszewski², Andy Fulmer, Gary Heaton
¹joslyn@lanl.gov, Los Alamos National Laboratory; ²smm@lanl.gov, Los Alamos National Laboratory Abstract: We present the Gene Ontology Clusterer (GOC), which structurally classifies the GO based on pseudo-distances between comparable nodes in posets, in conjunction with scoring algorithms, to rank-order the GO nodes with respect to a set of requested genes. We will also share lessons we've learned about working with the GO. File: joslynATlanl.gov_287 ************************************************* Tue May 6 01:29:36 2003 UPDATE ----- Number: 303 Name: Batalov, Serge Affiliation: GNF Address: 10675 JJ Hopkins Dr City: San Diego State/Provice: CA Postal/Zip Code: 92121 Country: USA Email: batalov@gnf.org Phone: +1-858-8121569 Fax: +1-858-8121502 Category: Microarrays Poster Title: Target selection for the custom oligonucleotide array by clustering experimentally determined and computationally predicted transcript sets in mouse Poster Authors and organization: Serge Batalov¹
¹batalov@gnf.org, GNF Abstract: Custom oligonucleotide array design is aimed at effectively interrogating a largest possible non-redundant set of transcripts under a physical size constraint. 200,000+ publicly available and proprietary mouse transcript sequences were clustered. The custom chip was subsequently extensively used to profile the expression in 70+ different tissues. File: batalovATgnf.org_303 ************************************************* Tue May 6 01:33:09 2003 UPDATE ----- Number: 311 Name: Kim, Chan-Wha Affiliation: Graduate School of Life Sciences and Biotechnology Address: 5-1 ga, Anam-dong City: Seoul State/Provice: - Postal/Zip Code: 136-701 Country: South Korea Email: cwkim@korea.ac.kr Phone: 82-2-3290-3439 Fax: 82-2-3290-3957 Category: Predictive Methods Poster Title: Improved Approach to Protein Identification Using Peptide Mass Fingerprint Poster Authors and organization: Won-A Joo¹, Kap-Soon Noh², Chan-Wha Kimm
¹wajoo0824@hanmail.net, Graduate School of Life Sciences and Biotechnology; ², Graduate School of Life Sciences and Biotechnology Abstract: Peptide mass fingerprint (PMF) has been a useful method for rapid and high-throughput protein identification. In our study, we compared software used frequently to identify the proteins of Homo sapiens and Halobacterium salinarum. These attempts could provide more effective algorithm for protein identification of each species using PMF. File: cwkimATkorea.ac.kr_311 ************************************************* Tue May 6 01:35:04 2003 UPDATE ----- Number: 315 Name: Chae, Sujin Affiliation: Bioinfomatix, Inc. Address: Seocho 1-dong City: SEOUL State/Provice: Seocho-gu Postal/Zip Code: 137-864 Country: KOREA Email: sujin@bioinfomatix.com Phone: 82-2-3445-4533 Fax: 82-2-514-1977 Category: Databases Poster Title: updateBASE : Real-time automatic updating system of biological databases under the client-server environment. Poster Authors and organization: Sujin Chae¹, Mira Roh², Ji-Hoon Jun, Geunwoo Lee, Yong-ho In
¹sujin@bioinfomatix.com, Bioinfomatix Inc.; ²mrroh@bioinfomatix.com, Bioinfomatix Inc. Abstract: We developed the updateBASE system which provides real-time, automatic updating of biological databases under the client-server architecture. Using this system, an annotator can get up-to-date database sources and get more confident annotation results. The updateBASE will play an effective supporting role in predicting functions and relationships of unknown sequences. File: sujinATbioinfomatix.com_315 ************************************************* Tue May 6 01:37:37 2003 UPDATE ----- Number: 317 Name: Rubin, Eitan Affiliation: Bioinformatics and Biological Computing, Weizmann Institute of Science Address: PO Box 26 City: Rehovot State/Provice: - Postal/Zip Code: 76100 Country: Israel Email: Eitan.Rubin@weizmann.ac.il Phone: 972-8-9343456 Fax: 972-8-9346006 Category: Databases Poster Title: CleanBank: a database of sequence artifacts Poster Authors and organization: Hanne Volpin¹, Eitan Rubin²
