ISMB 2006
ISMB 2006AB3CX-MeetingISMB 2006
ISMB 2006

ISCB

Hosted by

Embrapa

LNCC

Posters

Accepted Posters

 

Comparative Genomics

Poster A-1
Comparative genomics of Ciona savignyi and Ciona intestinalis
Lesheng Kong (Temasek Life Sciences Laboratory); Balamurugan Kumarasamy (Temasek Life Sciences Laboratory); Elia Stupka (Telethon Institute of Genetics and Medicine); Arend Sidow (Stanford University Medical Center); Kerrin Small (Stanford University Medical Center); Michael Brudno (University of Toronto); Alan Christoffels (Temasek Life Sciences Laboratory);
Short Abstract: The studies of Ciona species may provide insights to the origins and evolutions of chordate phylum, from which all vertebrates sprouted. To this end, the genome sequence and annotation of an as yet unpublished Ciona savignyi assembly was compared to that of Ciona intestinalis using comparative genomics approaches and a number of interested findings were identified and reported.
Long Abstract: Click Here

Poster A-2
Gland expression profile derived from ESTs
Eduardo R Capanema (UFMG); Maurício A Mudado (UFMG); J Miguel Ortega (UFMG);
Short Abstract: A pattern of expression from different types of glands, generated from ESTs retrieved from public databases has provided an overview onto a variety of gland expression trials amongst several animal groups. This profile is currently being compared to that obtained from venom glands of Brazilian scorpions and snakes.
Long Abstract: Click Here

Poster A-3
Correlation between the expression of splicing factors and the presence of specific patterns of alternative splicing in human and mouse.
Júlio César Nunes (Ludwig Institute For Cancer Research - São Paulo Branch); Pedro Alexandre Favoretto Galante (Ludwig Institute For Cancer Research - São Paulo Branch); Sandro J. de Souza (Ludwig Institute For Cancer Research - São Paulo Branch);
Short Abstract: We observed a significant coefficient correlation between the expression of splicing factors in brain, breast and prostate from human and mouse samples. We intend to analyze different types of expression data of splicing factors in an attempt to gain some insights on the expression of tumor-associated splicing variants.
Long Abstract: Click Here

Poster A-4
The strength of selection on ultraconserved elements
Christina TL Chen (Washington University at Saint Louis); Barak A. Cohen (Washington University at Saint Louis);
Short Abstract: Comparative analyses of polymorphisms and fixed differences among human, chimpanzee, and rodents indicate that ultraconserved elements are maintained by relatively weak purifying selection.
Long Abstract: Click Here

Poster A-5
Annotation, comparative and evolutionary analysis of fungal Carbohydrate Active enZymes (CAZymes).
Etienne G.J. Danchin (AFMB, CNRS); Pedro M. Coutinho (AFMB, CNRS); Corinne Rancurel (AFMB, CNRS); Bernard Henrissat (AFMB, CNRS);
Short Abstract: Carbohydrate Active enZymes (CAZymes) play a central role in the biology of species having an intimate relation with sugars such as Fungi. Moreover, the wealth and biodiversity of fungal genomes already available now allows deciphering the evolutionary history and adaptations to the environment of fungal CAZymes.
Long Abstract: Click Here

Poster A-6
Identification of conserved TAF1 promoters with functional roles in human Embryonic Stem cells
Victor M. Ruotti (WiCell Research Institute); Aaron Darling (Dept. of Computer Science, University of Wisconsin-Madison); Ron Stewart (WiCell Research Institute); Tae Hoon Kim (. Ludwig Institute for Cancer Research, UCSD School of Medicine); Bing Ren (. Ludwig Institute for Cancer Research, UCSD School of Medicine); James Thomson (WiCell Research Institute);
Short Abstract: We combine ChIP-chip hybridization data with a Mauve genome alignment of mammalian genomes to identify putative conserved TAF1 promoters and mammalian microrearrangements. In addition to previously reported TAF1 binding data, we utilized our own ChIP-on-chip array, which was designed to study promoters of human embryonic stem cells.
Long Abstract: Click Here

Poster A-7
Breakpoint Re-use and Generalized Transpositions Depend on Synteny Block Size in Mammalian Genome Rearrangements
Oliver Attie (Department of Infectious Diseases, Mount Sinai School of Medicine, NY, NY 10029); Aaron E. Darling (Department of Computer Science, University of Wisconsin-Madison, Madison, WI 53706); John Sikorski3 (Regeneron Pharmaceuticals, Tarrytown, NY10591); Sophia Yancopoulos (Chiorazzi Lab, Feinstein Institute for Medical Research, Manhasset, NY 11030);
Short Abstract: We analyzed human (NCBI 35), mouse (NCBI 33), and rat (RGSC 3.4) genome assembly versions using Mauve to determine syntenic regions, GRIMM and GRITT (Genome Rearrangement by Inversion, Translocation and generalized Transposition) for genome rearrangement. Transpositions occur in GRITT at high resolution and breakpoint re-use varies with scale.
Long Abstract: Click Here

Poster A-8
Multiple Sample Methodology for Determining Significant Within-Class Concordance of Aberration in Array CGH Data
Mitchell Guttman (Computational Biology and Informatics Lab, University of Pennsylvania); Carolyn Mies (Department of Pathology, University of Pennsylvania); Katarzyna Dudycz-Sulicz (Department of Pathology, University of Pennsylvania); Sharon Diskin (Division of Oncology, Children); Don Baldwin (Microarray Facility, University of Pennsylvania); Gregory R. Grant (Computational Biology and Informatics Lab, University of Pennsylvania);
Short Abstract: Genomic duplications and deletions are typical of tumor genomes. In this study we present a method for assessing the significance of concordant genomic aberrations across multiple aCGH. By exploiting the replication across multiple samples we can detect concordant aberrations at much higher resolution than single sample approaches allow.
Long Abstract: Click Here

Poster A-10
Codon instability at high GC level in the comparison between Human and Chimpanzee
Rosina Piovani (Laboratorio de Organización y Evolución del Genoma. Sección Biomatemática. Facultad de Ciencias, Uni); Hugo Naya (Laboratorio de Organización y Evolución del Genoma. Sección Biomatemática. Facultad de Ciencias, Uni); Victor Sabbía (Laboratorio de Organización y Evolución del Genoma. Sección Biomatemática. Facultad de Ciencias, Uni); Héctor Musto (Laboratorio de Organización y Evolución del Genoma. Sección Biomatemática. Facultad de Ciencias, Uni);
Short Abstract: We obtained a set of 2482 orthologous genes between Human and Chimpanzee and analyzed the codon usage of sites where the amino acid was conserved. We found that as long as GC3 increases the level of conservation decreases for most amino acids. We discuss the results as a consequence of natural selection.
Long Abstract: Click Here

Poster A-11
Identification and Analysis of Retroid Agents in the Insect Genomes: Drosophila melanogaster, Anopheles gambiae, and Apis mellifera.
Holly A. Basta (Montana State University, Bozeman, MT); Marcella A. McClure (Montana State University, Bozeman, MT);
Short Abstract: Retroid agents (RAs) integrate or transpose in a host organism's DNA via reverse transcription (RT) of RNA. The Genome Parsing Suite was developed to identify, characterize, and annotate the RAs that encode potential RTs in any genome. A summary of the RAs found in three insects will be presented.
Long Abstract: Click Here

Poster A-12
Annotating the Eukaryotic Retrome
Marcella A. McClure (MSU); Crystal Hepp (MSU); Holly Basta (MSU); Tara Swope (MSU); Steve Martin (MSU); Anoop Winston (MSU); Alex Buzak (MSU);
Short Abstract: The Genome Parsing Suite software identifies and annotates all Retroid agents (reverse transcriptase encoding genetic elements) in a given genome, thereby creating the data necessary to map the human and Eukaryotic Retromes. The data presented here are from the complete and ordered genomes of human, chimp, rat and mouse.
Long Abstract: Click Here

Poster A-13
Construction and Analysis of Protein-Protein Interaction Network of Aspergillus fumigatus Proteins
Alper Soyler (Department of Food Engineering, Middle East Technical University); Tolga Can (Department of Computer Engineering, Middle East Technical University); Zumrut B. Ogel (Department of Food Engineering, Middle East Technical University);
Short Abstract: This project aims to construct a probabilistic high-coverage Aspergillus fumigatus protein-protein interaction network by computational methods with the ultimate goal of integrating multiple data sources such as microarrays, GO annotations, and literature data. This will help to develop new drugs and finding cures for diseases caused by A.fumigatus.
Long Abstract: Click Here

Poster A-14
A rapid genome re-annotation system for comparative study of bacterial genomes
Satoshi Tamaki (Institute for Advanced Biosciences, Keio University, Kanagawa 252-8520, Japan); Kazuharu Arakawa (Japan Society for the Promotion of Science); Masaru Tomita (Institute for Advanced Biosciences, Keio University, Kanagawa 252-8520, Japan);
Short Abstract: Comparative genomics requires genome data annotated with uniform criteria and methods including computer friendly semantics, and a rapid and automatic means for this purpose. We have developed a very fast genome re-annotation system for the comparative study of bacterial genomes, available under GNU GPL at: http://www.g-language.org.
Long Abstract: Click Here

Poster A-16
Conservation of genomic neighbourhood is related to the rate by which intraparalogous proteins evolve in two bacterial species
Vasilis J. Promponas (University of Cyprus, Cyprus); Nikolas Papanikolaou (University of Crete, Greece); Ioannis Iliopoulos (University of Crete, Greece);
Short Abstract: We have estimated evolutionary rates of proteins encoded by paralogous genes in the complete genome of Salmonella typhimurium LT2 considering gene order conservation. Here we show that linked paralogs have significantly higher sequence identities (84.5%) compared to their Escherichia coli K12 homologous proteins than non-linked paralogs (46.3%).
Long Abstract: Click Here

Poster A-17
Alternative Splicing Events of Stress Responsive Genes in Arabidopsis and Rice Universal Stress Protein Domains
Shaneka S. Simmons (Department of Biology, Jackson State University, Jackson, Mississippi 39217, USA); Raphael D. Isokpehi (Department of Biology, Jackson State University, Jackson, Mississippi 39217, USA);
Short Abstract: We have combined alternative splicing information from Gramene and Alternative Splicing in Plants (ASIP) databases for genes of Arabidopsis and Rice encoding the Universal Stress Protein (USP) domain. Majority of USP genes generate transcript diversity using intron retention. Gene categories based on alternative splicing events represent targets for trait improvement.
Long Abstract: Click Here

Poster A-18
3D-ANNOTATE: A Web Portal for Structure-based Protein Annotation using Grid Technology
Shikta Das (Imperial College London);
Short Abstract: We present a stand-alone web application, back ended by a robustly designed database, called 3D-ANNOTATE, a part of the collaborative work of the e-Protein, that allows the user to select a wide range of homology based analytical tools and automatically apply them to proteins in the database.
Long Abstract: Click Here

Poster A-19
Logical and probabilistic reasoning for the functional annotation of genomic comparisons.
Keith Flanagan (University of Newcastle); Matthew Pocock (University of Newcastle); Phil Lord (University of Newcastle); Robert Stevens (University of Manchester); Anil Wipat (University of Newcastle);
Short Abstract: We present an approach for the systematic functional analysis of the variations between bacterial genome sequences. Our approach utilises a combination of logical and probabilistic reasoning techniques, backed by an ontology containing the definitions of domain terms. Ontology terms are also used to form complex queries over analysis result sets.
Long Abstract: Click Here

Poster A-20
Comparative analysis of environmental sequences
Konrad U Foerstner (European Molecular Biology Laboratory); Christian von Mering (European Molecular Biology Laboratory); Sean D Hooper (European Molecular Biology Laboratory); Peer Bork (European Molecular Biology Laboratory);
Short Abstract: The availability of large-scale metagenomics data will deeply improve our understanding of microbial communities in their natural environment. A comparative analysis of different habitats will provide the context sufficient for understanding each individual sample. Here we present such an investigation of different features ofenvironmental sequence data.
Long Abstract: Click Here

Poster A-21
Anchor-based whole genome divergence and phylogeny: Analysis of Mycobacterial genomes
Anchal Vishnoi (Research Scholar); Rahul Roy (Professor); Alok Bhattacharya (Professor);
Short Abstract: Comparative genome analysis is a powerful approach to measure the diversity among the genomes, their evolution and pathogensis. We had applied a sampling approach based on local and global information of the whole genome to identify the course of evolution and divergent regions among the strains of Mycobacteria.
Long Abstract: Click Here

Poster A-22
Comparison of Alternative Splicing Structures in Eukaryotes
Sammeth, M (GRIB - IMIM); Foissac, S (GRIB - CRG); Guigó, R (GRIB - IMIM);
Short Abstract: In order to investigate the evolution of alternative splicing (AS), we compared the structural changes in AS patterns of orthologous genes in 10 species. Amongst other, we show species-specific biases in the distribution of the patterns and novel metrices to quantify the distance between different AS patterns.
Long Abstract: Click Here

Poster A-23
Phylogenetic profiling approach to generate RNA-regulated protein networks in E. coli
Nozomu Yachie (Institute for Advanced Biosciences, Keio University); Koji Numata (Institute for Advanced Biosciences, Keio University); Yoshiteru Negishi (Institute for Advanced Biosciences, Keio University); Hiroyuki Nakamura (Institute for Advanced Biosciences, Keio University); Junichi Sugahara (Institute for Advanced Biosciences, Keio University); Rintaro Saito (Institute for Advanced Biosciences, Keio University); Masaru Tomita (Institute for Advanced Biosciences, Keio University);
Short Abstract: Although investigation of whole-cell network of RNAs and proteins are all-important in order to understand cellular roles of RNAs, no significant methodologies have been established. We here present a novel approach on the basis of phylogenetic profiling to generate RNA-protein functional linkages using numerous complete genome sequences.
Long Abstract: Click Here

Poster A-24
A multi-species study of chromosomal domains of co-expression
Aditya Ramani (Department of Computer Science, University of Illinois at Urbana-Champaign); Kilannin Krysiak (School of Molecular and Cell Biology, University of Illinois at Urbana-Champaign); Chengxiang Zhai (Department of Computer Science, University of Illinois at Urbana-Champaign); Lei Liu (W. M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaig);
Short Abstract: Chromosomal regions of co-expression are related to gene order and shared chromatin domains.We studied this phenomena across a number species with increased genome size and organism complexity. We foud that most of localized co-expression can be explained by gene duplication and the clustering of housekeeping genes.
Long Abstract: Click Here

Poster A-25
Patterns of Gene Colocalization in the Human Genome
Par Engstrom (Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Bergen, N); David Fredman (Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Bergen, N); Boris Lenhard (Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Bergen, N);
Short Abstract: We present a new strategy to explore gene order in annotated genomes. Our algorithm searches for clusters consisting of genes from different functional groups and reports recurring constellations observed more often than expected. We describe human gene clusters that are conserved in evolution and encode proteins with different regulatory functions.
Long Abstract: Click Here

Poster A-26
Plasticity of transcriptional regulatory machinery revealed from whole genome comparison
Sarath Chandra Janga (Program of Computational Genomics, CCG-UNAM); Ernesto Perez-Rueda (Department of Cellular Engineering & Biocatalysis, IBT-UNAM);
Short Abstract: We compare the repertoires of transcription factors (TFs) between model organisms Escherichia coli and Bacillus subtilis at different levels and present the first comprehensive and complete analysis of comparison of TFs between any two prokarya. We analyze and discuss the results in the light of the evolution of transcriptional regulatory networks.
Long Abstract: Click Here

Poster A-27
Prediction of Non-Coding RNAs Using Drosophila Whole-Genome Alignments
Yuri Bendana (Bioengineering Graduate Group, UC Berkeley/UCSF); Ian Holmes (Bioengineering, UC Berkeley);
Short Abstract: We investigate the feasibility of using a whole-genome alignment of Drosophila species for predicting functionally conserved features such as non-coding RNAs de novo and by annotation transfer.
Long Abstract: Click Here

Poster A-28
Delineating the Functional Components of Eukaryotic Genomes
Jonathan M. Keith (Department of Mathematics, University of Queensland); Stuart Stephen (Institute for Molecular Bioscience, University of Queensland); Peter Adams (Department of Mathematics, University of Queensland); John S. Mattick (Institute for Molecular Bioscience, University of Queensland);
Short Abstract: This poster presents an extensive collection of slowly evolving (and thus potentially functional) non-protein-coding elements in mammalian and insect genomes. These were discovered using recently developed Bayesian segmentation algorithms. An important aspect of the analysis is that it accounts for variation of GC content observed in mammalian genomes.
Long Abstract: Click Here

Top

Databases & Data Integration

Poster B-1
MPVAD: System of integration of biological data
R Puga (Faculty of Medicine of Ribeirão Preto, Department of Genetic, University of São Paulo, Ribeirão Pret); S Amui (Faculty of Pharmaceutical Sciences, University of São Paulo, Ribeirão Preto, SP, Brazil); D Jorge (Faculty of Medicine of Ribeirão Preto, Department of Genetic, University of São Paulo, Ribeirão Pret); M Junior (Department of Biotechnology, University of Ribeirão Preto, Ribeirão Preto, SP, Brazil); A Soares (Faculty of Pharmaceutical Sciences, University of São Paulo, Ribeirão Preto, SP, Brazil); S Giuliatti (Faculty of Medicine of Ribeirão Preto, Department of Genetic, University of São Paulo, Ribeirão Pret);
Short Abstract: In order to establish a relationship between scientific data of medicinal plants ant poison and poisons of animals and Venom was developed the Medicinal system Plants of Animals Database (MPVAD)
Long Abstract: Click Here

Poster B-2
IDconverter and IDClight: Conversion and enrichment of
Patricio Yankilevich (Centro Nacional de Investigaciones Oncologicas (CNIO)); Andreu Alibés (Centro Nacional de Investigaciones Oncologicas (CNIO)); Andrés Cañada (Centro Nacional de Investigaciones Oncologicas (CNIO)); Ramón Diaz Uriarte (Centro Nacional de Investigaciones Oncologicas (CNIO));
Short Abstract: IDconverter and IDClight are two extremely user-friendly, high-throughput oriented, freely available web server applications designed and developed to help researchers map accession numbers and identifiers among clones, genes, proteins and chromosomal positions. They also map the identifiers on to pathways and Gene Ontology terms and literature references.
Long Abstract: Click Here

Poster B-3
A Graph-relational Integrated Database of Human and Mouse Omics data
Junaid Gamieldien (NBN South Africa); Darren Otgaar (NBN South Africa); Nadeen Southgate (NBN South Africa); Daniel A. Jacobson (NBN South Africa);
Short Abstract: We describe a graph-relational integrated data model of human and mouse data, which includes orthology, expression, trait/phenotype information, and several ontologies. Although a prototype, the existing model allows users to perform infinitely complex queries across the integrated resources in a way that approaches ‘in-silico hypothesis generation’.
Long Abstract: Click Here

Poster B-4
Cyberinfrastructure for Emerging and Re-Emerging Infectious Diseases
Oswald R. Crasta (Cyberinfrastructure Group, Virginia Bioinformatics Institute, Virginia Polytechnic Institute and Sta); Eric Snyder (Cyberinfrastructure Group, Virginia Bioinformatics Institute, Virginia Polytechnic Institute and Sta); Stephen Cammer (Cyberinfrastructure Group, Virginia Bioinformatics Institute, Virginia Polytechnic Institute and Sta); Darius Dziuda (Cyberinfrastructure Group, Virginia Bioinformatics Institute, Virginia Polytechnic Institute and Sta); Zhangjun Fei (Cyberinfrastructure Group, Virginia Bioinformatics Institute, Virginia Polytechnic Institute and Sta); Mike Czar (Cyberinfrastructure Group, Virginia Bioinformatics Institute, Virginia Polytechnic Institute and Sta); Eric Nordberg (Cyberinfrastructure Group, Virginia Bioinformatics Institute, Virginia Polytechnic Institute and Sta); Boyu Yang (Cyberinfrastructure Group, Virginia Bioinformatics Institute, Virginia Polytechnic Institute and Sta); Chengdong Zhang (Cyberinfrastructure Group, Virginia Bioinformatics Institute, Virginia Polytechnic Institute and Sta); Chaitanya Kommidi (Cyberinfrastructure Group, Virginia Bioinformatics Institute, Virginia Polytechnic Institute and Sta); Ranjan Jha (Cyberinfrastructure Group, Virginia Bioinformatics Institute, Virginia Polytechnic Institute and Sta); Yan Zhang (Cyberinfrastructure Group, Virginia Bioinformatics Institute, Virginia Polytechnic Institute and Sta); Anjan Purkayastha (Cyberinfrastructure Group, Virginia Bioinformatics Institute, Virginia Polytechnic Institute and Sta); Rebecca Wattam (Cyberinfrastructure Group, Virginia Bioinformatics Institute, Virginia Polytechnic Institute and Sta); Kelly Williams (Cyberinfrastructure Group, Virginia Bioinformatics Institute, Virginia Polytechnic Institute and Sta); Ron Kenyon (Cyberinfrastructure Group, Virginia Bioinformatics Institute, Virginia Polytechnic Institute and Sta); Rebecca Will (Cyberinfrastructure Group, Virginia Bioinformatics Institute, Virginia Polytechnic Institute and Sta); Joao Setubal (Cyberinfrastructure Group, Virginia Bioinformatics Institute, Virginia Polytechnic Institute and Sta); Bruno W. Sobral (Cyberinfrastructure Group, Virginia Bioinformatics Institute, Virginia Polytechnic Institute and Sta);
Short Abstract: We have established functional cyberinfrastructure (CI) systems in the area of bioinformatics. The resources and outreach activities developed include tools for the curation of the genomes and pathosystems, database and knowledgebase systems for organizing the high-throughput data from pathosystems biology and software systems for analysis and visualization of the data.
Long Abstract: Click Here

Poster B-5
UniProt: the Universal Protein Resource.
Raja Mazumder (Protein Information Resource, Georgetown University); Claire ODonovan (European Bioinformatics Institute);
Short Abstract: UniProt is a comprehensive catalog of protein sequence and function, produced by EBI, PIR and SIB. It consists of the UniProt Knowledgebase (expertly curated database), the UniProt Reference Clusters (merged sequences based on sequence identity) and the UniProt Archive (comprehensive sequence repository). An additional component consisting of environmental sequences will be made available later this year.
Long Abstract: Click Here

Poster B-6
NMR Manager – Metabolomics software for interpreting NMR spectra
Robert Stones (Central Science Laboratory); Adrian Charlton (Central Science Laboratory); James Donarski (Central Science Laboratory);
Short Abstract: Metabolomics software developed to analyze/store NMR spectra; with the capability to graphically display and compare experimental and database spectra. Harnessing automated peak detection algorithms and statistical methods to compare experimental NMR against statistically generated populations of NMR, and identifying significant peak variations between NMR for rapid metabolite profiling.
Long Abstract: Click Here

Poster B-8
The BioMAZE System: an environment for representation and analysis of biological processes.
Christian LEMER (Service de Conformation des Macromolécules Biologiques et de Bioinformatique, Université Libre de Br); Hassan ANHEROUR (Service de Conformation des Macromolécules Biologiques et de Bioinformatique, Université Libre de Br); Fabian COUCHE (Service de Conformation des Macromolécules Biologiques et de Bioinformatique, Université Libre de Br); Simon DE KEYZER (Service de Conformation des Macromolécules Biologiques et de Bioinformatique, Université Libre de Br); Yves DEVILLE (Computing Science and Engineering Department, Université catholique de Louvain, Place Saint-Barbe 2,); Frederic FAYS (Service de Conformation des Macromolécules Biologiques et de Bioinformatique, Université Libre de Br); Olivier HUBAUT (Service de Conformation des Macromolécules Biologiques et de Bioinformatique, Université Libre de Br); Jacques VAN HELDEN (Service de Conformation des Macromolécules Biologiques et de Bioinformatique, Université Libre de Br); Shoshana J. WODAK (Department of Biochemistry and Structural Biology, Department of Medical Genetics, University of Tor);
Short Abstract: The BioMAZE System is a workbench for the representation and analysis of networks of molecular interactions and cellular processes, genetic expression and regulation, enzymatic transformations and regulation, metabolic pathways, signal transduction. The BioMAZE system integrates the aMAZE database and various tools for analyzing and visualizing the stored information.
Long Abstract: Click Here

Poster B-9
MiDaR: Microarray Database Resource for Customized Chip Design
Eric C. Rouchka (Department of Computer Engineering and Computer Science, University of Louisville); Ravishrikanth Gundlapalli (Department of Computer Engineering and Computer Science, University of Louisville); Nigel G.F. Cooper (Deparment of Anatomical Sciences and Neurobiology, University of Louisville);
Short Abstract: Often it is desirable to design a customized microarray chip for a subset of genes or a particular organism of interest. We have created a solution, MiDaR (Microarray Database Resource), to aid in the process of creating and storing custom microarrays based on gene information and GO annotations.
Long Abstract: Click Here

Poster B-10
PhenoLink - Linking phenotype to genotype
Pieter Neerincx (Laboratory of Bioinformatics, WUR); Blaise Alako (Laboratory of Bioinformatics, WUR); Jack Leunissen (Laboratory of Bioinformatics, WUR);
Short Abstract: PhenoLink Project Linkage analysis studies provide genomic regions to narrow the search for genes involved in a certain trait. But there might still be dozens of candidate genes left after linkage analysis and screening all of them is a laborious task. The PhenoLink project provides a data-mining framework using mapping, co-expression and interaction data to rank candidate genes.
Long Abstract: Click Here

Poster B-11
Implementation of a query processing model and view based data integration system
Myung-Eun Lim (Bioinformatics Team, Electronics and Telecommunications Research Institute); Myung-Guen Chung (Bioinformatics Team, Electronics and Telecommunications Research Institute); Yong-Ho Lee (Bioinformatics Team, Electronics and Telecommunications Research Institute); Soo-jun Park (Bioinformatics Team, Electronics and Telecommunications Research Institute);
Short Abstract: We designed a query processing model to dispersed biological databases and implemented data integration system based on mediator-wrapper concept. To reduce the response time when extracting data from data source, we induced a kind of wrapper cache. By using them, we got a reasonable response time in extracting data.
Long Abstract: Click Here

Poster B-12
Integr8 – Access to Complete Genomes and Proteomes
Manuela Pruess (EMBL Outstation - European Bioinformatics Institute (EBI)); Lawrence Bower (EMBL Outstation - European Bioinformatics Institute (EBI)); Paul Kersey (EMBL Outstation - European Bioinformatics Institute (EBI)); Rajesh Radhakrishnan (EMBL Outstation - European Bioinformatics Institute (EBI)); Rolf Apweiler (EMBL Outstation - European Bioinformatics Institute (EBI));
Short Abstract: Integr8 is a web portal for exploring the biology of organisms with completely deciphered genomes. For 250 species, Integr8 provides access to general information, publications, and a statistical overview of the genome and proteome of the organism constructed using data resources such as UniProtKB, GenomeReviews, IPI, InterPro, CluSTr and GOA.
Long Abstract: Click Here

Poster B-13
Development of Data Templates for Data Collection, Storage and Database Submission.
Miguel Anducho (Crop Research Informatics Laboratory, CIMMYT.); Kyle Braak (Crop Research Informatics Laboratory, CIMMYT.); Richard Bruskiewich (Crop Research Informatics Laboratory, IRRI.); Victoria Carollo (Center for Computational Biology, Montana State University.); Tom Hazekamp (International Plant Genetic Resources Institute.); Andrew Farmer (National Center for Genomic Resources.); David Marshall (Scottish Crop Research Center.); Dave Matthews (GrainGenes, Cornell University.); Ayton Meintjes (Bioinformatics and Computational Biology Unit, University of Pretoria.); Thomas Metz (Crop Research Informatics Laboratory, IRRI.); Jane Morris (African Centre for Gene Technologies.); Manuel Ruiz (TropDB, CIRAD.); Mary Schaeffer (MaizeGDB, University of Missouri.); Theo van Hintum (Centre for Genetic Resources, The Netherlands.); Susan McCouch (Gramene, Cornell University.); Guy Davenport (Crop Research Informatics Laboratory, CIMMYT.);
Short Abstract: A large amount of data is generated each year that needs to be made accessible to the scientific community. We have developed database submission templates that define the format of the data and provide sufficient information to allow scientists capture the data, metadata and available controls.
Long Abstract: Click Here

Poster B-14
Contextual Analysis and Visualization of High Throughput Experimental Data
Nenad Bartonicek (Bioinformatics Group, Faculty of Science, Zagreb University, Horvatovac 102a, 10000 Zagreb, Croatia.); Igor Segota (Department of Physics, Faculty of Science, Zagreb University, Bijenička cesta 32, 10000 Zagreb,); Kristian Vlahovicek (Bioinformatics Group, Faculty of Science, Zagreb University, Horvatovac 102a, 10000 Zagreb, Croatia.);
Short Abstract: MADNet (MicroArray Database Network) is a user-friendly data mining tool for rapid analysis of diverse biological data such as microarray, phage display or even metagenomes. It presents biological information in the context of metabolic and signaling pathways, gene orthologs, transcription factors and drugs through minimal user input.
Long Abstract: Click Here

Poster B-15
Patho-Gene and Pathos Databases – Support for Biodefense and Emerging Infectious Disease Research
Elizabeth M. Glass (Argonne National Laboratory); Mark D’Souza (University of Chicago); Alexis Rodriguez (Argonne National Laboratory); Dinanath Sulakhe (University of Chicago); Mustafa Syed (Argonne National Laboratory); Natalia Maltsev (Argonne National Laboratory);
Short Abstract: Presentation describes an interactive, integrated, bioinformatics environment to support biodefense and emerging infectious disease research. This environment has two components, PathoGene, a database of pathogenic factors that provides a knowledgebase for analysis of pathogenic organisms and Pathos. Pathos provides an integrated bioinformatics environment for analysis of genomes of pathogenic bacteria.
Long Abstract: Click Here

Poster B-18
The TIGR Rice Genome Annotation Database
Shu Ouyang (The Institute for Genomic Research); Haining Lin (The Institute for Genomic Research); Kevin L. Childs (The Institute for Genomic Research); Wei Zhu (The Institute for Genomic Research); John Hamilton (The Institute for Genomic Research); Dan Lee (The Institute for Genomic Research); Mathew Campbell (The Institute for Genomic Research); Renae Malek (The Institute for Genomic Research); Li Zheng (The Institute for Genomic Research); Joshua Orvis (The Institute for Genomic Research); Brian Haas (The Institute for Genomic Research); Jennifer Wortman (The Institute for Genomic Research); Robin Buell (The Institute for Genomic Research);
Short Abstract: We have been funded to annotate the rice genome. Our Osa1 database contains pseudomolecules representing the 12 rice chromosomes. Ab initio gene finders, full length cDNA, EST and protein evidence were used to generate gene models and functional assignments for those models. The annotation is available http://rice.tigr.org.
Long Abstract: Click Here

Poster B-19
APID: Agile Protein Interaction DataAnalyzer
Prieto C. (Cancer Research Center (CIC, CSIC/USAL)); De Las Rivas J. (Cancer Research Center (CIC, CSIC/USAL));
Short Abstract: Nowadays the assessment of the reliability and broader coverage of the interactome network are two of the main research areas in protein interactions. With these purposes APID (http://bioinfow.dep.usal.es/apid/) has been developed to analyze and integrate in a comparative web platform all the currently known data about protein-protein interactions.
Long Abstract: Click Here

Poster B-20
The PIRSF system for protein classification, rule-based annotation, and ontology mapping
Darren A. Natale (PIR/GUMC); Cecilia Arighi (PIR/GUMC); Winona Barker (PIR/GUMC); Zhangzhi Hu (PIR/GUMC); Hongzhan Huang (PIR/GUMC); Robel Kahsay (PIR/GUMC); Raja Mazumder (PIR/GUMC); Anastasia Nikolskaya (PIR/GUMC); Sona Vasudevan (PIR/GUMC); C. R. Vinayaka (PIR/GUMC); Lai-Su Yeh (PIR/GUMC); Cathy H. Wu (PIR/GUMC);
Short Abstract: PIRSF are a set of curated, hierarchical, whole protein families that form the basis for automated, rule-based annotation of individual proteins and for connecting various ontologies to protein entities.
Long Abstract: Click Here

Poster B-21
INOH pathway data ontologies
Ken FUKUDA (CBRC, AIST); Satoko YAMAMOTO (BIRD, JST); Noriko SAKAI (BIRD, JST); Hiromi NAKAMURA (Information and Mathematical Science Laboratory, Inc.); Toshihisa TAKAGI (Graduate School of Frontier Sciences, University of Tokyo);
Short Abstract: INOH is a manually curated database of signal transduction pathways. While conventional pathway data are highly structured, they use open vocabularies to annotate their pathway components. To resolve the problem of data integration or mapping between data from different sources, INOH pathway objects are annotated by our pathway annotation ontologies.
Long Abstract: Click Here

Poster B-22
Online dynamic visualization and statistical analyses of rat phenome data
Anne E Kwitek (Medical College of Wisconsin); Zhanchi Wang (Medical College of Wisconsin); Allen W. Cowley Jr. (Medical College of Wisconsin); Andrew S. Greene (Medical College of Wisconsin); Richard J. Roman (Medical College of Wisconsin); Howard J. Jacob (Medical College of Wisconsin);
Short Abstract: PhysGen has generated and characterized over 200 phenotypes in two panels of rat chromosome substitution strains. All data is released to the public via our website (http://pga.mcw.edu). To facilitate more streamlined mining of the PhysGen data, we have developed flexible and dynamic visualization tools, with linked online statistical analysis.
Long Abstract: Click Here

Poster B-23
A cell type transcriptional atlas database for rice
Matthew Holford (Yale University); Teresa Ceserani (Yale University); Mei Chen (Yale University); Neeru Gandotra (Yale University); Yuling Jiao (Yale University); Naixin Li (Yale University); Tie Liu (Yale University); Ligeng Ma (Yale University); Ning Sun (Yale University); Susan Tausta (Yale University); Xing-Wang Deng (Yale University); Hongyu Zhao (Yale University); Timothy Nelson (Yale University);
Short Abstract: We have constructed a transcriptional atlas database for rice using cells isolated by laser microdissection to facilitate the comparison of data between differing cell types. This database backs a web application that offers a variety of views to browse the data and analyze it within the context of biological pathways.
Long Abstract: Click Here

Poster B-24
WebLab: a workflow-based platform integrating bioinformatics resources
Jianmin Wu (Center of Bioinformatics, Peking University, Beijing 100871, China); Ge Gao (Center of Bioinformatics, Peking University, Beijing 100871, China); Xiaoqiao Liu (Center of Bioinformatics, Peking University, Beijing 100871, China); Lei Kong (Center of Bioinformatics, Peking University, Beijing 100871, China); Zhe Li (Center of Bioinformatics, Peking University, Beijing 100871, China); Di Liu (Center of Bioinformatics, Peking University, Beijing 100871, China); Wen Tang (Center of Bioinformatics, Peking University, Beijing 100871, China); Jingchu Luo (Center of Bioinformatics, Peking University, Beijing 100871, China);
Short Abstract: We developed a bioinformatics platform WebLab integrating various sequence analysis tools. WebLab was designed biological end-users with a single and simple Web interface which allows users to input sequence data and manage analysis results. WebLab can also be used by bioinformaticians as a workflow-based system for further development.
Long Abstract: Click Here

Poster B-25
eSLDB: eukaryotic Subcellular Localization DataBase.
Andrea Pierleoni (Biocomputing Group, Department of Biology, University of Bologna); Pier Luigi Martelli (Biocomputing Group, Department of Biology, University of Bologna); Piero Fariselli (Biocomputing Group, Department of Biology, University of Bologna); Rita Casadio (Biocomputing Group, Department of Biology, University of Bologna);
Short Abstract: eESLB is the first database of eukaryotic proteomes fully annotated for subcellular localization, containing experimental annotations derived from primary protein databases, homology based annotations and computational predictions. In its first release, the database contains subcellular annotations of proteins from five entire eukaryotic proteomes. eSLDB is publicly available at http://gpcr.biocomp.unibo.it/esldb/.
Long Abstract: Click Here

Poster B-26
NUDLE: A Tool for Inferring Nutrient Disease Relationships from Metabolic Networks
Anoop Kumar ( Department of Computer Science, Tufts University, Medford, MA, USA); Jennifer S. Buell (Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, USA); Lenore J. Cowen ( Department of Computer Science, Tufts University, Medford, MA, USA); Inga Peter ( Institute for Clinical Research and Health Policy Studies, Tufts-New England Medical Center, Boston);
Short Abstract: We have developed NUtrient-Disease Link Estimator (NUDLE), a tool that infers nutrient disease relationships using data from metabolic, genomic and disease databases. It constructs metabolic networks and allows the inference of relationships between genes, diseases and nutrients from distance properties within the networks.
Long Abstract: Click Here

Poster B-27
Development of Computational Tools for a Dynamic Association between Genomic and Proteomic Data and Metabolic Pathways
Renato Milani (Department of Biochemistry - Unicamp); Itaraju J. B. Brum (Department of Biochemistry - Unicamp); Anderson R. Martins (Alellyx Applied Genomics); Eduardo Galembeck (Department of Biochemistry - Unicamp);
Short Abstract: This project aimed to build tools for an easier association of proteomics and genomics information with metabolic pathways. GenPath and ECPath, unlike the currently available tools, offer the possibility to customize the data source analyzed, free from the pre-defined maps based on data present in metabolic pathways databases.
Long Abstract: Click Here

Poster B-28
A Computational Pipeline for the Analysis of Data from a 500,000 SNP Whole Genome Association Study of Multiple Sclerosis
David Sexton (Center for Human Genetics Research, Vanderbilt University, International Multiple Sclerosis Genetics); Jacob McCauley (Center for Human Genetics Research, Vanderbilt University, International Multiple Sclerosis Genetics); Justin Giles (Center for Human Genetics Research, Vanderbilt University, International Multiple Sclerosis Genetics); Yuki Bradford (Center for Human Genetics Research, Vanderbilt University, International Multiple Sclerosis Genetics); Jonathan Haines (Center for Human Genetics Research, Vanderbilt University, International Multiple Sclerosis Genetics);
Short Abstract: The International Multiple Sclerosis Genetics Consortium (IMSGC) has undertaken a whole genome association study for regions with association to multiple sclerosis phenotypes. This study consists of genotyping 500,000 SNPs in 1000 affected family trios. New methods were developed to automatically upload, quality control, analyze, and report this data.
Long Abstract: Click Here

Poster B-29
UniHI: Unifying Large-Scale Maps of the Human Protein Interactome
Gautam Chaurasia (Max-Delbrück-Centrum); Christian Hänig (Max-Delbrück-Centrum); Hanspeter Herzel (Institute for Theoretical Biology); Erich Wanker (Max-Delbrück-Centrum); Matthias E. Futschik (Institute for Theoretical Biology);
Short Abstract: We present here a web-based database called UniHI (Unified Human Interactome) which aims to integrate available protein interaction maps. It is currently based on 10 interaction maps including over 16000 unique proteins and 150000 distinct interactions in total. UniHI offers researchers a direct entry gate into the human interactome.
Long Abstract: Click Here

Poster B-30
Prediction from complex bioinformatic databases, with application to protein--protein interactions
Berzuini Carlo (MRC BSU); Tom M.W. Nye (MRC BSU); Sarah A. Teichmann (MRC LMB);
Short Abstract: We consider predictions based on a synthesis of information from a heterogeneous collection of databases. Our method involves a weighted combination of predictive distributions generated by each individual database, where each weight measures the independent predictive contribution of the corresponding database. We apply the methodology to predict domain--domain contacts within a given multimeric protein complex, by synthesizing information from a database of atomic-level, three--dimensional, multimer structures and from rather crude, genome--wide, experiments indicating which pairs of proteins have potential to multimerise.
Long Abstract: Click Here