¹hanne@agri.gov.il, Bioinformatics, Agricultural Research Organization, Bet Dagan, Israel; ²Eitan.Rubin@weizmann.ac.il, Bioinformatics and Biological Computing, Weizmann Institute of Science, Rehovot, Israel Abstract: CleanBank is a database that documents suspected artifacts found in sequences and/or their annotation in the international sequence databases. The artifacts are either reported by researchers, or identified by curated algorithms. Current algorithms detect E. coli and vector contamination. For a detailed description and a preview, see http://bip.weizmann.ac.il/MIW/CleanBank/index.html http://bip.weizmann.ac.il/MIW/CleanBank/index.html
File: Eitan.RubinATweizmann.ac.il_317 ************************************************* Tue May 6 01:42:59 2003 UPDATE ----- Number: 325 Name: Kim, Yong Wook Affiliation: Bioinfomatix, Inc. Address: Sung Woo Bldg., 1424-2, Seocho 1-dong City: Seoul State/Provice: - Postal/Zip Code: 137-864 Country: Korea Email: yongari@bioinfomatix.com Phone: 82-2-3445-4533 Fax: 82-2-514-1977 Category: New Frontiers Poster Title: Using XML-RPC for Distributed BLAST -Desterilizing idle resources- Poster Authors and organization: Yong Wook Kim¹
¹yongari@bioinfomatix.com, Bioinfomatix, Inc. Abstract: Usually, personal computers use the MS Windows opperating system, but the computing power is used for simple work. We try to use these available resources as member resources of a clustering system. XML-RPC provides the straight forward way for distributed BLAST and heterogeneous operating systems to be used as a member of the distributed system for BLAST. File: yongariATbioinfomatix.com_325 ************************************************* Tue May 6 01:43:49 2003 UPDATE ----- Number: 325 Name: Kim, Yong Wook Affiliation: Bioinfomatix, Inc. Address: Sung Woo Bldg., 1424-2, Seocho 1-dong City: Seoul State/Provice: - Postal/Zip Code: 137-864 Country: Korea Email: yongari@bioinfomatix.com Phone: 82-2-3445-4533 Fax: 82-2-514-1977 Category: New Frontiers Poster Title: Using XML-RPC for Distributed BLAST -Desterilizing idle resources- Poster Authors and organization: Yong Wook Kim¹
¹yongari@bioinfomatix.com, Bioinfomatix, Inc. Abstract: Usually, personal computers use the MS Windows operating system, but the computing power is used for simple work. We try to use these available resources as member resources of a clustering system. XML-RPC provides the straight forward way for distributed BLAST and heterogeneous operating systems to be used as a member of the distributed system for BLAST. File: yongariATbioinfomatix.com_325 ************************************************* Tue May 6 01:46:54 2003 UPDATE ----- Number: 327 Name: Chung, Myungguen Affiliation: Hanyang University Address: Sa-1dong Sangnok-Gu City: Ansan State/Provice: Kyunggido Postal/Zip Code: 426-791 Country: Korea Email: aobo@chollian.net Phone: +82 16 776 3726 Fax: +82 31 419 0940 Category: Functional Genomics Poster Title: Prediction of a full length gene from partial sequence Poster Authors and organization: Chung, Myungguen¹, Cho, Sooyoung², Ban, hyojeong ; Kim, hyun and Lee Youngseek
¹aobo@ihanyang.ac.kr, Hanyang University; ²singylu@hanmail.net, Hanyang University Abstract: We obtained 3� end partial sequence of cDNA which have not found homologs in �nr� by using BLAST. We predicted full length genes from partial sequence and cloned full length genes by using a predicted sequence File: aoboATchollian.net_327 ************************************************* Tue May 6 01:51:56 2003 UPDATE ----- Number: 341 Name: Fukuda, Ken I Affiliation: CBRC, AIST Address: Aomi Frontier Bldg. 17F, 2-43 Aomi City: Koto-ku State/Provice: TOKYO Postal/Zip Code: 135-0064 Country: JAPAN Email: fukuda-cbrc@aist.go.jp Phone: +81-3-3599-8049 Fax: +81-3-3599-8081 I plan to use my laptop computer as part of my poster Category: Databases Poster Title: A Pathway DB: Annotating Signal Transduction Pathways with bio-processes using hierarchical multi-layered structures. Poster Authors and organization: Ken Ichiro Fukuda¹, Yuki Yamagata², Toshihisa Takagi