Poster B-31
MS-PED: A Management System for Proteomics Experimental Data
W. Yan (Bioinformatics User Facility, University of California, Los Angeles, CA); S. Than (School of Dentistry, University of California, Los Angeles, CA); R. Qiao (School of Medicine, University of Southern California, Los Angeles, CA); D.S. Parker (Department of Computer Science, University of California, Los Angeles, CA); D. Wong (School of Dentistry, University of California, Los Angeles, CA);
Short Abstract: MS-PED: A Management System for Proteomics Experimental Data
W. Yan1, S. Than2, R. Qiao3, D.S. Parker4, D. Wong2 1Bioinformatics User Facility, 4Department of Computer Science, and 2School of Dentistry, University of California, Los Angeles, CA; 3School of Medicine, University of Southern California, Los Angeles, CA.
MS-PED is a web-based management system for proteomics experimental data. It differs from existing platforms in handling both bottom-up and top-down proteomics experimental data, its support for a PEDRo-like level of information detail, its integration of tools with the database, its portable web-based design, and its commitment to open-source availability.
Long Abstract: Click Here

Poster B-32
A Classification for Conceptually Layouting Protein-Protein Interaction Networks
SunLee Bang (Electronics & Telecommunications Research Institute); JaeHun Choi (Electronics & Telecommunications Research Institute); JongMin Park (Electronics & Telecommunications Research Institute); SooJun Park (Electronics & Telecommunications Research Institute);
Short Abstract: To better understand interactions and protein function in the protein-protein interactions network, we nearly layout the proteins that do same function with keeping physical structure using annotated information of the protein. With this method, we can conceptually analyze the network and visualize it faster than existing graph drawing algorithms
Long Abstract: Click Here

Poster B-33
STING Database Quality Assessment
Stanley R. M. Oliveira (Embrapa Agricultural Informatics); Paula R. K. Falcão (Embrapa Agricultural Informatics); Michel E. B.Yamagishi (Embrapa Agricultural Informatics); Goran Neshich (Embrapa Agricultural Informatics); Diego N. Rodrigues (Embrapa Agricultural Informatics); Kassyus R. R. Souza (Embrapa Agricultural Informatics); Douglas U. Morita (Embrapa Agricultural Informatics); Gustavo V. Almeida (Embrapa Agricultural Informatics); Ivan Mazoni (Embrapa Agricultural Informatics); Edgard H. Santos (Embrapa Agricultural Informatics); Fábio D. Vieira (Embrapa Agricultural Informatics); José G. Jardine (Embrapa Agricultural Informatics);
Short Abstract: Inaccurate or inconsistent data can hinder our ability to interpret the research results. An effective data quality strategy can help the research to better handle its scientific objective, reducing costly operational inefficiencies. Here we present the results of our effort to access the quality of data in STING Database.
Long Abstract: Click Here

Poster B-34
A computational system to select candidate genes for complex human traits
Kyle J Gaulton (Department of Genetics, University of North Carolina); Karen L Mohlke (Department of Genetics, University of North Carolina); Todd J Vision (Department of Biology, University of North Carolina);
Short Abstract: A wealth of genomic data exists that can be mined to uncover functionally relevant links between genes and traits. We developed a computational system, named CAESAR, which exploits these resources by combining text mining, data mining and data integration to prioritize potential candidate genes for complex human traits.
Long Abstract: Click Here

Poster B-35
FlagelLink – An integrated organellar database dealing with refined pattern recognition of specific motifs/domains targeted to the eukaryotic flagellum
Fabiana Freire de Araújo (NUGEN-UECE); Wesley Jefferson Oliveira Alcoforado (NUGEN-UECE); João David de Lira (NUGEN-UECE); Dácio Barros Tavares (NUGEN-UECE); Ana Luiza Bessa de Paula Barros (LARCES-UECE); Diana Magalhães de Oliveira (NUGEN-UECE);
Short Abstract: In order to provide a convenient bioinformatics resource covering available information about the flagellum (an organelle of intriguing motile features), an integrated relational database has been created. FlagelLink (http://nugen.lcc.uece.br/lpgate/?p=flagdb) gives this first insight on compiling the modularity of flagellar genes/proteins for allowing further analyses.
Long Abstract: Click Here

Poster B-36
XMLPipeDB: A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources
Kam D. Dahlquist (Loyola Marymount University); Joey Barrett (Loyola Marymount University); Joe Boyle (Loyola Marymount University); Adam Carasso (Loyola Marymount University); David Hoffman (Loyola Marymount University); Babak Naffas (Loyola Marymount University); Jeffrey Nicholas (Loyola Marymount University); Roberto Ruiz (Loyola Marymount University); Scott Spicer (Loyola Marymount University); John David N. Dionisio (Loyola Marymount University);
Short Abstract: XMLPipeDB is an open source suite of Java-based tools for automatically building relational databases from an XML schema (XSD). XMLPipeDB can be used for the management of biological data from different sources. We have used it to generate GenMAPP Gene Databases containing UniProt and Gene Ontology data for Escherichia coli and other bacterial species.
Long Abstract: Click Here

Poster B-37
InterProScan New and Planned Features
Sarah Hunter (European Bioinformatics Institute); Nicola Mulder (European Bioinformatics Institute); Alberto Labarga (European Bioinformatics Institute);
Short Abstract: InterProScan is arguably the best-known tool for predicting protein functional annotation. It is a perl-based software package which wraps search algorithms for 10 protein signature databases and 4 other programs. This poster describes the architecture of the software, together with new and up-and-coming features.
Long Abstract: Click Here

Poster B-38
Novel "shim" Service to Develop Fexible Workflows with Web Services
Toshiaki Katayama (University of Tokyo); Minoru Kanehisa (Kyoto University);
Short Abstract: It is difficult to develop flexible pipelines for biological analysis only by the methods currently available in the public web services. We developed a new web service containing a collection of "shim" services to process various data types especially for the integration with the KEGG API.
Long Abstract: Click Here

Poster B-39
Automating the Maintenance of Bioinformatics Services with Aap
Estienne Swart (National Bioinformatics Network (South Africa)); Ruediger Brauning (National Bioinformatics Network (South Africa));
Short Abstract: Bioinformatics Services are complex systems that require a significant amount of effort to maintain. Much of this burden can be eased by using a unified framework for concise, declarative specification and flexible, imperative scripting. For our purposes we employed a generic build system, Aap (http://www.a-a-p.org).
Long Abstract: Click Here

Poster B-40
Middleware approach to data integration for plant genomics
Pierre Larmande (Phd Student); Isabelle Mougenot (Assitant Professor); Christine Tranchant-Dubreuil (Ingineer); Manuel Ruiz (Phd); Therese Libourel (Professor);
Short Abstract: Plant functional genomics requires efficient integration and processing of related information. The difficulty lies in the integration of this information, often semantically inconsistent or expressing different viewpoints, and, very often, only available in heterogenous formats. We present a distributed integrated environment that permits interoperability between different data sources.
Long Abstract: Click Here

Poster B-41
Context-sensitive Evidence Integration for Predicting Biological Networks
Chad L. Myers (Lewis-Sigler Institute for Integrative Genomics, Department of Computer Science); Olga G. Troyanskaya (Lewis-Sigler Institute for Integrative Genomics, Department of Computer Science);
Short Abstract: We developed a general probabilistic system for context-sensitive discovery of biological networks from diverse genomic data. We measure significant variation in relevance of common experimental technologies across biological processes, and exploit this information to improve prediction accuracy. Using our approach, we predicted and experimentally confirmed novel network behavior for S. cerevisiae.
Long Abstract: Click Here

Poster B-42
Evidence handling in EMBL Third Party Annotation: a two-tiered structure.
Cochrane G.R. (EMBL-EBI); Bates K. (EMBL-EBI); Faruque N. (EMBL-EBI); Kanz C. (EMBL-EBI); Kulikova T. (EMBL-EBI); Zhu W. (EMBL-EBI); Apweiler R (EMBL-EBI);
Short Abstract: The EMBL Third Party Annotation database (EMBL TPA) recruits and presents peer-reviewed annotation and re-annotation of primary nucleotide sequence available in the public nucleotide sequence databases and trace archives. A recent broadening of scope of EMBL TPA increases coverage to include submitted annotation derived from non-experimental and indirect experimental evidence.
Long Abstract: Click Here

Poster B-44
An Integrated database of structural parameters for protein analysis
Stanley R. M. Oliveira (Embrapa Agricultural Informatics); Gustavo V. Almeida (Embrapa Agricultural Informatics); Kassyus R. R. Souza (Embrapa Agricultural Informatics); Diego N. Rodrigues (Embrapa Agricultural Informatics); Goran Neshich (Embrapa Agricultural Informatics); Paula R. Kuser-Falcão (Embrapa Agricultural Informatics); Michel E. B.Yamagishi (Embrapa Agricultural Informatics); Edgard H. Santos (Embrapa Agricultural Informatics); Fábio D. Vieira (Embrapa Agricultural Informatics); José G. Jardine (Embrapa Agricultural Informatics);
Short Abstract: STING_DB is a relational database composed of structural parameters for protein analysis operating with a collection of both publicly available data (PDB, HSSP, Prosite) and its own data (contacts, interface contacts, surface accessibility). STING_DB has over 300 parameters compiled at the single site and was implemented using free software.
Long Abstract: Click Here

Poster B-45
Digr: A web interface for mining Digrabase graph databases
Kieran O'Neill (National Bioinformatics Network); Dan Jacobson (National Bioinformatics Network); Hugh Murrell (University of KwaZulu-Natal);
Short Abstract: Digr is an extensible, platform independent, free open source interface to the graph mining functionality of DigraBase. Digr facilitates the finding of co-annotations of objects of interest to ontology terms. It has been applied to a molecular mammalian health model, and an endangered species tissue bank sample tracking system.
Long Abstract: Click Here

Poster B-46
GEMINA: Genomic Metadata for Infectious Agents
Aaron Gussman (The Institute for Genomic Research, Rockville, Maryland 20850, USA.); Sam Angiuoli (The Institute for Genomic Research, Rockville, Maryland 20850, USA.); Lynn M. Schriml (The Institute for Genomic Research, Rockville, Maryland 20850, USA.The Institute for Genomic Researc); Kumar Hari (Ibis Division of Isis Pharmaceuticals, 1891 Rutherford Rd., Carlsbad, CA 92008, USA.); Alan Goates (Ibis Division of Isis Pharmaceuticals, 1891 Rutherford Rd., Carlsbad, CA 92008, USA.); Kathy Phillippy (The Institute for Genomic Research, Rockville, Maryland 20850, USA.); Tanja Davidsen (The Institute for Genomic Research, Rockville, Maryland 20850, USA.); Anu Ganapathy (The Institute for Genomic Research, Rockville, Maryland 20850, USA.); Steven Salzberg (Center for Bioinformatics and Computational Biology, University of Maryland Institute for Advanced C); Owen White (The Institute for Genomic Research, Rockville, Maryland 20850, USA.); Neil Hall (The Institute for Genomic Research, Rockville, Maryland 20850, USA.);
Short Abstract: The Gemina (Genomic Metadata for Infectious Agents) system, developed at TIGR, integrates pathogen and epidemiological information with genomic sequence and annotation data. It enables the identification of microbial pathogen species based on their epidemiology and pathogenesis, and supports the development of nucleotide signature-based assays for the detection of pathogens.
Long Abstract: Click Here

Poster B-47
A Web-based Workbench for Conducting "In-Silico" Experiments Using Microarray Data
Cheryl Hornbaker (Department of Pharmacology, University of Colorado Health Sciences Center); Lawrence Hunter (Department of Pharmacology, University of Colorado Health Sciences Center); Tzu Phang (Department of Pharmacology, University of Colorado Health Sciences Center); Sanjiv Bhave (Department of Pharmacology, University of Colorado Health Sciences Center); Ravan Lapadat (Department of Pharmacology, University of Colorado Health Sciences Center); Laura Saba (Department of Pharmacology, University of Colorado Health Sciences Center); Jeanette Gaydos (Department of Pharmacology, University of Colorado Health Sciences Center); Daniel McGoldrick (Department of Pharmacology, University of Colorado Health Sciences Center); Andrew Dolbey (Department of Pharmacology, University of Colorado Health Sciences Center); Brian Soriano (Department of Pharmacology, University of Colorado Health Sciences Center); John Belnap (Behavioral Neuroscience, Oregon Health & Science University); Aaron Gabow (Department of Pharmacology, University of Colorado Health Sciences Center); Allison Ellington (Department of Pharmacology, University of Colorado Health Sciences Center); Eric Ellington (Department of Pharmacology, University of Colorado Health Sciences Center); Kendra Jones (Department of Pharmacology, University of Colorado Health Sciences Center); Paula Hoffman (Department of Pharmacology, University of Colorado Health Sciences Center); Boris Tabakoff (Department of Pharmacology, University of Colorado Health Sciences Center);
Short Abstract: The Colorado INIA Informatics website offers a suite of tools for sharing, analyzing, and interpreting microarray experiment data for worldwide collaborative research. The website allows users to combine gene expression data from an assortment of previously uploaded MIAME-compliant experiments to test novel hypotheses regarding gene expression and complex behaviors.
Long Abstract: Click Here

Poster B-48
SOAP-based services provided by the European Bioinformatics Institute
Alberto Labarga (European Bioinformatics Institute - EMBL); S. PIlai (European Bioinformatics Institute - EMBL); M. Anderson (European Bioinformatics Institute - EMBL); F. Valentin (European Bioinformatics Institute - EMBL); H. McWilliam (European Bioinformatics Institute - EMBL); P. Stoehr (European Bioinformatics Institute - EMBL); K. Henrick (European Bioinformatics Institute - EMBL); P. Rice (European Bioinformatics Institute - EMBL); R. Lopez (European Bioinformatics Institute - EMBL);
Short Abstract: SOAP based Web Services has gained much attention as an open standard enabling interoperability among applications. The European Bioinformatics Institute (EBI) is using this technology to provide robust data retrieval and data analysis mechanisms to the scientific community and to enhance utilization of the biological resources it already provides.
Long Abstract: Click Here

Poster B-49
BISI: an integrative, extensible and minable database of South African wildlife and indigenous livestock biomaterial information
Athlee Maclear (National Bioinformatics Network); Darren Otgaar (National Bioinformatics Network); Dr. Junaid Gamieldien (National Bioinformatics Network); Dr. Paul Bartels (National Zoological Gardens/BioBankSA); Dan Jacobson (National Bioinformatics Network); Dr. Antoinette Kotze (National Zoological Gardens, South Africa);
Short Abstract: BISI is a collaborative project employing the graph storage and mining capabilities of DigraBase, to establish an integrative, extensible and minable database of South African wildlife and indigenous livestock biomaterial information, that will facilitate the identification of specific priorities for biodiversity conservation, research and biotechnology development in South Africa.
Long Abstract: Click Here

Poster B-51
Arabidopsis Functional Genomics Data Integration
Nicolas Tsesmetzis (Computational Biology Department, John Innes Centre); Matthew Couchman (Computational Biology Department, John Innes Centre); Sean Walsh (Computational Biology Department, John Innes Centre);
Short Abstract: We are currently working on two systems: i) The Arabidopsis thaliana Integration Database (http://atidb.org) integrates the latest gene models and annotation with the location of insertional mutagens, the Gene Ontology Database, InterProScan results, primer locations etc. ii) The Arabidopsis Reactome is a knowledge base that models biological processes as a series of events and it is based on the human Reactome data-structure (http://www.reactome.org).
Long Abstract: Click Here

Poster B-52
CUDXML: Codon Usage Database in XML Format
Denis Shestakov (Turku Centre for Computer Science); Tapio Salakoski (University of Turku);
Short Abstract: In this work, we present Codon Usage Database in XML Format (CUDXML), an XML-based database for codon usage data. Our motivation was to provide researchers involved in codon usage studies with a comprehensive database of codon usage patterns for all known complete protein coding sequences (calculated based on current GenBank release).
Long Abstract: Click Here

Poster B-53
GAFFA: Genome Annotation Framework for Flexible Analysis
Anders Lanzén (Computational Biology Unit, Bergen Center for Computational Science, University of Bergen); Svenn Helge Grindhaug (Computational Biology Unit, Bergen Center for Computational Science, University of Bergen); Pål Puntervoll (Computational Biology Unit, Bergen Center for Computational Science, University of Bergen);
Short Abstract: The aim of GAFFA is to provide a flexible and modular framework for integrating all steps involved in a genome analysis project. Further, it provides a system for keeping track of the analysis process and results generated. GAFFA is developed using a service-oriented architecture.
Long Abstract: Click Here

Poster B-54
SNP-Ontology for semantic integration of genomic variation data
Adrien Coulet (KIKA Medical, 35 rue de Rambouillet 75012 Paris, France. LORIA (UMR 7503 CNRS-INPL-INRIA-Nancy2-UHP)); Malika Smaïl-Tabbone (LORIA (UMR 7503 CNRS-INPL-INRIA-Nancy2-UHP)); Pascale Benlian (Université Pierre et Marie Curie - Paris6, INSERM UMRS 538, Biochimie - Biologie Moléculaire, Paris,); Amedeo Napoli (LORIA (UMR 7503 CNRS-INPL-INRIA-Nancy2-UHP)); Marie-Dominique Devignes (LORIA (UMR 7503 CNRS-INPL-INRIA-Nancy2-UHP));
Short Abstract: A formal ontology is proposed as a means for guiding data selection and for semantically integrating data about genomic variations. The designed SNP-Ontology is used for initializing a SNP-dedicated knowledge base which integrates information on genomic variations whatever their original representations.
Long Abstract: Click Here

Poster B-56
A Functional Genomics Information Management System
Meintjes, AP (University of Pretoria); Schriek, CA (University of Pretoria); De Bruin, J (University of Pretoria); Harrison, CM (University of Pretoria); Tiedt, DA (University of Pretoria); Ganesan, H (University of Pretoria); Hefer, CA (University of Pretoria); de Beer, TAP (University of Pretoria); Burger, PB (University of Pretoria); Joubert, F (University of Pretoria);
Short Abstract: A web-based system system for integrated management and analysis of a variety of Functional Genomic data types is being developed, including generic, sequence, microarray, genotyping, ligand and structural data.
Long Abstract: Click Here

Poster B-57
Generation Challenge Programme (GCP) Domain Modeling and Crop Information Platform
Kyle Braak (Centro Internacional de Mejoramiento de Maíz y Trigo (CIMMYT)); Richard M. Bruskiewich (International Rice Research Institute (IRRI)); Guy Davenport (Centro Internacional de Mejoramiento de Maíz y Trigo (CIMMYT)); Alexis Dereeper (Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD)); Andrew Farmer (National Center for Genome Resources (NCGR)); Tom HazeKamp (International Plant Genetic Resources Institute (IPGRI)); Graham Mclaren (International Rice Research Institute (IRRI)); Thomas Metz (International Rice Research Institute (IRRI)); Sebastian Ritter (Centro Internacional de Mejoramiento de Maíz y Trigo (CIMMYT)); Manuel Ruiz (Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD)); Martin Senger (International Rice Research Institute (IRRI)); Reinhard Simon (Centro Internacional de la Papa (CIP)); Masaru Takeya (National Institute for Agrobiological Sciences (NIAS)); Theo Van Hintum (Wageningen Universiteit & Researchcentrum (WUR));
Short Abstract: The Generation Challenge Programme (GCP;http://www.generationcp.org) is an international agricultural research consortium currently comprising 20 agricultural research institutes. The corresponding poster discusses the GCP's Domain Modeling (DM) undertaking and its incorporation into its ‘crop information platform’. Lastly, it introduces a new and promising bioinformatics application called ISYSEclipse based on the platform.
Long Abstract: Click Here

Poster B-58
Development of BioMOBY and its Associated Applications
Mylah Rystie Anacleto (International Rice Research Institute (IRRI)); Kyle Braak (Centro Internacional de Mejoramiento de Maíz y Trigo (CIMMYT)); Richard Bruskiewich (International Rice Research Institute (IRRI)); Mathieu Rouard (International Plant Genetic Resources Institute (IPGRI)); Martin Senger (International Rice Research Institute (IRRI)); Milko Skofic (International Plant Genetic Resources Institute (IPGRI));
Short Abstract: Developed with the Generation Challenge Programme (GCP;http://www.generationcp.org) BioMoby is an integration tool helping to connect databases, analysis programs, and other resources into a unified distributed system, linking gene discovery with genetic resource characterization and crop evaluation data. This poster highlights BioMoby, its associated applications, and its integration with other tools.
Long Abstract: Click Here

Poster B-59
Design Principles of Ontology-based Query and Development of Ontology Wrapper
Myung-Guen Chung (Electronics and Telecommunications Research Institute); Myung-Eun Lim (Electronics and Telecommunications Research Institute); Myung-Nam Bae (Electronics and Telecommunications Research Institute); Yong-Ho Lee (Electronics and Telecommunications Research Institute); Soo-Jun Park (Electronics and Telecommunications Research Institute);
Short Abstract: A typical mediator-wrapper system required practical linkage information among the database. Unfortunately, each database bestows a different. To solve this inconsistency problem in terminology, researchers have used several methods, one of which is ontology. But most system still remains ontology resource in the system. We propose ontology wrapper.
Long Abstract: Click Here

Poster B-60
Classification of snake venon-neutralizing effects of medicinal plants via artificial neural networks
Gabriela Félix dos Santos (Department of Physics and Mathematics of Ribeirão Preto - University of São Paulo); Renato Tinós (Department of Physics and Mathematics of Ribeirão Preto - University of São Paulo); Silvana Giuliatti (Faculty of Medicine of Ribeirão Preto - University of São Paulo);
Short Abstract: Artificial Neural Networks (ANNs) are employed to map relationship between amino acid sequences of snake venoms and anti-venom medicinal plants. The inputs of the ANN are obtained by encoding the amino acid sequences by two different methods The validation results indicate that 75% of the patterns were correctly classified.
Long Abstract: Click Here

Poster B-61
Genome-wide Comparison of DNA Melting Bubbles and Ensembl’s Genomic Annotations
Geir Ivar Jerstad (Dept. of Informatics, University of Oslo); Eivind Tøstesen (Dept. of Tumor Biology, Norwegian Radium Hospital); Torbjørn Rognes (Dept. of Informatics, University of Oslo); Eivind Hovig (Dept. of Tumor Biology, Norwegian Radium Hospital);
Short Abstract: The statistical occurrence of DNA melting bubbles can be represented using stitch profile diagrams. By computing genomic stitch profiles, a direct comparison between physical bubbles and genomic annotations is facilitated. Visualisation of the overlap has been achieved by the integration of a stitch profile view into the Ensembl genome browser.
Long Abstract: Click Here

Poster B-62
Database PROBACTER: proteomes of plants-associated bacteria.
Fernanda Nascimento Almeida (Labindo, LNCC); Rangel Celso Souza (Labindo, LNCC); Alexandre Rossi Paschoal (Labindo, LNCC); Ana Tereza Ribeiro de Vasconcelos (Labindo, LNCC); Claudia Barros Monteiro-Vitorello (Labindo, LNCC);
Short Abstract: We report the construction of PROBACTER, a comparative database containing data of 19 complete proteomes of plant-associated bacteria. Most of them are Gram-negative bacteria being this database oriented to groups working mostly with Xylella and Xanthomonas.
Long Abstract: Click Here

Poster B-63
2D Maps of Protein Surface
Marcelo Gonçalves Narciso (Embrapa Informática Agropecuária); Michel E. B. Yamagishi (Embrapa Informática Agropecuária); Paula R. Kuser-Falcão (Embrapa Informática Agropecuária); Goran Neshich (Embrapa Informática Agropecuária);
Short Abstract: In this work, we present 2DIM (Two Dimensional Interface Maps). It is a graphical interface that permits to visualize the protein-protein interfaces in 2D maps.
Long Abstract: Click Here

Poster B-64
Expression Databases for Three Crop Species: Maize, Rice and Potato
Jia Liu (TIGR); Eugene Ly (TIGR); Li Zheng (TIGR); Amy Hart (TIGR); Shu Ouyang (TIGR); Kimberly Rehfeld (TIGR); Willem Rensink (TIGR); Robin Buell (TIGR); Qiaoping Yuan (TIGR); Hue Vuong (TIGR);
Short Abstract: We have been funded to develop databases for expression data for three crop species: potato, rice and maize. We have constructed relational databases and accept expression data associated with these arrays from the public. We have developed a suite of web-based data mining tools for all projects.
Long Abstract: Click Here

Poster B-65
CocoaGen DB, an Integrative Information System to Exploit both Phenotypic and Genomic Data on Cocoa.
Xavier Argout (CIRAD); Manuel Ruiz (CIRAD); Mathieu Rouard (INIBAP); Chris Turnbull (School of Plant Sciences, University of Reading); Claire Lanaud (CIRAD); Eric Rosenquist (ARS, USDA); Brigitte Courtois (CIRAD);
Short Abstract: CocoaGen DB is an integrative information system on cocoa initiated through a collaborative project involving CIRAD, the University of Reading and USDA. This database comprises molecular, genetic, phenotypic and passport data on cocoa. An intuitive web consultation interface with several tools allows end-users to best exploit genetic information available on cocoa germplasm.
Long Abstract: Click Here

Poster B-66
TraceSearch: Implementation and Applications.
Adam Spargo (WTSI); Steve Leonard (WTSI); Guy Coates (WTSI); Jody Clements (WTSI); Roger Pettett (WTSI); Antony Cox (WTSI); Martin Widlake (WTSI); Zemin Ning (WTSI);
Short Abstract: TraceSearch enables access to the trace archive via homology. Our distributed implementation of the SSAHA2 algorithm allows data to be added incrementally on a daily basis and hardware failures to be handled efficiently. As well as technical details we present examples of how the system is used in research.
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Poster B-67
Disease Portals: A Platform for Genetic and Genomic Research
Andrew Patzer (Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin); Weihong Jin (Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin); Mary Shimoyama (Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin); Simon Twigger (Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin); Anne Kwitek (Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin); Howard Jacob (Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin); Victoria Petri (Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin); Jiali Chen (Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin);
Short Abstract: The Disease Portals at the Rat Genome Database provide a comprehensive platform for physiological genomics discovery through the integration of heterogeneous datasets into the context of the genome using multiple ontologies and sophisticated data mining and visualization tools.
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Evolution and Phylogeny

Poster C-1
Elucidating the complex nature of gene fusion events for moving towards automatic quantification of protein function
Ashwin Sivakumar ( Bioinformatics group, Division of Genetics, Institute of Biotechnology, University of Helsinki PO B); Christopher Wilton (Bioinformatics group, Division of Genetics, Institute of Biotechnology, University of Helsinki PO Bo); Swapan Mallick (Bioinformatics group, Division of Genetics, Institute of Biotechnology, University of Helsinki PO Bo); Liisa Holm (Bioinformatics group, Division of Genetics, Institute of Biotechnology, University of Helsinki PO Bo);
Short Abstract: A complete functional unit of a protein can be multi-domain, and it is the co-occurrence and interaction of these multiple domains that determines the function and functional diversity of their gene products. We automatically mine these “functional units” (modules) using only sequence information for introducing a biologically novel automatic functional classification system of contemporary proteins.
Long Abstract: Click Here

Poster C-2
Phylogenetic Analysis On Five STR- Loci Of Chromosome Y In Homo Sapiens Sapiens, Pan Troglodytes And Macaca Tonkeana
Everty M. Rocha (LASP/FIOCRUZ); Flora M. C. Fernandes (LASP/FIOCRUZ);
Short Abstract: Phylogenetic analyses were conducted using five STR-loci of chromosome Y: DSY19, DSY385a-b, DSY391a-b. We used sequences from NCBI. Maximum likelihood approach was employed. In general, different species formed clades well supported except in the case of DSY391a in wich human and chimpanzee were in the same clade.
Long Abstract: Click Here

Poster C-3
Phylogenetic Analysis Of The Mitochondrial DNA HVS2 Loci.
Thiago J Santana (LASP/FIOCRUZ); Flora M.C. Fernandes (LASP/FIOCRUZ);
Short Abstract: HVS2 is a D-loop hipervariable region of the mtDNA. We analized 346 sequences of HVS2 (297bp). Phylogeny was carried out using maximum likelihood, and 13 haplotypes lineages presented no resolution. The aim of the presente work is to analyze HVS2 polimorphism involving HTLV-1+ and - individuals for prevention programs.
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Poster C-4
A phylogenetic reconstruction method based on genetic algorithms and hierarchical clustering
Ryosuke Watanabe (Computer Science Department, ITESM Campus Estado de México); Edgar E. Vallejo (Computer Science Department, ITESM Campus Estado de México); Enrique Morett (Department of Cellular Engineering and Biocatalysis, IBT UNAM);
Short Abstract: We present a method for phylogenetic reconstruction based on genetic algorithms and hierarchical clustering. We formulate the fitness function as a combination of UPMGA and MP scores. We use taxas from several lineages to evaluate the proposed method. Experimental results indicate that our model is capable of producing accurate phylogenies.
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Poster C-5
Generation and evolutionary fate of insertions of organelle DNA in the nuclear genome of rice and Arabidospsis
Christos Noutsos (AG Leister, Botanik I, Biologie, Ludwig Maximillian University); Dario Leister (AG Leister, Botanik I, Biologie, Ludwig Maximillian University);
Short Abstract: Nuclear genomes are exposed to a continuous influx of DNA from mitochondria and plastids.Transfer of DNA from mitochondria and/or plastids to the nucleus is a ubiquitous, ongoing evolutionary process, which has markedly influenced the evolution of eukaryotic genomes.
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Poster C-6
Intracellular transporters evolve slowly
Hajime Ohyanagi (Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics); Takashi Gojobori (Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics);
Short Abstract: The membranous organelles in eukaryotes could affect on the evolution of particular proteins, such as intracellular transporters (ITs) because of particular functional constraints. We compared evolutionary rates of ITs and non-ITs. The results suggest that ITs, especially transporters for large molecules are slowly evolving now.
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Poster C-7
In silico identification and analysis of new Artemis/Artemis-like sequences from fungal and metazoan species
Diego Bonatto (Universidade de Caxias do Sul); Martin Brendel (Universidade Estadual de Santa Cruz); João Antonio Pêgas Henriques (Universidade de Caxias do Sul);
Short Abstract: The mammalian Artemis proteins have important functions in the repair of DNA double-strand breaks and in the V(D)J recombination. We have characterized new Artemis/Artemis-like sequences from the genomes of fungi and non-mammalian metazoan species using an in-depth phylogenetic analysis coupled to hydrophobic cluster analysis and three-dimensional modeling of selected sequences.
Long Abstract: Click Here

Poster C-8
Molecular recognition and evolution in the olfactory receptor gene superfamily
Tsviya Olender (Department of Molecular Genetics and the Crown Human Genome Center, Weizmann Institute of Science); Ester Feldmesser (Department of Molecular Genetics and the Crown Human Genome Center, Weizmann Institute of Science); Ronny Aloni (Department of Molecular Genetics and the Crown Human Genome Center, Weizmann Institute of Science); Doron Lancet (Department of Molecular Genetics and the Crown Human Genome Center, Weizmann Institute of Science);
Short Abstract: We compared five mammalian repertoires of olfactory receptors (ORs), including the marsupial opossum,. We identified 48 CLICs (CLusters In Conservation) containing most of the mammalian ORs. Human and mouse OR expression data were collected from a multitude of sources. Data showed an unexpectedly high degree of ectopic expression in non-olfactory tissues.
Long Abstract: Click Here

Poster C-9
How protein evolution measured by similarity change and stop codon incidence depends on the genetic code
Francisco Prosdocimi (UFMG); Henrique Melo (UFMG); Eduardo R Capanema (UFMG); J Miguel Ortega (UFMG);
Short Abstract: One important source for protein evolution is the successive incurrence of mutations on the coding DNA. Our results support the hypothesis that one important factor on protein evolution is the codon composition, since both similarity change and stop codon incidence seem to depend on the genetic code.
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Poster C-10
Evolutionary History of Multi-Domain Proteins
Diana Ekman (Stockholm Bioinformatics Center, Stockholm University); Åsa Björklund (Stockholm Bioinformatics Center, Stockholm University); Arne Elofsson (Stockholm Bioinformatics Center, Stockholm University);
Short Abstract: A majority of the eukaryotic proteins are multidomain proteins. Here, we present a study of the evolution of new domain architectures through fusion and internal duplication. We found that architectures are created mainly through insertions/deletions of domains at the terminals. Expansion of domain repeats is also an important contribution.
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Poster C-11
Evolution of Death-domain-superfamily in apoptosis pathway
Juilee Thakar (Department of Bioinformatics, University of Wuerzburg and Department of Physics, Pennsylvania state); Yogeshwar Kelkar (Integrated biosciences,Department of Biology, Pennsylvania state university); Christoph Borner (Center for biochemistry and molecular cell biology, University of Freiburg); Thomas Dandekar (Department of Bioinformatics, Wuerzburg);
Short Abstract: Apoptosis takes place during normal development and pathological conditions. Proteins with domains from death-domain-superfamily are involved in apoptosis pathway regulation. We performed sequence, phylogenetic and structural analysis on domains from this family to look for conserved elements to comment on their role in signaling cascades.
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Poster C-12
Do Genome-Escale Phylogenies Actually Detect True Trees?
Karla Yotoko (PUC-RS); Sandro Bonatto (PUC-RS);
Short Abstract: We tested, using different phylogenetic methods, and three different sets, if the use of complete genomes recovers a convergent "true" tree. Our data point to differences between DNA and aminoacid trees, as well to long branch attractions, suggesting that complete genomes do not assure the recover of the "true" tree.
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Poster C-13
RHOGAP DOMAIN-CONTAINING PROTEINS PHYLOGENY – AN BAYESIAN APPROACH
MARCELO MENDES BRANDÃO (Hematology and Hemotherapy Center - UNICAMP); KARINA LUCAS DA SILVA-BRANDÃO (Zoology department - UNICAMP); FERNANDO FERREIRA COSTA (Hematology and Hemotherapy Center - UNICAMP); SARA TEREZINHA OLALLA SAAD (Hematology and Hemotherapy Center - UNICAMP);
Short Abstract: Proteins containing a RHOGAP domain work as molecular switches involved in the regulation of diverse cellular functions. The ability of these GTPases to regulate a wide number of cellular processes comes from their interaction with multiple proteins, including their inhibitors, the RHOGAPs protein family, which stimulates their intrinsic GTPase activity.
Long Abstract: Click Here

Poster C-14
A new approach for using genome scans to detect recent positive selection in the human genome
Tang, Kun (Max Planck Institute for Evolutionary Anthropology); Stoneking, Mark (Max Planck Institute for Evolutionary Anthropology);
Short Abstract: We present a new approach for using genome scans to detect recent positive selection in the human genome. We applied this method on both the Perlegen and the HapMap SNP data. A set of candidate genomic regions with strong signals of selection were identified across the genome.
Long Abstract: Click Here

Poster C-15
Molecular evolution and structural aspects of plant alcohol dehydrogenase
Claudia Elizabeth Thompson (Universidade Federal do Rio Grande do Sul); Loreta Brandão de Freitas (Universidade Federal do Rio Grande do Sul); Francisco Mauro Salzano (Universidade Federal do Rio Grande do Sul); Osmar Norberto de Souza (Pontifícia Universidade Católica do Rio Grande do Sul);
Short Abstract: The alcohol dehydrogenase genes encode glycolytic enzymes. Phylogenetic analysis indicate duplication events within angiosperms. Coefficients of functional divergence indicate site-specific shift of evolutionary rate in the Adh1 and Adh2 gene groups and different families. Amino acids residues important for functional divergence were identified in the ADH tridimensional structure.
Long Abstract: Click Here

Poster C-16
Comparative analysis of nucleotide polymorphism levels across different taxonomic units.
Natalia Petit (Departamento de Genètica i Microbiología. Facultat de Ciències, Universitat Autònoma de Barcelona); Sonia Casillas (Departamento de Genètica i Microbiología. Facultat de Ciències, Universitat Autònoma de Barcelona); Raquel Egea (ica i Microbiología. Facultat de Ciències, Universitat Autònoma de Barcelona); Alfredo Ruiz (ica i Microbiología. Facultat de Ciències, Universitat Autònoma de Barcelona); Antonio Barbadilla (ica i Microbiología. Facultat de Ciències, Universitat Autònoma de Barcelona);
Short Abstract: Two databases (DPDB and Mampol) compile sequences and estimate the levels of polymorphism of many organisms. Using this information, we designed and implemented a strategy to perform a global analysis of polymorphism data. The present study aims to describe and explain the polymorphism pattern in a wide range of species.
Long Abstract: Click Here

Poster C-17
Simplified Models of Evolution lead to Improved Prediction of Functional Linkage from Correlated Gain and Loss of Genes among Eukaryotes
Daniel Barker (School of Biology, University of St Andrews); Andrew Meade (School of Biological Sciences, University of Reading); Mark Pagel (School of Biological Sciences, University of Reading);
Short Abstract: Correlated gain and loss of genes from species' genomes may be used to predict functional linkage between gene products. We propose and test a novel variation on the phylogenetic maximum likelihood approach for seeking correlation among gain/loss of genes, tailored to eukaryotic gene content evolution. This improves results significantly.
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Poster C-18
reconstructing prokaryotic phylogeny applying a novel integrative approach
naryttza n. diaz (center for biotechnology (cebitec), universität bielefeld); lutz krause (center for biotechnology (cebitec), universität bielefeld); alfred pühler (lehrstuhl für genetik, universität bielefeld); kasten niehause (lehrstuhl für genetik, universität bielefeld); timm w. nattkemper (technische fakultät, universität bielefeld);
Short Abstract: we present a novel method for reconstructing phylogenetic trees, based on a novel integrative distance measurement of whole genomes and proteomes. an exhaustive analysis using 350 prokaryotic genomes not only show the validity of the method, but also suggest novel phylogenetic insights and its application to environmental sample analysis.
Long Abstract: Click Here

Poster C-20
Maximum likelihood inference of ancestral gene content for the bacterial septosome
Robson Francisco de Souza (Departament of Biochemistry, University of São Paulo, Brazil); Sandro José de Souza (Computational Biology Laboratory - Ludwig Institute for Cancer Research - São Paulo Branch, Brazil); Frederico José Gueiros Filho (Departament of Biochemistry, University of São Paulo, Brazil);
Short Abstract: We apply maximum likelihood methods for inferring the ancestral gene content of a specific protein complex, the bacterial septosome, and correlate shifts in septosome composition to phenotype. We now are estimating the variance of rates of gain and loss of genes through simulations and validating putative horizontal transfer
Long Abstract: Click Here

Poster C-21
C.A.S.S.I.O.P.E.
lopez rascol (EA 3781); gouret (EA 3781); grusea (EA 3781); danchin (AFMB); pontarotti (EA 3781);
Short Abstract: We present here CASSIOPE, an intelligent multi-agents system which integrates concept, process and automation of genome comparison based on evolution concepts and specific mathematical models, i.e. a systematic phylogenetic analysis to determine orthologous and paralogous relationship and specific statistical tests to evaluate the significant of a region conservation.
Long Abstract: Click Here

Poster C-22
Comparative Genomic Profiling of an Emerging Pathogen using a 7 Genomes Escherichia coli Microarray
Hanni Willenbrock (Center for Biological Sequence Analysis); Camilla Sekse (Norwegian School of Veterinary Science); Kristoffer Kiil (Center for Biological Sequence Analysis); Yngvild Wasteson (Norwegian School of Veterinary Science); David W. Ussery (Center for Biological Sequence Analysis);
Short Abstract: Shiga toxin-producing E. coli have emerged as important food borne pathogens. In this study, we characterize the novel strain, D1, encoding a shiga-toxin lamboid bacteriophage. Our analyses indicated that D1 is a K-12 like strain and that its 3538 phage element most likely originates from the E. coli 3538 strain.
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Poster C-23
Conformational diversity and evolutionary sequence divergence of proteins
Maria Silvina Fornasari (Centro de Estudios e Investigaciones, Universidad Nacional de Quilmes); Gustavo Parisi (Centro de Estudios e Investigaciones, Universidad Nacional de Quilmes);
Short Abstract: Using the Structurally Constrained Protein Evolution model, we found that the consideration of the quaternary structure and the multiple conformations that a protein could adopt, enhance the description of the sequence divergence. We used the protein triosephosphate isomerase from the archaeal Thermoproteus tenax which adopts a dimer/tetramer equilibrium.
Long Abstract: Click Here

Poster C-24
Comparative sequence analysis of microbial genomes to identify potential virulence genes in Mycobacterium tuberculosis.
Gordon Jamieson (IIDMM); Halimah Rabiu (IIDMM); Venu Vuppu (IIDMM); Nicola Mulder (IIDMM);
Short Abstract: Microbes are masters of adaptation to their environment, which results in ever changing targets for drug and vaccine research. This project aims to identify and characterise virulence genes from Mycobacterium tuberculosis through cataloguing of all microbial genes and determination of their phylogenetic distributions.
Long Abstract: Click Here

Poster C-26
3D Phylogeny Explorer: Distinguishing paralogs, lateral transfer, and violations of the “molecular clock” assumption with 3D visualization
Namshin Kim (Molecular Biology Institute, Center for Genomics and Proteomics, Department of Chemistry and Biochem); Christopher Lee (Molecular Biology Institute, Center for Genomics and Proteomics, Department of Chemistry and Biochem);
Short Abstract: 3D Phylogeny Explorer projects trees onto three axes: species (X); paralogs (Z); evolutionary distance (Y), enabling one to distinguish speciation, gene duplication and lateral gene transfer at a glance. Live 3D views (VRML2) of microbial gene phylogenies (COGS) at http://bioinfo.mbi.ucla.edu/3DPhylogenyExplorer.
Long Abstract: Click Here

Poster C-27
LOSS: an heuristic approach to incorporate prior information into prokaryotic genomic GC prediction
Hugo Naya (Unidad de Bioinformática, Institut Pasteur de Montevideo, Uruguay); Héctor Romero (Laboratorio de Organización y Evolución del Genoma, Sección Biomatemética, Facultad de Ciencias, Uru);
Short Abstract: Genomic GC content is one of the most important features of a genome. We introduce an heuristic algorithm that allow to incorporate information from completely sequenced genomes to improve the genomic GC content prediction from a sample of genes. In general, performance of LOSS algorithm compared favorably with previous methods.
Long Abstract: Click Here

Poster C-28
Modeling the evolution of gene and protein interactions
Todd A. Gibson (University of Colorado Health Sciences Center); Debra S. Goldberg (University of Colorado);
Short Abstract: Current protein network analyses either use abstract evolutionary models lacking gene context, or model current-day protein interactions without a dynamic evolutionary component. We present a generalizable method for evolving an organism's putative ancestral protein interaction network to its current-day interactions. We compare evolutionary parameters and topology of distinct protein families.
Long Abstract: Click Here

Poster C-29
PhyloTree – An Integrated and Automatic Tool to Generate Phylogenetic Trees
Ana Luiza Bessa de Paula Barros (Computação-UECE); Gerardo Valdísio Rodrigues Viana (Computação-UECE); Tariana Mara Fernandes Batista (Computação-UECE); Gustavo Agusto de Lima Campos (Computação-UECE); Raimundo Bezerra da Costa (NUGEN-UECE); Rodrigo Maggioni (NUGEN-UECE); Diana Magalhães de Oliveira (NUGEN-UECE);
Short Abstract: PhyloTree is an integrated tool to help generate phylogenetic trees in an automated way. It combines successive steps, based on well-developed algorithms including ClustalW and PHYLIP, while it is intended to assist biologists from a broad range of disciplines and is likely to be particularly helpful for non-experts.
Long Abstract: Click Here

Poster C-30
Evolutionary inferences from the amino acid sequence of HC-Pro, a plant virus multifunctional protein
Antonio Sergio Kimus Braz (Depto Genetica - IBB - UNESP Botucatu); Ivan de Godoy Maia (Depto Genetica - IBB - UNESP Botucatu);
Short Abstract: The Helper component-proteinase (HC-Pro) encoded by viruses within the Potyviridae family is a multifunctional protein involved in several steps of the virus life cycle. We report an extensive phylogenetic analysis using the amino acid sequences of HC-Pro and provide evolutionary inferences concerning virus transmission and host range.
Long Abstract: Click Here

Poster C-31
Evolutionary Patterns At Different Codon Positions
Lee Bofkin (Cambridge University, European Bioinformatics Institute); Nick Goldman (European Bioinformatics Institute);
Short Abstract: Functional constraints imposed by the genetic code affect evolutionary patterns at different codon positions. We analysed >5000 protein-encoding sequence alignments and assessed differences in common evolutionary parameters (e.g. evolutionary rate, base composition) at the three codon positions. Our results are important to understanding evolutionary processes and phylogeny inference.
Long Abstract: Click Here

Poster C-32
Clustering to minimize genetic overlap between clades
Mukund Narasimhan (Microsoft Corp.); Nebojsa Jojic (Microsoft Corp.);
Short Abstract: Phylogenetic tree construction methods which rely on multiple alignment as a foundation are restricted to gene/gene-fragments/small proteins. We show that parsimony satisfies a property called submodularity, and hence we can use recently discovered algorithms for submodular function minimization to construct maximum parsimony phylogenetic trees.
Long Abstract: Click Here

Poster C-33
Evolutionary Trends in Proteomes: exploring the Multidimensional Contributions
Tekaia (Institut Pasteur); Yeramian (Institut pasteur);
Short Abstract: Various aspects of the complex evolutionary trends that mutually link species can be grasped from the detailed analysis of their proteomes. Using Correspondence Analysis, we derive global pictures for the evolutionary links between species in terms of Genome trees (based on conservation profiles) and of proteomes amino-acid compositions.
Long Abstract: Click Here

Poster C-34
Parallelizing Computationally Intensive Bootstrap Phylogenetic Analyses
Ricardo Gonzalez-Mendez (Department of Radiological Sciences, University of Puerto Rico School of Medicine); Hugh B. Nicholas (NRBSC, Pittsburgh Supercomputing Center); Alexander J. Ropelewski (NRBSC, Pittsburgh Supercomputing Center);
Short Abstract: Computationally intensive programs in PHYLIP have been parallelized using MPI, enabling large-scale phylogenetic studies that rely on bootstrapping to be performed in a moderate amount of time. The methodology used to paralyze PHYLIP programs and the performance of the PHYLIP protein distance method on several parallel architectures is discussed.
Long Abstract: Click Here

Poster C-35
Phylogenetic studies on UniProtKB/Swiss-Prot families and data from complete proteomes
Boeckmann (SIB); Kriventseva (University of Geneva); Amendolia (SIB); Bairoch (SIB & University of Geneva);
Short Abstract: Swiss-Prot families and data from complete proteomes have recently been analyzed in various studies. Results suggest that the protein groupings are of high quality, but there is room for improvements. Classification issues could be addressed by the integration of relevant analysis methods into the annotation platform.
Long Abstract: Click Here

Poster C-36
Life with 22 amino acids
Hector Romero (Fac. Ciencias - UdelaR); Hector Musto (Fac. Ciencias - UdelaR); Vadim Gladyshev (University of Nebraska); Gustavo Salinas (Fac. Química - UdelaR);
Short Abstract: Selenocysteine (Sec) and pyrrolysine (Pyl) are two unusual amino acids co-traslationally incorporated. We analyze and compare Pyl and Sec decoding and particularly, we investigate especific features associated with Pyl synthesis and incorporation, making emphasis in their evolutionary aspects, and the implications for the genetic code evolution.
Long Abstract: Click Here

Poster C-37
Genome alignment with lineage-specific rearrangement and gene flux rates
Aaron E. Darling (Dept. of Computer Science, Univ. of Wisconsin-Madison); Bob Mau (Dept. of Animal Health and Biomedical Sciences, Univ. of Wisconsin-Madison); Nicole T. Perna (Dept. of Animal Health and Biomedical Sciences and Genome Center, Univ. of Wisconsin-Madison);
Short Abstract: We assess the relative rates of genome rearrangement, gene acquisition, gene loss, and nucleotide substitution among finished genome sequences from the family Enterobacteriacae. We find significant evidence for lineage specific mutation rates, and develop a new multiple-genome alignment method to account for the observed heterotachy.
Long Abstract: Click Here

Poster C-38
Comparison Between Complete Genomes of Vibrio Species
Patrícia P. Côgo (Institute of Computing, University of Campinas); João Meidanis (Institute of Computing, University of Campinas); Fabiano Thompson (Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro);
Short Abstract: This work proposes a methodology based on the “Genomic Rearrangement Theory” to compare complete genomes of vibrio species. In other words, our focus are large-scale mutations involving entire genes or blocks of consecutive genes, instead of events that affect individual bases.
Long Abstract: Click Here

Poster C-39
Evaluation of Brazilian web based program for classification of HIV-1 sequences
Luciano V Araujo (Department of Computer Science - Department of Computer Science - University of São Paulo); João E Ferreira (Department of Computer Science - University of São Paulo); Sabri S Sanabani (Fundação Pro-Sangue, Hemocentro, São Paulo, Brazil); Ester C Sabino (Fundação Pro-Sangue, Hemocentro, São Paulo, Brazil);
Short Abstract: An automated web based tool for assigning HIV-1 pure and recombinant subtypes within unaligned sequences is presented. The system combines the BLAST search algorithm and the recombination identification program for genetic subtyping of HIV-1. The softer was validated through combined analysis of simulated and other HIV-1 real data.
Long Abstract: Click Here

Poster C-40
Evaluating Orthology Detection Approaches in the Absence of a Gold Standard
Feng Chen (Biological Chemistry Graduate Program, University of Pennsylvania); Aaron J Mackey (Department of Biology, and Genomics Institute, University of Pennsylvania); Jeroen K Vermunt (Department of Methodology and Statistics, Tilburg University, Netherlands); David S Roos (Department of Biology, and Genomics Institute, University of Pennsylvania);
Short Abstract: Latent Class Analysis permits performance evaluation for multiple tests based on observed patterns of agreement. Applying this statistical methodology to various orthology identification methods reveals that INPARANOID, Orthostrapper, and OrthoMCL exhibit the best balance between sensitivity and specificity. OrthoMCL offers additional advantages of speed and applicability to multi-species datasets.
Long Abstract: Click Here

Poster C-41
Metamorphosis - Sorting by Weighted Inversions, Transpositions, and Inverted Transpositions
Martin Bader (University of Ulm); Simon Gog (University of Ulm); Enno Ohlebusch (University of Ulm);
Short Abstract: We have implemented a 1.5-approximation algorithm for Sorting by Weighted Reversals, Transpositions, and Inverted Transpositions. The algorithm can handle any weight ratio from 1:1 to 2:1 (transpositions:reversals). The algorithm performs very well in practice and is available as a web application.
Long Abstract: Click Here

Poster C-42
Anâtaxis, a Simple Deterministic Phylogenetic Reconstruction Algorithm
Bernhard Sonderegger (Département d'informatique, Université de Genève, Swiss Institute of Bioinformatics); Gabriel Bittar (Swiss Institute of Bioinformatics); Bastien Chopard (Département d'informatique, Université de Genève, Swiss Institute of Bioinformatics);
Short Abstract: We propose Anâtaxis, a simple phylogenetic tree reconstruction algorithm capable of analysing very large data-sets. Anâtaxis uses an intuitive two-step procedure to resolve the problems of variable rates of evolution and homoplasy. We show a biologically meaningful result and furthermore demonstrate the efficiency of each step using numerical methods.
Long Abstract: Click Here

Poster C-44
Bayesian Partitioning for Phylogenetic Footprinting
Yussanne Ma (Division of Molecular Biosciences, Imperial College London); Dr. Maria De Iorio ( Division of Epidemiology, Public Health and Primary Care, Imperial College London); Dr. Michael Stumpf (Division of Molecular Biosciences, Imperial College London);
Short Abstract: Reliable promoter prediction is one of the big challenges in bioinformatics today. Phylogenetic footprinting is a method which uses the property of evolutionary conservation of promoters to identify them through the comparison of distant species. We present a novel algorithm for phylogenetic footprinting which uses a Bayesian hierarchical framework combined with Markov chain Monte Carlo method. Our method uses Bayesian partitioning to estimate evolutionary rate variation along the DNA sequence.
Long Abstract: Click Here

Poster C-45
On the origin of microbial ORFans: Quantifying the strength of the evidence for viral lateral transfer
Yanbin Yin (University at Buffalo); Daniel Fischer (University at Buffalo);
Short Abstract: We provide evidence suggesting that lateral transfer from viruses alone is unlikely to explain the origin of the majority of microbial ORFans in the majority of prokaryotes. Consequently, other, not necessarily exclusive, mechanisms are likely to better explain the origin of the increasing number of ORFans.
Long Abstract: Click Here

Poster C-46
In-paralogs analysis of Insecta
Stanislav Vershenya (Bioinformatics, University of Wuerzburg); Joerg Schultz (Bioinformatics, University of Wuerzburg);
Short Abstract: In this work the in-paralogs of fruitfly, mosquito and honeybee were compared with each other. For every species we were able to identify expanded groups of genes and thus characterized the trends in the adaptational process. Furthermore, we found in-paralogs reflecting adaptations on the genome level of feeding pattern, scent, vision.
Long Abstract: Click Here

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Human Health

Poster D-1
Development of prediction system in TYPE 2 DIABETES using molecular epidemiological data
Ju-young Lee (nih,korea); Seung-Woo Shin (nih,korea); Seol-hee Bae (nih,korea); Keun-Joon Park (nih,korea); In Ae Hur (nih,korea); Jeoung Ho Cha (nih,korea); Haesook Min (nih,korea); Eun Ji Hwang (nih,korea); Keun yong Park (nih,korea); Hyun-Woo Han (nih,korea); Hang-Suk Choi (nih,korea);
Short Abstract: Finding high risk factors related Type 2 Diabetes(T2DM), we tried to optimizing model ; SVM and decision tree. Population–based 1145 cases and 1122 controls are selected. Using epidemic and genetic data, they are analyzed their association related T2DM. We suggest the genetic information in molecular epidemiological data might be useful for the classification of high risk of T2DM.
Long Abstract: Click Here

Poster D-2
A time series analysis tool for the analysis of neuronal activity in Parkinson disease
Patricio Yankilevich (Departmento de Ciencias de la Computación, Facultad de Ciencias Exactas y Naturales, Universidad de); Gustavo Murer (Departamento de Fisiología, Facultad de Medicina, Universidad de Buenos Aires); Luis Riquelme (Departamento de Fisiología, Facultad de Medicina, Universidad de Buenos Aires);
Short Abstract: We present a computational tool that integrates classic and novel graphical statistical methods to make a qualitative and quantitative analysis of neural activity signal recordings from in vivo rats with induced Parkinson disease, allowing systematically assessing neuronal behavior and detecting synchrony between firing patterns of neurons affected by Parkinson disease.
Long Abstract: Click Here

Poster D-3
Mixture Modeling in Fused Genotype and Phenotype Data
Benjamin Georgi (Max-Planck Institute for Molecular Genetics); M. Anne Spence (University of California at Irvine); Pam Flodman (University of California at Irvine); Alexander Schliep (Max-Planck Institute for Molecular Genetics);
Short Abstract: We present results from applying mixture model based clustering on a data set of ADHD patients. The data includes both geno- and phenotypic features and the interactions between these two sources of data will be one focus point of the analysis.
Long Abstract: Click Here

Poster D-4
Discovering cell dynamics in pancreas fibrosis by means of microarray gene expression profiling
Aenne Glass (Bioinformatics Core Facility, Medical Faculty, University of Rostock); Thomas Karopka (Bioinformatics Core Facility, Medical Faculty, University of Rostock);
Short Abstract: Comparing numbers of immediately versus belatedly regulated genes during activation of pancreatic stellate cells microarray gene expression profiling revealed the "e;delay"e; phenomenon. Cells pass an unexpected several days lag phase in stimulus response before they alter to fibrotic tissue. This aspect motivates for new anti-fibrotic therapeutic approaches in cancer research.
Long Abstract: Click Here

Poster D-5
Gene prioritization via genomic data fusion
Peter Van Loo (Human Genome Laboratory, Department of Human Genetics, Flanders Interuniversity Institute for Biotec); Stein Aerts (Laboratory of Neurogenetics, Department of Human Genetics, Flanders Interuniversity Institute for Bi); Diether Lambrechts (The Center for Transgene Technology and Gene Therapy, Flanders Interuniversity Institute for Biotech); Sunit Maity (The Center for Transgene Technology and Gene Therapy, Flanders Interuniversity Institute for Biotech); Bert Coessens (Bioinformatics group, K.U.Leuven ESAT-SCD); Frederik De Smet (The Center for Transgene Technology and Gene Therapy, Flanders Interuniversity Institute for Biotech); Leon-Charles Tranchevent (Bioinformatics group, K.U.Leuven ESAT-SCD); Bart De Moor (Bioinformatics group, K.U.Leuven ESAT-SCD); Peter Marynen (Human Genome Laboratory, Department of Human Genetics, Flanders Interuniversity Institute for Biotec); Bassem Hassan (Laboratory of Neurogenetics, Department of Human Genetics, Flanders Interuniversity Institute for Bi); Peter Carmeliet (The Center for Transgene Technology and Gene Therapy, Flanders Interuniversity Institute for Biotech); Yves Moreau (Bioinformatics group, K.U.Leuven ESAT-SCD);
Short Abstract: We developed a novel bioinformatics method, ENDEAVOUR, to prioritize candidate genes underlying pathways or diseases, based on similarity to genes known to be involved in these processes. ENDEAVOUR can fuse information from multiple heterogeneous data sources. We successfully validated ENDEAVOUR computationally, as well as in vitro and in vivo.
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Poster D-6
Analysis for Single nucleotide polymorphism related type 2 diabetes in insulin signaling pathway
Hang Suk Choi (NIH Korea); Seung-Woo Shin (NIH Korea); Eun Jung Jang (NIH Korea); Hyo-jeong Ban (NIH Korea); Keun-Joon Park (NIH Korea); Ji Hong Kim (NIH Korea); Chang-Bum Hong (NIH Korea); Sung-Hoon Lee (NIH Korea); Keun yong Park (NIH Korea); Hyun-Woo Han (NIH Korea); Ju-young Lee (NIH Korea);
Short Abstract: Genetic factors contribute to human disease interacted with environmental factors. Environmental factors are confound variable finding genetic factors. We controled variables which has influence on disease phenotype to analyze SNPs. And we compared with insulin resistant group and insulin sensitive group using HOMA-IR value. This result found 2 SNPs of INSR and 1 SNP of CBL and 1 SNP of PRIKCZ.
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Poster D-7
Exploratory analysis of multi-modal data including breast cancer microarray data
Christian Martin (Technical Faculty, Bielefeld University); Harmen grosse Deters (Technical Faculty, Bielefeld University); Tim W. Nattkemper (Technical Faculty, Bielefeld University);
Short Abstract: Data analysis in modern biomedical research has to integrate data from different sources, like microarray, clinical and categorical data, so called multi-modal data. The reef SOM, a metaphoric display, is applied and further improved such to allow the simultaneous display of biomedical multi-modal data for an exploratory analysis.
Long Abstract: Click Here

Poster D-8
Genome wide analysis of factors regulating gene expression in liver
Andreas Teufel (Department of Medicine I, Johannes Gutenberg University, Mainz, Germany); Arndt Weinmann (Department of Medicine I, Johannes Gutenberg University, Mainz, GermanyDepartment of Medicine I); Markus Krupp (Department of Medicine I, Johannes Gutenberg University, Mainz, Germany); Matthias Budinger (Institute of Medical Biometry, Epidemiology and Informatics (IMBEI), Johannes Gutenberg University,); Peter R Galle (Department of Medicine I, Johannes Gutenberg University, Mainz, Germany);
Short Abstract: We performed a genome-wide screen to identify genetic factors regulating gene expression in liver. We conclude that the existence of central factors in liver gene expression is unlikely and expression of individual genes in liver is more likely to be dependent on individual combinations of regulating factors for each gene.
Long Abstract: Click Here

Poster D-10
Gene Expression Profiling in Autoimmunity: Molecular Signatures of Systemic Lupus Erithematosus, Rheumatoid Arthritis and Type 1 Diabetes Mellitus
Guilherme Liberato Silva (Department of Genetics of Faculty of Medicine of Ribeirão Preto, University of São Paulo); Cristina Moraes Junta (Department of Genetics of Faculty of Medicine of Ribeirão Preto, University of São Paulo); Paula Sandrin Garcia (Department of Genetics of Faculty of Medicine of Ribeirão Preto, University of São Paulo); Diane Meyre Rassi (Department of Genetics of Faculty of Medicine of Ribeirão Preto, University of São Paulo); Eduardo A. Donadi (Department of Medicine of Faculty of Medicine of Ribeirão Preto, University of São Paulo); Geraldo Aleixo S. Passos Junior (Department of Genetics of Faculty of Medicine of Ribeirão Preto, University of São Paulo);
Short Abstract: Gene expression profiling can allow new insights on molecular pathogenesis of autoimmune diseases. Based on this assumption, we are using the cDNA microarray technology to trace hybridization signatures of systemic lupus erithematosus, rheumatoid arthritis and type 1 diabetes mellitus patients.
Long Abstract: Click Here

Poster D-11
From systems to symptoms: A combined genomics approach to expression-based breast cancer outcome prediction
Victor J. Weigman (Department of Biology, Program in Bioinformatics and Computational Biology, UNC-CH); Melissa Troester (Department of Pathology and Laboratory Medicine, UNC-CH); Xiaping He (Lineberger Comprehensive Cancer Center, UNC-CH); Chien-Hui Huang (Lineberger Comprehensive Cancer Center,UNC-CH); Charles M. Perou (Department of Pathology and Laboratory Medicine, Department of Genetics, Lineberger Comprehensive Ca);
Short Abstract: Headway has been made in the microarray realm to further stratify breast cancer patients into affect groups, which have significantly improved outcome prediction and response to therapy from traditional pathology. Incorporation of genome variant information would greatly assist this approach by providing biological evidence concordant with transcriptome analysis.
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Poster D-12
MOLECULAR HOMOLOGOUS MODELING OF 3B-HSD2 MUTANT ENZYME: STRUCTURE-FUNCTION ASPECTS OF PRO222GLN MUTATION CORRELATES WITH THE EXPERIMENTAL DATA FROM A PATIENT WITH CONGENITAL ADRENAL HYPERPLASIA.
LUCIO FABIO CALDAS FERRAZ (CBMEG, UNICAMP); FERNANDA SOARDI (CBMEG, UNICAMP); PAULA FALCÃO (EMBRAPA); GORAN NESHICH (EMBRAPA); MARICILDA PALANDI DE MELLO (CBMEG, UNICAMP);
Short Abstract: We describe the mutation Pro222Gln in HSD3B2 gene on a patient with congenital adrenal hyperplasia. Molecular modeling of 3B-HSD2 mutant allowed us to identify critical role of residue Pro222 on the folding pattern and catalytic activity of the enzyme. The proposed models correlate with the experimental data previously reported.
Long Abstract: Click Here

Poster D-13
Ad Hoc Biomedical Computational Tools: An Unfilled Niche
Craig R. Street (Biomedical Informatics Facility, Department of Pathology and Laboratory Medicine, University of Penn); David Wang (Biomedical Informatics Facility, Department of Pathology and Laboratory Medicine, University of Penn); David Birtwell (Biomedical Informatics Facility, Department of Pathology and Laboratory Medicine, University of Penn); Kevin Lux (Biomedical Informatics Facility, Department of Pathology and Laboratory Medicine, University of Penn); Alison W. Loren (Division of Hematology and Oncology, Department of Medicine, University of Pennsylvania, Philadelphi); Eline L. Prak (Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104); David Fenstermacher (Biomedical Informatics Facility, Department of Pathology and Laboratory Medicine, University of Penn);
Short Abstract: Biomedical Researchers are frustrated managing their data. Our facility at Penn is devising a unique approach in solving local problems. We are utilizing computational technologies to store, mine and retrieve data from genomic, proteomic, and molecular biology experiments. Our development is open-source and can be adopted by groups elsewhere.
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Molecular and Supramolecular Dynamics

Poster E-3
Analysis of Prion Protein: deeper understanding of protein motion from the molecular dynamics simulation
Masakazu Sekijima (Computational Biology Research Center / AIST); Chie Motono (Computational Biology Research Center / AIST); Yutaka Akiyama (Computational Biology Research Center / AIST); Tamotsu Noguchi (Computational Biology Research Center / AIST);
Short Abstract: We will present classification of local minim structures by molecular dynamics simulation. In our simulation, huge molecular dynamics trajectory data were obtained by Tera FLOPS computer (like Blue Gene and Earth Simulator). Our presentation will suggest that huge data are different from classical short range molecular dynamics simulation.
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Poster E-4
Mutational Effects on Calbindin D9k Investigated by Molecular Dynamics Simulations
Sérgio Modesto Vechi (Instituto de Química e Biotecnologia, Universidade Federal de Alagoas); Fernando Luis Barroso da Silva (Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo);
Short Abstract: Protein activity is related to its tertiary structure and intermolecular interactions. Theoretical site-directed mutagenesis can be used to probe the structure and dynamics of proteins. Here, we apply molecular dynamics simulations to explore the effects of mutations on calbinding in an explicit aqueous environment.
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Poster E-6
Flexibility adaptation of enzymes to low temperatures
Adrian Kalstein (Centro de Estudios e Investigaciones, Universidad Nacional de Quilmes); Sandra Maguid (Centro de Estudios e Investigaciones, Universidad Nacional de Quilmes); Gustavo Parisi (Centro de Estudios e Investigaciones, Universidad Nacional de Quilmes); Sebastian Fernandez-Alberti (Centro de Estudios e Investigaciones, Universidad Nacional de Quilmes);
Short Abstract: Psychrophiles organisms have evolved by producing cold-adapted enzymes that efficiently catalyze biochemical reactions at low temperatures. We report a systematic comparative analysis of flexibility profiles and rigid domains of pairs of homologous psychrophilic and mesophilic enzymes belonging to the structural families of xylanases, α-amylases, citrate synthase and, adenylate kinase.
Long Abstract: Click Here

Poster E-7
Sequence-structure-flexibility relationship in protein evolution.
Sandra Maguid (Centro de Estudios e Investigaciones, Universidad Nacional de Quilmes); Gustavo Parisi (Centro de Estudios e Investigaciones, Universidad Nacional de Quilmes); Sebastian Fernandez-Alberti (Centro de Estudios e Investigaciones, Universidad Nacional de Quilmes); Julian Echave (Instituto Nacional de Investigaciones Fisicoquimicas Teoricas y Aplicadas, Universidad Nacional de L);
Short Abstract: We study the evolutionary divergence of protein backbone dynamics by comparing the Cα flexibility profiles for a large dataset of homologous proteins classified into families and superfamilies. Proteins were structurally aligned and for each alignment we calculated sequence similarity (Id%), structural dissimilarity (RMSd) and different measures of backbone flexibility similarity.
Long Abstract: Click Here

Poster E-8
Dynamics of catalysis and inhibition in oligopeptidases: Natural peptide structures as promising antihypertensive agents.
Jorge H. Fernandez (Center of Applied Toxinology –Instituto Butantan, S.P., Brazil); Vanessa Rioli (Center of Applied Toxinology –Instituto Butantan, S.P., Brazil); Goran Neshich (Structural Bioinformatics Laboratory, CNPTIA – EMBRAPA, Campinas, S.P., Brazil); Emmer S. Ferro (Departamento de Biologia Celular e Desenvolvimento, ICB - USP, S.P., Brazil); Fernanda C. Portaro (Center of Applied Toxinology –Instituto Butantan, S.P., Brazil); Antonio C. M. Camargo (Center of Applied Toxinology –Instituto Butantan, S.P., Brazil);
Short Abstract: Molecular modeling, combined with docking and molecular dynamics experiments was used to study the dynamics of catalysis/inhibition in “druggable” human Oligopeptidases. The dynamics of ligand recognition and structural determinants for selective inhibition of these enzymes lead us to propose more selective oligopeptidase inhibitors with improved stability and pharmacological profile.
Long Abstract: Click Here

Poster E-9
Dynamical System Modeling of the Estrogen Transcription Control Network
Marcelo Ris (IME-USP); Junior Barrera (IME-USP); Helena Brentani (Hospital do Câncer);
Short Abstract: Identify the estrogen transcription control network, that is, modeling the relationships of the estrogen genes regulated. We adopt the PGN model and estimate its parameters from gene expression profiles, using the U-curve algorithm. Based on the relationships, we can group the genes in the different mechanisms of transcription control.
Long Abstract: Click Here

Poster E-10
Structural Comparative Studies of Brazilian HIV-1 Protease Mutants: Molecular Modeling and X-Ray Data
Paulo Ricardo Batista (IBCCF / UFRJ); Pedro A. G. Lapido Loureiro (IBCCF / UFRJ); Mario Sanches (Physics Department / USP / Sao Carlos); Igor Polikarpov (Physics Department / USP / Sao Carlos); Pedro Geraldo Pascutti (IBCCF / UFRJ);
Short Abstract: We exploit Molecular Modeling to perform structural comparative studies with Brazilian HIV-1 Protease mutants. Were built 3D models of each mutant and were played Molecular Dynamics simulations with the crystallographic structures in order to compare with the modeled ones, making possible analyze Molecular Modeling efficacy as structure predictor tool.
Long Abstract: Click Here

Poster E-11
Simulation of Amino Acid Solvation Structure in Transmembrane Helices and Implications for Membrane Protein Folding
Anna Johansson (Stockholm Bioinformatics Center, Stockholm University); Erik Lindahl (Stockholm Bioinformatics Center, Stockholm University);
Short Abstract: We report on extensive molecular dynamics simulations used to quantitativly study the atomic scale structure and dynamics of interactions between hydrophilic residues in transmembrane helices and the bilayer environment. The main conclusion is that hydrophilic residues retain solvation water in amounts that correlate well with experimental hydrophobicity scales.
Long Abstract: Click Here

Poster E-12
A Hierarchical Approach to Predict Protein Conformational Changes in terms of Localized Rearrangements using Temporal and Spatial Constraints
Arvind Ramanathan (Department of Computational Biology, Carnegie Mellon University); Tatyana Mamonova (Department of Chemistry, Carnegie Mellon University); Maria Kurnikova (Department of Chemistry, Carnegie Mellon University);
Short Abstract: Stability and fluctuations of non-covalent contacts (hydrogen bonds and hydrophobic contacts) within a protein play an important role in stabilizing its structure, defining its flexibility and, hence, function. Based on dynamical behavior of non-covalent contacts extracted from molecular dynamics we present an approach to predict global conformational motions.
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Ontologies

Poster F-1
Time-courses of gene expression during development of murine tooth germs by analysis of microarray data.
Harald Osmundsen (Univ. of Oslo); Maria (Landin); Steinar (Risnes);
Short Abstract: Analysis of microarray expression data from a series of microarrays, covering the duration of development of the murine tooth germ from 11.5-26.5dpc, has been used to describe time-courses of gene expression during development of this organ. Resulting data appears useful in assigning ontologies to observed, significant, changes in gene expression.
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Poster F-3
Protein Structure Homology Modelling assisted by Ontology
Kellen Pinagé (Computing Science Department, Federal University of Amazonas); Virgínia Brilhante (Computing Science Department, Federal University of Amazonas);
Short Abstract: Determining a protein 3D structure is fundamental to knowing its function. The Homology Modelling method applies knowledge reuse to determine protein structures. Improve the method by introducing an ontology to it and demonstrate that an ontology-based knowledge reuse technique is applicable to the protein structure prediction is the goal
Long Abstract: Click Here

Poster F-5
GOLIAS: Gene Ontology Library Analyzer for SAGE
Gustavo GL Costa (Universidade Estadual de Campinas- Hemocentro); Anderson Ferreira da Cunha (Universidade Estadual de Campinas- Hemocentro); Tarcísio de Souza Peres (Universidade Estadual de Campinas- Hemocentro); Tiago Ferraz Machado (Universidade Estadual de Campinas- Hemocentro); Fernando Ferreira Costa (Universidade Estadual de Campinas- Hemocentro);
Short Abstract: Retrieving information from SAGE experiments demands integration among tools, databases and protocols. We developed GOLIAS, a program that uses the Gene Ontology DAG structure to provide this integration and to automate the SAGE analysis. GOLIAS reports quantitative data about the sequenced tags, statistics and graph charts.
Long Abstract: Click Here

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Proteomics

Poster G-1
An Integrated Strategy In 2DE Maps Analysis For The Identification Of Potential Discriminants Between Different Clinical Conditions
Pattini L (Bioengineering Department, Polytechnic University of Milan, Milan, Italy); Cannistraci CV (Bioengineering Department, Polytechnic University of Milan, Milan, Italy); Conti A (Proteome Biochemistry, San Raffaele Scientific Institute, Milan, Italy); Iannaccone S (Neurology Department, San Raffaele Scientific Institute, Milan, Italy); Alessio M (Proteome Biochemistry, San Raffaele Scientific Institute, Milan, Italy); Cerutti S (Bioengineering Department, Polytechnic University of Milan, Milan, Italy);
Short Abstract: Through techniques of dimensionality reduction, the gels, described in terms of features opportunely defined to be informative and to tackle the problem of the intrinsic variability of the 2DE technology, are represented as items in a three dimensional space, where it is possible to appreciate segregations, coherent in respect of clinical conditions.
Long Abstract: Click Here

Poster G-2
Comparison of Gene Expression in Murine Retina by SAGE and 2D-PAGE
Tim Alcon (Bioinformatics and Computational Biology, Iowa State University); Heather West Greenlee (Biomedical Sciences, Iowa State University); Vasant Honavar (Computer Science, Iowa State University);
Short Abstract: Knowledge of gene expression can give insight into the networks of interactions active during development. We compare mRNA expression data from SAGE with protein abundance data from 2D-PAGE for five timepoints during the development of the murine retina. We find low overall correlation between mRNA abundance and protein abundance.
Long Abstract: Click Here

Poster G-3
Molecular mechanics studies of pyrophosphorylase, template enzyme involved in chitin metabolic pathway
Manoelito C. Dos Santos Junior (Programa de Pós-Graduação em Biotecnologia); Sandra A. Assis (Departamento de Saúde); Aristóteles Goes Neto (Departamento de Biologia); Sandra Helena Cruz (Universidade de São Paulo); Alex Guterres Taranto (Departamento de Saúde);
Short Abstract: Pyrophosphorylase of Crinipellis perniciosa (agent of witches’ broom disease) was sequenced, and a homologous protein (1JV1) was obtained from PDB with 50.1% sequence similarity. 1JV1 structure was refined using molecular mechanics methods and this will be used as a template to obtain the 3D model of pyrophosphorylase structure of C. perniciosa by comparative modeling approach.
Long Abstract: Click Here

Poster G-4
Sequence structure of the proteins based on the conservative elements
Yehoshua Sobolevsky (Genome Diversity Center, Haifa University); Edward N. Trifonov (Genome Diversity Center, Haifa University);
Short Abstract: The set of decamers which are present in at least 8 prokaryotic genomes of total 15 is selected. They are clustered into 200 groups of closely related decamers. For each group the set of proteins which contain decamer from a this group is described.
Long Abstract: Click Here

Poster G-6
Proteomics Approach for Exploring Sperm Antigens Involved in Epididymal Maturation
Amol R. Suryawanshi (Department of Gamete Immunobiology, National Institute for Research in Reproductive Health (ICMR), M); Shagufta A. Khan (Department of Gamete Immunobiology, National Institute for Research in Reproductive Health (ICMR), M); Priyanka P. Parte (Department of Gamete Immunobiology, National Institute for Research in Reproductive Health (ICMR), M); Vrinda V. Khole (Department of Gamete Immunobiology, National Institute for Research in Reproductive Health (ICMR), M);
Short Abstract: Using proteomics approach, several spots specific to epididymal sperm were identified. Of these, some spots were cored and are being sequenced. LC-MS/MS data will be used to decipher the identity as well as presence of human homologue using in silico approach. This approach will help in identifying epididymal proteins involved in sperm maturation and fertilization which could be used as post testicular targets for contraception or as markers for infertility diagnosis.
Long Abstract: Click Here

Poster G-7
Learning Classifiers for Assigning Protein Sequences to Subcellular Localization Families
Carson Andorf (Iowa State University); Drena Dobbs (Iowa State University); Vasant Honavar (Iowa State University);
Short Abstract: We explore machine learning approaches to build classifiers for protein subcellular localization prediction using a class conditional probabilistic representation of amino acid sequences. We combine these methods with a homology tool to develop HDTree. HDTree builds a classifier that outperforms current more computationally expensive methods used to predict subcellular localization.
Long Abstract: Click Here

Poster G-8
Prediction system for chemical structures of glycolipids using MALDI-TOF MS and MS/MS data.
Masahiro ITO (Department of Bioscience and Bioinformatics, Ritsumeikan University); Yuki Matsumuro (Department of Bioscience and Bioinformatics, Ritsumeikan University);
Short Abstract: A preliminary study of the prediction system of chemical structures of glycolipids using MALDI-TOF MS and MS/MS data is reported. The high accuracy of our system was confirmed with some known chemical structures of the glycolipid which had a normal chain type or two divergence type.
Long Abstract: Click Here

Poster G-9
Study on the role of bgl operon of E.coli in stationary phase
Ranjna Madan (Indian Institute of Science); S. Mahadevan (Indian Instiute of Science);
Short Abstract: We have found that the apparently cryptic bgl operon of Escherichia coli gives the organism a Growth Advantage in stationary phase.In order find out the function of this opeon, proteomics analysis is being carried out.
Long Abstract: Click Here

Poster G-10
Detection of post-translational modifications of proteins by mass shift decomposition in peptide mass fingerprints
Axel Rack (Max Planck Institute for Infection Biology); Peter R. Jungblut (Max Planck Institute for Infection Biology); Klaus-Peter Pleissner (Max Planck Institute for Infection Biology);
Short Abstract: Exhaustive prediction of post-translational modifications (PTMs) from peptide mass fingerprints is combinatorically demanding. We present an algorithm that identifies PTMs by decomposing mass differences between experimental and theoretical peaks over an alphabet of known PTM induced mass shifts that allows high numbers of PTMs to be searched in parallel.
Long Abstract: Click Here

Poster G-12
Beating the Noise: New Statistical Methods for Detecting Signals in MALDI-TOF Spectra below Noise Level
Tim OF Conrad (Free University of Berlin, Department of Mathematics and Computer Science); Alexander Leichtle (Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital); Andre Hagehuelsmann (Microsoft Research); Elmar Diederichs (Free University of Berlin, Department of Mathematics and Computer Science); Sven Baumann (Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital); Joachim Thiery (Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital); Christof Schuette (Free University of Berlin, Department of Mathematics and Computer Science);
Short Abstract: A new analysis workflow for MALDI-TOF massspectrometry data has been developed capable of identifying and analyzing signals (peaks) even below noise level and accurately determination of their parameters.We believe that this will foster identification of new biomarkers having not been detectable by most algorithms currently available.
Long Abstract: Click Here