¹fukuda-cbrc@aist.go.jp, CBRC, AIST; ²snowfox@hgc.jp, BIRD, JST Abstract: A database that formalizes Signal Transduction Pathway knowledge in scientific literatures is presented. The database focuses on annotating pathways or sub-pathways according to their related biological processes. Every process and element in a pathway has a pointer to ontologies, such as GO, and one can search (sub-)pathways, molecules by using them. File: fukuda-cbrcATaist.go.jp_341 ************************************************* Tue May 6 01:53:13 2003 UPDATE ----- Number: 343 Name: Park, Chungoo Affiliation: Biological Research Information Center, Pohang University of Science and Technology Address: San 31, Hyojadong, Namgu City: Pohang State/Provice: Kyungbuk Postal/Zip Code: 790-784 Country: South Korea Email: madreach@bric.postech.ac.kr Phone: +82-54-279-8195 Fax: +82-54-279-5540 Category: Genome Annotation Poster Title: New approach to build models for predicting prokaryotic genes Poster Authors and organization: Chungoo Park¹, Mihwa Park², Jongwon Chang, Jeongho Huh, Dong Soo Jung, Hong Gil Nam, Young Bock Lee, Jiin Choi, Seungsik Yoo, Jaewoo Kim
¹madreach@bric.postech.ac.kr, Biological Research Information Center, Pohang University of Science and Technology; ²bfpark@posdata.co.kr, Solution Development Research Institute,POSDATA Abstract: We propose a new method for increasing the gene prediction accuracy without using information of known genes. To increase the gene prediction accuracy we used the additional learning data through the phylogenetic concept. Tests on 3 complete prokaryotic genomes performed with the GLIMMER program demonstrate the ability of the new approach to detect additional genes. File: madreachATbric.postech.ac.kr_343 ************************************************* Tue May 6 01:55:27 2003 UPDATE ----- Number: 351 Name: Zou, Yanming Affiliation: University of Melbourne Address: Sneydes Road City: Melbourne State/Provice: Victoria Postal/Zip Code: 3030 Country: Australia Email: y.zou@pgrad.unimelb.edu.au Phone: 61 3 97313391 Fax: 61 3 97313254 Category: Structural Biology Poster Title: Prediction of RNA Secondary Structures with XNAfold Poster Authors and organization: Yanming Zou¹, Alan J. Hillier², P. Scott Chandry
¹y.zou@pgrad.unimelb.edu.au, University of Melbourne; ²Alan.Hillier@foodscience.afisc.csiro.au, University of Melbourne Abstract: XNAfold is a JAVA-C hybrid program that takes an RNA sequence as input and predicts RNA secondary structure. The minimum free energy structure predicted by XNAfold matched the experimentally determined structure for 77 out of 133 different RNA molecules. XNAfold is freely available at http://www.student.unimelb.edu.au/~yanmz/index.html File: y.zouATpgrad.unimelb.edu.au_351 ************************************************* Tue May 6 01:59:06 2003 UPDATE ----- Number: 361 Name: Mizushima, Hiroshi Affiliation: National Cancer Center Research Institute Address: 5-1-1 Tsukiji City: Chuo-ku State/Provice: Tokyo Postal/Zip Code: 104-0045 Country: Japan Email: hmizushi@ncc.go.jp Phone: +81-3-5550-2020 Fax: +81-5550-2027 Category: Data Visualisation Poster Title: Molecular Modeling using Virtual Reality with Force Feed Back Poster Authors and organization: Hiroshi Mizushima¹, Hiroshi Tanaka², Masaaki Hatsuta, Daisuke Arai, Hiroshi Nagata
¹hmizushi@ncc.go.jp, National Cancer Center Research Institute; ²tanaka@tmd.ac.jp, Tokyo Medical Dental University Abstract: We developed a computer aided molecular modeling system using virtual reality technologies. Although it is still a prototype, the most characteristic function of the system is enabling its user to �touch� and �feel� the electrostatic potential field of a protein or a drug molecule. File: hmizushiATncc.go.jp_361 ************************************************* Tue May 6 02:02:25 2003 UPDATE ----- Number: 373 Name: Kim, Hye Young Affiliation: Hanyang University College of Medicine Address: 17, Hengdang-dong, Sungdong-ku City: Seoul State/Provice: - Postal/Zip Code: 133-791 Country: Korea Email: hykim121@hanyang.ac.kr Phone: +82-2-2290-0614 Fax: +82-2-2281-3603 Category: Microarrays Poster Title: Compensation of scanner before robust M regression normalization in cDNA microarray Poster Authors and organization: Hye Young Kim¹, Jin Hyuk Kim², Yong Sung Lee, Young Seek Lee, Tae Sung Park, Ki Woong Kim, and Hyun Ju Chang