Poster G-13
A Wrapper-based Approach for Protein Identification in PPI Networks
YongHo Lee (Electronics and Telecommunications Research Institute (ETRI)); JaeHun Choi (Electronics and Telecommunications Research Institute (ETRI)); MyungEun Lim (Electronics and Telecommunications Research Institute (ETRI)); SooJun Park (Electronics and Telecommunications Research Institute (ETRI));
Short Abstract: For the purpose of maintaining consistency of protein data among local databases, global databases, and PPI networks, we proposed a wrapper-based approach for protein identification in PPI networks. This method synchronizes a PPI network with a global database by identifying protein data of a global database using a wrapper.
Long Abstract: Click Here

Poster G-14
Storage, management and exchange of experimental and validated proteomics data considering HUPO-PSI standards
Klaus-Peter Pleissner (Max Planck Institute for Infection Biology , Berlin, Germany); Benjamin Arndt (University of Applied Sciences, Berlin, Germany); Daniel Paape (Max Planck Institute for Infection Biology , Berlin, Germany); Toni Aebischer (Max Planck Institute for Infection Biology , Berlin, Germany); Monika Schmid (Max Planck Institute for Infection Biology , Berlin, Germany); Robert Stein (Max Planck Institute for Infection Biology , Berlin, Germany); Peter R. Jungblut (Max Planck Institute for Infection Biology , Berlin, Germany);
Short Abstract: Comprehensive data management and intelligent data analysis are nowadays indispensable preconditions in proteomics research. By the investigation of the proteome of Leishmania mexicana amastigotes we demonstrate the versatile application of information management and databases for experimental and validated proteomics data considering the requirements of the HUPO-Proteome Standardization Initiative (PSI).
Long Abstract: Click Here

Poster G-15
Modified Random Forest Algorithm for Biomarker Identification in Clustered Mass Spectrometry Data
Yuliya Karpievitch (Dept. of Biostatistics and Applied Mathematics, M. D. Anderson Cancer Center, University of Texas); Elizabeth Hill (Dept. of Biostatistics, Bioinformatics and Epidemiology, Medical University of South Carolina); Timothy Millar (Dept. of Gastroenterology and Hepatology, Medical University of South Carolina); Adam Smolka (Dept. of Gastroenterology and Hepatology, Medical University of South Carolina); Jonas Almeida (Dept. of Biostatistics and Applied Mathematics, M. D. Anderson Cancer Center, University of Texas); Brenda Hoffman (Dept. of Gastroenterology and Hepatology, Medical University of South Carolina);
Short Abstract: We present a novel modification of the Random Forest (Breiman 2001) algorithm for biomarker identification in clustered or longitudinal data commonly seen in biological experiments. Clustered data are not independent identically distributed (iid) and are typically positively correlated, thus we provided enhancements to accommodate for explicit relationships between input parameters.
Long Abstract: Click Here

Poster G-16
Evaluation of predicted human protein networks
Mario Albrecht (Max Planck Institute for Informatics); Fidel Ramirez (Max Planck Institute for Informatics); Andreas Schlicker (Max Planck Institute for Informatics); Yassen Assenov (Max Planck Institute for Informatics); Hagen Blankenburg (Max Planck Institute for Informatics); Carola Huthmacher (Max Planck Institute for Informatics); Thomas Lengauer (Max Planck Institute for Informatics);
Short Abstract: We used recently published experimental datasets for the human interactome to assess the reliability of previously predicted protein-protein interactions and to compare prediction methods. In our comprehensive analysis, we found significant differences between the experimental and predicted human networks regarding prediction accuracy, functional consistency, information contents, and network topology.
Long Abstract: Click Here

Poster G-17
SuperQual: A tool to assess similarity of liquid chromatography mass spectrometry data
Lukas Mueller (IMSB); Markus Mueller (IMSB); Reto Ossola (IMSB); Ruedi Aebersold (IMSB);
Short Abstract: We have developed a novel software tool, SuperQual, to assess the reproducibility of LC/MS data. The application of SuperQual to a large dataset of LC/MS runs demonstrates how the software enables the quantification of data reproducibility and the detection of poor quality LC/MS runs.
Long Abstract: Click Here

Poster G-18
Comparative Assessment of Large-Scale Maps of the Human Protein Interactome
Matthias E. Futschik (Institute for Theoretical Biology, Humboldt-University); Gautam Chaurasia (Max-Delbrück-Centrum);
Short Abstract: We present here a first comparative assessment of different human protein-protein interaction networks. This analysis shows that the current maps have only a small, but nevertheless significant overlap. Furthermore, we detected intrinsic tendencies which are necessary to consider in future application of these maps.
Long Abstract: Click Here

Poster G-19
Identification of Thermostability in Microorganisms using Compression Algorithms
Van der Linden, M. G. (Laboratório Nacional de Computação Científica); Batista, L. V. (Universidade Federal da Paraíba); Farias, S. T. (Universidade Federal de Minas Gerais); Marques, J. R. T. (Universidade Federal da Paraíba);
Short Abstract: Popular data compression algorithms were applied to the problem of classifying microbial proteomes according to their optimal growth temperatures. The implications of the results are discussed for the problem of understanding patterns of protein sequences that relate to resistance of microbial proteins to extreme temperatures.
Long Abstract: Click Here

Poster G-20
Enhanced protein identification and gene annotation from MS/MS data
Jens Allmer (Institute for Plant Biochemistry and Biotechnology, Westfälische Wilhelms University, Münster, Germa); Bianca Naumann (Institute for Plant Biochemistry and Biotechnology, Westfälische Wilhelms University, Münster, Germa); Monica Zhang (Institute for Plant Biochemistry and Biotechnology, Westfälische Wilhelms University, Münster, Germa); Michael Hippler (Institute for Plant Biochemistry and Biotechnology, Westfälische Wilhelms University, Münster, Germa);
Short Abstract: A novel error tolerant computer algorithm is presented which enables high throughput proteomics data mining in genomic databases, using mass spectrometric data. This method successfully identifies peptides that are split by an intron when deduced from genomic DNA or originate from alternative splicing while adding confidence to the individual identifications.
Long Abstract: Click Here

Poster G-21
The iProXpress Knowledge System for Proteomic Studies
Hongzhan Huang (Georgetown University Medical Center); Zhang-Zhi Hu (Georgetown University Medical Center); Xin Yuan (Georgetown University Medical Center); Peter McGarvey (Georgetown University Medical Center); An Chi (University of Virginia); Satya Saxena (National Institute on Aging); Cathy H. Wu (Georgetown University Medical Center);
Short Abstract: iProXpress is an integrated system for proteomic and genomic analysis consisted of the PIR integrated protein information, analytical tools for sequence analysis and functional annotation, and a graphical user interface for categorization and visualization of expression data. This system has been successfully applied to several global profiling and functional analyses.
Long Abstract: Click Here

Poster G-22
From peptides - identified by mass spec - to biomolecular pathways
Claus A. Andersen (Sienabiotech SpA); Stefano Gotta (Sienabiotech SpA); Roberto Raggiaschi (Sienabiotech SpA); Andreas Kremer (Sienabiotech SpA); Eduardo Gonzalez Couto (Sienabiotech SpA); Rainer Kern (Sienabiotech SpA); Georg C. Terstappen (Sienabiotech SpA);
Short Abstract: Today several tools support protein identification by mass spec, but bringing the acquired experimental results into an improved understanding of the biomolecular pathways is missing. Grouping the MS identified proteins can support this step by connecting splice variants, paralogs, orthologs, homologs, GO functions etc. as presented here.
Long Abstract: Click Here

Poster G-23
Alignment-Independent Homology Estimator
Avihay Apatoff (The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University); Eddo Kim (The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University); Yossef Kliger (Compugen Ltd.);
Short Abstract: We present a method that estimates the fraction of homologs in a set of protein alignments. The method requires an abundant protein feature that is conserved among homologs (e.g. the N-terminal signal peptide). The method is beneficial for the development and assessment of homology search methods.
Long Abstract: Click Here

Poster G-24
Mapping epitope candidates from HIV-1 Brazilian sequences for vaccine Development
Artur T.L. Queiróz (LASP/CPqGM/FIOCRUZ, Salvador, Bahia, Brazil.); Luciane A. Santos (LASP/CPqGM/FIOCRUZ, Salvador, Bahia, Brazil.); Tulio de Oliveira (Oxford University, U.K.); Ramon Moreau (LASP/CPqGM/FIOCRUZ, Salvador, Bahia, Brazil.); Bernardo Galvão-Castro (LASP/CPqGM/FIOCRUZ, Salvador, Bahia, Brazil; FBDC/EBMSP, Salvador, Bahia, Brazil.); Luis Carlos Alcântara (LASP/CPqGM/FIOCRUZ, Salvador, Bahia, Brazil; FBDC/EBMSP, Salvador, Bahia, Brazil.);
Short Abstract: Epitope mapping presented on HIV proteins provide information for vaccine development. All Brazilian HIV sequences were collected from GenBank for epitope mapping. The HIVbase epitope mapping showed 30 CD8 and eight CD4 epitopes with high frequency. The objective of this work is perform molecular characterization of Brazilian HIV env sequences
Long Abstract: Click Here

Poster G-26
Bioinformatic analysis of Gluconacetobacter diazotrophicus proteome
Lery, LMS (IBCCF/UFRJ); von Kruger, WMA (IBCCF/UFRJ); Bisch, PM (IBCCF/UFRJ);
Short Abstract: A molecular analysis of the G. diazotrophicus metabolism was performed and we have mass-spectrometry identified more than 600 housekeeping and 50 regulated proteins, which could help validation of genome predicted ORFs and hypothetical proteins, assignment of non-predicted ORFs, start and stop codons definition, information about post-translational modifications and protein processing.
Long Abstract: Click Here

Poster G-27
IntAct - An extensible open source framework for molecular interactions
H. Hermjakob (EBI); S Kerrien (EBI);
Short Abstract: IntAct is an extensible open source framework for molecular interactions. The project aims at defining a standard for the representation and annotation of molecular interaction data and providing a public repository populated with experimental data from project partners and curated literature data. It contains more than 110.000 interactions and is available at http://www.ebi.ac.uk/intact
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Sequence Analysis

Poster H-1
Analysis of the Conservation of Regulation Systems in Firmicutes
Nicolas Sierro (The Institute of Medical Science, The University of Tokyo); Kenta Nakai (The Institute of Medical Science, The University of Tokyo);
Short Abstract: Recently, the number of sequenced bacterial genome has considerably increased, so that comparative analysis of bacterial promoters can provide new insight in the evolution of regulatory networks. Investigation of firmicute promoters was therefore carried out using the available sequenced genomes and the database of transcriptional regulation in Bacillus subtilis (DBTBS).
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Poster H-2
GINGA - Graphical INterface for comparative Genome Analysis
Alexandre Rossi Paschoal (LabInfo, LNCC); Marcelo Marques Zerillo (Institute of Biology, USP); Luiz Gonzaga Paula de Almeida (LabInfo, LNCC); Oberdan de Lima Cunha (LabInfo, LNCC); Ana Tereza Ribeiro de Vasconcelos (LabInfo, LNCC); Claudia Barros Monteiro-Vitorello (LabInfo, LNCC);
Short Abstract: We report a system for comparative analysis of one complete bacterial genome and one of a close species that is being partially sequenced. The system permit the mapping of end sequences, contigs and scaffolds onto the complete genome, identifying conserved blocks of synteny, specific regions, repeats, and rearrangements.
Long Abstract: Click Here

Poster H-3
Splice Form Prediction using Machine Learning
Gunnar.Raetsch@tuebingen.mpg.de (Friedrich Miescher Laboratory of the Max Planck Society); Sören Sonnenburg (Fraunhofer FIRST); Jagan Srinivasan (Caltech); Klaus-Robert Müller (Fraunhofer FIRST); Ralf Sommer (MPI Developmental Biology); Bernhard Schölkopf (MPI Biological Cybernetics);
Short Abstract: Accurate ab initio gene finding is still a major challenge in computational biology. We employ cutting edge machine learning similar to Hidden-Markov-SVMs to assay and improve the accuracy of genome annotations. We applied our system on the C_elegans genome and were able to drastically improve its annotation.
Long Abstract: Click Here

Poster H-4
Machine Learning Algorithms for Polymorphism Detection
Georg Zeller (Friedrich Miescher Laboratory of the Max Planck Society); Gabriele Schweikert (MPI Biological Cybernetics); Richard Clark (MPI Developmental Biology); Stefan Ossowski (MPI Developmental Biology); Norman Warthman (MPI Developmental Biology); Paul Shinn (The Salk Institute); Kelly Frazer (Perlegen Sciences Inc.); Joe Ecker (The Salk Institute); Daniel Huson (University of Tübingen); Detlef Weigel (MPI Developmental Biology); Bernhard Schölkopf (MPI Bilogical Cybernetics); Gunnar Rätsch (Friedrich Miescher Laboratory of the Max Planck Society);
Short Abstract: Based on high-density oligo-nucleotide array measurements and sophisticated machine learning methods, we obtain a genome-wide inventory of polymorphisms (including SNPs, deletions and highly polymorphic regions) in natural populations of Arabidopsis thaliana, representing an unprecedented resource for the study of genetic variation in a multicellular model organism.
Long Abstract: Click Here

Poster H-5
Accurate Global Alignment Statistics: An Application to Searching for Protein Domains
Maricel G. Kann (NCBI); Sergey L. Sheetlin (NCBI); Yonil Park (NCBI); Stephen H. Bryant (NCBI); John L. Spouge (NCBI);
Short Abstract: The most powerful approach for inferring function of protein sequences is the transfer of annotation using sequence comparison methods. This paper develops general, accurate statistical approximations for semi-global alignment and other biological applications, and in searching a protein domain database, its methods retrieved domains better than current local alignment methods.
Long Abstract: Click Here

Poster H-6
Regulatory Content of Vertebrate Enhancers
Altuna Akalin (Computational Biology Unit, Bergen Center for Computational Science, Univ. of Bergen, Norway); Boris Lenhard (Computational Biology Unit, Bergen Center for Computational Science, Univ. of Bergen, Norway);
Short Abstract: Long-range developmental enhancers in vertebrate genomes often coincide with highly conserved non-coding regions. We have devised a graph-based approach to discover regulatory information in such elements, and applied it to a collection of experimentally characterized enhancers to assign their expression patterns to specific motifs or combinations thereof.
Long Abstract: Click Here

Poster H-7
Classification of HCV Using Whole Genome Method
Raymond Wan (Gilead Sciences Inc.); Eugenia Bastos (SAS Institute);
Short Abstract: Q-gram is used in clustering procedures to generate a hierarchical tree for HCV genomes. A classifier is also built using the measure to classify sequences into subtypes, showing that q-gram can be very good measure of sequence similarity and it can be used effectively in clustering viral genomes.
Long Abstract: Click Here

Poster H-8
Prediction of Peptide Binding to MHC Class I Using Sliding Motifs and Regression Trees
Ana Paula Sales (Computational Biology and Bioinformatics Program, Duke University); Georgia D. Tomaras (Department of Surgery, Duke University Medical Center); Thomas B. Kepler (Department of Biostatistics and Bioinformatics, Duke University);
Short Abstract: Accurate prediction of peptide binding to Major Histocompatibility Complex class I molecules (MHCI) can accelerate vaccine development. We present a novel approach that integrates experimental and computational methods to elucidate the factors that affect MHCI-peptide binding and to identify potential epitopes for vaccines against pathogens causing emerging infectious diseases.
Long Abstract: Click Here

Poster H-9
Improved membrane protein topology prediction by domain assignments
Andreas Bernsel (Stockholm Bioinformatics Center, Stockholm University); Gunnar von Heijne (Department of Biochemistry and Biophysics, Stockholm University);
Short Abstract: We have identified a set of domains that, when found in soluble proteins, have conpartment-specific localization of a kind relevant for membrane protein topology prediction. Using these domains as prediction constraints, we are able to provide high-quality topology models for 11% of the membrane proteins extracted from 38 eukaryotic genomes.
Long Abstract: Click Here

Poster H-10
Successful clustering of ortholog groups by Bidirectional Best Hit (BBH) using organisms modeled from a single ancestral via stepwise mutation
Francisco Prosdocimi (UFMG); Maurício A Mudado (UFMG); J Miguel Ortega (UFMG);
Short Abstract: We set up for modeling synthetic CDS sequences aside their respective deduced proteins and an ancestral organism containing was created. Afterward, ten different organisms were modeled from the single ancestral via stepwise mutation. Results suggest that BBH driven clustering of ortholog groups seems to properly stand for homology searches.
Long Abstract: Click Here

Poster H-11
Hidden Markov Models for Gene Finding in Viral Genomes
Saskia de Groot (Department of Statistics, University of Oxford); Stephen McCauley (Department of Statistics, University of Oxford); Jotun Hein (Department of Statistics, University of Oxford);
Short Abstract: Viruses tend to code in overlapping reading frames. The constrictions forced upon multiple coding regions will result in atypical both codon bias and sequence evolution. Exploiting these latter constraints we present three different gene-finding HMMs – single, pairwise and EHMM – to annotate viral genomes coding in unidirectional overlapping reading frames.
Long Abstract: Click Here

Poster H-12
Regulatory motif discovery pipeline for co-regulated gene sets and chromatin-IP data: from motifs to functional instances.
Laurence Ettwiller (EMBL); Benedict Paten (EBI); Mirana Ramialison (EMBL); Ewan Birney (EBI); Jochen Wittbrodt (EMBL);
Short Abstract: We present a new pipeline for discovering overrepresented motifs in pulled-down sequences from Chromatin-IP. The signal is first evaluated using random samples and motifs that constitute the signal are retrieved. These motifs are clustered and PWM(s) built. Positions of functional instances are evaluated using conservation across species.
Long Abstract: Click Here

Poster H-13
Combined ab initio and comparative analysis of putative cis regulatory modules (CRMs)
Nora (Pierstorff); Rodrigo (Nunes da Fonseca); Casey (Bergman); Thomas (Wiehe);
Short Abstract: We have developed a method to predict cis-regulatory modules (CRMs) which identifies regions containing perfect local ungapped sequences based on multiple species comparison and overrepresentation of transcription factor binding sites without using prior information. Applied to a dataset of CRMs of Drosophila, our method outperforms all other methods tested.
Long Abstract: Click Here

Poster H-14
Markov Models of Genome Segmentation
Vivek Thakur (School of Information Technology, Jawaharlal Nehru University, India); R. K. Azad (Dept. of Biological Sciences, University of Pittsburgh, USA); R. Ramaswamy (School of Physical Sciences, Jawaharlal Nehru University, India);
Short Abstract: Entropic segmentation dissects the DNA sequences into compositionally homogeneous sequences and finds application in locating the boundaries of CpG islands, isochores etc. It however has limitations in resolving boundaries when tested for biological chimeric DNA sequences of different origin. To improve its performance we implemented Markovian approach and observed substantial rise in sensitivity and specificity.
Long Abstract: Click Here

Poster H-16
RASTA-Bacteria: a tool for the annotation of Toxin/Antitoxin modules in bacterial genomes
Emeric SEVIN (UMR6061-CNRS); Frédérique Barloy-Hubler (UMR6061-CNRS);
Short Abstract: Toxin-Antitoxin (TA) systems are major prokaryotic cell regulators during nutritional stress conditions, but they are poorly annotated. We developed RASTA-bacteria (Rapid Annotation for Systems of Toxin/Antitoxin in Bacteria), a tool that automatically identifies such systems in bacterial genomes, yielding a list of candidates ranked by expectation score.
Long Abstract: Click Here

Poster H-17
Construction of dephosphorylation site prediction system
Seong-Jin Park (Hanyang university); Soo-Young Cho (Hanyang university); Young-Seek Lee (Hanyang university);
Short Abstract: Predictions of possible sites of pholspholylation have been studied by many researchers. However, prediction research of dephosphorylation site contains little. We construt the dephosphorylation site prediction system and predicte signal transduction network. The prediction system information will allow biologists to easily retrieve extensive information about dephosphorylation signal transduction network.
Long Abstract: Click Here

Poster H-18
Evolution of the Inorganic Pyrophosphatase Family
Joel Hedlund (IFM Bioinformatics, Linköping university, Linköping, Sweden); Roberto Cantoni (CGB, Karolinska Institute, Stockholm, Sweden; Department of physical sciences, "Federico II" Univers); Margareta Baltscheffsky (Arrhenius Laboratories, Stockholm university, Stockholm, Sweden); Herrick Baltscheffsky (Arrhenius Laboratories, Stockholm university, Stockholm, Sweden); Bengt Persson (IFM Bioinformatics, Linköping university, Linköping, Sweden; CGB, Karolinska Institute, Stockholm, S);
Short Abstract: Inorganic pyrophosphatases contain ancient sequence motifs and produce energy through catabolism of pyrophosphate molecules, a mechanism thought to predate ATP driven cellular energy production. We have used bioinformatic methods to discover new family members, to study motifs and evolutionary relationships, and to identify potentially determining features for differences among subfamilies.
Long Abstract: Click Here

Poster H-19
Regular Expression Pattern Matching Using Suffix Array amd Its Application to Motif Search
Aki Hasegawa (Informatics Infrastructure Team, Genome Core Technology Facilities, Genomic Sciences Center, RIKEN); Akihiko Konagaya (Informatics Infrastructure Team, Genome Core Technology Facilities, Genomic Sciences Center, RIKEN);
Short Abstract: We present a fast regular expression pattern matching system using distributed suffix arrays. Our system enables to find out all occurrences of a pattern in seconds from massive sequences including human genome, nucleic acid, and amino acid. Performance of PROSITE patterns search from SwissProt and nr is measured and evaluated.
Long Abstract: Click Here

Poster H-20
A De Bruijn Subgraph Approach to Repeat Identification in Incompletely Sequenced Genomes
José Augusto Amgarten Quitzau (University of Bielefeld); Jens Stoye (University of Bielefeld);
Short Abstract: We present an approach for repeated regions identification that can also be applied for incompletely sequenced genomes. The approach is based on Pevzner and colleagues approach for genome assembly implemented in the Euler assembler. We conjecture that the approach may be extended to the de novo identification of repeat families.
Long Abstract: Click Here

Poster H-21
n-Nucleotide Frequency Analysis for Detecting Conserved String Pattern in Mus musculus Genome
Fumikazu KONISHI (RIKEN GSC); Aki Hasegawa (RIKEN GSC); Akihiko KONAGAYA (RIKEN GSC);
Short Abstract: We have developed a method of detecting conserved string pattern using a correlation coefficient of the progression of the recursive association of the substring frequencies among all the possible nucleotide sequence patterns within the specific size toward significant short nucleotide sequence detections.
Long Abstract: Click Here

Poster H-22
Protein solubility assessment using support vector machine
Pawel Smialowski (Technical University Muenchen); Antonio Martin-Galiano (Technical University Muenchen); Tobias Girschick (Technical University Muenchen); Dmitrij Frishman (Technical University Muenchen);
Short Abstract: We propose a machine-learning approach to sequence-based prediction of protein solubility in which we exploit subtle differences between proteins reported to be soluble and insoluble in TargetDB and PDB databases as well as in literature accounts. An overall prediction accuracy of 73% was achieved in a 10-fold cross-validation experiment.
Long Abstract: Click Here

Poster H-23
Are competitive tandem splice donors utilized to shift out-of-frame and trigger nonsense-mediated decay?
Ralf H. Bortfeldt (Friedrich Schiller University of Jena); Stefan Schuster (Friedrich Schiller University of Jena); Dirk Holste (Institute of Molecular Pathology Vienna);
Short Abstract: Alternative splicing (AS) is a central mode of genetic regulation, and the classification and subsequent characterization of patterns is the first step to obtain a global picture of AS exons. Here, we investigate whether alternative 5'ss exons might be produced by competitive tandem donor splice sites in the human genome.
Long Abstract: Click Here

Poster H-24
Characterization of putative chromosomal rearrangements related to chromosomes ends between Leishmania species. An in silico approach.
Patrícia de Cássia Ruy (FMRP/FFCLRP-USP); Loislena Oliveira Brito (FMRP-USP); Elton José Rosas de Vasconcelos (FMRP-USP); Raony Guimarães Correa do Carmo Lisboa Cardenas (FMRP/FFCLRP-USP); Ângela Kaysel Cruz (FMRP-USP); Jeronimo Conceição Ruiz (FMRP-USP);
Short Abstract: In this study we are characterizing genomic rearrangements at chromosome ends in Leishmania spp. This comparative analysis could contribute to the understanding of genetic diversity of parasites and the identification of patterns associated with the molecular evolution process. An analysis pipeline and preliminaries results of recombination events will be presented.
Long Abstract: Click Here

Poster H-25
ProtComp: Hybrid approach of predicting sub-cellular localization of animal, plants and bacterial proteins.
Victor Solovyev (Royal Holloway, University of London, Egham, Surrey,TW20 0EX, UK); Alexander Bachinsky (Softberry Inc., 116 Radio Circle, Suite 400, Mount Kisco, NY,10549,USA);
Short Abstract: We developed a group of programs, PortComp, for predicting protein sub-cellular localization. Three taxon-specific programs: for plant, animal, and bacterial proteins, use common general architecture. The test results show that ProtComp significantly outperforms other programs for predicting sub-cellular localization in both accuracy and number of compartments covered.
Long Abstract: Click Here

Poster H-26
Evolution of the Inorganic Pyrophosphatase Family
Joel Hedlund (IFM Bioinformatics, Linköping University, Linköping, Sweden); Roberto Cantoni (CGB, Karolinska Institute, Stockholm, Sweden; Department of Physical Sciences, "Federico II" Univers); Margareta Baltscheffsky (Arrhenius Laboratories, Stockholm University, Stockholm, Sweden); Herrick Baltscheffsky (Arrhenius Laboratories, Stockholm University, Stockholm, Sweden); Bengt Persson (IFM Bioinformatics, Linköping University, Linköping, Sweden; CGB, Karolinska Institute, Stockholm, S);
Short Abstract: Inorganic pyrophosphatases contain ancient sequence motifs and produce energy through catabolism of pyrophosphate molecules, a mechanism thought to predate ATP driven cellular energy production. We have used bioinformatic methods to discover new family members, to study motifs and evolutionary relationships, and to identify potentially determining features for differences among subfamilies.
Long Abstract: Click Here

Poster H-27
Predicting Nuclear Localization
John Hawkins (University of Queensland); Mikael Boden (University of Queensland);
Short Abstract: Predicting nuclear localization of proteins is complicated due to the diversity of targeting signals. Many nuclear proteins shuttle in and out of the nucleus. However, current nuclear localization predictors use exclusively nuclear localized proteins in their training sets. We present the first complete model for identifying nuclear localized proteins.
Long Abstract: Click Here

Poster H-28
On the the fidelity of assembly, binning and gene calling of metagenomes using simulated datasets
Konstantinos Mavromatis (Joint Genome Institute); Natalia Ivanova (Joint Genome Institute); Kerrie Barry (Joint Genome Institute); Harris Shapiro (Joint Genome Institute); Eugene Goltsman (Joint Genome Institute); Alice McHardy (IBM Thomas J. Watson Research Center.); Isidore Rigoutsos (IBM Thomas J. Watson Research Center.); Asaf Salamov (Joint Genome Institute); Frank Korzenieski (Joint Genome Institute); Miriam Land (Oak Ridge National Laboratory); Philip Hugenholtz (Joint Genome Institute); Nikos C Kyrpides (Joint Genome Institute);
Short Abstract: We constructed three synthetic metagenomic datasets of increased complexity by combining reads from a selection of 113 isolate genome sequencing projects available through the Joint Genome Institute. The datasets were used to evaluate assembly, binning and gene calling methods used for metagenomic analysis
Long Abstract: Click Here

Poster H-29
Gnomon - NCBI gene prediction tool for eukaryotic genomes
Alexander Souvorov (NCBI); Yuri Kapustin (NCBI); Boris Kiryutin (NCBI); Vyacheslav Chetvernin (NCBI); Tatiana Tatusova (NCBI); David Lipman (NCBI);
Short Abstract: We have developed a new gene prediction tool, Gnomon, for eukaryotic genome annotation. Gnomon constrains its core ab initio gene-finding algorithm using transcript and protein alignment data with a goal to minimize instances where a biological expert could generate an obviously improved gene model.
Long Abstract: Click Here

Poster H-30
Prediction of Transcription Factor Binding Sties by a Novel Computational Algorithm
Daekwan Seo (Virginia Commonwealth University); Moritoshi Yasunaga (University of Tsukuba); Insook Kim (University of Araknsas Medical Sciences); Jung H. Kim (University of Arkansas);
Short Abstract: The identification of transcription factor binding sites (TFBS) still remains a fundamental challenge in modern biology. The proposed algorithm predicts TFBS based on a hybrid Dynamic Programming combined with statistical method. We predicted experimentally verified TFBS and unknown but highly putative TFBS in each group of Dictyostelium gene sequences.
Long Abstract: Click Here

Poster H-31
Microarray Layout and the Quadratic Assignment Problem
Sergio A. de Carvalho Jr (Graduiertenkolleg Bioinformatik and International NRW Graduate School in Bioinformatics and Genome R); Sven Rahmann (Algorithms and Statistics for Systems Biology group, Genome Informatics, Technische Fakultät, Bielef);
Short Abstract: We propose a new model for evaluating the quality of oligonucleotide microarrays based on the arrangement of its probes. We show that the microarray design is an instance of the quadratic assignment problem (QAP) and present the results of using a QAP heuristic to design small artificial chips.
Long Abstract: Click Here

Poster H-32
Characterization of homogeneous and heterogeneous regions in the human genome and compositional features of individual chromosomes
Victor Sabbia (Laboratorio de Organización y Evolución del Genoma); Rosina Piovani (Laboratorio de Organización y Evolución del Genoma); Hugo Naya (Insituto Pasteur Montevideo); Hector Musto (Laboratorio de Organización y Evolución del Genoma);
Short Abstract: In the present work we A) describe the homogeneous vs heterogeneous categorization of long fragments along the human genome and the uneven distribution of genes between them. B) We show the results of a study of compositional correlations of individual chromosomes, their genes, introns and surrounding isochores.
Long Abstract: Click Here

Poster H-33
Probabilistic reasoning on occurrences of related binding site model matches
Rainer Pudimat (University of Freiburg); Rolf Backofen (University of Freiburg);
Short Abstract: We present a novel approach for modeling clusters of protein binding sites on nucleotide sequence (DNA, RNA). Single binding motifs are represented as PSSM-like Naive Bayes classifiers. These models are connected by probabilistic evaluating the fulfillness of logical expressions which describe the relations between models.
Long Abstract: Click Here

Poster H-34
An in silico and in vivo study on the Caulobacter crescentus SOS regulon
Apuã C. M. Paquola (Depto. de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São P aulo); Raquel P. Rocha (Depto. de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São P aulo); Rodrigo S. Galhardo (Depto. de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São P aulo); Carlos F. M. Menck (Depto. de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São P aulo);
Short Abstract: We have studied the composition of Caulobacter crescentus SOS regulon by computational prediction of LexA binding sites and posterior real-time PCR evaluation of candidate genes. We observed a remarkable correlation between predicted LexA box distance from start codon and level of SOS induction.
Long Abstract: Click Here

Poster H-35
Identifying functional domains in a family of restriction endonucleases where DNA recognition, methyltransferase and endonuclease functions reside in a single polypeptide.
Richard D. Morgan (New England Biolabs);
Short Abstract: Restriction-Modification systems of the MmeI family consist of a single polypeptide performing DNA recognition, DNA methylation and DNA cleavage. We speculate these enzymes use a single DNA recognition domain to mediate both methylation and endonuclease functions. Replacing the recognition domain may allow engineering endonucleases with new DNA specificity.
Long Abstract: Click Here

Poster H-36
Sequence Comparison by Sequence Harmony Identifies Sub-type Specific Sites for Smad Receptor Binding
Walter Pirovano (IBIVU, Free University Amsterdam); K. Anton Feenstra (IBIVU, Free University Amsterdam); Jaap Heringa (IBIVU, Free University Amsterdam);
Short Abstract: We introduce a new entropy-based method, called Sequence Harmony, to accurately detect subclass-specific positions based on compositional differences. Applying the method on the Smad-family of TFs yields 40 sites of which 26 have a known function. Structural considerations led to the assignment of a putative function of 11 more sites.
Long Abstract: Click Here

Poster H-37
TreeDomViewer: A tool for the visualization of phylogeny and protein domain structure
Blaise T.F Alako (Laboratory of Bioinformatics, Wageningen University); Daphne Rainey (Keygene NV); Harm Nijveen (Laboratory of Bioinformatics, Wageningen University); Jack A.M. Leunissen (Laboratory of Bioinformatics, Wageningen University);
Short Abstract: TreeDomViewer is a biological web-based visualization tool that combines a phylogenetic tree, sequence alignment and InterProScan analysis of sequences and generates a phylogenetic tree projecting the predicted protein domains onto the multiple sequence alignment. TreeDomViewer is a valuable addition to the annotation pipeline of unknown gene or gene product. Availability: http://www.bioinformatics.nl/tools/treedom/
Long Abstract: Click Here

Poster H-38
A Motif Sampler for the Discovery of Conserved Motif Pairs with Periodic Spacing
Erik Larsson (Department of Biomedicine, Göteborg University); Olle Nerman (Department of Mathematical Statistics, Chalmers University of Technology); Per Lindahl (Department of Biomedicine, Göteborg University);
Short Abstract: Due to the turning DNA helix, distances between binding sites within cis-regulatory modules sometimes have periodic properties. We propose a motif discovery tool based on Gibbs sampling which finds motifs pairs with periodic spacing. Evaluation on simulated datasets demonstrates increased sensitivity compared to single motif and colocalization models.
Long Abstract: Click Here

Poster H-39
Comparative structure-based analysis of amino acid composition in proteins adapted to cold and hot environments
Gisle Sælensminde (University of Bergen); Inge Jonassen (University of Bergen);
Short Abstract: We present a methodology for performing comparative analysis of amino acid composition of homologous proteins in species adapted to different temperatures. It allows inclusion of structural information enabling differentiation between protein core and surface. We present an analysis showing clear trends in proteins adapted to cold environments.
Long Abstract: Click Here

Poster H-40
GFMerge - A method for merging of gene predictions
Sebastian Spiegler (Technical University Ilmenau, Germany; Wellcome Trust Sanger Institute, Cambridge, UK); Marie-Adele Rajandream (Wellcome Trust Sanger Institute, Cambridge, UK); Neil Hall (The Institute for Genomic Research (TIGR), Maryland, USA); Kim Rutherford (Genetics Department, Cambridge University, UK); Arnaud Kerhornou (Genome Bioinformatics Research Group, Barcelona, Spain);
Short Abstract: Genome data from large-scale sequencing is primarily scanned for possible genes using gene prediction programs. Results often contradict each other in structure and location. "GFMerge" calculates a single consensus of non-overlapping high-quality predictions. Within an internal hierarchical scoring system it uses additional similarity information, considers gene structure and evaluates each gene prediction program.
Long Abstract: Click Here

Poster H-41
Large-scale detection of mutations potentially responsible of genetic disorders
Kais Ghedira (Institute Pasteur of Tunis); Walid Bedhiafi (Institut Pasteur de Tunis); Hela Ouaili (Ecole de Supérieure des Statistique et de l'Analyse de l'Information); Koussay Dellagi (Institute Pasteur of Tunis); Alia Benkahla (Institute Pasteur of Tunis);
Short Abstract: The scientific challenge of the present analysis is to extract meaningful and realistic hypotheses about links between mutations and human genetic disorders by taking advantage of all knowledge and data available in public databases.
Long Abstract: Click Here

Poster H-42
Discriminatory features of sequence profiles for transcription factor binding site discovery
Gerald Quon (Department of Biochemistry, University of Toronto); Shoshana Wodak (Structural Biology and Biochemistry, The Hospital for Sick Children);
Short Abstract: Transcription factor binding site (TFBS) prediction methods typically report a high rate of false-positive motifs. Using novel information content profile-based features, our method discriminates true- and false-positive motifs from yeast with an overall accuracy of 90%. Furthermore, we demonstrate significant improvement in predictions in a set of synthetic mammalian datasets.
Long Abstract: Click Here

Poster H-43
Vector Graphics to improve Blast graphic representations
Rafael Jimenez (NBN);
Short Abstract: Vegra Blast is a Python Object Orientation Library based in BioPython to yield graphical visualization results for Blast utilizing Vector Graphics. Vegra is not just an improvement for blast visualization but a model of how other visualization approaches could be developed.
Long Abstract: Click Here

Poster H-44
“Co-transcriptional” prediction of splice sites and analysis of spliceosomal introns in human pre-mRNAs
Kai Wang (Center for Biological Sequence Analysis, Biocentrum, Technical University of Denmark); Rasmus Wernersson (Center for Biological Sequence Analysis, Biocentrum, Technical University of Denmark); Søren Brunak (Center for Biological Sequence Analysis, Biocentrum, Technical University of Denmark);
Short Abstract: We developed a new prediction program to detect splice site, including alternative splice sites, by combining neural networks. We presented a detailed review of various anticipated and novel statistical features of exon-intron structures, splicing enhancers and silencer, ultra-conserved elements, and pseudogenes in human to enhance our understanding of the many intriguing questions in different splicing scenarios. We also investigated the spliceosomal intron evolution on co-transcriptional splicing processes.
Long Abstract: Click Here

Poster H-45
yrGATE: Web Based Community Gene Annotation for Eukaryotes
Matthew Wilkerson (Department of Genetics, Development, and Cell Biology, Iowa State University); Shannon Schlueter (Department of Genetics, Development, and Cell Biology, Iowa State University); Volker Brendel (Department of Genetics, Development, and Cell Biology and Department of Statistics, Iowa State Unive);
Short Abstract: Your Gene structure Annotation Tool for Eukaryotes (yrGATE) provides an Annotation Tool and Community Utilities for web based community gene annotation. Annotators can evaluate gene evidence through several methods. yrGATE is appropriate for annotating emerging genomes and correcting inaccurate published annotations. yrGATE is portable and is available at http://www.plantgdb.org/prj/yrGATE.
Long Abstract: Click Here

Poster H-46
Telomerase RNA searching using an Infernal-based pipeline
Ariane Machado Lima (Instituto de Matemática e Estatística, Universidade de São Paulo); Sean R. Eddy (Department of Genetics, Washington University); Hernando A. del Portillo (Instituto de Ciências Biomédicas II, Universidade de São Paulo); Alan Mitchell Durham (Instituto de Matemática e Estatística, Universidade de São Paulo);
Short Abstract: Infernal is a tool that builds RNA probabilistic models from structural multiple alignments. We are developing an Infernal-based pipeline to search telomerase RNAs. In this work we make a preliminary assessment of this pipeline and of the phylogenetic reach of the vertebrate TERC alignment through cross-validation technique.
Long Abstract: Click Here

Poster H-47
Development of an integrated Comparative Genomics environment
Hamilton Ganesan (Bioinformatics, University of Pretoria); Fourie Joubert (Bioinformatics, University of Pretoria);
Short Abstract: The recent spurt in sequence availability has sparked the era of comparative genomics (CG). Many stand-alone CG tools are available but there is no common environment existing to integrate available software. This project aims to integrate existing CG software into a common environment enabling streamline and efficient CG studies.
Long Abstract: Click Here

Poster H-48
Chaos Game Representation and Vector Quantization (CGR-VQ): a new computational tool for the identification of transcription factor binding sites
Dominik Beck (Biomathematics Group, ITQB-UNL / INESC-ID); Jonas S Almeida (Dept Biostatistics and Applied Mathematics, Univ. Texas MDAnderson Cancer Center / Biomathematics Gr); Ana Teresa Freitas (IST/ INESC-ID); Arlindo L. Oliveira (IST/ INESC-ID); Susana Vinga (INESC-ID /FCM-UNL);
Short Abstract: A new computational methodology for the Identification of Transcription Factor Binding Sites in DNA promoter regions is presented. This algorithm combines Chaos Game Representation and cluster analysis using Vector Quantization. This technique was tested on real and artificial datasets, showing good agreement with biological knowledge and other motif finding algorithms.
Long Abstract: Click Here

Poster H-49
New EST trimming procedure applied to SUCEST sequences
Christian Baudet (Institute of Computing - Unicamp); Zanoni Dias (Institute of Computing - Unicamp);
Short Abstract: In order to improve EST trimming, we proposed a new set of procedures to detect regions that do not belong to the sequenced organism. We evaluated the proposed method using SUCEST ESTs. Based on the results, we concluded that our method suits projects that want to produce more reliable clusters.
Long Abstract: Click Here

Poster H-50
M-Coffee: combining multiple sequence alignment methods with T-Coffee.
Iain Wallace (University College Dublin,Ireland); Orla OSuillivan (University College Dublin,Ireland); Desmond Higgins (University College Dublin,Ireland); Cedric Notredame (Laboratoire Information Génomique et Structurale, CNRS Marseille,France);
Short Abstract: We introduce M-Coffee, an extension of T-Coffee, a meta-method for assembling multiple sequence alignments (MSA) by combining the output of several individual methods into one single MSA. M-Coffee outperforms all the individual methods on three major reference datasets: HOMSTRAD, Prefab and Balibase.
Long Abstract: Click Here

Poster H-51
Constrained Alignment Using Cluster Tree Elimination
Sebastian Will (University of Freiburg); Anke Busch (University of Freiburg); Rolf Backofen (University of Freiburg);
Short Abstract: We revisit sequence comparison with side constraints. Often, when prior knowledge about the molecules is available, it is desirable to incorporate this information into the alignment. We introduce a constraint-based approach that allows for easy integration of various kinds of additional information, while preserving the efficiency of dynamic programming.
Long Abstract: Click Here

Poster H-52
Web Based Computational Tools for Predicting G-quadruplexes in Mammalian Genes
Oleg Kikin (Ramapo College of NJ); Rumen Kostadinov (University of Pennsylvania); Nishtha Malhotra (Ramapo College of NJ); Manuel Viotti (Ramapo College of NJ); Lawrence DAntonio (Ramapo College of NJ); Paramjeet S. Bagga (Ramapo College of NJ);
Short Abstract: Highly stable G-quadruplex structures formed by guanine rich nucleic acids have recently come into limelight because of their potential role in biologically important processes, including regulated RNA processing. We have developed a suite of web based computational tools for predicting G-quadruplexes and studying their distribution patterns in mammalian genes.
Long Abstract: Click Here

Poster H-53
Using latent semantic indexing (LSI) to evaluate the similarity of sets of sequences without multiples alignments character-by-character
Braulio RGM Couto (UNI-BH); Ana Paula Ladeira (UNI-BH);
Short Abstract: We present an algorithm that estimates relatedness between large numbers of biomolecules without the requirement of multiples alignments. Proteins recoded as n-peptide frequency values using all possible overlapping n-peptides, which generates a matrix, reduced by SVD. Cosine and Euclidean distance between proteins vectors are used as similarity measure.
Long Abstract: Click Here

Poster H-54
Software usage testing for studies of genetic variability in marine shrimp aquaculture
Michel Toth Kamimura (NUGEN-UECE); Samara Cardoso da Silva (NUGEN-UECE); Fátima de Cássia Evangelista de Oliveira (NUGEN-UECE); Sara Ramos Medeiros (NUGEN-UECE); Daniel Pascoalino Pinheiro (NUGEN-UECE); Rodrigo Maggioni (NUGEN-UECE); Diana Magalhães de Oliveira (NUGEN-UECE);
Short Abstract: An application was performed in order to test the GeneMapper® software v3.7 (Applied Biosystems) in the development of a genetic improvement program in Northeastern Brazil marine shrimp farms. Results are interesting for helping to implement rational breeding programs, contributing even for more general population genetic studies.
Long Abstract: Click Here

Poster H-55
HMM-based subsequence feature map for Protein Classification and Remote Homology Detection
Omer Sinan Sarac (Dept. of Computer Engineering, Middle East Technical Univeristy); Volkan Atalay (Dept. of Computer Engineering, Middle East Technical Univeristy); Rengul Cetin-Atalay (Dept. of Molecular Biology and Genetics, Bilkent Univeristy);
Short Abstract: This study represents a feature mapping for protein sequence classification that uses the models of conserved regions in proteins. An kmeans-like algorithm with an HMM map is used to cluster the subsequences and learn the models of these regions from a given family of proteins in an unsupervised manner.
Long Abstract: Click Here

Poster H-56
ARTS: Accurate Recognition of Transcription Starts
Sören Sonnenburg (Fraunhofer FIRST); Alexander Zien (MPI for biological Cybernetics and Friedrich Miescher Laboratory); Fabio de Bona (Friedrich Miescher Laboratory); Gunnar Rätsch (Friedrich Miescher Laboratory);
Short Abstract: We present ARTS, a novel method for accurate recognition of transcription start sites in several species. Large scale training of a complex model is enabled by rapid kernel computations with suffix tries. In carefully designed experiments, we show that ARTS considerably outperforms recently published methods (for instance McPromotor and FirstEF).
Long Abstract: Click Here

Poster H-57
Construction of multiple transcription factor prediction system
Min-Young Park (Hanyang university); Soo-Young Cho (Hanyang university); Young-Seek Lee (Hanyang university);
Short Abstract: Gene expression in mammalian cells is regulated by colplicated function of multiple transcription factor(TF)s. In this study, we developed prediction system for putative function of multiple TFs in the promoter regions of known genes. Prediction algorithm was prepared using Markov chain(MC) and Greedy algorithm.
Long Abstract: Click Here

Poster H-58
An Automated Combination of Sequence Motif Kernels for Protein Subcellular Localization
Alexander Zien (MPI for Biological Cybernetics); Cheng Soon Ong (Friedrich Miescher Laboratory and MPI for Biological Cybernetics);
Short Abstract: We propose an elegant multiclass prediction approach for protein subcellular localization. First we define a family of protein sequence kernels which consider variable length motifs with gaps. Second, we generalize the multiclass SVM to automatically optimize over multiple kernels. We compare to other subcellular localization predictors on different protein datasets.
Long Abstract: Click Here

Poster H-59
XGrid Implementation of the InterProScan for the Epichloe festucae Genome Project
Wayne E. Beech (Computing Services, University of Kentucky); V. Cody Bumgardner (Department of Computer Science, University of Kentucky); Uliana Hesse (Plant Pathology, University of Kentucky); Ch. David Van Horn (Department of Computer Science, University of Kentucky); Jerzy W. Jaromczyk (Department of Computer Science, University of Kentucky); Christopher Schardl (Plant Pathology, University of Kentucky);
Short Abstract: We present our XGrid implementation for InterProScan needed in determining the complete sequence of a model endophyte, Epichloe festucae, commonly found in grasses of genera Lolium (ryegrasses) and Festucae (fescues). Preliminary results indicate a phenomenal decrease in genome annotation time as we observe an almost linear speedup.
Long Abstract: Click Here

Poster H-60
Improvements in ELM Resource Filtering and Web Service Technology Implementation
Claudia Chica (EMBL); Kate Gould (EMBL); Allegra Via (University of Rome Tor Vergata); Jan Christian Bryne (Bergen Centre for Computational Science); Francesca Diella (EMBL); Pal Puntervoll (Bergen Centre for Computational Science); Rein Aasland (University of Bergen); Manuela Helmer-Citterich (University of Rome Tor Vergata); Toby Gibson (EMBL);
Short Abstract: ELM predicts functional sites in eukaryotic proteins. Overprediction is limited by biological context information filtering. By refinement of the structural filter and the addition of conservation filtering, the predictive power of ELM can be greatly improved. Grid technology implementation is in progress to aid extensibility and interoperability of the tool.
Long Abstract: Click Here

Poster H-61
Identification of replication origins in archaea using a moving window model along the double strands
Yonghong Wang (Department of Physics, Tianjin University, Tianjin, 300072, China; School of Computer Science and I); Xiaolei Liu (Department of Physics, Tianjin University, Tianjin, 300072, China);
Short Abstract: A new method has been developed to identify replication origins in prokaryotic genomes based on a moving-window model along double strands. Two curves corresponding to base distribution in two DNA strands, intersect at replication origins. The approach can be used to identify single and multiple replication origins in archaea.
Long Abstract: Click Here

Poster H-62
Chisel - a Framework for Identification and Characterization of Taxonomic and Phenotypic Versions of Enzymes
Alexis Rodriguez (Argonne National Laboratory); Yi Zhang (Argonne National Laboratory); Natalia Maltsev (Argonne National Laboratory); Elizabeth Marland (Argonne National Laboratory);
Short Abstract: Chisel is a bioinformatics environment that supports both automated and expert-driven identification, characterization and comparative analysis of taxonomic and evolutionary variations of enzymes. Application of Chisel for the needs of biomedical research, bioremediation, high-throughput analysis of genomes and metagenomes will be discussed.
Long Abstract: Click Here

Poster H-64
Precisely Mapping Structural Variations in the Human Genome by Splitting Shotgun Reads
Zemin Ning (The Wellcome Trust Sanger Institute);
Short Abstract: We have developed a new computational method to detect structural variations by splitting shotgun reads against the reference sequence. A total number of 7,293 structural variants have been identified: 2,500 deletions, 2,358 insertions and 2,435 VNTRs, using 44 million shotgun reads from 10 different individuals
Long Abstract: Click Here

Poster H-65
DP-BIND: a sequence-based application of multiple machine learning methods to predict DNA-binding sites in DNA-binding proteins.
Igor Kuznetsov (University at Albany); Seungwoo Hwang (University at Albany); Zhenkun Gou (University at Albany);
Short Abstract: An application of three machine-learning methods to sequence-based prediction of DNA-binding sites in a DNA-binding protein. The performance of our predictors is better than that of other sequence-based methods. Outputs of the three individual methods are combined into consensus prediction to further improve performance.
Long Abstract: Click Here

Poster H-66
Analyzing the effects of generalizations implicit within the BLAST algorithm
Mileidy Gonzalez (University of Maryland Baltimore County); Stephen J. Freeland (University of Maryland Baltimore County);
Short Abstract: We have mapped the entire network of simplifying mathematical assumptions used by the BLAST algorithm (the most widely-used pairwise sequence comparison method) to identify the properties of unusual, natural sequences that could compromise the program's reliability. We present preliminary data that evaluates the magnitude of potential problems.
Long Abstract: Click Here

Poster H-67
Decomposition of DNA Sequences into Hidden Components: Applications to Human Genome's Promoter Recognition
Yasuo Matsuyama (Waseda University); Kenji Onuki (Waseda University); Youichi Ito (Waseda University); Yugo Ishihara (Waseda University); Kouhei Kawasaki (Waseda University); Takayuki Hasegawa (Waseda University);
Short Abstract: Decomposition of discrete-symbol biosequences into hidden components is discussed. Presented methods are based upon the principal component analysis and the independent component analysis. The decomposition procedure is described and tested on human genome's promoters and other specific sites to show better recognition scores than traditional non-decomposing methods.
Long Abstract: Click Here

Poster H-68
A Comparison a New Genetic Algorithm With Existing Methods For Determining a Consensus Sequence
Josh W Gilkerson (University of Kentucky, Dept. of Computer Science); Dr. Jerzy W. Jaromczyk (University of Kentucky, Dept. of Computer Science);
Short Abstract: We present two original methods for finding consensus sequences and compare them with existing algorithms. Experimental tests are performed on both synthetic data and sequences taken from biological sources. The algorithms construct high quality consensus sequences -- superior to other methods -- in particular for repeat elements in the Magnaporthe grisea genome.
Long Abstract: Click Here

Poster H-69
On the Quality of Motifs for Protein Phosphorylation Site Prediction
Yasser EL-Manzalawy ( Artificial Intelligence Laboratory, Department of Computer Science, Iowa State University); Cornelia Caragea ( Artificial Intelligence Laboratory, Department of Computer Science, Iowa State University); Drena Dobbs (Department of Genetics, Development and Cell Biology, Bioinformatics and Computational Biology Gradu); Vasant Honavar (Artificial Intelligence Laboratory, Department of Computer Science, Bioinformatics and Computationa);
Short Abstract: Motif-based bioinformatics tools allow users to set threshold values for specific motifs, even though users may not know how these values affect performance. We propose statistical measures for assessing "motif quality" and the relationship between p-values and true positive rate, using phosphorylation site prediction as a test case.
Long Abstract: Click Here

Poster H-70
Computational identification of structural variation in genomes
David Fredman (Bergen Center for Computational Science); Boris Lenhard (Bergen Center for Computational Science);
Short Abstract: We present a new approach to explore structural variation (duplication, deletion, inversion) in annotated genomes. Our algorithm classifies sequence as prone to structural variation based on sequence attributes. We provide a detailed view of genomic features associated with structural variation and novel sites for targeted identification in the laboratory.
Long Abstract: Click Here

Poster H-71
A composite benchmark for local gapped alignments and scoring systems based on extended alphabets
Lorenzo Cerutti (Swiss Institute of Bioinformatics); Marco Pagni (Swiss Institute of Bioinformatics);
Short Abstract: We setup a benchmark to provide a complete evaluation of the scoring system for local alignment algorithms. We describe a general framework to extend standard amino acid alphabet with predicted information, which combined to our benchmark, permits to design new and more performing scoring systems rationally.
Long Abstract: Click Here

Poster H-72
MAVIANT – a Multi-purpose Alignment VIewing and (SNP) Annotation Tool
Panitz, F (Dept. Genetics and Biotechnology, Danish Institute of Agricultural Sciences); Stengaard, H (Dept. Genetics and Biotechnology, Danish Institute of Agricultural Sciences); Bendixen, C (Dept. Genetics and Biotechnology, Danish Institute of Agricultural Sciences);
Short Abstract: MAVIANT, a platform-independent Multi-purpose Alignment VIewing and (SNP) Annotation Tool, was designed for large-scale SNP mining projects. In addition to chromatogram and alignment views MAVIANT facilitates manual annotation, which is stored directly in an integrated database. The annotations are immediately accessible and can be easily shared with external collaborators.
Long Abstract: Click Here

Poster H-73
Unusually Large Conserved Syntenic Blocks at the Vertebrate Hox loci are associated with Conserved Regulatory Elements Within and Outside Hox clusters
B.Venkatesh (Institute of Molecular and Cell Biology); Alison Lee (Institute of Molecular and Cell Biology); Esther E.G.L. Koh (Institute of Molecular and Cell Biology); Alice Tay (Institute of Molecular and Cell Biology); Sydney Brenner (Institute of Molecular and Cell Biology);
Short Abstract: By comparative analysis of human, mouse and fugu Hox loci we have uncovered unusually large evolutionary conserved syntenic blocks (up to 5.2 Mb) at these loci. Conserved putative regulatory elements spread over large regions are likely to be the evolutionary constraint that has maintained the exceptionally long syntenic blocks.
Long Abstract: Click Here

Poster H-75
In silico characterization of sequence conservation in the 5’ and 3’ untranslated regions between Leishmania species
Elton José Rosas de Vasconcelos (FMRP - USP); Patrícia de Cássia Ruy (FMRP/FFCLRP - USP); Loislene Oliveira Brito (FMRP - USP); Raony Guimarães Correa do Carmo Lisboa Cardenas (FMRP/FFCLRP - USP); Angela Kaysel Cruz (FMRP - USP); Jeronimo Conceição Ruiz (FMRP - USP);
Short Abstract: In this study we are characterizing sequence conservation in the 5' and 3’ untranslated genomic regions between Leishmania species. The study of these regions could shed light on the understanding of the post-transcriptional control mechanisms in these parasites. A sequence analysis pipeline and preliminary results of motifs conservation will be presented.
Long Abstract: Click Here

Poster H-76
SEQUENCE ANALYSIS OF THE RIBOFLAVIN BIOSYNTHESIS GENES FROM ACIDITHIOBACILLUS FERROOXIDANS.
MARCOS TADEU SANTOS (CBMEG, UNICAMP); LUCIO FABIO CALDAS FERRAZ (CBMEG, UNICAMP); FERNANDA DE CASTRO REIS (CBMEG, UNICAMP); ANA PAULA FELÍCIO (IQ, UNESP); PAULA FALCÃO (EMBRAPA); MARIA TERESA MARQUES NOVO (UFSCAR); GORAN NESHICH (EMBRAPA); OSWALDO GARCIA JR (IQ, UNESP); LAURA MARIA MARISCAL OTTOBONI (CBMEG, UNICAMP);
Short Abstract: Acidithiobacillus ferrooxidans is a bacteria with economic relevance in metal bioleaching. We describe here the sequence analysis of the riboflavin operon in this bacteria. Expression analysis of the rib genes was performed by Real-Time PCR. The results could contribute to a better understanding of the bioleaching process by Acidithiobacillus ferrooxidans.
Long Abstract: Click Here

Poster H-77
Biological signal prediction using Stochastic Regular Grammar
Andre Kashiwabara (IME-USP); Alan Durham (IME-USP);
Short Abstract: Two technologies have been widely applied for ab initio splice site prediction, WMM and WAMs. We show that WMMs and WAMs are part of the search space of inference algoritms for Sochastic Regular Grammars and present an algorithm that converge to any of them.
Long Abstract: Click Here

Poster H-78
Evaluating ORF Function Predictions using Domain-specific Knowledge
Sivakumar Kannan (Robert Cedergren Centre for Bioinformatics and Genomics, Département de Biochimie, Université de Mon); Gertraud Burger (Robert Cedergren Centre for Bioinformatics and Genomics, Département de Biochimie, Université de Mon);
Short Abstract: Evaluating the machine learning based function predictions of hypothetical proteins is a challenging task. Therefore, we have developed evaluation criteria based on domain-specific knowledge. Using these criteria, we were able to rank predictions and thus identifying the most like working hypotheses for experimental validation.
Long Abstract: Click Here

Poster H-79
CONTRAlign 2: Discriminative Training for Multiple Sequence Alignment
Chuong B. Do (Stanford University); Samuel S. Gross (Stanford University); Robert C. Edgar (Stanford University); Kazutaka Katoh (Kyoto University); Serafim Batzoglou (Stanford University);
Short Abstract: We present CONTRAlign 2, an extension of the CONTRAlign conditional random field pairwise aligner to consistency-based progressive multiple sequence alignment. CONTRAlign 2 improves upon its predecessor by incorporating an array of new sequence features designed to exploit the additional signal found in the alignment of multiple protein sequence sets.
Long Abstract: Click Here

Poster H-80
An integrated custom design tool for PCR resequencing
Daniel Ingber (Applied Biosystems); Jingwei Ni (Applied Biosystems); Mary Ann Rydland (Applied Biosystems); Robert Sanders (Applied Biosystems); Xiaoying Lin (Applied Biosystems);
Short Abstract: Increasing attention has been devoted to SNP discovery and genotyping in an effort to associate disease/phenotypes with gene variations and mutations, but reliable primer design and data analysis remain two of the major challenges to overcome. We developed a flexible design tool that allows selection of different genomic targets.
Long Abstract: Click Here

Poster H-81
TOFI: A Software Tool for Oligonucleotide Fingerprint Identification
Waibhav Tembe (Biotechnology HPC Institute, US Army Medical Research and Materiel Command); Nela Zavaljevski (Biotechnology HPC Institute, US Army Medical Research and Materiel Command); Elizabeth Bode (Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases); Catherine Chase (Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases); Jeanne Geyer (Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases); Leonard Wasieloski (Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases); Gary Benson (Departments of Biology and Computer Science, Boston University); Jaques Reifman (Biotechnology HPC Institute, US Army Medical Research and Materiel Command);
Short Abstract: TOFI implements an automated computational approach to identify from a target genomic se-quence its in silico DNA fingerprints satisfying microarray experimental constraints. The GUI-driven software pipeline integrates various bioinformatics algorithms on a high performance computing platform. We employed TOFI to identify in silico DNA fingerprints for several patho-gens, which were then experimentally evaluated.
Long Abstract: Click Here

Poster H-82
An Integrated System for High Throughput Genome Annotation and Comparative Genome Analysis
Samuel V Angiuoli (TIGR); Jonathan Crabtree (TIGR); Joshua Orvis (TIGR); Jennifer R Wortman (TIGR); Owen R White (TIGR);
Short Abstract: We describe an architecture for large scale, high throughput sequence analysis and highlight two components: Ergatis, a workflow system for running computational analysis in a distributed computing environment and Sybil, a suite of web interfaces for comparative genome analysis that utilizes the Chado database schema and community ontologies.
Long Abstract: Click Here

Poster H-83
Conserved genes in a path from commensalism to pathogenicity
ZhiWei Cao (Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, Shanghai, China); Wu Wei (Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Graduate School of the Chi);
Short Abstract: We focused on small variations of conserved genes from a conditional pathogen, Staphylococcus epidermidis. In addition to the previously investigated global changes, single-nucleotide polymorphisms in orthologs may reveal genes that contribute to adaptation of the bacteria to different environmental stimuli, allowing them to shift from commensalism to pathogenicity.
Long Abstract: Click Here

Poster H-84
A functional genomics sequence analysis workbench
CA Hefer (University of Pretoria); F Joubert (University of Pretoria);
Short Abstract: A web-based biological sequence analysis workbench and management system integrated within a functional genomics platform is described. In addition to providing access to analysis packages, both locally and through web-services, relationships between functional genomic data types can be investigated, enabling users to identify patterns across different data types.
Long Abstract: Click Here

Poster H-85
Motif Discovery with Arbitrary Insertions and Deletions
Martin C Frith (IMB / RIKEN); Timothy L Bailey (IMB);
Short Abstract: We present GLAM2, the first Gibbs sampling-based motif discovery algorithm that allows arbitrary indels. Our approach is novel in the way in which it models the probability of indels and optimizes the number of aligned columns. We show that GLAM2 is substantially more sensitive than other methods.
Long Abstract: Click Here

Poster H-86
GREENPHYL: A Generic Phylogenomic Pipeline for Ortholog Prediction Between two Model Plant Species Arabidopsis thaliana and Oryza sativa
Matthieu Conte (CIRAD); Sylvain Gaillard (CIRAD); Brigitte Courtois (CIRAD); Manuel Ruiz (CIRAD); Emmanuel Guiderdoni (CIRAD); Christophe Perin (CIRAD);
Short Abstract: Gene ortholog identification is now a major objective for mining the increasing amount of sequence data provided by full or partial genome sequencing projects. Currently, most of the methods available for functional prediction are based on sequence similarity even if this kind of annotation transfer is often misleading. We developed GREENPHYL, an optimized phylogenomic pipeline which can generate weighted-supported orthologs and paralogs relationships to provide a robust and accurate way for gene function assignment.
Long Abstract: Click Here

Poster H-87
CaPSuLo, an integrative web tool for predicting the subcellular location of proteins
Perret (Swiss Institute of Bioinformatics); Bairoch (Swiss Institute of Bioinformatics); Veuthey (Swiss Institute of Bioinformatics);
Short Abstract: CaPSuLo provides a common access to a set of selected subcellular location prediction programs in an integrative tool, preventing an easy interpretation of inconsistent results. It displays results together with information on sequence homology and topology to help users take the most reliable prediction (http://biosapiens.isb-sib.ch/capsulo).
Long Abstract: Click Here

Poster H-88
Porter+: A Server for Protein Structural Motif Prediction
Catherine Mooney (UCD); Gianluca Pollastri (UCD); Alessandro Vullo (UCD);
Short Abstract: Porter+ is a server for the prediction of a new alphabet of local structural motifs. The predictive system, based on ensembles of bi-directional recurrent neural networks, and trained on a large non-redundant set of protein structures, achieves 60% correct motif prediction for tetra-peptides into 14 classes.
Long Abstract: Click Here

Poster H-89
Conservation and Correlation Analyses of the V3 Sequences of HIV-1 Envelope Proteins
Shuo L. Lin (Wyeth Vaccines Research); Robert Zagursky (Wyeth Vaccines Research);
Short Abstract: A large collection of HIV-1 gp120 V3 loop sequences was analyzed by a variety of computational methods to reveal patterns of genetic conservation and correlation. These patterns were related to viral phenotypes and to the interactions between gp120 and host molecules.
Long Abstract: Click Here

Poster H-90
PCR primer design for 2,4-D degradation genes using BLOCKS and the CDD database
VIANEZ JUNIOR, J. L. S. G (Departamento de Microbiologia Geral, LBSBM, UFRJ); MACRAE, A (Departamento de Microbiologia Geral, LBSBM, UFRJ);
Short Abstract: Conserved regions within genes were identified after sequential, protein structural and functional analysis and used for PCR primer design of 6 genes involved in the biodegradation of the globally important pesticide 2,4-D. The six primer pairs designed are intended to be used as tools to study the capacity of the local microbial community to biodegradate this herbicide.
Long Abstract: Click Here

Poster H-91
A Digital Northern tool for assessment of Citrus differentially expressed genes
Marcelo S. Reis (Centro APTA Citros "Sylvio Moreira"); Marco A. Takita (Centro APTA Citros "Sylvio Moreira"); Alessandra A. Souza (Centro APTA Citros "Sylvio Moreira"); Irving J. Berger (Centro APTA Citros "Sylvio Moreira"); Juliana Freitas-Astua (Embrapa Milho e Sorgo, and Centro APTA Citros "Sylvio Moreira"); Marcos A. Machado (Centro APTA Citros "Sylvio Moreira");
Short Abstract: We present a web-based tool for the in silico assessment of differentially expressed genes. It allows the comparison between the results of the most important measuring methods for gene abundance, and also performs comparison of the gene with public protein repositories, and automatic functional classification.
Long Abstract: Click Here

Top

Structural Bioinformatics

Poster I-1
Modelling of S1 Subunits of Three Different Avian Infectious Bronchitis Coronavirus Strains
Caio Júlio Martins Veloso (UFMG/PUCMG); Josiane Tavares de Abreu (UFMG/PUCMG); Jose Sergio de Resende (EMV/UFMG); Marcelo Santoro (ICB/UFMG);
Short Abstract: Avian Infectious Bronchitis (AIB) is a disease of economic importance. The development of drugs and vaccines depends on the existence molecular models. The S1 subunits of the spike of three strains was modeled by conventional homology. The analysis of models suggest the localization of the relevant regions for their activity.
Long Abstract: Click Here

Poster I-2
Protein function prediction based on 'reverse engineering' of the protein fold-recognition approach:examples from CASP6
Michal Andrzej Kurowski (Genesilico, IIMCB);
Short Abstract: The most reliable approach to predict protein function is via its structure. Fold recognition - class predictions by themselves are often not good enough to enable function assignment, though. We developed an approach combining evolutionary protein families analysis with structural prediction. T0197 and T0209 CASP6 cases are described in here.
Long Abstract: Click Here

Poster I-3
Designing C2H2 Zinc Finger Proteins to Target Specific Genomic Sites
Jeff Sander (Iowa State University); Peter Zaback (Iowa State University); Fengli Fu (Iowa State University); Daniel Voytas (Iowa State University); Drena Dobbs (Iowa State University);
Short Abstract: Consisting of modular nucleic acid binding domains, C2H2 zinc finger proteins provide an excellent framework for engineering new sequence-specific DNA binding proteins. Using binding specificities determined by others, we have developed a program, ZiFit, to locate and rank candidate targets for zinc finger binding within a given DNA sequence.
Long Abstract: Click Here

Poster I-4
Crystal structure of PrTX-I complexed with alpha-tocopherol and comparison studies with native Lys49-PLA2s
Juliana Izabel dos Santos (Depto. de Física e Biofísica - Iinstituto de Biociências, UNESP / Botucatu); Andreimar Martins Soares (Depto. de Análises Clínicas, Bromatológicas e Toxicológicas, FCFRP, USP / Ribeirão Preto); Marcos Roberto de Mattos Fontes (Depto. de Física e Biofísica - Iinstituto de Biociências, UNESP / Botucatu);
Short Abstract: This work reports the crystal structure of PrTX-I complexed with alpha-tocopherol and the comparison with native PrTX-I. Additionally, other native Lys49-PLA2s are used in the comparison. This study may bring insights into the myotoxic / cytotoxic mechanisms of Lys49-PLA2s and the role of C-terminal region.
Long Abstract: Click Here

Poster I-5
Protein structure topology comparison based on contact maps
Raquel C. Melo (UFMG); Ivan Mazoni (Embrapa); Goran Neshich (Embrapa); Marcelo M. Santoro (UFMG); Wagner Meira Jr (UFMG);
Short Abstract: Topologs (Topology Homologous) is a tool which is part of the Star Sting Suite (http://sms.cbi.cnptia.embrapa.br/SMS). It is a structural classification of proteins totally based on the pattern of intrachain interactions. Its precision is higher than 85% for all tested fold types and has been precomputed for all ASTRAL 40 chains.
Long Abstract: Click Here

Poster I-6
Contacts as the key elements for comparing two protein structures
Raquel C. Melo (UFMG); Ivan Mazoni (Embrapa); Goran Neshich (Embrapa); Marcelo M. Santoro (UFMG); Wagner Meira Jr (UFMG);
Short Abstract: TopSiMap (Topological Similarity Map) is and interactive tool which is part of the Star Sting Suite (http://sms.cbi.cnptia.embrapa.br/SMS).As contacts pattern is very conserved in each protein fold type, it makes possible to compare protein structures through their contact maps and also analyze what changes in contacts between two protein chains.
Long Abstract: Click Here

Poster I-7
Analyzing high-throughput biological data: complexities, issues, challenges and some lessons learned
Fazel Famili (IIT); Sieu Phan (IIT); Ziying Liu (IIT); Junjun Ouyang (IIT); Youlian Pan (IIT); Alan J. Barton (IIT);
Short Abstract: This poster consists of three parts. In part one, we provide an overview of data mining in genomics and the BioMine project. In part two we describe some of our case studies using the BioMiner data mining software that we have built. Part three includes our experiences in this project.
Long Abstract: Click Here

Poster I-8
Genome-wide de novo structure prediction for over 100 genomes and automatic integration of structure prediction with Gene Ontology database.
Lars Malmström (University of Washington); David Baker (University of Washington); Richard Bonneau (NYU, Dept of Computer Science);
Short Abstract: We describe application of Rosetta de novo structure prediction to over 100 genomes and our novel method for automatic integration of that structural compendium with information contained in GO (using grid-computing, wcgrid.org). We highlight Rosetta+GO (validated and novel) function predictions in several organisms.
Long Abstract: Click Here

Poster I-9
A one-shot algorithm for visualizing large-scale RNA structures with pseudoknots as planar graphs
Kyungsook Han (Inha University); Yanga Byun (Inha University);
Short Abstract: Drawing large RNA structures with pseudoknots often requires additional intervention by the user to make the drawing overlap-free, but it becomes difficult as the size and complexity of the RNA structure increase. We developed a new one-shot algorithm that produces overlap-free drawings for RNA structures with pseudoknots.
Long Abstract: Click Here

Poster I-10
Negative Result on Maximum Common Subgraph of Two Graphs
Xiuzhen Huang (Department of Computer Science, Arkansas State University);
Short Abstract: The problem of finding maximum common subgraph has important applications in biological structure matching. We investigate the maximum common subgraph of two graphs. We derive the hardness result for the exact algorithms of this problem. Our lower bound result is asymptotically tight.
Long Abstract: Click Here

Poster I-12
Predicting co-evolving pairs in Pfam based on Mutual Information of mutation events measured along the phylogenetic tree
Scooter willis (Department of Computer and Information Science and Engineering, University of Florida);
Short Abstract: Mutual Information(MI) is used to detect co-evolving pairs in a protein family by re-sampling based on mutation events in the phylogenetic tree. The predictive quality with MI(Z>=4), a sequence distance >10 and within 12 angstroms using the RPE method is on average 81% in a Pfam family.
Long Abstract: Click Here

Poster I-13
Predicting Enzyme Class From Protein Structural Parameters Using STING_DB parameters and Bagging Predictors
Michel E. B. Yamagishi (Embrapa Informática); Stanley R. M. Oliveira (Embrapa Informática); Luiz C. Borro (Embrapa Informática); Edgard H. Santos (Embrapa Informática); José G. Jardine (Embrapa Informática); Fábio D. Vieira (Embrapa Informática); Ivan Mazoni (Embrapa Informática); Marcelo G. Narciso (Embrapa Informática); Paulo R. Kuser-Falcão (Embrapa Informática); Goran Neshich (Embrapa Informática);
Short Abstract: In this work we present a new method to classify enzymes that uses the STING_DB physical-chemical parameters and Bagging predictors. By building models based on "decision tree" and "neural network", we obtained an accuracy of 74% on average. These results outperform the similar models proposed in literature.
Long Abstract: Click Here

Poster I-14
Analysing Protein-Protein Interface using JPIV
Michel E. B. Yamagishi (Embrapa Informática); Paula R. Kuser-Falcão (Embrapa Informática); Luiz C. Borro (Embrapa Informática); Stanley R. M. Oliveira (Embrapa Informática); Edgard H. Santos (Embrapa Informática); José G. Jardine (Embrapa Informática); Fábio D. Vieira (Embrapa Informática); Ivan Mazoni (Embrapa Informática); Marcelo G. Narciso (Embrapa Informática); Goran Neshich (Embrapa Informática);
Short Abstract: In this work we present Java Protein Interface Viewer (JPIV). It is a web-based software designed to visualize and analyze protein-protein interfaces. It uses Delaunay triangulation in order to define the interface, and the STING_DB physical-chemical parameters to the analysis process.
Long Abstract: Click Here

Poster I-17
Identification of novel imprinted genes in human.
Jorge E. S. de Souza (Pós-Graduação em Bioinformática - Universidade de São Paulo); Pedro A. F. Galante (Bioquímica - Universidade de São Paulo); Lilian C. Pires (Biologia Molecular e Genômica - Instituto Ludwig de Pesquisa sobre o Câncer); Sandro J. de Souza (Biologia Computacional - Instituto Ludwig de Pesquisa sobre o Câncer); Anamaria A. Camargo (Biologia Molecular e Genômica - Instituto Ludwig de Pesquisa sobre o Câncer);
Short Abstract: Identification of imprinted genes is expensive mainly due the difficulty to the paternal allele expression evaluation. In this work we developed a large scale approach, based in the integration of public data from SNPs, SAGE and MPSS, for the identification of new imprinted genes candidates.
Long Abstract: Click Here

Poster I-18
Identification of Druggabable “Hot Spots” in Ligand Binding Pockets by Computational Solvent Mapping of Proteins.
Melissa R. Landon (Graduate Program in Bioinformatics, Boston University); Spencer C. Thiel (Graduate Program in Bioinformatics, Boston University); David R. Lancia, Jr. (Department of Biomedical Engineering, Boston University); Sandor Vajda (Department of Biomedical Engineering, Boston University);
Short Abstract: Here we describe the application of the CS-Map algorithm to the identification of druggable subsites within a ligand binding pocket. The accuracy of CS-Map results is illustrated on a set of fifty proteins for which high affinity drug-like compounds have been developed and structural information is available.
Long Abstract: Click Here

Poster I-19
A Trypanosoma cruzi Genome Study by Sequence-Structure HighThroughput Comparative Modelling: A First Step Towards the Identification of Potential Molecular Targets for Chagas Disease
Priscila V. S. Z. Capriles (LNCC/MCT); Shaila C. Rössle (Ludwig - Maximilians - University of Munich); Ana C. R. Guimarães (DBBM/FIOCRUZ); Marcos Catanho (DBBM/FIOCRUZ); Paulo M. Bisch (IBCCF/UFRJ); Wim Degrave (DBBM/FIOCRUZ); Laurent E. Dardenne (LNCC/MCT);
Short Abstract: In this work, we investigated the Trypanosoma cruzi genome, by highthroughput comparative modelling, and identified/classified the subset of T. cruzi enzymes with theoretically determined 3D-structures (9.13% of the total genome) which can be investigated as potential molecular targets for structure based rational drug design researches.
Long Abstract: Click Here

Poster I-21
STRUCTURAL PARAMETERS TO FILTER CRUCIAL CATALYTIC SITE AMINOACIDS FROM FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE.
MARCELO MENDES BRANDÃO (Hemotherapy and Hematology Center - UNICAMP); PAULA R. KUSER (Embrapa information technology); GORAN NESHICH (Embrapa information technology);
Short Abstract: In this work we demonstrate the minimum structural parameters needed to isolate the active site of the fructose 1,6-bisphosphate aldolase, using the Diamond STING suite. DSs is a web based set of programs for a comprehensive analysis of a relationship between protein sequence, structure, function, physical chemical characteristics and stability.
Long Abstract: Click Here

Poster I-22
BlueStar STING - A multiplatform environment for protein structure analysis
Paula Kuser (EMBRAPA); Michel E. B. Yamagishi (EMBRAPA); Stanley R. M. Oliveira (EMBRAPA); Ivan Mazoni (EMBRAPA); Edgard H. Santos (EMBRAPA); Fábio D. Vieira (EMBRAPA); José G. Jardine (EMBRAPA); Luiz C. Borro (EMBRAPA); Goran Neshich (EMBRAPA);
Short Abstract: BlueStar STING is the latest version of the STING suite of programs and corresponding database. STING continues to build on what is considered its major asset: a principal DB of per-residue-reported descriptors (available for display both numerically and graphically) for either the public PDB or local files.
Long Abstract: Click Here

Poster I-23
INFO-RNAseq - Fast Inverse RNA Folding Satisfying Sequence Constraints
Anke Busch (Albert-Ludwigs-University Freiburg, Inst. of Computer Science, Chair for Bioinformatics); Rolf Backofen (Albert-Ludwigs-University Freiburg, Inst. of Computer Science, Chair for Bioinformatics);
Short Abstract: INFO-RNAseq is a fast algorithm for the INverse FOlding of RNA that includes sequence constraints. It designs RNA sequences that fold into a given structure and additionally satisfy some constraints on the primary sequence. INFO-RNAseq benefits from the design of a good initializing sequence by dynamic programming and the use of different local search methods.
Long Abstract: Click Here

Poster I-24
How parallel are the helices of your favourite protein?
Peter Røgen (Department of Mathematics, Technical University of Denmark); Per W. Karlsson (Department of Mathematics, Technical University of Denmark);
Short Abstract: How parallel and anti-parallel are the helices of your favourite protein? - And which other proteins have a similar parallelity of their helices? To answer such questions, we introduce a notion of Local Self Parallelity of protein secondary structures, and use it for automatic classification of protein structures.
Long Abstract: Click Here

Poster I-26
Using Knowledge-Based Constraints To Optimise Comparative Models Of Protein Structure
Braddon K. Lance (Macquarie University, Department of Statistics); Graham R. Wood (Macquarie University, Department of Statistics); Charlotte M. Deane (University of Oxford, Department of Statistics);
Short Abstract: Comparative modelling can be improved by better refinement of the inherited template backbone. To facilitate structure refinement, we generate local backbone conformations that are consistent with the observed structural variation by estimating the multivariate distribution of fragment atoms. We use this distribution in a simulated annealing algorithm for structure refinement.
Long Abstract: Click Here

Poster I-28
Protein-Protein Docking Guided by Biochemical Data
Domantas Motiejunas (EML Research); Ting Wang (UC Davis); Anna Feldman-Salit (EML Research); Tim Johann (EML Research); Razif Gabdoulline (EML Research); Rebecca Wade (EML Research);
Short Abstract: We present a protein-protein docking protocol comprised of rigid-body docking with Brownian Dynamics and flexible refinement with Molecular Dynamics. Docking is done subject to biochemical constraints. The protocol is applied to a structurally and functionally diverse set of test cases.
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Poster I-29
VSM-G: the Virtual Screening Manager platform for computational Grids. Use for the identification of putative ligands of the Liver X Receptor
Alexandre Beautrait (Mr); Bernard Maigret (Mr);
Short Abstract: The VSM-G platform performs high throughput virtual screening based on both ligand- and receptor-based algorithms running on computational grids. A central molecular funnel composed of successive filters allows the screening of large molecular libraries for compounds prioritization in experimental assays. Illustrations will deal with the LXRβ target protein involved in cholesterol regulation.
Long Abstract: Click Here