¹hykim121@hanyang.ac.kr, Hanyang Univeirsity College of Medicine; ²jhkim1@hanyang.ac.kr, Hanyang University College of Medicine Abstract: In cDNA microarray, the conversion of the amount of fluorescence to image intensity with the scanning process must be carefully handled to find the gene expression ratio. We developed a reverse scanning method for the microarray image and applied robust M regression to normalize the data from the compensated image. File: hykim121AThanyang.ac.kr_373 ************************************************* Tue May 6 02:05:51 2003 UPDATE ----- Number: 383 Name: Kim, Mingoo Affiliation: SNUBI Seoul National University Biomedical Informatics Address: 28 Yongon-dong, Chongno-gu City: Seoul State/Provice: kyunggi Postal/Zip Code: 110799 Country: South Korea Email: satyrs1@snu.ac.kr Phone: 8227408320 Fax: 8227474830 Category: Systems Biology Poster Title: Social Network Analysis of DNA Microarray Data Poster Authors and organization: Jung Hun Ohn¹, Tae Su Chung², Jihoon Kim, Mingoo Kim, Jihun Kim, Hye Won Lee, Ji Yeon Park, Ju Han Kim
¹jhohn2@snu.ac.kr, SNUBI Seoul National University Biomedical Informatics; ²epiai@korea.com, SNUBI Seoul National University Biomedical Informatics Abstract: Genomic interactions are quite complicated and special skills are needed to understand the network. Application of social affiliation network analysis on the yeast gene expression compendium dataset of hundreds of systematic perturbations shows the core-peripheral and the significant intermediary genes by network density and centrality indices. File: satyrs1ATsnu.ac.kr_383 ************************************************* Tue May 6 02:06:38 2003 UPDATE ----- Number: 385 Name: Zauhar, Randy J Affiliation: Dept. of Chemistry and Biochemistry, University of the Sciences in Philadelphia Address: 600 S. 43rd Street City: Philadelphia State/Provice: PA Postal/Zip Code: 19104 Country: USA Email: r.zauhar@usip.edu Phone: 215-596-8691 Fax: 215-596-8543 I plan to use my laptop computer as part of my poster Category: New Frontiers Poster Title: Shape Signatures, a New Approach for Ligand- and Receptor-Based Molecular Design Poster Authors and organization: Randy J. Zauhar¹, Karthi Nagarajan², Izabela Gierach, Mukesh Kumar, ZhiJian Li, LiFeng Tian, William J. Welsh
¹r.zauhar@usip.edu, University of the Sciences in Philadelphia; ²nagaraka@umdnj.edu, University of Medicine and Dentistry of New Jersey Abstract: We present several applications of "Shape Signatures", a new method for compactly encoding and rapidly comparing the shapes of ligand molecules and receptors. Our approach uses a technique much like ray-tracing to explore the volumes of both drug molecules and the protein active sites they target. File: r.zauharATusip.edu_385 ************************************************* Tue May 6 02:11:27 2003 UPDATE ----- Number: 397 Name: Luciano, Joanne S Affiliation: BioPAX Address: 45 Orchard Street City: Belmont State/Provice: MA Postal/Zip Code: 02478-3008 Country: USA Email: jluciano@biopathways.org Phone: 617 993-9994 Fax: 208.728.1133 Category: Databases Poster Title: BioPAX - Biological Pathway Data Exchange Format Poster Authors and organization: BioPAX Group¹
¹pax@cbio.mskcc.org, BioPAX Abstract:
BioPAX (http://biopax.org) is a new community-based initiative to address the growing need for a unified framework for sharing pathway information. Several groups are participating in BioPAX to develop a data exchange format that will allow communication between existing pathway databases and facilitate deposition of data into a common public repository.