Poster I-30
Automatically Clustering Protein Structure Using the Distribution of Atom Bonds in Backbone
Sung Hee Park (ETRI bioinformatics team); Chan Yong Park (ETRI bioinformatics team); Dae Hee Kim (ETRI bioinformatics team); Soo Jun Park (ETRI bioinformatics team);
Short Abstract: Recently, a protein structural similarity, 3D atom bond histogram, has proposed by the authors. the 3D atom bond histogram descriptor is enough efficient to retrieve neighbors within a second from huge protein structure database with more than 9700 proteins.In this paper, this descriptor is applied to automatically clustering proteins.
Long Abstract: Click Here

Poster I-31
Prediction of functional residues from Plasmodium falciparum plasmepsins: implications in the antimalarial drugs design.
Pedro Alberto Valiente Flores (Centro de Estudios de Proteínas (CEP), Facultad de Biología, Universidad de La Habana, Cuba.); Amaury Pupo Meriño (Centro de Estudios de Proteínas (CEP), Facultad de Biología, Universidad de La Habana, Cuba.); Tirso Pons Hernández (Centro de Estudios de Proteínas (CEP), Facultad de Biología, Universidad de La Habana, Cuba.); Pedro G. Pascutti (Instituo de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Brasil.);
Short Abstract: Sequence and structural analysis of aspartic proteases allowed us to identify the conserved positions M75, V105, T108, Y115, A219, T221, and L287 (plasmepsin II numbering scheme). The predicted positions are in proximity to the inhibitor’s functional groups and they line the protease binding-cavity. This knowledge may contribute to the development of more selective antimalarial drugs.
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Poster I-32
Homology modeling of Chromobacterium violaceum and Thiobacillus ferrooxidans atypical ArsR proteins
Rafael S. Rocha (Laboratório de Polimorfismo de DNA, CCB-UFPa, Belém-PA, Brasil); Marta P. Carepo (Centro de Química Fina e Biotecnologia FCT/UNL Portugal); Evonnildo C. Gonçalves (Laboratório de Polimorfismo de DNA, CCB-UFPa, Belém-PA, Brasil); Artur Silva (Laboratório de Polimorfismo de DNA, CCB-UFPa, Belém-PA, Brasil); Cláudio N. Alves (Laboratório de Química, CCEN-UFPa, Belém-PA, Brasil); Maria P. Schneider (Laboratório de Polimorfismo de DNA, CCB-UFPa, Belém-PA, Brasil);
Short Abstract: The 3D structures of ArsR proteins from Chromobacterium violaceum and Thiobacillus ferrooxidans were investigated by homology modeling. The models have the same secondary structure seen in the template SmtB protein. We identified a putative C-terminal arsenite/antimonite binding site in these atypical but functional ArsR proteins.
Long Abstract: Click Here

Poster I-33
Information-Theoretic Analysis of Protein Fold Potentials
Armando D. Solis (Mount Sinai School of Medicine); S. Rackovsky (Mount Sinai School of Medicine);
Short Abstract: We examine fundamental information-theoretic roots of protein fold potentials to explore effective ways to build better empirical functions. We estimate parameters from finite data for potential functions chosen to minimize information loss while also avoiding information redundancy. The effect of these improvements on performance in fold recognition is assessed.
Long Abstract: Click Here

Poster I-34
Structural Analysis of proplasmepsin from the human malarial pathogen plasmodium vivax
Juliana M. Papine (Faculdade de Ciências Farmacêuticas-PUCCampinas,); Mariana S. Vieira (Faculdade de Ciências Farmacêuticas-PUCCampinas,); José G. Jardine (Embrapa Information Technology); Goran Neshich (Embrapa Information Technology); Paula R. Kuser-Falcão (Embrapa Information Technology); Michel E. B.Yamagishi (Embrapa Information Technology); Stanley R. M. Oliveira (Embrapa Information Technology); Ivan Mazoni (Embrapa Information Technology); Fábio D. Vieira (Embrapa Information Technology); Edgar H. Santos (Embrapa Information Technology);
Short Abstract: We have concentrated our effort in understanding some crucial features of the protein plasmepsin from the human malarial pathogen plasmodium vivax. The analysis for identification and alignment of homologous sequences for proteins with decided structure was led with the Star Sting Suite.
Long Abstract: Click Here

Poster I-35
Structural Analysis of the Protein Twitching Motility
Jose Gilberto Jardine (Embrapa Information Technology); Goran Neshich (Embrapa Information Technology); Paula R. Kuser-Falcão (Embrapa Information Technology); Michel E. B.Yamagishi (Embrapa Information Technology); Stanley R. M. Oliveira (Embrapa Information Technology); Ivan Mazoni (Embrapa Information Technology); Edgard H. Santos (Embrapa Information Technology); Fábio D. Vieira (Embrapa Information Technology); Sérgio Marangoni (Departamento de Bioquímica, UNICAMP); Daniel Martins (Departamento de Bioquímica, UNICAMP); Flavia V. Winck (Departamento de Bioquímica, UNICAMP); José C. Novello (Departamento de Bioquímica, UNICAMP); Juliana M. Papine (Faculdade de Ciências Farmacêuticas-PUCCampinas); Mariana S. Vieira (Faculdade de Ciências Farmacêuticas-PUCCampinas);
Short Abstract: We have concentrated our effort in understanding some crucial features of protein Twitching Motility of Xylella fastidiosa. Our study is based on the model of this protein, constructed by homology modeling in which we used the crystallographic structure of a Víbrio cholerae homologous protein as a mold.
Long Abstract: Click Here

Poster I-36
DomainDiscovery: A Novel Algorithm for Protein Domain Boundary Assignment Using Support Vector Machine
Abdur R Sikder (Advanced Networks Research Group, School of Information Technologies, University of Sydney, NSW 2006); Stella Veretnik (San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA); Albert Y Zomaya (Advanced Networks Research Group, School of Information Technologies, University of Sydney, NSW 2006); Philip E Bourne (Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 9209);
Short Abstract: Knowledge of protein domain boundaries is critical for the characterisation and understanding of protein function, specifically in the post genomic era. The ability to identify structural domains without the knowledge of the structure – by using sequence information only – is essential step in many types of protein analysis. We present a novel method for domain identification from sequence-based information.
Long Abstract: Click Here

Poster I-38
Structural and Evolutionary analysis of Importin-alpha and its interaction with the nuclear localization sequence peptides.
Agnes Alessandra Sekijima Takeda (Dept. de Física e Biofísica, Instituto de Biociências, UNESP, Botucatu-SP, Brasil); Antônio Sergio Kimus Braz (Laboratório de Biotecnologia e Genética Molecular (BIOGEM), Dept. de Genética, Instituto de Biociênc); Bostjan Kobe (Dept .Biochemistry and Molecular Biology, University of Queensland, Brisbane,QLD, Australia); Marcos Roberto de Mattos Fontes (Dept. de Física e Biofísica, Instituto de Biociências, UNESP, Botucatu-SP, Brasil);
Short Abstract: Importin-alpha isoforms display cargo preferences in vitro and in vivo. In this study we present a phylogenetic analysis of Importin-alpha family, showing the independent duplication events in Metazoa and Viridiplantae. We also present structural sequence conservation and molecular dynamics studies of Importin-alpha and NLS interaction.
Long Abstract: Click Here

Poster I-41
Single-family analysis of binding site structural similarities
Rafael Najmanovich (EBI); Richard Morris (EBI); Janet Thornton (EBI);
Short Abstract: We describe a method for the detection of pairwise local structural similarities between members of a given protein family using all non-hydrogen atoms in protein clefts allowing larger, over-predicted and apo-form binding sites to be analyzed. We uncover previously unknown similarities between members of the human cytosolic sulfotransferase family.
Long Abstract: Click Here

Poster I-42
Use of docking tools and MD simulations to predict the interaction between the MH2 domain of Smad3 and the PDZ domain of Erbin
Matthieu Chavent (eDAM group); Claire Nourry (Inserm - UMR 599 - Molecular Pharmacology); Nadine Deliot (Inserm - UMR 599 - Molecular Pharmacology); Jean Paul Borg (Inserm - UMR 599 - Molecular Pharmacology); Bernard Maigret (eDAM group);
Short Abstract: Erbin has been identified as a binding partner for Smad3, a major component of the transforming growth factor-beta signaling pathway. We present how the use of bioinformatics and molecular modelling tools such as molecular dynamics helped us to conceptualize the association between the Smad3 MH2 and Erbin PDZ domains.
Long Abstract: Click Here

Poster I-43
Novel Protein Structural Classification by Discovering Coherence in Hydrophobicity Scales
Sumeet Dua (College of Engineering and Science, Louisiana Tech University); Pradeep Chowriappa (College of Engineering and Science, Louisiana Tech University); Ramakrishnan Rajagopalan (College of Engineering and Science, Louisiana Tech University);
Short Abstract: In this work, we present a novel feature extraction and classification computational paradigm that discovers the points of spectral coherence among different hydrophobicity scales for proteins and employ them for structural class identification of proteins, yielding a significant increase in prediction accuracy over previous results in this area.
Long Abstract: Click Here

Poster I-44
Protein Dynamics from X-Ray Crystallography Data: Modeling Structural Heterogeneity with Inverse Kinematics
Henry van den Bedem (Stanford Linear Accelerator Center); Ankur Dhanik (Stanford University); Ashley M. Deacon (Stanford Linear Accelerator Center); Jean-Claude Latombe (Stanford University);
Short Abstract: We present a method to accurately model heterogeneity in experimental protein main-chain fragments. A computer program using our method was developed to automatically identify and model multiple conformations of a fragment that fit the experimental X-ray data, together with their likelihoods. Additionally, our software can be used to calculate energetically plausible pathways between the conformations, thus providing insight in the local dynamics of the main chain.
Long Abstract: Click Here

Poster I-45
Profiling Tertiary Protein Motifs Using PHMM
Jalal Mahmud (Department of Computer Science, Stony Brook University, Stony Brook , NY 11794, USA); Chang Zhao (Department of Computer Science, Stony Brook University, Stony Brook , NY 11794, USA); I.V. Ramakrishnan (Department of Computer Science, Stony Brook University, Stony Brook , NY 11794, USA);
Short Abstract: Structural motif comparison can detect homology when there is no sufficient sequence similarity or overall structural similarity. Profile based methods have been proved to be more effective in recognizing remote homologs. We adapt PHMM to profile the tertiary structure of protein motifs. Our experiments demonstrate reasonable result.
Long Abstract: Click Here

Poster I-46
Protein Designability in the 2-D Triangular Lattice
Myron F. Peto (ISU); Robert L. Jernigan (ISU); Andrzej Kloczkowski (ISU);
Short Abstract: Using a lattice model with relatively higher coordination number than that of many studies, we explore the question of protein designability. Our definition of designability is based on the uniqueness of conformations that a sequence folds to with lowest energy. We identify and classify designable conformations for different shapes.
Long Abstract: Click Here

Poster I-47
The Cry 1Ac Protein from Bacillus thuringiensis and its structure stability centers
Katia Regina Evaristo de Jesus (EMBRAPA CNPMA); Paula Kuser (EMBRAPA CNPTIA); Goran Neshich (EMBRAPA CNPTIA);
Short Abstract: The Cry 1Ac Protein from Bacillus thuringiensis and its structure stability centers were analysed by means of identification of order of cross links and co-evolving amino acids, both parameters available in Blue Star STING
Long Abstract: Click Here

Poster I-48
Serine Proteases analysis based on phylogenetic trees constructed from the sequence and structure alignments
Cristina Ribeiro (UFMG); Paula Kuser (EMBRAPA CNPTIA); Goran Neshich (EMBRAPA CNPTIA); Marcelo Santoro (UFMG);
Short Abstract: We compared two approaches to construct phylogenetic trees from a set of serine proteases with deciphered 3D_structure. The first approach: sequence alignment generates a phylogenetic tree; the seccond approach is based on a sequence alignment strictly following the structure alignment. The differences b/w the two is discussed.
Long Abstract: Click Here

Poster I-49
PROTEIN LIGAND CONTACTS ANALYSED IN AN INTEGRATED ENVIRONMENT WITH OTHER STRUCTURE AND SEQUENCE RELATED PARAMETERS
Paula Kuser (Embrapa Cnptia); Luiz Cesar Borro (Embrapa Cnptia); Ivan Mazoni (Embrapa Cnptia); Michel Yamagishi (Embrapa Cnptia); José G. Jardine (Embrapa Cnptia); Edgard H. dos Santos (Embrapa Cnptia); Stanley R. M. Oliveira (Embrapa Cnptia); Goran neshich (Embrapa Cnptia);
Short Abstract: The Protein Ligand Contacts – the new STING module allows a user to compare the contacts established between the ligand and the protein together with the variety of other structure parameters within a simple yet intuitive set of interactive plots. The biologically important examples are presented in this work.
Long Abstract: Click Here

Poster I-50
MSSP: simultaneous comparison of the same structure descriptor for different protein structures
Ivan Mazoni (Embrapa CNPTIA); Paula Kuser (Embrapa CNPTIA); Michel Yamagishi (Embrapa CNPTIA); Luiz Borro (Embrapa CNPTIA); Jose Jardine (Embrapa CNPTIA); Edgard H. dos Santos (Embrapa CNPTIA); Stanley R. M. Oliveira (Embrapa CNPTIA); Goran Neshich (Embrapa CNPTIA);
Short Abstract: The Multiple Structures - Single Parameter STING module allows a user to compare variety of structure parameters from different protein structures in a simple yet intuitive 2D plot. The parameters which can be used for the analysis are those stored in the STING_DB (Neshich et al., 2005).
Long Abstract: Click Here

Poster I-51
COMPARISSON OF THE AMINO ACIDS CO-EVOLUTION AND THE CORRELATED STRUCTURE DESCRIPTORS
Ivan Mazoni (Embrapa CNPTIA); Paula Kuser (Embrapa CNPTIA); Michel Yamagishi (Embrapa CNPTIA); Luiz Borro (Embrapa CNPTIA); Jose Jardine (Embrapa CNPTIA); Edgard H. dos Santos (Embrapa CNPTIA); Stanley R. M. Oliveira (Embrapa CNPTIA); Goran Neshich (Embrapa CNPTIA); Marcelo Narciso (Embrapa CNPTIA);
Short Abstract: The AA Co-evolution is a very powerful method of identifying those critical residues which are responsible for maintaining the minimum information for the specific function. By comparing the set of co evolving amino acids together with the variety of other structure parameters, couple of biologically important examples are presented.
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Poster I-52
Insights into protein-protein interfaces using a Bayesian network prediction method
James Bradford (University of Leeds); Chris Needham (University of Leeds); Andrew Bulpitt (University of Leeds); David Westhead (University of Leeds);
Short Abstract: We combine surface patch analysis with a Bayesian network to predict protein-protein binding sites with high accuracy even when no sequence homologues to the query protein are available. We show that our method can be applied to un-annotated structures solved by structural genomics projects, and can identify potential drug targets.
Long Abstract: Click Here

Poster I-53
A computational method to identify amino acid residues involved in protein-RNA interactions
Michael Terribilini (Iowa State Univeristy); Jeffry Sander (Iowa State Univeristy); Byron Olson (Iowa State Univeristy); Jae-Hyung Lee (Iowa State Univeristy); Robert Jernigan (Iowa State Univeristy); Vasant Honavar (Iowa State Univeristy); Drena Dobbs (Iowa State Univeristy);
Short Abstract: Protein-RNA interactions are vital for many biological processes. This work is the first reported attempt to combine sequence and three-dimensional structure information for prediction of RNA-binding residues in proteins. It should be valuable both for investigations of specific RNA-binding proteins and for large scale efforts.
Long Abstract: Click Here

Poster I-54
RNA Secondary structure prediction
Stéfan ENGELEN (IBISC -CNRS. University of Evry/Genopole); Fariza TAHI (IBISC -CNRS. University of Evry/Genopole);
Short Abstract: We present an algorithm,called P-DCFold, for predicting RNA secondary structures including all kinds of pseudoknots. It is based on the comparative approach. P-DCFold has been applied on several RNAs and in less than two seconds, their respective secondary structures, including their pseudoknots,have been recovered very efficiently.
Long Abstract: Click Here

Poster I-55
Discrimination of beta-barrel Membrane Proteins based on Statistical Methods and Machine Learning Algorithms
M. Michael Gromiha (CBRC, AIST); Makiko Suwa (CBRC, AIST);
Short Abstract: We have developed statistical methods and machine learning techniques for discriminating -barrel membrane proteins from other folding types of globular and membrane proteins using amino acid composition, residue pair preference and motifs. We obtained the accuracy of 95% for correctly identifying the beta-barrel membrane proteins using statistical methods and 99% for excluding globular proteins using machine learning techniques.
Long Abstract: Click Here

Poster I-56
Fast Structural Similarity Search based on Topology String Matching
Sung Hee Park (Bioinformatics Research Centre, Department of Computing Science, University of Glasgow); Keun Ho Ryu (Database Laboratory, Department of Computer Science, Chungbuk National University); David Gilbert (Bioinformatics Research Centre, Department of Computing Science, University of Glasgow);
Short Abstract: We describe a framework for fast similarity search based on a string representation of topological relationships of proteins and report on the comparison of protein structures based on these topology strings using bipartite graph matching. The system is implemented on top of the Oracle 9i spatial DBMS.
Long Abstract: Click Here

Poster I-57
Targeting Proteins from the Human Cancer Protein Interaction Network (HCPIN) for Structural Genomics
Y. J. Huang (Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Ru); L. J. Lu (Department of Molecular Biology and Biochemistry,Yale University,Northeast Structure Genomics Consor); M. B. Gerstein (Department of Molecular Biology and Biochemistry,Yale University,Northeast Structure Genomics Consor); G. T. Montelione (Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Ru);
Short Abstract: The Northeast Structure Genomics Consortium is targeting hundreds of proteins from the Human Cancer Protein Interaction Network. This interaction network has been constructed by combined analysis of seven signal transduction pathways from the KEGG Database, together with data from the Human Protein Reference Database, including >2000 proteins and ~5000 interactions.
Long Abstract: Click Here

Poster I-58
i-BioS: A system for Inverse Biological Virtual Screening Based on Inverse Docking Approach
Julio CD Lopes (Cheminformatics and Medicinal Chemistry Group - Departamento de Química - UFMG);
Short Abstract: In the present work we develop a new system for inverse docking studies. Our system, called i-BioS (Inverse Biological virtual Screening), is based on Surflex docking program. It was able to reproduce some of the biological activities of violacein and found new ones, associated to its anti-oxidant character.
Long Abstract: Click Here

Poster I-59
Prediction of protein complexes using evolutionary information
Richard Bickerton (Department of Biochemistry, University of Cambridge); Tom Blundell (Department of Biochemistry, University of Cambridge); David Burke (Department of Biochemistry, University of Cambridge);
Short Abstract: We exploit structural and evolutionary information to predict protein-protein interaction sites for use as restraints in data-driven docking. To benchmark docking algorithms we created a comprehensive non-redundant database of observed protein interactions. This is useful in assessing impacts of non-synonymous SNPs on protein interactions.
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Poster I-60
Docking protein domains in contact space
Stefano Lise (University College London); Alice Walker-Taylor (University College London); David T Jones (University College London);
Short Abstract: We present a novel method that attempts to dock protein domains using a contact map representation. It is based on a scoring function that combines structural, physicochemical and evolutionary information. The method correctly predicts some contacts across the interface and can complement effectively other computational methods.
Long Abstract: Click Here

Poster I-61
Expected packing density allows to predict both amyloidogenic and unfolded regions in protein chain
Galzitskaya (Institute of Protein Research); Garbuzynskiy (Institute of Protein Research); Lobanov (Institute of Protein Research);
Short Abstract: It has been shown that regions with strong expected packing of residues would be responsible for the amyloid formation, at the same time regions with weak expected packing of residues would be responsible for the appearance of unfolded regions.
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Poster I-62
Self-organizing Maps - the Heuristic Approach for Understanding Ligand-protein Interactions in Vitamin D Receptor.
Ferdinand Molnár (Department of Biochemistry, Universitz of Kuopio);
Short Abstract: Since ligand-docking is more dynamic process than crystallography can monitor, we analyzed the action of different agonists using molecular-dynamics simulations, self-organizing maps and in-vitro assays. The combined movement of 40 residues results in the ligand-binding pocket modulation and may serve as an important parameter in smart drug design.
Long Abstract: Click Here

Poster I-63
The Influence of Alternative Splice Sites in Protein Structure
Elza H.A.B. Durham (IME -USP/LICR); Richard Garrat (IFSC-USP); Sandro J. de Souza (LICR);
Short Abstract: Alternative splicing of pre-mRNAs is one of the most important mechanisms that increase protein diversity in eukaryotes. Using information from expressed sequences and protein structures, we studied the structural impact of alternative splicing in proteins.
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Poster I-64
Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: application to complete genomes
Håkan Viklund (Stockholm University); Erik Granseth (Stockholm University); Arne Elofsson (Stockholm University);
Short Abstract: 3D-structures of transmembrane proteins have been used to define and study the concept of reentrant regions. The results include statistics for the amino acid composition of reentrant regions, a novel prediction method and estimations of the occurence of reentrant regions in three genomes.
Long Abstract: Click Here

Poster I-65
Visualization and clustering of Protein Local Conformational Space using Geometric Invariant Theory
Ashish V Tendulkar (KReSIT, IIT Bombay); Pramod P Wangikar (Dept of Chemical Engg, IIT Bombay);
Short Abstract: Structures of peptide fragments from a protein can potentially occupy a vast conformational continuum. Here, we propose a general framework to visualize the protein local conformational space using geometric invariants as structure descriptors. We observe that the number of preferred local conformations is far less than that predicted previously.
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Poster I-66
Crystal structure of hemoglobin from Cerdocyon thous at 2.2 Å resolution using syncrotron radiation.
Esteves, G. F. (Universidade de Brasília); Freitas, S. M. (Universidade de Brasília);
Short Abstract: The blood of Cerdocyon thous was purified, and crystals were grown by the vapor-diffusion .The structure has been determined to a resolution of 2.2 Å. The R and Rfree factor are 0.232 and 0.168. Final quality was checked by PROCHECK. Thanks to EMBRAPA, LNLS,CNPq and RENABIME.
Long Abstract: Click Here

Poster I-67
3D Model quality evaluation using evolutionary information
Nicolas Palopoli (Centro de Estudios e Investigaciones, Universidad Nacional de Quilmes); Ezequiel Juritz (Centro de Estudios e Investigaciones, Universidad Nacional de Quilmes); Diego Gomez-Casati (IIB-INTECH, UNSAM-CONICET); Gustavo Parisi (Centro de Estudios e Investigaciones, Universidad Nacional de Quilmes);
Short Abstract: We use the structurally constrained model of protein evolution (SCPE) to assess 3D model quality. Our method uses site-specific substitution matrices generated with SCPE simulations for each model. We found the best structural model using maximum likelihood calculations using a reference alignment and the derived substitution matrices.
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Poster I-68
Prediction of order and disorder at the domain level
Zsuzsanna Dosztanyi (Institute of Enzymology); Mark Sandor (Institute of Enzymology); Istvan Simon (Institute of Enzymology);
Short Abstract: During target selection of structural genomics projects it is important to be able to discern ordered globular domains from disordered regions. A method based on the IUPred algorithm is suggested to locate ordered and disodered domains from amino acid sequences and was tested on datasets containing both order and disorder.
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Poster I-69
Datamining the Fourth Dimension from Crystal Structures: Function-Structure-Entropy Relationships in Membrane Proteins
Ilan Samish (Dept of Biochemistry & Biophysics, School of Medicine & Dept of Chemistry, School of Arts and Scienc); Avigdor Scherz (Weizmann Institute of Science, Rehovot, Israel);
Short Abstract: We show how variation in conformational flexibility is involved in dynamic mechanisms of membrane-proteins. Intra-protein cavities within photosynthetic-reaction-centers are involved entropic-reorganization facilitating acclimatization of energy conversion to ambient temperatures. More generally, carefully-normalized high temperature-factors in membrane-proteins point at pivotal loci to dynamic mechanisms.
Long Abstract: Click Here

Poster I-70
Dimeric Lys49-Phospholipases A2: Which Is The Correct Biological Assembly?
Mário T. Murakami (Departamento de Física, IBILCE, UNESP, São José do Preto-SP, Brazil); Raghuvir K. Arni (Departamento de Física, IBILCE, UNESP, São José do Preto-SP, Brazil); Marcos R.M. Fontes (Departamento de Física e Biofísica, Instituto de Biociências, UNESP, Botucatu-SP, Brazil);
Short Abstract: Several myotoxic-phospholipases A2-like have been extensively structurally and biochemically characterized and, a dimer conformation has been considered as the biological assembly. We propose an alternative dimer conformation based on small angle X-ray scattering, crystal structures of complexes with ligands, interface analysis and energy minimization.
Long Abstract: Click Here

Poster I-71
In Silico Identification of Radial Spoke Proteins and Prediction of their Arrangement Patterns towards Assembly of the Flagellar Axoneme in Leishmania spp.
Allan Rodrigo Soares Maia (NUGEN-UECE); Ana Carolina Landim Pacheco (NUGEN-UECE); Hálisson Lucas Ribeiro (NUGEN-UECE); George de Paulo Ferreira (NUGEN-UECE); Ana Luiza Bessa de Paula Barros (LARCES-UECE); Raimundo Bezerra da Costa (NUGEN-UECE); Rodrigo Maggioni (NUGEN-UECE); Diana Magalhaes de Oliveira (NUGEN-UECE);
Short Abstract: We present sequence and structural comparisons of radial spoke proteins (RSPs) in order to refine predictions that, if correct, suggest RSPs as part of the emerging group of flagellar proteins that are localized in specific axonemal compartments to carry out diversified activities related to flagellar maintenance in Leishmania spp.
Long Abstract: Click Here

Poster I-72
Protein Active Site Comparison and Retrieval System Based on 3D Pattern Matching
Dae-Hee Kim (Electronics and Telecommunications Research Institute); Sung-Hee Park (Electronics and Telecommunications Research Institute); Chan-Yong Park (Electronics and Telecommunications Research Institute); Soo-Jun Park (Electronics and Telecommunications Research Institute); Seon-Hee Park (Electronics and Telecommunications Research Institute);
Short Abstract: we propose a method which finds and shows some active sites structurally similar to active site of the target protein. The similarities between the active site of target protein and that of other proteins are calculated by our proposed system based on geometric hashing (GH).
Long Abstract: Click Here

Poster I-73
A Filtering Approach for Improved Modelling of Predicted Contact Maps Alberto J. Martin, Dr Alessandro Vullo, Dr Gianluca Pollastri School of Computer Science and Informatics University College Dublin Belfield, Dublin 4, Ireland {albertoj,alessandro.vullo,gianluca.pollastri}@ucd.ie
Alberto J. Martin (School of Computer Science and Informatics University College Dublin); A. Vullo (School of Computer Science and Informatics University College Dublin); G. Pollastri (School of Computer Science and Informatics University College Dublin);
Short Abstract: Residue contact maps are an important intermediate step towards de novo prediction of protein structure. The problem of accurately predicting contact maps from primary sequences is still unsolved. We focus on the problem of learning to predict physically realisable residue contact maps by directly incorporating rules encoding protein structural principles.
Long Abstract: Click Here

Poster I-74
Molecular dynamic and structural analysis from the ab initio model of HC-Pro, a plant virus multifunctional protein
Antonio Sergio Kimus Braz (Depto Genetica - IBB - UNESP Botucatu); Sérgio Oyama Jr. (Centro de Biologia Molecular Estrutural, Laboratório Nacional de Luz Síncrotron); Ivan de Godoy Maia (Depto Genetica - IBB - UNESP Botucatu);
Short Abstract: The HC-Pro encoded by Potyvirus is a multifunctional protein involved in several steps of the virus life cycle. In this study, we build a three-dimensional model of HC-Pro using an ab initio method, followed by molecular dynamics of two domains derived from this structure.
Long Abstract: Click Here

Poster I-75
A set of approaches for analysis of functional relationship in proteins.
Joanna M. Sasin (International Institute of Molecular and Cell Biology); Janusz M. Bujnicki (International Institute of Molecular and Cell Biology);
Short Abstract: We would like to present a set of methods for analysis of functional relationships in protein families that focus on comparisons of protein surfaces and structures.
Long Abstract: Click Here

Poster I-76
Structural Annotation Pipeline for Malarial proteomes
Yolandi Joubert (Department Biochemistry, University of Pretoria); Fourie Joubert (Department Biochemistry, University of Pretoria);
Short Abstract: The pipeline consists of a series of established bioinformatics tools, such as Blast vs. PDB, family assignment, secondary structure and TM predictions, and is applied to several malarial proteomes. Annotations such as protein interactions and small molecule interactions are added for P.falciparum. Results are made accessible through a web application developed in ZOPE.
Long Abstract: Click Here

Poster I-77
LIGLIB: Generation of in silico analogous ligand libraries
Wolf Cochrane (University Pretoria); Fourie Joubert (University Pretoria);
Short Abstract: LIGLIB (LIGand LIbrary Builder) is an open source tool that builds in silico analogous ligand libraries. The user selects permutation positions on the structure, and for each a range of linkers and fragments. LIGLIB permutes over combinations of linkers and fragments at each position and creates a molecule for each.
Long Abstract: Click Here

Poster I-78
Structural and phylogenetic studies with a theoretical model of the BjussuMP-I, a metalloprotease isolated from the Bothrops jararacussu venom
Angelo J. Magro (Departamento de Física e Biofísica - Instituto de Biociências de Botucatu - UNESP - Botucatu/SP - Br); Antônio S. K. Braz (Departamento de Genética - Instituto de Biociências de Botucatu - UNESP - Botucatu/SP - Brasil); Andreimar M. Soares (Departamento de Análises Clínicas, Toxicológicas e Bromatológicas - Faculdade de Ciências Farmacêuti); Marcos R. M. Fontes (Departamento de Física e Biofísica - Instituto de Biociências de Botucatu - UNESP - Botucatu/SP - Br);
Short Abstract: In this work the phylogenetic and structural analyses of a theoretical BjussuMP-I metalloprotease/catalytic domain model were performed to get new insights into the molecular evolution of the metalloproteases and to identify eventual structural differences responsible for the several biochemical activities carried out by these enzymes.
Long Abstract: Click Here

Poster I-79
Conformational changes in the structure of Shikimate Kinase from Mycobacterium tuberculosis caused for ions and substrates.
Marcio Vinicius Bertacine (Ibilce - UNESP); Livia Maria Faim (Ibilce - UNESP); Igor Bordim Vasconcelos (PUC - Porto Alegre RS); Jaim Simões de Oliveira (PUC - Porto Alegre RS); Luis Augusto Basso (PUC - Porto Alegre RS); Diógenes Santiago Santos (PUC - Porto Alegre RS); Walter Filgueira de Azevedo Jr. (PUC - Porto Alegre RS);
Short Abstract: Shikimate kinase converts shikimate in shikimate-3-phospahte. In this reaction is required ADP, magnesium and chloride. This molecules influence in the structure of shikimate kinase. Magnesium influence in the position of hydroxyl groups of shikimate. The chloride influence in the positioning of ADP. The shikimate closes of LID domain.
Long Abstract: Click Here

Poster I-80
XXStout: Improving the Prediction of Long range residue contacts
Ian Walsh (University College Dublin School of Computer Science and Informatics); Alessandro Vullo (University College Dublin School of Computer Science and Informatics); Gianluca Pollastri (University College Dublin School of Computer Science and Informatics);
Short Abstract: This poster discusses our XXStout server, which is a state of the art residue contact predictor. It uses the novel feature of contact density as input, contact density is the principal eigenvector of the residue contact matrix. We show that using contact density significantly increases the performance.
Long Abstract: Click Here

Poster I-81
Improvement of Portable virtual reality system with haptic device for molecular modeling and education.
Isao Okada (Tokyo Medical and Dental University); Takayuki Ohnishi , (Tokyo Medical and Dental University); Hiroshi Nagata, (Tokyo Medical and Dental University); Hiroshi Tanaka (Tokyo Medical and Dental University); Hiroshi Mizushima (Tokyo Medical and Dental University);
Short Abstract: We have been developing Virtual Reality System for molecular modeling using haptic device. This time we have improved our easy-to-carry system for demonstration at the conference or at other labs using portable PC. We also tried some actual simulation of membrane proteins.
Long Abstract: Click Here

Poster I-82
Protein Structure Prediction Aided Text Mining for Functional Inference
Andreas Rechtsteiner (CGB, Indiana University); Jeremy Luinstra (B-Div, Los Alamos National Lab); Judith D. Cohn (B-Div, Los Alamos National Lab); Charlie E. M. Strauss (B-Div, Los Alamos National Lab);
Short Abstract: Ab-initio structure prediction with Rosetta and Mammoth can be highly effective on structural variations beyond the limits of homology modeling and threading approaches. We report here that putative annotation rankings based on literature keyword similarity dramatically improve the annotation accuracy over either sequence or structure based annotation alone.
Long Abstract: Click Here

Poster I-83
Chemoinformatics approach to Differential Drug Response of the Tyrosine Kinase Domain BCR-ABL to Imatinib in Chronic Myeloid Leukemia Patients
Sergio de Alencar (UFMG); Julio Lopes (UFMG); Abdrelly Martins (UFMG);
Short Abstract: Chemoinformatics approach to differential drug response of the tyrosine kinase domain BCR-ABL to imatinib in chronic myeloid leukemia (CML) patients in order to investigate the effects of three substitutions (Tyr315Ile, Phe317Leu and Phe359Val) at direct drug contact sites in CML patients that develop imatinib resistance.
Long Abstract: Click Here

Poster I-85
A Study of SNPs in Sirtuins Structures
Beatriz J. Pinto (Faculty of Medicine of Ribeirão Preto - University of São Paulo); André L. T. Vinci (Faculty of Medicine of Ribeirão Preto - University of São Paulo); Marcela C. de Santo (Laboratory of Bioinformatics - University of Ribeirão Preto); Milton Faria Jr (Laboratory of Bioinformatics - University of Ribeirão Preto); Silvana Giuliatti (Faculty of Medicine of Ribeirão Preto - University of São Paulo);
Short Abstract: The goal is to locate SNPs in the proteins structures of the sirtuins and verifying if they occur in active sites. Alignment between SNPs and proteins was obtained and it was used to locate SNPs in the structures. However, none of the substitutions had presented alterations affecting the active sites.
Long Abstract: Click Here

Poster I-86
Comparative Analysis of Human SIRT Proteins Tertiary Structures
André L. T. Vinci (Faculty of Medicine of Ribeirão Preto - University of São Paulo); Beatriz J. Pinto (Faculty of Medicine of Ribeirão Preto - University of São Paulo); Marcela C. de Santo (Laboratory of Bioinformatics - University of Ribeirão Preto); Milton Faria Jr (Laboratory of Bioinformatics - University of Ribeirão Preto); Silvana Giuliatti (Faculty of Medicine of Ribeirão Preto - University of São Paulo);
Short Abstract: Humans have proteins homologous to SIR2, the sirtuins. Some sirtuins have unknown function. The aim is a comparative analysis of the sirtuins structures. A alignment determinated a consensus for each sirtuin. The conserved regions were located in the tertiary structures. It was found amino acid presenting chemical properties replacement.
Long Abstract: Click Here

Poster I-87
Using a computer model of human CYP21 to correlate structural features with clinical severity
Jonas Carlsson (IFM Bioinformatics, Linköping University); Tiina Robins (Molecular Medicine and Surgery, Centre of Molecular Medicine, (CMM), KI / KS); Maria Sunnerhagen (Molecular Biotechnology, IFM, Linköping University); Anna Wedell (Molecular Medicine and Surgery, Centre of Molecular Medicine, (CMM), KI / KS); Bengt Persson (IFM Bioinformatics, Linköping University; Centre for Genomics and Bioinformatics, Karolinska Institu);
Short Abstract: A structural model of human CYP21 was calculated based on the crystal structure of CYP2C5, to better understand the molecular causes of CAH. 60 disease causing mutations and six normal variants, were analysed using this model. A structural explanation for the corresponding phenotype was found for all but two mutants.
Long Abstract: Click Here

Poster I-88
Protein Structural Analysis Made Easy
Tjaart de Beer (University of Pretoria); Fourie Joubert (University of Pretoria);
Short Abstract: Biologists do not always have the appropriate training to do in silico analysis of protein structures. We aim to provide a one-stop, browser-based tool and visualization facility, which will allow the user to analyse protein structures and retrieve data about the protein via webservices from other international sites.
Long Abstract: Click Here

Poster I-89
Tsallis Statistics Applied to Protein Folding, Protein Model Refinement and Molecular Complex Optimization
Pedro G. Pascutti (Instituto de Biofísica Carlos Chagas Filho - Universidade Federal do Rio de Janeiro - Brasil); Tacio V. Amorim Fernandes (Instituto de Biofísica Carlos Chagas Filho - Universidade Federal do Rio de Janeiro - Brasil); Flávia P. Agostini (Laboratório Nacional de Computação Científica/CNPq - Petrópolis-RJ - Brasil);
Short Abstract: We applied a proposal of generalization for Statistical Mechanics using stochastic simulated annealing coupled to a molecular Force Field in protein folding studies, and show that in this strategy is necessary a new parameter to control the freezing process, to avoid polypeptide chains to be trapped in energy local minima.
Long Abstract: Click Here

Poster I-90
MOLECULAR MODELING OF THE RIBOFLAVIN GENES FROM ACIDITHIOBACILLUS FERROOXIDANS.
LUCIO FABIO CALDAS FERRAZ (CBMEG, UNICAMP); FERNANDA DE CASTRO REIS (CBMEG, UNICAMP); MARCOS TADEU SANTOS (CBMEG, UNICAMP); ANA PAULA FELÍCIO (IQ, UNESP); PAULA FALCÃO (EMBRAPA); MARIA TERESA MARQUES NOVO (UFSCAR); GORAN NESHICH (EMBRAPA); OSWALDO GARCIA JR (IQ, UNESP); LAURA MARIA MARISCAL OTTOBONI (CBMEG, UNICAMP);
Short Abstract: Acidithiobacillus ferrooxidans is a bacteria with economic relevance in metal bioleaching. Very little is known about the riboflavin genes from Acidithiobacillus ferrooxidans. Molecular modeling of enzymes involved in riboflavin biosynthesis could contribute to a better understanding of riboflavin biosynthesis when A. ferroxidans is maintained in the presence of metal sulfides.
Long Abstract: Click Here

Poster I-93
Anti-tick vaccines: homology modeling of a tick antigen Bm91 from Boophilus microplus
Jurgens de Bruin (Bioinformatics,University of Pretoria); Anabella R.M. Gaspar (Biochemistry,University of Pretoria); Albert W.H. Neitz (Biochemistry,University of Pretoria);
Short Abstract: An alternative method of tick control involves the artificial induction of immunologically-based resistance to infestation. The 3D-structure of Bm91, a tick-antigen from B. microplus, was predicted by means of homology modeling using HACE as template. This work has contributed towards future drug design and development of ectoparasite specific anitigens.
Long Abstract: Click Here

Poster I-94
In Silico Comparative Macromolecular Modeling of the Leishmania Flagellum: 3D Perspective of an Axonemal Nanomachine
Cleilton Lima Rocha (NUGEN-UECE); Marcília Pinheiro da Costa (NUGEN-UECE); George de Paulo Ferreira (Computação-UECE); Fabiana Freire de Araújo (Computação-UECE); Allan Rodrigo Soares Maia (NUGEN-UECE); Patricy de Andrade Salles (NUGEN-UECE); Hálisson Lucas Ribeiro (Computação-UECE); Ana Luiza Bessa de Paula Barros (Computação-UECE); Diana Magalhães de Oliveira (NUGEN-UECE);
Short Abstract: Here we introduce a few tentative computer-generated and physical models of the flagellar axoneme of the protozoan Leishmania in an attempt to represent the nanostructured complexity of the assemblies of macromolecular structures that resemble a rotatory and bending natural nanomachine. Resulting tangible models will be available at request.
Long Abstract: Click Here

Poster I-95
MOLECULAR MODELING OF POLYPEPTIDE DEFORMYLASE FROM ACIDITHIOBACILLUS FERROOXIDANS
FERNANDA DE CASTRO REIS (CBMEG, UNICAMP); LÚCIO FÁBIO CALDAS (CBMEG, UNICAMP); MARCOS TADEU DOS SANTOS (CBMEG, UNICAMP); PAULA K. FALCÃO (EMBRAPA INFORMÁTICA AGROPECUÁRIA, CAMPINAS); GORAN NESHICH (EMBRAPA INFORMÁTICA AGROPECUÁRIA, CAMPINAS); LAURA M. M. OTTOBONI (CBMEG, UNICAMP);
Short Abstract: We report the molecular modeling of the polypeptide deformylase from A. ferrooxidans. The model presents all the conserved residues that characterize this family of protein including, the HEXXH domain and the Gln50, Cys90, Leu91, Ser92 residues. Interactions among many residues showed some important differences when compared with the reference structure.
Long Abstract: Click Here

Poster I-96
Ab Initio Modelling of Protein C-alpha Traces Through Structural Constraints Predicted by Machine Learning
Davide Bau (School of Computer Science and Informatics, UCD Dublin); Alessandro Vullo (School of Computer Science and Informatics, UCD Dublin); Gianluca Pollastri (School of Computer Science and Informatics, UCD Dublin);
Short Abstract: We describe Distill, a fully automated computational system for ab initio prediction of protein C-alpha traces composed of: a set of predictors of protein features; a simple optimisation algorithm. On a small PCs Distill can solve protein coordinates on a genomic scale in the order of days.
Long Abstract: Click Here

Poster I-97
Fast Protein Structure Alignment by Joining Similar Substructure Pair
Chan-Yong Park (ETRI); Sung-Hee Park (ETRI); Dae-Hee Kim (ETRI); Soo-Jun Park (ETRI); Hong-Ro Lee (Chung Nam University); Chi-Jung Hwang (Chung Nam University);
Short Abstract: We propose a new fast protein structure alignment algorithms. This algorithm uses a 3D chain code representation for fast measuring the local geometric similarity of protein and apply a backtracking algorithm for joining a similar local substructure efficiently.
Long Abstract: Click Here

Poster I-98
Sequence based prediction of distortion in alpha-helix using Support Vector Machine
Ashish V Tendulkar (KReSIT, IIT Bombay); Pramod P. Wangikar (Dept of Chemical Engg, IIT Bombay);
Short Abstract: The structure conservation in alpha-helix subclasses reveals sequence and context dependent factors causing variations. We capture these factors in form of sequence features and train support vector machine(SVM) for sequence based discrimination between regular and distorted helix. The SVM performs with 80.97% precision and 88.05% recall.
Long Abstract: Click Here

Poster I-99
FILTREST3D: a simple method for discrimination of multiple structural models against spatial restraints
Michal J. Gajda (Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell); Marta Kaczor (Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell); Anastasia Bakulina (Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell); Andrzej Kasperski (Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell); Alan M. Friedman (Department of Biological Sciences, Purdue University, West Lafayette, IN, USA); Chris Bailey-Kellogg (Department of Computer Science, Dartmouth College, Hanover, NH, USA); Janusz M. Bujnicki (Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell);
Short Abstract: FILTREST3D http://filtrest3d.genesilico.pl/ is a new method for discrimination of alternative models against mixed sets of restraints (e.g. spatial distances) derived from experimental analyses as well as from computational predictions (e.g. solvent accessibility) or arbitrarily defined by the user. It can be used to analyze models of individual proteins and complexes.
Long Abstract: Click Here

Poster I-100
Meta-MQAP: an SVM-based meta-server for the quality assessment of protein models
Marcin Pawlowski (International Institute of Molecular and Cell Biology in Warsaw); Ryszard Matlak (International Institute of Molecular and Cell Biology in Warsaw); Janusz Bujnicki (International Institute of Molecular and Cell Biology in Warsaw);
Short Abstract: Presented Meta-MQAP uses the results of the five primary MQAPs to predict the absolute deviation (in Angstrom) of C-alpha atoms of all residues in the model from their counterparts in the native structure, without the knowledge of the actual native structure.
Long Abstract: Click Here

Poster I-101
High resolution crystal structure of BthTX-I-BPB and comparison analysis with native BthTX-I - insights into the lack of the toxic activities
Marchi-Salvador, D.P. (IBB-UNESP); Fernandes, C.A.H. (IBB-UNESP); dos Santos, J.I. (IBB-UNESP); Amui, S.F. (FCF-USP); Soares, A.M. (FCF-USP); Fontes, M.R.M. (IBB-UNESP);
Short Abstract: Structure of a non-catalytic and myotoxic Lys49-PLA2 was solved with BPB inhibitor in two different oligomeric states. BthTX-I with the His48 chemically modified by BPB shows strong myotoxic and citotoxic activities reduction. The comparison between monomeric and dimeric BthTX-I-BPB and three different native conformations is analyzed.
Long Abstract: Click Here

Poster I-102
Classifiers of the protein interactions with their substrate/inhibitors
Vera S. Garcia (Unicamp/Embrapa); Paula Kuser Falcão (Embrapa);
Short Abstract: Basically all biological processes require protein-ligand identifications. One major challenge to biophysics-chemistry is try to predict these interactions. One step towards solving this mystery is analyzing the structural features involved in the complex formation. A good biological model to start these studies is the cystein-protease family.
Long Abstract: Click Here

Poster I-103
Screening the human UTR database for stabilized RNA secondary structures
Sven Siebert (Department of Bioinformatics, Institute of Computer Science, Albert-Ludwigs University Freiburg); Rolf Backofen (Department of Bioinformatics, Institute of Computer Science, Albert-Ludwigs University Freiburg);
Short Abstract: We screened the human 5'UTR and 3'UTR database for stabilized RNA structures. A window sliding approach is used to fold sequence regions of various lengths. The stability of a folded RNA sequence is determined by introducing a significant value. We compared our stable regions with sequence patterns given in the database UTRSite.
Long Abstract: Click Here

Poster I-104
Self-consistent Assignment of Asparagine and Glutamine Side-Chain Amide Rotamers
Christian X. Weichenberger (Dept. of Molecular Biology, University of Salzburg); Manfred J. Sippl (Dept. of Molecular Biology, University of Salzburg);
Short Abstract: We present a method based on potentials of mean force to validate and correct the amide side-chain orientation of asparagine and glutamine in protein structures which is often indistinguishable in electron densities obtained from X-ray experiments. Our method shows excellent agreement with expert annotated data. Availability: http://flipper.services.came.sbg.ac.at
Long Abstract: Click Here

Top

Systems Biology

Poster J-1
BiologicalNetworks: integrated environment for system level analysis and predictive modeling of molecular machines. Case study of eukaryotic early meiosis.
Michael Baitaluk (San Diego Supercomputer Center, UCSD); Mayya Sedova (San Diego Supercomputer Center, UCSD); Biranchi Patra (Keck Graduate Institute); Kirilynn Svay (Keck Graduate Institute); Amarnath Gupta (San Diego Supercomputer Center, UCSD); Animesh Ray (Keck Graduate Institute);
Short Abstract: We describe BiologicalNetworks: an information integration system for modeling of gene regulatory networks and show how system level models of genetic regulatory processes involved in development and differentiation can be derived from an integrated gene/protein network generated from: mRNA expression profiles and chromatin-immunoprecipitation experiments, protein-protein interaction, and genetic interaction data.
Long Abstract: Click Here

Poster J-2
Analysis of pleiotropy during C. elegans development and interpretation with interactome networks
Lihua Zou (Harvard University); Brian Ross (Whitehead Institute); Jun Liu (Harvard Univeristy); Hui Ge (Whitehead Institute);
Short Abstract: Pleiotropy refers to the phenomenon of a single gene controlling multiple phenotypes. We analyze phenotypic data from C. elegans development and identify pleiotropic proteins. We develop a model to estimate the importance of a given protein to the propagation of biological signals in interactome networks. We propose that pleiotropic proteins act as “information exchange centers” between complexes or pathways.
Long Abstract: Click Here

Poster J-3
Searching for Genes Involved in Novel Mechanisms of Tumor Cell Death Triggered by FGF2: Introducing New Methodological Approaches
F. Nakano (BIOINFO-USP, SP, Brasil); P. F. Asprino (Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil); C. H. A. Higa (Instituto de Matetmática e Estatística, Universidade de São Paulo, SP, Brasil); R. F. Hashimoto (nstituto de Matetmática e Estatística, Universidade de São Paulo, SP, Brasil); H. A. Armelin (Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil);
Short Abstract: Coefficient of Determination (CoD) is introduced to analyze gene expression data aiming to uncover genetic networks underlying the Y1 adrenocortical tumor cell death triggered by FGF2. CoD networks are searched for subnetworks modeled as logic circuits and the shortest path between FGF stimulus and phenotype (survival/death), modeled as Bayesian Networks. Initial probing revealed induction of the p190RhoA-GAP gene antagonising FGF2-cell death triggering, a likely relevant inference since RhoA activation is required for FGF2-cell death triggering.
Long Abstract: Click Here

Poster J-4
Systematic Analysis of Phenotypes of E. coli Single Gene Deletion Mutants
Hirotada Mori (Nara Institute of Science and Technology); Hiroko Matsui (Mitsubishi space Co. Ltd.); Hiroaki Gobara (Nara Institute of Science and Technology); Shigeki Tanishima (Mitsubishi space Co. Ltd.); Sivasundaram Suharnan (Axio Helix Co. Ltd.); Shigehiko Kanaya (Nara Institute of Science and Technology); Barry L. Wanner (Purdue University);
Short Abstract: Complete single gene knock out library of E. coli was established and applied for systematic functional network analysis using BIOLOG system. Data mining has been performed by statistical data processing followed by clustering based on Graph theory. The initial target genes were glycolysis and TCA cycle enzyme genes.
Long Abstract: Click Here

Poster J-6
Dynamical Modeling of the Gene Regulatory Network of Halobacterium from Diverse Global Systems Biology Datasets
David J Reiss (Institute for Systems Biology); Vesteinn Thorsson (Institute for Systems Biology); Paul Shannon (Institute for Systems Biology); Lee Hood (Institute for Systems Biology); Nitin S Baliga (Institute for Systems Biology); Richard Bonneau (Depts. of Biology and Computer Science, New York University);
Short Abstract: We have developed a computational strategy for inferring a global model of the regulatory network of the archaeon Halobacterium NRC-1, using genome-wide high-throughput data, de novo. The procedure integrates mRNA and protein levels with functional associations, physical interactions, and regulatory sequence to generate a dynamic, predictive regulatory model that is biologically and statistically parsimonious.
Long Abstract: Click Here

Poster J-7
Statistical Analysis of Retroviral Insertional Mutagenesis Data
Jeroen de Ridder (Information and Communication Theory Group, Delft University of Technology); Jaap Kool (Division of Molecular Genetics, The Netherlands Cancer Institute); Anthony Uren (Division of Molecular Genetics, The Netherlands Cancer Institute); Lodewyk Wessels (Division of Molecular Biology, The Netherlands Cancer Institute); Marcel Reinders (Information and Communication Theory Group, Delft University of Technology);
Short Abstract: The presence of multiple mutations within one tumor hints toward cooperation between the mutated genes. We propose a two-dimensional Gaussian Kernel Convolution method, a computational technique that identifies the cooperating mutations in mutagenesis data. This resulted in the discovery of new regions in the genome that may be involved in tumorigenesis.
Long Abstract: Click Here

Poster J-8
Inferring transcriptional modules from ChIP-chip-, motif- and microarray data
Karen Lemmens (Dept. Electrical Engineering, K.U.Leuven); Thomas Dhollander (Dept. Electrical Engineering, K.U.Leuven); Tijl De Bie (Dept. Psychology); Pieter Monsieurs ( Dept. Electrical Engineering, K.U.Leuven); Kristof Engelen (ept. Microbial and Molecular Systems, K.U.Leuven); Bart De Moor ( Dept. Electrical Engineering, K.U.Leuven); Kathleen Marchal (ept. Microbial and Molecular Systems, K.U.Leuven);
Short Abstract: We present ‘ReMoDiscovery’, a module detection algorithm that exploits in a concurrent way three independent data sources: ChIP-chip data, motif information and gene expression profiles. When compared to published module discovery algorithms, ReMoDiscovery is fast and easily tunable. When evaluated on yeast data, biologically meaningful findings were generated.
Long Abstract: Click Here

Poster J-9
In silico motif search along with in vivo confirmation of NF-kB regulated gene sets in NPC microarray data.
Yuching Lai (Life Science Department, Chang Gung University); Greg Tyrelle (Life Science Department, Chang Gung University); Kuang-Den Chen (Life Science Department, Chang Gung University);
Short Abstract: NF-kB has been implicated as a link between chronic inflammation and cancer. We use in silico promoter analysis of genes up-regulated in a NPC microarray study to determine NF-kB activated gene clusters. Results show significant clusters of up-regulated cytokines in NPC are activated by NF-kB.
Long Abstract: Click Here

Poster J-10
Dedicated Computer System for Genome Wide Simulation of Signal Transduction Networks
Tetsuya Maeshiro (University of Tsukuba); Katsunori Shimohara (Doshisha University);
Short Abstract: We have developed a computer system dedicated to simulate and predict signal transduction networks in biological cells. The simulation speed is at least ten thousand times faster than software based simulations executed on conventional computers. We present a simulation result of a simple cell model, and the potentiality of our system.
Long Abstract: Click Here

Poster J-11
Computational predicted protein associations of Mycobacteriun tuberculosis under hypoxic conditions associated with latency.
Christian SOLIS CALERO (Facultad de Farmacia y Bioquímica - Universidad Nacional Mayor de San Marcos); Luisa NEGRON BALLARTE (Facultad de Farmacia y Bioquímica - Universidad Nacional Mayor de San Marcos);
Short Abstract: A set of Mycobacteriun tuberculosis functional annotated proteins up-expressed under hypoxic conditions associated with latency, were analysed using computational methods for the inference of protein–protein associations. This approach reveals certain signatures, including associations of proteins involved in fatty acid b-oxidation, nitrite/nitrate metabolism, and protection against stress.
Long Abstract: Click Here

Poster J-12
GEM System version 2 for the analysis of metabolic pathways
Kazuharu Arakawa (Institute for Advanced Biosciences, Keio University, and Japan Society for the Promotion of Science); Nobuaki Kono (Institute for Advanced Biosciences, Keio University); Satoshi Tamaki (Institute for Advanced Biosciences, Keio University); Hiromi Yoshida (Institute for Advanced Biosciences, Keio University); Masaru Tomita (Institute for Advanced Biosciences, Keio University);
Short Abstract: The Genome-based E-cell Modeling System (GEM System) realizes a automatic conversion of genome sequence data into a quantitative in silico cell-wide metabolic pathway model. Manually curated database of kinetic in silico models maintained for this purpose facilitates the dynamic modeling process.
Long Abstract: Click Here

Poster J-13
A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data – a case study of E2F1
Victor X Jin (UC Davis Genome Center); Alina Rabinovich (UC Davis Genome Center); Sharon L. Squazzo (UC Davis Genome Center); Peggy J. Farnham (UC Davis Genome Center);
Short Abstract: We have developed a computational genomics approach (ChIPModules), to identify transcriptional regulatory modules using data obtained from chromatin immunoprecipitation microarrays. We have used E2F1 in cancer cells as a study case to demonstrate our approach has identified five regulatory modules for E2F1 and verified one module by another ChIP-chip.
Long Abstract: Click Here

Poster J-14
METABOLIC FLUX ANALYSIS TO STUDY THE PRODUCTION OF CDA, BY STREPTOMYCES COELICOLOR
Raul Munoz-Hernandez (The University of Manchester); Ana Katerine de Carvalho Lima Lobato (The University of Manchester); Ferda Mavituna (The University of Manchester);
Short Abstract: Streptomyces coelicolor, produces many secondary metabolites. Of these, CDA is of great interest; especially for its potential applications in novel Drug Development. In this work, a metabolic model for it was constructed using the Metabolic Flux Balancing method. This model is being applied to develop strategies to increase CDA productivity.
Long Abstract: Click Here

Poster J-15
The Role of LIMK1 in Endothelial Barrier Function
Matvey Gorovoy (University of Illinois); Tatyana Voyno-Yasenetskaya (University of Illinois);
Short Abstract: Microtubule destabilization promotes the formation of actin stress fibers and enhances the contractility of cells. Our findings indicate that LIM kinase 1, LIMK1 can coordinate microtubules and actin cytoskeleton. We showed that the loss of LIMK1 protein leads to less permeable pulmonary blood vessels. Therefore, LIMK1 might be a target for therapeutic drug development for acute lung injury and lung edema.
Long Abstract: Click Here

Poster J-16
Computational analysis of gene regulatory elements
Reddy, D. A. (University of Hyderabad); Mitra, C. K. (University of Hyderabad);
Short Abstract: The core promoter regions and also the TFBS have been studied by calculating the average mutual information content. For mouse and human, both TATA-box and TSS-region are likely to play important roles. For plant, the importance of TSS-region in transcriptional initiation is more compared to the TATA box. The TFBS clustering results gives us a new way to look at the protein classification-not based on their structure or function of TFs but by the nature of their TFBS.
Long Abstract: Click Here

Poster J-17
An Agent-based Model of T cell Proliferatin Experiments
Beatriz Stransky (UFRJ); Eduardo Auilar (UFRJ); Luis Alfredo V Carvalho (UFRJ); Alberto Nobrega (UFRJ);
Short Abstract: The peripheral T-cell repertoire is maintained in equilibrium by both the production of thymic T-cells and self-renewal in periphery. We present an immune system model based on computational agents to simulate this population dynamics and address the role of self-renewing process in the generation of homeostasis.
Long Abstract: Click Here

Poster J-18
Regulation of E.coli respiration: molecular genetic network reconstruction and mathematical modeling
Alexander V. Ratushny (Institute of Cytology and Genetics SB RAS); Tamara M. Khlebodarova (Institute of Cytology and Genetics SB RAS); Vitaly A. Likhoshvai (Institute of Cytology and Genetics SB RAS);
Short Abstract: By using the GeneNet technology, we reconstructed the molecular genetic network of the regulation of E. coli cell respiration. The mathematical models describing the influence of oxygen concentration in the environment on the regulation of E.coli respiratory system and main catabolic pathways functioning were constructed.
Long Abstract: Click Here

Poster J-19
Probabilistic comparison of gene sets for detecting key metabolic pathways in the stress response of yeast
Jean-Marc Schwartz (Kyoto University); Claire Gaugain (University of Bordeaux); Jose Nacher (Kyoto University); Antoine de Daruvar (University of Bordeaux); Minoru Kanehisa (Kyoto University);
Short Abstract: We analyse the flexible response of yeast to different stress conditions, including temperature shocks, nutrient starvation, and exposure to toxins. We show that a combination of correlation-based expression analysis with a probabilistic comparison of sets implemented by the BlastSets tool leads to uncovering key metabolic pathways related to stress response.
Long Abstract: Click Here

Poster J-20
Does the Yeast PPI Network Look Like a Jellyfish?
Shaohua Zhou (Department of Developmental and Cell Biology, University of California Irvine); Arthur D. Lander (Department of Developmental and Cell Biology, University of California, Irvine); Natasa Przulj (Department of Computer Science, University of California Irvine);
Short Abstract: It has been shown that the Autonomous System Internet topology "looks like a jellyfish" (Siganos et al., 2006). Since the purpose of both the Internet and protein-protein interaction (PPI) networks is to deliver information, we ask if the PPI networks are also structured like a jellyfish. We show that the PPI network of yeast Saccharomyces cerevisiae looks like a jellyfish.
Long Abstract: Click Here

Poster J-21
Biological Organization and Information
Maurício V. Kritz (LNCC/MCT);
Short Abstract: A novel concept of information modeled on biological phenomena is introduced. Its definition assumes that all biological entities are whole-part organizations. This concept depends on observers, signals, an interpreter and a perception hypothesis. Information is conveyed by organizations, composed from hierarchies and associations, and doesn’t presuppose a sender.
Long Abstract: Click Here

Poster J-22
Beyond classical statistics - A systems biology approach for pathway level analysis
Sorin Draghici (Karmanos Cancer Institute and Dept. of Comp. Science, Wayne State Univ.); Kashyap Amin (Dept. of Comp. Science,); Arina Done (Dept. of Comp. Science); Purvesh Khatri (Dept. of Comp. Science);
Short Abstract: A statistical approach is universally used to identify the most relevant regulatory pathways in high-throughput experiments. We show this approach is unsatisfactory, and can provide incorrect results. Using a systems biology approach, we developed a more powerful analysis that includes the classical statistics but also considers other crucial factors.
Long Abstract: Click Here

Poster J-23
Small Molecule Regulation of Metabolic Networks
Alex Gutteridge (Kyoto University); Susumu Goto (Kyoto University); Minoru Kanehisa (Kyoto University);
Short Abstract: We have used data from the KEGG and BRENDA databases to study the way in which small molecules regulate metabolism. We find a scale-free topology in the regulatory network that is conserved across several organisms, though the details of which compounds act as regulators is found to vary.
Long Abstract: Click Here

Poster J-24
SymBioSys: K.U.Leuven Center for Computational Systems Biology
Yves Moreau (K.U.Leuven ESAT-SCD); Sigrid De Keersmaeker (K.U.Leuven BIW-CMPG); Kathleen Marchal (K.U.Leuven BIW-CMPG); Chantal Mathieu (K.U.Leuven MED-Legendo); Frans Schuit (K.U.Leuven MED-GEU); Jos Vanderleyden (K.U.Leuven BIW-CMPG); Iven Van Mechelen (K.U.Leuven PSY-QuantPsy); Geert Verbeke (K.U.Leuven MED-BioStat); Joris Vermeesch (K.U.Leuven MED-CME-UZ); Mieke Verstuyf (K.U.Leuven MED-Legendo); Bart De Moor (K.U.Leuven ESAT-SCD);
Short Abstract: SymBioSys, the K.U.Leuven Center for Computational Systems Biology, is an interfaculty platform that integrates expertise in bioinformatics, statistics, and life sciences. The consortium targets three problems in computational systems biology: gene prioritization by genomic data fusion, regulatory module discovery, and network inference. http://www.kuleuven.be/symbiosys.
Long Abstract: Click Here

Poster J-25
Biological Network Comparison Using Graphlet Degree Distribution
Natasa Przulj (UC Irvine, Computer Science);
Short Abstract: We devise a highly constraining network comparison metric based on local structural properties that are a direct generalization of the degree distribution. We use this new metric to demonstrate that geometric random graphs better model protein-protein interaction networks of various species than do Erdos-Renyi, random scale-free, or Barabasi-Albert scale-free networks.
Long Abstract: Click Here

Poster J-26
Studying microRNA-target interactions using gene expression data
Gabor Halasz (Columbia Univesity); Harmen J Bussemaker (Columbia Univesity);
Short Abstract: We investigated the effect of microRNAs on mRNA target stability using transcript sequence and steady-state expression data from normal human tissues. Activity levels of miRNAs inferred from the differential expression of putative targets revealed tissue-specific regulation in several tissues and helped distinguish functional targets from non-functional ones.
Long Abstract: Click Here

Poster J-27
KEGG-based pathway visualization tool for complex omics data
Nobuaki Kono (Institute for Advanced Biosciences, Keio University); Kazuharu Arakawa (Japan Society for the Promotion of Science); Yohei Yamada (Institute for Advanced Biosciences, Keio University); Hirotada Mori (Nara Institute of Science and Technology); Masaru Tomita (Institute for Advanced Biosciences, Keio University);
Short Abstract: We have developed a pathway mapping tool for the visualization of multiple omics data, including transcriptome, proteome, and metabolome. The software maps given data onto an integrated pathway map based on the KEGG pathway diagrams in SVG format. The software is available as a web application at: http://www.g-language.org/data/marray/.
Long Abstract: Click Here

Poster J-28
Evidential Reasoning and Validation for Gene Expression Data
Noppadon Khiripet (National Electronics and Computer Technology Center, Thailand);
Short Abstract: Inferring the network structure of genes poses a serious challenge in microarray analysis where the main limitation is the amount of available experimental data. Integrating evidence from the NCBI and KEGG in learning Bayesian network framework helps improve the reliability of clustering as well as gene network inferring procedures.
Long Abstract: Click Here

Poster J-29
Protein Interaction Prediction with Supervised Learning Methods
Oksana Kohutyuk (Department of Comp. Science, Iowa State University); Vasant Honavar (Department of Comp. Science, Iowa State University);
Short Abstract: We evaluated the effects of class distribution in training and test data in protein interaction prediction on performance of different classifiers (DT, NB, SVM, RF), and developed a recursive algorithm that utilizes predictions made at a given iteration for future classifications, which showed improved performance on small data sets.
Long Abstract: Click Here

Poster J-30
Cellular sensing machinery for exogenous and endogenous conditions is differentially encoded on the chromosome and poorly conserved across genomes.
Heladia Salgado Osorio (CCG/UNAM); Sarath Chandra Janga (CCG/UNAM); Agustino Martínez Antonio (INSERM U511, Université Pierre et Marie Curie, CHU-Pitié Salpetrière Paris, France); Julio Collado Vides (CCG/UNAM);
Short Abstract: Transcriptional factors (TFs) have been classified previously into three classes, depending on the source of their allosteric or equivalent metabolite: TFs of external, internal and hybrid sensing classes. Here we report a chromosomal proximity of transcription factors and their signal genes to sense external conditions in contrast to the components for internal sensing that tend to be distant.
Long Abstract: Click Here

Poster J-31
PATIKAweb: A Web service for querying, visualizing and analyzing a graph-based pathway database
Asli (Ayaz); Ozgun (Babur); Esat (Belviranli); Ahmet (Cetintas); Recep (Colak); Emek (Demir); Alptug (Dilek); Ugur (Dogrusoz); E.Zeynep (Erson); Erhan (Giral); Kutay (Karatepe); Hande (Kucuk); Cihan (Kucukkececi); Serhat (Tekin);
Short Abstract: PATIKAweb provides a Web service for retrieving and analyzing biological pathways in the PATIKA database, currently containing data integrated from many prominent pathway databases. It features a user-friendly interface, dynamic visualization, advanced graph-theoretic queries, microarray data analysis tools and exporting facilities to various exchange formats and static images.
Long Abstract: Click Here

Poster J-32
Phylogenetic profiles for the prediction of protein-protein interactions: how to select reference organisms?
Jingchun Sun (Virginia Commonwealth University); Yixue Li (Bioinformation Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences); Zhongming Zhao (Virginia Commonwealth University);
Short Abstract: We performed a systematic investigation of the effects of reference organism selection on the phylogenetic profiles and the prediction of protein-protein interactions (PPIs). The results provide important guidance on the construction of phylogenetic profiles for PPI prediction and functional genomics, which has become challenging due to the large data.
Long Abstract: Click Here

Poster J-34
Condition transition analysis reveals TF activity related to nutrient-limitation-specific effects of oxygen presence in yeast
Theo Knijnenburg (Mediamatics,TU Delft); Lodewyk Wessels (Mediamatics,TU Delft / Molecular Biology, The Netherlands Cancer Institute); Marcel Reinders (Mediamatics,TU Delft);
Short Abstract: Differential gene expression between the combinatorial cultivation conditions of a small and homogenous yeast microarray dataset are modeled as transitions. The interrelatedness of the cultivation conditions is exploited to reveal the combinatorial effects on expression behavior and TF activity at these transitions.
Long Abstract: Click Here

Poster J-35
FunCoup: data integration and the network of functional coupling in Eukaryotes
Andrey V Alexeyenko (Stockholm Bioinformatics Center, Stockholm University); Erik LL Sonnhammer (Stockholm Bioinformatics Center, Stockholm University);
Short Abstract: Functional coupling of genes is predicted from high-throughput data of multiple sources. Optimized pattern recognition techniques employ information on orthologous genes of model organisms to improve accuracy and sensitivity of the method. FunCoup is a flexible tool transferring information between genomes and automatically optimizing for different data sources.
Long Abstract: Click Here

Poster J-36
The consequences of alternative splicing on biological pathways
Melissa Cline (Pasteur Institute);
Short Abstract: We evaluated the consequences of alternative splicing on biological networks using ENSEMBL. 3910 of 21205 human genes produce two or more proteins with different domain compositions. According to domain network analysis, at least 490 of 2450 protein interactions surveyed would be lost for loss of a critical domain.
Long Abstract: Click Here

Poster J-37
A Homology-based Method for Predicting Complexes in Large Protein-Protein Interaction Networks
Jae-Hun Choi (ETRI); Jong-Min Park (ETRI); Soo-Jun Park (ETRI);
Short Abstract: In this paper, we propose a method for predicting biological complexes, in which interactions among their proteins are described specifically. The prediction suggests candidate complexes for a target species, which are homologically transformed from the complex experimented on well-known other species such as yeast, drosophila, mouse etc.
Long Abstract: Click Here

Poster J-38
Nonlinear dimesnionalilty reduction in apoptosis signalling networks
Sergii Ivakhno (University of Edinburgh; School of Informatics); Douglas Armstrong (University of Edinburgh; School of Informatics);
Short Abstract: System wide modelling and analysis of signalling networks is essential for understanding complex cellular behaviour, such as biphasic responses to different combinations of growth factors. We applied unsupervised learning approach via non-linear dimensionality reduction using ISOMAP for analysis and clustering of apoptosis signalling network activities.
Long Abstract: Click Here

Poster J-39
Metabolic flux balance model as a potentially approach for the design and optimization of Cosmomycin production by Streptomyces olindensis ICB20
Ana Katerine de Carvalho Lima Lobato (The School of Chemical Engineering and Analytical Science, The University of Manchester); Raul Munoz-Hernandez (The School of Chemical Engineering and Analytical Science, The University of Manchester); Renata L. Araujo Furlan (University of Sao Paulo); Gabriel Padilla (Institute of Biomedical Sciences, University of Sao Paulo); Leandro M. Garrido (Institute of Biomedical Sciences, University of Sao Paulo); Gorete Ribeiro de Macedo (Department of Chemical Engineering, Federal University of Rio Grande do Norte); Ferda Mavituna (The School of Chemical Engineering and Analytical Science, The University of Manchester);
Short Abstract: Cosmomycin is an anti-tumor drug produced by Streptomyces olindensis. In this work a computational model based on metabolic flux balancing methodology was developed to investigate some strategies for the selection of media, precursor addition, and genetic engineering targets in order to direct and optimize the production of the product.
Long Abstract: Click Here

Poster J-40
Comparative Evaluation of the Accuracy of Reverse Engineering Gene Regulatory Networks with various Machine Learning Methods
Adriano V. Werhli (BioSS); Marco Grzegorczyk (University of Dortmund); Dirk Husmeier (BioSS); Wolfgang Urfer (University of Dortmund);
Short Abstract: We compare the accuracy of predicting gene regulatory networks with three different machine learning methods: (1) relevance networks, (2) graphical Gaussian models, and (3) Bayesian networks. The evaluation is carried out on a cellular signalling network that describes the interaction of 11 phosphorylated proteins and phospholipids in human immune system cells.
Long Abstract: Click Here

Poster J-41
Identification of transcription logic-gate dynamics in Escherichia coli
Ilaria Mogno (University of Rome La Sapienza); Lorenzo Farina (University of Rome La Sapienza); Timothy Gardner (Boston University);
Short Abstract: We develop a method to characterize combinatorial regulation in bacteria. Time series data is collected using GFP as a reporter for gene expression. We use nonlinear regression and an iterative Kalman filter to identify the logic gate and dynamics of the regulatory function. Our method provides a simple way to characterize promoters in an effort to control the cellular behavior.
Long Abstract: Click Here

Poster J-43
On the Creation of Provably-Correct Models of Biological Structure and Process
Randall L. Owen (University of Oxford); Charlotte Deane (University of Oxford);
Short Abstract: We present an application of formal software engineering methods to an established bioinformatics model: the HP lattice model for protein folding. Our results demonstrate the rigorous creation and implementation of provably correct biological models, demonstrating how we can formally verify that complex models is performing as intended.
Long Abstract: Click Here

Poster J-44
GenePro: a Cytoscape Plugin for Advanced Visualization and Analysis of Interaction Networks
Jim Vlasblom (Center for Computational Biology, The Hospital for Sick Children); Samuel Wu (Center for Computational Biology,The Hospital for Sick Children); Shuye Pu (Center for Computational Biology, The Hospital for Sick Children); Mark Superina (Center for Computational Biology, The Hospital for Sick Children); Gina Liu (Center for Computational Biology, The Hospital for Sick Children); Chris Orsi (Center for Computational Biology, The Hospital for Sick Children); Shoshana J. Wodak (Center for Computational Biology, The Hospital for Sick Children, Departments of Biochemistry and Me);
Short Abstract: Systems biology studies frequently require integrative, interactive analysis and visualization of large scale protein/gene interaction networks. We present GenePro, a plugin to Cytoscape, featuring multi-resolution display of interaction networks at both cluster and protein/gene level. GenePro also allows mapping between different partitioning of the network.
Long Abstract: Click Here

Poster J-45
Assistant Research Fellow
ChungYen Lin (Institute of Information Science, Academia Sinica); Chi-Shiang Cho (National Health Research Institutes); Chia-Ling Chen (National Health Research Institutes); Fan-Kai Lin (National Health Research Institutes); Chieh-Hua Lin (National Health Research Institutes); Pao-Yang Chen (National Health Research Institutes); Shu-Hwa Chen (Institute of Zoology, Academia Sinica); Chen-Zen Lo (National Health Research Institutes); Chao A. Hsiung (National Health Research Institutes);
Short Abstract: We used the fruit fly, as the target species to build protein networks integrated experimental and inferred interactions to form whole network under various scenarios. Based on the experimental Y2H interactions, we converted the protein interactions to domain interacting network to infer new protein interactions and perform the topology analysis.
Long Abstract: Click Here

Poster J-46
Multi-layered network structure of amino acid (AA) metabolism characterized by each essential AA-deficient condition
Nahoko Shikata (Graduate School of Systems Life Sciences, Kyushu University); Yukihiro Maki (Department of Digital Media, Fukuoka International University); Yasushi Noguchi (Research Institute for Health Fundamentals, Ajinomoto Co., Inc.); Masato Mori (Research Institute for Health Fundamentals, Ajinomoto Co., Inc.); Taizo Hanai (Graduate School of Systems Life Sciences, Kyushu University); Michio Takahashi (Research Institute for Health Fundamentals, Ajinomoto Co., Inc.); Masahiro Okamoto (Graduate School of Systems Life Sciences, Kyushu University);
Short Abstract: We inferred the network structure of plasma amino acids from plasma samples of rats fed diet deficient in one of nine essential amino acids, with using multi-level digraph analysis method. This revealed several interesting interrelations between plasma amino acids, which could not be drawn from the metabolic pathway map.
Long Abstract: Click Here

Poster J-47
Relationship between topology and functions in chloroplast metabolic network evolution
Zhuo Wang (Biomedical Instrument Institute, Shanghai Jiao Tong University); Yazhu Chen (Biomedical Instrument Institute, Shanghai Jiao Tong University); Yuanyuan Li (Shanghai Center for Bioinformation Technology); Yixue Li (Shanghai Center for Bioinformation Technology); Lei Liu (W. M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaig);
Short Abstract: We found the enzymes in the highly conserved functional pathways and modules are highly connected and the relationship between topology and functions is very similar in metabolic networks of chloroplast and cyanobacteria, while different from other species. The relationship can be used as an indicator of the closeness in evolution.
Long Abstract: Click Here

Poster J-49
Analysis of Adaptation Behaviour of Fungi Under Biotic Stress Caused by Biofilm Formation
Betul Soyler (Department of Food Engineering); Zumrut B. Ogel (Department of Food Engineering);
Short Abstract: Biofilms have been found to be cause of many human infections. The composition of biofilm is not known entirely, but supposed to be mixture of various polysaccharides. Fungi are capable of degrading complex polysaccharides. Aim of this study is to explore adaptation of Aspergillus to Salmonella biofilms via microarray analysis.
Long Abstract: Click Here

Poster J-50
Monet Ontology as a tool to construct and explore integrated biological networks
Ney Lemke (IBB-Unesp); Renata Vieira (Unisinos); João Paulo Müller da Silva (Unisinos); José Guilherme Camargo de Souza (UNISINOS); Marialva Sinigaglia (IF-UFRGS); José Carlos Mombach (IF-UFRGS);
Short Abstract: We present MONET (Molecular Network) ontology, an integrated model for the integration of molecular cellular networks: metabolism, protein-protein interaction and regulation. Using the ontology we build a network model for E.coli molecular interactions. Applying machine learning techniques we predict gene essentiality with 85.7 recall.
Long Abstract: Click Here

Poster J-51
Combined visualization and analysis of Gene Ontology annotations using multivariate representations of annotations and bipartite networks
Rohan Williams (UNSW); Kai (Kevin) Xu (National ICT Australia); Jane Huang (University of Sydney); Chris Cotsapas (UNSW); Seokhee Hong (National ICT Australia); Geoff McCaughan (University of Sydney); Mark Gorrell (University of Sydney); Peter Little (UNSW);
Short Abstract: We present a "multi-scale" methodology that analyze GO annotations for high-throughput experiments in a network context at various levels of details and employs visualization, statistical analysis, and unsupervised learning techniques. We illustrate this methodology with microarray data from the human liver with hepatitis C virus (HCV) infection.
Long Abstract: Click Here

Poster J-52
Probabilistic Genetic Networks analysis of three Plasmodium falciparum strains from dynamical expression signals
Junior Barrera (Instituto de Matemática e Estatística - Universidade de São Paulo); Roberto Marcondes Cesar Jr (Instituto de Matemática e Estatística - Universidade de São Paulo); David Corrêa Martins Jr (Instituto de Matemática e Estatística - Universidade de São Paulo); Ricardo Z. N. Vêncio (Instituto de Matemática e Estatística - Universidade de São Paulo); Carlos A. B. Pereira (Instituto de Matemática e Estatística - Universidade de São Paulo); Hernando A. Del Portillo (Instituto de Ciências Biomédicas - Universidade de São Paulo);
Short Abstract: In this work we present a framework to construct genetic networks from dynamical expression signals. The applicability of this tool for discovering gene networks of the malaria expression regulation system has been validated for simulated and real microarray data. Currently, we are applying the same technique for three malarial strains.
Long Abstract: Click Here