File: jlucianoATbiopathways.org_397 ************************************************* Tue May 6 02:12:26 2003 UPDATE ----- Number: 397 Name: Luciano, Joanne S Affiliation: BioPAX Address: 45 Orchard Street City: Belmont State/Provice: MA Postal/Zip Code: 02478-3008 Country: USA Email: jluciano@biopathways.org Phone: 617 993-9994 Fax: 208.728.1133 Category: Databases Poster Title: BioPAX - Biological Pathway Data Exchange Format Poster Authors and organization: BioPAX Group¹
¹pax@cbio.mskcc.org, BioPAX Abstract:
BioPAX (http://biopax.org) is a new community-based initiative to address the growing need for a unified framework for sharing pathway information. Several groups are participating in BioPAX to develop a data exchange format that will allow communication between existing pathway databases and facilitate deposition of data into a common public repository.
File: jlucianoATbiopathways.org_397 ************************************************* Tue May 6 06:53:13 2003 Number: 419 Name: Wang, Junbai Affiliation: Tumor Department of Norwegian Radium Hospital Address: Montebello City: OSLO State/Provice: OSLO Postal/Zip Code: 0310 Country: Norway Email: junbaiw@radium.uio.no Phone: 47-22935392 Fax: 47-22522421 Category: Microarrays Poster Title: MGraph: graphical models for microarray data analysis Poster Authors and organization: junbai wang¹, Ola Myklebost², Eivind Hovig, Norwegian Radium Hospital, j.e.hovig@labmed.uio.no
¹junbaiw@radium.uio.no, Norwegian Radium Hospital; ²olam@radium.uio.no, Norwegian Radium Hospital Abstract: MGraph is a MATLAB toolbox, which applies graphical models to solve problems in microarray data analysis. MGraph with its graphical interface allows user to predict genetic regulatory networks by a graphical gaussian model, and to quantify the effects of different experimental treatment conditions on gene-expression profiles by graphical log-linear model. File: junbaiwATradium.uio.no_419.html ************************************************* Tue May 6 11:11:37 2003 Number: 420 Name: Biro, Jan C Affiliation: Karolinska Inst. and Homulus Informatics Address: 88 Howard, Room 1205 City: San Francisco State/Provice: CA Postal/Zip Code: 94 104 Country: USA Email: jan.biro@kbh.ki.se Phone: +1-234-5678901 Fax: +1-234-5678901 Category: Sequence Comparison Poster Title: The BlastNP. A new sequence similarity searching and visualization method Poster Authors and organization: Jan C. Biro¹
¹jan.biro@kbh.ki.se, Homulus Informatics Abstract: An alternative method to TblastX has been developed, known as blastNP. Nucleic acids in database and query sequences were translated into overlapping protein-like sequences (overlappingly translated sequences, OTSs) before searching with blastP. Thus, each nucleic acid sequence is represented by a single �protein like� sequence (instead of three reading frames). File: jan.biroATkbh.ki.se_420.html ************************************************* Tue May 6 12:50:57 2003 Number: 421 Name: Biro, Jan C Affiliation: Karolinska Institute and Homulus Informatics Address: 88 Howared., Room 1205 City: San Francisco State/Provice: CA Postal/Zip Code: 94 105 Country: USA Email: jan.biro@kbh.ki.se Phone: +1-234-5678601 Fax: +1-234-5678601 Category: Predictive Methods Poster Title: The Prion Paradox:. Infection or Polymerization? Poster Authors and organization: Jan C. Biro¹
¹Jan.biro@kbh.ki.se, Homulus Informatics Abstract: There is a weak but significant similarity between the prion protein (PrP) and some transcription factors and Zn-finger proteins. A molecular model of the Cu++-binding monomeric (normal, cytoplasmic) PrPC and the Cu++-stabilized polymeric (scrapie - pathogenic) PrPSc is presented and is called to: the CUPRION model. File: jan.biroATkbh.ki.se_421.html *************************************************