Poster J-53
Using Synthetic Gene Expression Data to Assess Characteristics of Gene Network Inference Algorithms
Tim Van den Bulcke (ESAT-SCD, K.U.Leuven); Koenraad Van Leemput (ISLab, Universiteit Antwerpen); Thomas Dhollander (ESAT-SCD, K.U.Leuven); Bart De Moor (ESAT-SCD, K.U.Leuven); Piet van Remortel (ISLab, Universiteit Antwerpen); Kathleen Marchal (CMPG, K.U.Leuven);
Short Abstract: We report the application of synthetic datasets to three well-known gene network inference algorithms, providing insight in the impact of different aspects of the expression data on the quality of the inferred network. Synthetic data reveals operational characteristics of inference algorithms unlikely to be discovered using biological microarray data only.
Long Abstract: Click Here

Poster J-54
Identifying Individual Genome-Scale Models: Integrating Reverse Engineering with Classification Analysis
Bahrad A. Sokhansanj (Drexel University); Suman Datta (Drexel University); Diane C. Lim (Drexel University);
Short Abstract: “Personalized medicine” requires understanding molecular and cellular processes underlying physiological changes and inter-individual differences in human health. We implement a novel method combining large scale discriminant analysis methods with a fuzzy logic scheme for individual-based models for the function of biomolecular networks as they result in health changes.
Long Abstract: Click Here

Top

Text Mining & Information Extraction

Poster K-1
OAT - Shows the complementarity of MeSH and GO in interpretation of gene lists
Anders Bresell (IFM Bioinformatics, Linköpings Universitet, Sweden); Bo Servenius (AstraZeneca R&D Lund, Sweden); Bengt Persson (IFM Bioinformatics, Linköpings Universitet, Sweden);
Short Abstract: OAT is built to represent, condense and summarize the knowledge associated with a gene list. OAT uses MeSH and GO and we show that the two ontologies complement each other with surprisingly low overlap by mapping annotations to UMLS. OAT calculates test statistics and includes novel annotation sets for MeSH.
Long Abstract: Click Here

Poster K-2
Literature Mining at the Protein Information Resource (PIR)
Hu, ZZ (Protein Information Resource, Georgetown University Medical Center); Liu, H (Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University Medical Cente); Han, B (Center for Information Science and Technology, Temple University); Huang H (Protein Information Resource, Georgetown University Medical Center); Mazumder R (Protein Information Resource, Georgetown University Medical Center); Yuan, X (Protein Information Resource, Georgetown University Medical Center); Obradovic, Z (Center for Information Science and Technology, Temple University); Vijay-Shanker, K (Department of Computer and Information Sciences, University of Delaware); Vucetic, S (Center for Information Science and Technology, Temple University); Wu, CH (Protein Information Resource, Georgetown University Medical Center);
Short Abstract: The Protein Information Resource conducts research and provides resources on literature mining in areas, i) named entity recognition, providing BioThesaurus of gene/protein names and database associations; ii) information retrieval, developing algorithms for text categorization; iii) information extraction, developing online text mining tool for protein phosphorylation to assist protein annotation.
Long Abstract: Click Here

Poster K-3
Disambiguation of large gene/protein terminologies by automatic literature profiling
Roney S Coimbra (GlaxoSmithKline - Cheminformatics); Dana E. Vanderwall (GlaxoSmithKline - Cheminformatics);
Short Abstract: We present a method to disambiguation of gene/protein terminologies. Aliases of a given gene produce collections of Medline abstracts which share a common vocabulary. This gene/protein specific vocabulary defines a unique fingerprint that can be used to disclose ambiguous aliases.
Long Abstract: Click Here

Poster K-4
Genotyping and Annotation of Affymetrix SNP Arrays
Philippe Lamy (Bioinformatics Research Center, University of Aarhus); Carsten Wiuf (Bioinformatics Research Center, University of Aarhus); Claus L. Andersen (Molecular Diagnostic Laboratory, Aarhus University Hospital, Skejby); Friedrik P. Wikman (Molecular Diagnostic Laboratory, Aarhus University Hospital, Skejby);
Short Abstract: We have developed a new method for genotyping Affymetrix SNP array. The method is based on using multiple arrays at the same time to determine the genotypes and on a model that relates intensities of individual SNPs to each other. It is therefore possible to annotate SNPs that experimentally perform badly.
Long Abstract: Click Here

Poster K-5
Title: SAM as a plugin for BASE
Ana Carolina Q. Simoes (Programa de Pós-Graduação Interunidades em Bioinformática & Departamento de Bioquímica, Instituto de); Aline Maria da Silva (Programa de Pós-Graduação Interunidades em Bioinformática & Departamento de Bioquímica, Instituto de);
Short Abstract: This poster describes the implementation of Significance Analysis of Microarrays (SAM) as a plugin for BASE, a opensource system for the analysis of microarray experiments
Long Abstract: Click Here

Poster K-6
Construction and Evaluation of an Abbreviation Dictionary for Normalizing Protein Names
Joon-Ho Lim (ETRI); Jaesoo Lim (ETRI); Hyunchul Jang (ETRI); Soo-Jun Park (ETRI);
Short Abstract: To normalize protein names to a database, it is necessary to disambiguate an abbreviation to definition. To construct an abbreviation dictionary, we collect 2920541 PubMed abstracts, and extract abbreviation-definition pairs using Schwartz' algorithm. The constructed dictionary has 25844 pairs, and 13509 abbreviation names. An experimental result shows 82% accuracy.
Long Abstract: Click Here

Poster K-8
Dynamic query and exploration of literature paths between proteins
Robert Hoffmann (Memorial Sloan-Kettering Cancer Center); Chris Sander (Memorial Sloan-Kettering Cancer Center);
Short Abstract: Why do proteins X and Y show up together in a given experiment? The iHOP literature network contains the answer to many questions as to the relationships between specific proteins. However, to find these answers is difficult when considering different synonyms and allowing for indirect relationships. We present a novel literature query system that facilitates the interactive exploration of literature paths in the iHOP network.
Long Abstract: Click Here

Poster K-9
Human Computer Interface Analysis of Tier1/2/3 Bioinformatics Tools
Annette Greiner (Joint Genome Institute); Kristen Taylor (Joint Genome Institute);
Short Abstract: Rapid development cycles impact the human computer interfaces designed for bioinformatics data analysis and visualization tools. The paper evaluates data density, usability, intuitiveness and information absorption factors for various tools and presents a simple method for improving bioinformatics tool usability.
Long Abstract: Click Here

Poster K-10
Recursive Top-Down Quantum Clustering of Biological Data
Varshavsky Roy (School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel); Horn David (School of Physics and Astronomy, Tel Aviv University, Israel); Linial Michal (Deptartment of Biological Chemistry, The Hebrew University of Jerusalem, Israel);
Short Abstract: We present a top-down, recursive clustering algorithm, for various datasets (e.g., gene-expression, protein sequences). The algorithm is successfully tested on several benchmarks. This novel algorithm identifies some internal structures, while other algorithms fail. Investigating these new structures suggests a new biological interpretation.
Long Abstract: Click Here

Poster K-11
Annotation errors and their correction by association rule mining
Artamonova I.I. (Institute for Bioinformatics, GSF - National Research Center for Environment and Health); Frishman G. (Institute for Bioinformatics, GSF - National Research Center for Environment and Health); Gelfand M.S. (Institute of Information Transmission Problems RAS); Frishman D. (Department of Genome Oriented Bioinformatics, Technische Universität Munchen);
Short Abstract: The Association Rules mining was applied to identification of possible errors in protein annotations. The errors were identified as exceptions from strong rules found by the algorithm. Suspicious features were marked for manual curation. Tests demonstrated that most exceptions indeed were caused by annotation errors.
Long Abstract: Click Here

Poster K-12
FLAME: Frequency-Based Lexical Analysis of Microarray Gene Lists
Anar K. Khan (AgResearch Ltd., Invermay Agricultural Centre, Puddle Alley, Mosgiel, Otago, New Zealand); Alistair K. Knott (Computer Science Department, University of Otago, 90 Union Place East, Dunedin, New Zealand); Jonathan W. Warren (AgResearch Ltd., Invermay Agricultural Centre, Puddle Alley, Mosgiel, Otago, New Zealand); John C. McEwan (AgResearch Ltd., Invermay Agricultural Centre, Puddle Alley, Mosgiel, Otago, New Zealand);
Short Abstract: FLAME is a web-based Java program which provides a portal to the literature surrounding a differentially expressed (DE) gene list derived from a microarray experiment. FLAME leverages term usage information in PubMed abstracts to summarise and cluster a given DE gene list, thereby automatically revealing associations amongst DE genes.
Long Abstract: Click Here

Poster K-14
BioMint: a database curator’s assistant for biomedical text processing
Anne-Lise Veuthey (Swiss Institute of Bioinformatics); Violaine Pillet (Swiss Institute of Bioinformatics); Marc Zehnder (Swiss Institute of Bioinformatics);
Short Abstract: BioMinT is an information retrieval system which helps literature screening for Swiss-Prot curation. It provides a graphical user interface which expands a query on a gene/protein with synonyms, filters and ranks the retrieved abstracts according to their relevance to the query, and extracts information specific to database annotation topics.
Long Abstract: Click Here

Poster K-15
A New Methodology for Regulatory Network Inference
Ígor L. Almeida (PIPCA, Universidade do Vale do Rio dos Sinos - São Leopoldo, Brazil); Adelmo L. Cechin (PIPCA, Universidade do Vale do Rio dos Sinos - São Leopoldo, Brazil); Cláudia K. Barcellos (Hewlett-Packard Labs - Porto Alegre, Brazil); Irene S. Gabashvili (Computational Biosciences Research, Hewlett-Packard Labs - Palo Alto, USA);
Short Abstract: DNA array technologies are powerful tools to monitor simultaneously the expression patterns of thousands of genes. The challenge is to extract useful information from the vast amounts of data generated. This work proposes a new Markov Chain-based approach for analysis of microarray data.
Long Abstract: Click Here

Poster K-16
Predicting MEDLINE Abstracts Relevant to Salt Tolerance in Plants
Crystal L. Nevels (Department of Computer Science, Jackson State University, Jackson Mississippi, USA); Charles E. Bland (Department of Computer Science, Jackson State University, Jackson Mississippi, USA); Raphael D. Isokpehi (Department of Biology, Jackson Mississippi, USA);
Short Abstract: We have built positive and negative corpora of MEDLINE abstracts of articles suitable for identifying words in abstracts that indicate the relevance of an abstract to salt tolerance in plants. A total of 952 positive predictive words were identified including salt, nacl, stress, tolerance, saline, osmoprotectant, drought, halophyte and mesembryanthemum.
Long Abstract: Click Here

Poster K-17
Effects of Head Noun Features on Statistical Named Entity Recognition in Biomedical Literatures
Jaesoo Lim (Electronics and Telecommunications Research Institute); Hyunchul Jang (Electronics and Telecommunications Research Institute); Joon-Ho Lim (Electronics and Telecommunications Research Institute); Soo-Jun Park (Electronics and Telecommunications Research Institute);
Short Abstract: We suggest head noun features with positional information instead of using chunk tag features for biomedical named entity recognition (NER). We evaluated our statistical NER system on the GENIA corpus. The system using head nouns performed 1.7%p of f-scores better than the system using chunk tags.
Long Abstract: Click Here

Poster K-18
Clustering of Medline abstracts using Particle Swarm Optimisation
Ayton Meintjes (Bioinformatics and Computational Biology Unit, University of Pretoria); Fourie Joubert (Bioinformatics and Computational Biology Unit, University of Pretoria);
Short Abstract: The growth in the number of biomedical publications has heightened the need for automatic identification of articles of interest to researchers. Particle Swarm Optimisation has previously been shown to be effective in clustering text documents. We propose the application of this technique to clustering Medline abstracts.
Long Abstract: Click Here

Poster K-19
Construction of Scoring Functions using Neural Network for Determination of Affinities Constants Receptor-Ligand.
Thaís Gaudencio do Rêgo (Laboratório Nacional de Computação Científica); Marco Antônio Vilela (Laboratório Nacional de Computação Científica); Hélio José Corrêa Barbosa (Laboratório Nacional de Computação Científica); Laurent Emmanuel Dardenne (Laboratório Nacional de Computação Científica);
Short Abstract: One of the most important challenges of molecular modeling is provide quantitative or semiquantitative information, using a low computational cost, about ligand-receptor affinities. Have as main objective in this work for the solution that problem, the construction of empirical functions of free energy with neural networks.
Long Abstract: Click Here

Poster K-20
From Spectrum to Structure using Machine Learning
Caroline Farrelly (University of Manchester); Prof. Douglas Kell (University of Manchester); Dr. Joshua Knowles (University of Manchester);
Short Abstract: Current trends in the use of high throughput techniques have created demand for rapid analytical techniques. In the areas of combinatorial chemistry and metabolomics alike, huge datasets are generated, often relating to novel compounds. This project addresses structure elucidation of carbon NMR spectra for small organic molecules (>500 molecular weight).
Long Abstract: Click Here

Poster K-21
Frame-based Analysis of Complex Relationships in Biomedical Text: Annotating and Extracting Protein Transport Information in GeneRIFs
Zhiyong Lu (Center for Computational Pharmacology, School of Medicine, University of Colorado); William Baumgartner Jr. (Center for Computational Pharmacology, School of Medicine, University of Colorado); Michael Bada (Center for Computational Pharmacology, School of Medicine, University of Colorado); James Firby (Center for Computational Pharmacology, School of Medicine, University of Colorado); Philip Ogren (Center for Computational Pharmacology, School of Medicine, University of Colorado); Kevin Cohen (Center for Computational Pharmacology, School of Medicine, University of Colorado); Lawrence Hunter (Center for Computational Pharmacology, School of Medicine, University of Colorado);
Short Abstract: We present a novel concept recognition system named OpenDMAP (Open Access Direct Memory Access Parser), which was used to extract the biological entities and relations pertinent to protein transport, the biological process of moving proteins from one cellular location to another.
Long Abstract: Click Here

Poster K-22
EBIMed and Protein Corral: EBI’s information retrieval and information extraction engines for realtime analysis of Medline abstracts
Arregui (EBI); Gaudan (EBI); Kirsch (EBI); Rebholz-Schuhmann (EBI);
Short Abstract: EBIMed and Protein Corral are EBI’s new Web services based on Medline abstracts. Upon keyword search the retrieved abstracts are analyzed for associations between biomedical terms (EBIMed) and for relations between proteins (Protein Corral). The identified concepts are automatically linked EBI’s and NCBI’s biomedical databases.
Long Abstract: Click Here

Poster K-24
BioTermNet: a system for biomedical text mining
Asako Koike (Univ. of Tokyo); Toshihisa Takagi (Univ. of Tokyo);
Short Abstract: We have developed a text mining system called “BioTermNet”, which provides two functions: 1) to find implicit relationships by connecting explicit relationships for knowledge discovery, 2) to cluster concepts based on the document similarities for the interpretation of high-throughput data. These results are presented interactively by a graphic viewer.
Long Abstract: Click Here

Poster K-25
Search Engine for Mining Biological Significance of Genetic Markers in Medline
Weijian Xuan (Molecular and Behavioral Neuroscience Institute and Department of Psychiatry, University of Michigan); Pinglang Wang (Molecular and Behavioral Neuroscience Institute and Department of Psychiatry, University of Michigan); Stanley J. Watson (Molecular and Behavioral Neuroscience Institute and Department of Psychiatry, University of Michigan); Fan Meng (Molecular and Behavioral Neuroscience Institute and Department of Psychiatry, University of Michigan);
Short Abstract: MarkerInfoFinder is the first application that allows researchers to find genetic marker related Medline records using positional and linkage disequilibrium criteria. It greatly increases the efficiency of mining literature related to a list of genetic markers, facilitating the understanding of the molecular mechanisms underlying genetic disorders.
Long Abstract: Click Here

Poster K-26
Imitating manual curation of text-mined facts in biomedicine
Raul Rodriguez-Esteban (Center for Computational Biology and Bioinformatics, Columbia University); Ivan Iossifov (Center for Computational Biology and Bioinformatics, Columbia University); Andrey Rzhetsky (Center for Computational Biology and Bioinformatics, Columbia University);
Short Abstract: In biomedical applications, which rely on use of text-mined data, it is critical to assess the extraction quality of individual facts. Using a large set of almost 100,000 manually produced evaluations, we implemented algorithms that mimic human evaluation of facts provided by an automated information-extraction system.
Long Abstract: Click Here

Poster K-27
Mindmapping literature information: extract, visualize and explore for modeling
Steven Vercruysse (Ghent University - VIB); Martin Kuiper (Ghent University - VIB);
Short Abstract: When modeling genetic networks, we need tools to handle the wide variety of literature information. We designed a system to capture this information, and display it similar to how our brain works: a clickable 'mindmap', linking all proteins/events/.... Herewith a modeler can easily browse information gathered from many publications.
Long Abstract: Click Here

Poster K-28
Mining Provenance Logs from Bioinformatics Workflows
Sérgio Manuel Serra da Cruz (NCE-UFRJ); Carla Tavares dos Reis (Instituto Osvaldo Cruz - Farmanguinhos);
Short Abstract: Mining bioinformatics logs allow e-scientists to gain insight into the data and come up with new scientific hypotheses. To explore this opportunity we present PM-BioWSLogA, a framework which relies on mining provenance logs of scientific workflows based on Web Services log data captured from bioinformatics in silico experiments
Long Abstract: Click Here

Top

Transcriptomics

Poster L-1
A calibration method for estimating absolute expression levels from microarray data
Kristof Engelen (Department of Microbial and Molecular Systems, KULeuven); Hui Zhao (Department of Electrical Engineering, KULeuven); Bart De Moor (Department of Electrical Engineering, KULeuven); Kathleen Marchal (Department of Microbial and Molecular Systems, KULeuven);
Short Abstract: We describe an approach for estimating absolute expression levels from two-color, spotted microarray data. The procedure is based on a physically motivated calibration model of which the parameters and error distributions are estimated from external control spikes.
Long Abstract: Click Here

Poster L-2
Genome Expression Pathway Analysis Tool - Analysis and Visualization of Microarray Gene Expression Data under Genomic, Proteomic and Metabolic Context
Markus Weniger (Department of Bioinformatics, Biocenter, University Wuerzburg); Joerg Schultz (Department of Bioinformatics, Biocenter, University Wuerzburg);
Short Abstract: GEPAT, http://bioapps.biozentrum.uni-wuerzburg.de/GEPAT/, is a web-based platform for annotation, analysis and visualization of microarray gene expression data. Analysis and visualization methods under genomic, proteomic and metabolic context are integrated in an easy to use, interactive graphical user interface.
Long Abstract: Click Here

Poster L-3
Identification of Deuterostomia Conserved Genes in the Human Parasite Schistosoma mansoni
Thiago M. Venancio (Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Brazil); Ricardo DeMarco (Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Brazil); Giulliana T. Almeida (Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Brazil); Katia C.P. Oliveira (Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Brazil); João C. Setubal (Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg,); Sergio Verjovski-Almeida (Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Brazil);
Short Abstract: Schistomiasis is a health problem caused by Schistosoma mansoni. Here we describe in silico identification of 21 schistosome genes conserved in Deuterostomia and lost in Ecdysozoa. Transcription regulation, metabolism and angiogenesis genes were found. They might be related to the parasite’s adaptation to host or interaction with host signaling processes.
Long Abstract: Click Here

Poster L-4
A Large Scale Gene Expression Analysis of the Mouse Brain
Pedro A. F. Galante (Ludwig Institute for Cancer Research and Departamento de Bioquímica - IQ - USP); Sandro José de Souza (Ludwig Institute for Cancer Research); Bettina Malnic (Departamento de Bioquímica - IQ - USP);
Short Abstract: A first step towards a complete understanding of the nervous system is the knowledge about genes expressed in each sub region of the brain. In this work, using bioinformatics approaches, we searched and analyzed genes specifically or preferentially expressed in 10 sub regions of the mouse brain.
Long Abstract: Click Here

Poster L-5
Power CoClustering – detecting multiple regulatory influences in gene expression data
Shay Zakov (Computer Science Department, Ben Gurion University); Avraham A. Melkma (Computer Science Department, Ben Gurion University);
Short Abstract: Thermodynamic models of transcription regulation suggest that gene expression levels may obey a power law dependence on the activity level of the regulatory mechanism. We present a new method of CoClustering micro-array data, which aims to detect such power law relations, as well as encouraging preliminary results.
Long Abstract: Click Here

Poster L-6
KERNEL-IMBEDDED GAUSSIAN PROCESSES FOR MICROARRAY GENE EXPRESSION DATA ANALYSIS
LEO WANG-KIT CHEUNG (Department of Preventive Medicine and Epidemiology, Loyola University Medical Center); XIN ZHAO (Department of Information and Computer Sciences, University of Hawaii);
Short Abstract: We propose kernel-imbedded Gaussian processes for exploration of nonlinear relationships between expression data and the target features of a disease classification problem. This work has been applied to simulated data as well as real microarray data, and has shown great promises especially when non-linearity is dominant in the underlying relationships.
Long Abstract: Click Here

Poster L-7
SNPs in NAGNAG Acceptors Are Highly Predictive for Variations of Alternative Splicing
Michael Hiller (Albert-Ludwigs-University Freiburg);
Short Abstract: We identified 64 SNPs that probably influence alternative splicing at NAGNAG acceptors and demonstrated their splice-relevance by searching EST/mRNA databases and own experiments. We showed that the NAGNAG motif is necessary and sufficient for alternative splicing. Thus, the effect of these SNPs on alternative splicing is highly predictive.
Long Abstract: Click Here

Poster L-8
Detection of the candidates of Alternative promoters and TOP genes using Database of Transcription Start Sites (DBTSS)
Riu Yamashita (HGC, IMS,Univ. of Tokyo); Katsuki Tsuritani (HGC, IMS, Univ. of Tokyo); Yutaka Suzuki (Dep. of Med. Genome. Sci., Univ. of Tokyo); Sumio Sugano (Dep. of Med. Genome. Sci., Univ. of Tokyo); Kenta Nakai (HGC, IMS, Univ. of Tokyo);
Short Abstract: We have constructed the Database of Transcription Start Sites to determine precise transcription start sites. Using this database, we tried to detect alternative promoters. We also predicted terminal oligo-pyrimidine (TOP) gene which are thought to be related with translation.
Long Abstract: Click Here

Poster L-9
Discovering co-occurrences of gene annotations in large lists of genes
Pedro Carmona-Saez (BioComputing Unit. National Center of Biotechnology); Monica Chagoyen (BioComputing Unit. National Center of Biotechnology); Jose M. Carazo (BioComputing Unit. National Center of Biotechnology); Francisco Tirado (Computer Architecture Department. Universidad Complutense de Madrid); Alberto Pascual-Montano (Computer Architecture Department. Universidad Complutense de Madrid);
Short Abstract: We have developed a methodology to integrate biological annotations from several sources and extract sets of categories that frequently appear together in a list of genes. This method can be used to analyze large lists of genes to get insights into the associated biological mechanisms.
Long Abstract: Click Here

Poster L-10
Query-driven Search for Analysis of Large Microarray Collections
Matthew A. Hibbs (Lewis-Sigler Institute for Integrative Genoimcs, Department of Computer Science, Princeton Universit); Kai Li (Department of Computer Science, Princeton University); Olga G. Troyanskaya (Lewis-Sigler Institute for Integrative Genoimcs, Department of Computer Science, Princeton Universit);
Short Abstract: In order to explore vast compendiums of microarray data, new methodologies are required to provide fast, intuitive access to the collection. We developed a methodology for fast search and analysis of large collections of microarray data taking into account the functional context of each query.
Long Abstract: Click Here

Poster L-11
Development of a Rice Genome Database for the Interpretation of Cereal Microarray Data
Philip Law (Bioinformatics and Computational Biology Unit, University of Pretoria); Clotilde Claudel-Renard (Bioinformatics and Computational Biology Unit, University of Pretoria); Fourie Joubert (Bioinformatics and Computational Biology Unit, University of Pretoria); Dave Berger (Department of Botany, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretor);
Short Abstract: The MADIBA (MicroArray Data Interface for Biological Annotation) toolkit identifies GO terms, metabolic pathways, transcriptional co-regulation and genomic localisations, in clusters of Plasmodium or rice genes. These are identified using microarray experiments showing significant expression variation. Planned improvements include a pre-processing option and plant defence maps.
Long Abstract: Click Here

Poster L-12
Probabilistic Inference of transcription factor concentrations and gene-specific regulatory activities
Guido Sanguinetti (University of Sheffield); Neil Lawrence (University of Sheffield); Magnus Rattray (University of Manchester);
Short Abstract: We present a probabilistic dynamical model to infer active transcription factor concentrations and their regulatory effect for regulatory networks of known architecture. The advantage of the model is that it allows to estimate separately the strength and sign of the regulator interactions. The model is validated on two yeast datasets.
Long Abstract: Click Here

Poster L-13
Cerebellar Ethanol Sensitivity: A Central Role For Creb Transcription Regulation
George K. Acquaah-Mensah (Massachusetts College of Pharmacy & Health Sciences);
Short Abstract: The cerebellum is especially susceptible to ethanol toxicity. Inbred Long-Sleep (ILS) and Inbred Short-Sleep (ISS) mice, are a model for studying ethanol sensitivity. The C4.5 algorithm was applied to promoter sequences differentially expressed between ILS and ISS mice and indicates a central role for CREB transcription activity.
Long Abstract: Click Here

Poster L-14
Combining DNA copy number and gene expression data to reveal recurrent genetic abnormalities in pancreatic cancer
Liviu Badea (AI department, National Institute for Research in Informatics); Doina Tilivea (AI department, National Institute for Research in Informatics);
Short Abstract: We use the Pollack lab pancreatic cancer dataset for determining a set of genes with consistent expression changes in pancreatic cancer and relate these genes with the DNA copy number changes observed in the individual samples. A rank-covering algorithm provides an aggregated view of the candidate genes with DCN alterations that potentially explain the observed phenotype.
Long Abstract: Click Here

Poster L-15
MDframe: a computational framework for the high-throughput identification of human regulatory motifs
Linyong Mao (Medical University of South Carolina); Omar Moussa (Medical University of South Carolina); John S. Yordy (Medical University of South Carolina); Dennis K. Watson (Medical University of South Carolina); W. Jim Zheng (Medical University of South Carolina);
Short Abstract: We developed a computational framework, MDframe, for the high-throughput identification of potential human regulatory motifs. The framework integrates microarray/transcription profiling, comparative genomics, and de novo motif discovery to identify overrepresented DNA motifs in the sequence set upstream of co-regulated genes by employing an exhaustive oligomer enumeration technique
Long Abstract: Click Here

Poster L-17
Global analysis of antisense transcription in intronic regions of the human genome
Helder I. Nakaya (Departamento de Bioquímica, Instituto de Química, USP); Rodrigo Louro (Departamento de Bioquímica, Instituto de Química, USP); André Lopes (Departamento de Bioquímica, Instituto de Química, USP); Tarik El-Jundi (Departamento de Bioquímica, Instituto de Química, USP); Paulo P. Amaral (Departamento de Bioquímica, Instituto de Química, USP); Angela Fachel (Departamento de Bioquímica, Instituto de Química, USP); Aline M. da Silva (Departamento de Bioquímica, Instituto de Química, USP); Eduardo M. Reis (Departamento de Bioquímica, Instituto de Química, USP); Sergio Verjovski-Almeida (Departamento de Bioquímica, Instituto de Química, USP);
Short Abstract: Mapping of all EST sequences to the human genome revealed that 86% of all spliced RefSeq-genes have transcriptionally active intronic regions. These messages were non-coding long unspliced transcripts, and were preferentially found in 5’ introns of RefSeq-genes. A tissue signature of antisense intronic transcription was revealed using a custom oligoarray.
Long Abstract: Click Here

Poster L-18
Non-negative matrix factorization of biological data
Alberto Pascual-Montano (Computer Architecture Department.. Complutense University of Madrid. Spain); Pedro Carmona-Saez (BioComputing Unit. National Center of Biotechnology. Madrid. Spain); Monica Chagoyen (BioComputing Unit. National Center of Biotechnology. Madrid. Spain); Francisco Tirado (Computer Architecture Department.. Complutense University of Madrid. Spain); Jose M. Carazo (BioComputing Unit. National Center of Biotechnology. Madrid. Spain); Roberto D. Pascual-Marqui (The KEY Institute for Brain-Mind Research. Zurich. Switzerland);
Short Abstract: We describe a versatile tool for using non-negative matrix factorization technique (NMF) in solving different biological problems like biclustering and sample classification using gene expression, as well as other applications in protein sequences and text mining of biomedical literature. This tool is publicly available to the bioinformatics community.
Long Abstract: Click Here

Poster L-19
Computational detection of tissue- and process-specific cis-regulatory modules by a maximum specificity method
Peter Van Loo (Department of Human Genetics, Flanders Interuniversity Institute for Biotechnology and University of); Stein Aerts (Department of Human Genetics, Flanders Interuniversity Institute for Biotechnology and University of); Bart De Moor (Bioinformatics group, Department of Electrical Engineering, University of Leuven, Belgium); Yves Moreau (Bioinformatics group, Department of Electrical Engineering, University of Leuven, Belgium); Peter Marynen (Department of Human Genetics, Flanders Interuniversity Institute for Biotechnology and University of);
Short Abstract: We present the first method for CRM discovery based on whole genome optimization. We applied this method on 892 genes and predicted CRMs in 218 of those. These predictions are supported both by leave-one-out cross-validations and by validations in independent test sets.
Long Abstract: Click Here

Poster L-20
Improving nitrogen utilisation and amino acid composition in barley used for animal feed
Carsten Friis (CBS); Michael Hansen (Danish Institute of Agricultural Sciences); E. Vincze (Danish Institute of Agricultural Sciences,); P. B. Holm (Danish Institute of Agricultural Sciences,);
Short Abstract: Microarray data on the nitrogen utilization in barley have been analysed using clustering of differentially expressed genes. From the annotation of co-regulated genes a map of affected biological processes was drawn and compared with data on Arabidopsis to construct a conjectural overview of the nitrogen utilization in barley.
Long Abstract: Click Here

Poster L-21
Integrative Analysis of NCI-60 Panel Reveals Candidate Key Genetic Regulators Affected by Genomic Alterations
Doron Lipson (CS Dept, Technion, Israel); Mark Reimers (National Cancer Institute, Bethesda, MD); Anya Tsalenko (Agilent Laboratories, CA); Amir Ben-Dor (Agilent Laboratories, CA); Kimberly Bussey (National Cancer Institute, Bethesda, MD); William Reinhold (National Cancer Institute, Bethesda, MD); Michael Barrett (Agilent Laboratories, CA); John Weinstein (National Cancer Institute, Bethesda, MD); Zohar Yakhini (Agilent Laboratories, CA);
Short Abstract: Integrating new high-resolution DNA copy number data on the NCI-60 cell-line panel with existing expression and drug activity data we identify genomic alterations affecting key genetic regulators, by searching for those genes that exhibit noticeable downstream effects, as well as correlation with phenotypic characteristics.
Long Abstract: Click Here

Poster L-22
Splicing Arrays: Profiling transcriptome by statistical analysis of mRNA isoform expression
Murlidharan Nair (IUSB); Hai-Ri, Li (UCSD); Jessica A Whitaker (IUSB); Xiang-Dong Fu (UCSD);
Short Abstract: Alternative splicing is a major source of proteome diversity. mRNA-isoform levels reflect transcriptional and post-transcriptional processing. Ability to detect the levels of each isoform in the cell significantly increases our understanding of the state of the cell. Using statistical approaches of multiple comparisons we have profiled transcriptome from isofom data.
Long Abstract: Click Here

Poster L-23
Novel Gene Expression Analysis Using SAM and PAM Algorithms to Determine Estrogen-regulated Genes Involved in Response to Neoadjuvant Endocrine Therapy for Breast Cancer
Susan Trapp ("Computational Bioscience Program, Univ. of Colorado Health Sciences"); Tzu Phang ("School of Medicine, Univ. of Colorado Health Sciences"); Djuana Harvell ("Division of Endocrinology, Univ. of Colorado Health Sciences"); Larry Hunter ("Computational Bioscience Program, Univ. of Colorado Health Sciences"); Anthony Elias ("Dept of Oncology, Univ. of Colorado Health Sciences"); Jennifer Richer ("Division of Endocrinology, Univ. of Colorado Health Sciences");
Short Abstract: We present a gene expression analysis approach incorporating SAM and PAM algorithms to determine estrogen-regulated genes involved in response to hormonal therapy for breast cancer. The challenge is can we accurately predict gene biomarkers based upon drug treatments and response from a dataset of 7 paired breast cancer patient samples (pre- and post-treatment).
Long Abstract: Click Here

Poster L-24
Fuzzy puzzle of cis-elements in co-regulated promoters – the blueprint of key nodes in signal transduction networks.
Nico Voss (BIOBASE GmbH Halchtersche Str. 33, D-38304 Wolfenbüttel, Germany); Tatyana Konovalova (Institute of Cytology and Genetics, Novosibirsk, Russia); Philip Stegmaier (BIOBASE GmbH Halchtersche Str. 33, D-38304 Wolfenbüttel, Germany); Olga Kel-Margoulis (r. 33, D-38304 Wolfenbüttel, Germany); Evelin Katona (University Hospital Regensburg Franz-Josef-Strauss-Allee 11, D-93053 Regensburg, Germany); Thomas Langmann (University Hospital Regensburg Franz-Josef-Strauss-Allee 11, D-93053 Regensburg, Germany); Gerd Schmitz (University Hospital Regensburg Franz-Josef-Strauss-Allee 11, D-93053 Regensburg, Germany); Edgar Wingender (Dept. Bioinformatics, UKG/Univ. Göttingen, Goldschmidtstr. 1, 37077 Göttingen, Germany); Alexander Kel (BIOBASE GmbH Halchtersche Str. 33, D-38304 Wolfenbüttel, Germany);
Short Abstract: Novel method for causal interpretation of gene expression data identifies composite cis-regulatory elements in promoters of co-regulated genes and reveals key transcription factors and “upstream” signaling molecules – perspective drug targets. Regulatory regions are modeled as fuzzy puzzle of TF binding sites providing blueprints to explain signal transduction networks.
Long Abstract: Click Here

Poster L-25
ChromoViz-Web: mapping and multimodal visualizing gene expression data with integrated major bio resources onto chromosomes using scalable vector graphics
Do Kyoon Kim (Seoul National University Biomedical Informatics (SNUBI)); Jihoon Kim (Department of Biostatistics, University of Wisconsin); Ju Han Kim (Seoul National University Biomedical Informatics (SNUBI));
Short Abstract: ChromoViz-Web is a web-based service for the visualization of microarray gene expression data, cross-species and cross-platform comparisons, as well as non-expression genomic data obtained from public databases onto chromosomes using Scalable Vector Graphics. In addition, it provides a function for mapping gene expression data with integrated major bio databases.
Long Abstract: Click Here

Poster L-26
SigWin-finder: an interactive workflow in a virtual laboratory for e-bioscience
Marcia A. Inda (Integrative Bioinformatics Unit, Faculty of Science, University of Amsterdam); Marco Roos (Integrative Bioinformatics Unit, Faculty of Science, University of Amsterdam); Adam S. Z. Belloum (Institute of Informatics, Faculty of Science, University of Amsterdam); Dmitry Vasunin (Institute of Informatics, Faculty of Science, University of Amsterdam); Timo M. Breit (Integrative Bioinformatics Unit, Faculty of Science, University of Amsterdam);
Short Abstract: Running on a grid-based virtual laboratory, the SigWin-finder workflow analyzes any given sequence of values, spanning from gene expression data to time series of temperature. It implements a generalized and improved version of the ridgeogrammer method to identify regions of increased gene expression in trancriptome maps.
Long Abstract: Click Here

Poster L-27
graPT : A genome resourcing analyzer for Predictive Toxicology
Jung Hoon Woo (Seoul National University Biomedical Informatics, Interdisciplinary Program in Bioinformatics, Seoul); Ju Han Kim (Seoul National University Biomedical Informatics, College of Medicine, Seoul National University);
Short Abstract: Predictive toxicology have been main issues of emerging technology, toxicogenomics. We have developed predictive methods and tools, graPT which is based on the gene-toxicant, toxicant-disease relationships to provide association between toxic endpoints and unknown chemicals.
Long Abstract: Click Here

Poster L-28
The role of membrane proteins in sample classification inferred by genome-wide expression profiling data
Paolo Uva (IRBM (MRL-Rome)); Armin Lahm (IRBM (MRL-Rome)); Emanuele de Rinaldis (IRBM (MRL-Rome));
Short Abstract: Membrane proteins play a crucial role in cell biology. We define the “Human Membranome” as the set of in-silico predicted membrane protein genes, and we investigate its expression in tumors, cell lines and normal tissue samples. We illustrate here that the largest part of the global transcriptional differences between different samples can be ascribed to the Membranome expression levels.
Long Abstract: Click Here

Poster L-29
Identifying functional gene sets from hierarchically clustered expression data: map of abiotic stress regulated genes in Arabidopsis thaliana.
Matti Kankainen (University of Helsinki, Institute of Biotechnology); Günter Brader (University of Helsinki, Department of Biological and Environmental Sciences, Division of Genetics); Petri Törönen (University of Helsinki, Institute of Biotechnology); E. Tapio Palva (University of Helsinki, Department of Biological and Environmental Sciences, Division of Genetics); Liisa Holm (University of Helsinki, Institute of Biotechnology);
Short Abstract: MultiGO is a tool to automatically identify biologically relevant gene sets from hierarchically clustered gene trees (http://ekhidna.biocenter.helsinki.fi/poxo/multigo). Since the entire tree is analyzed, all gene clusters sharing a common biological function, as defined by GO, are reported. The tool also identifies a cluster set representing the experimental key functions.
Long Abstract: Click Here

Poster L-30
Features of sequence composition and population genetical measures of selection to analyse alternatively spliced exons and introns
Ivana Vukusic (University of Cologne, Institute for Genetics); Sushma-Nagaraja Grellscheid (Institute of Human Genetics, International Centre for Life, University of Newcastle upon Tyne); Thomas Wiehe (University of Cologne, Institute for Genetics);
Short Abstract: We have developed a binary classifier based on Genetic Programming (GP) to predict whether a given gene sequence is spliced constitutively or alternatively. The prediction accuracies are greater than 85% on the dataset of retained introns. Furthermore we showed that skipped exons show traces of positive selection.
Long Abstract: Click Here

Poster L-31
Large-scale analysis of the impact of alternative splicing on protein isoforms.
Johannes Frey-Skött (Stockholm Bioinformatics Center); Arne Elofsson (Stockholm Bioinformatics Center);
Short Abstract: Alternative splicing is the process where metazoan genomes expand their proteome. To study this phenomenon all genes in Ensembl that produce more than one transcript were extracted and the events occurring between the protein isoforms were identified. The events were studied for several features such as abundance and sequence identity.
Long Abstract: Click Here

Poster L-32
Gene Expression Trees in Blood Cell Development
Ivan G. Costa Filho (Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics); Stefan Roepcke (Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics); Alexander Schliep (Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics);
Short Abstract: We present a statistical framework -- mixtures of conditional probabilistic trees - designed to cluster gene expression in the course of cell development. Additionally, we include microRNA target prediction in our framework. We recover well-known biological facts and also identify novel putative but convincing egulatory and functional assignments of microRNAs.
Long Abstract: Click Here

Poster L-33
Meta-Learning of Clustering Algorithms: Analyzing Gene Expression Time Courses
Francisco A. T. de Carvalho (Centro de Informática, Universidade Federal de Pernambuco); Ricardo B. C. Prudencio (Centro de Informática, Universidade Federal de Pernambuco); Marcílio C. P. de Souto (Departamento de Informática e Matemática Aplicada, Universidade Federal do Rio Grande do Norte); Ivan G. Costa (Dept. of Computational Molecular Biology, Max Planck Institute for Molecular Genetics); Benjamin Georgi (Dept. of Computational Molecular Biology, Max Planck Institute for Molecular Genetics); Teresa Ludermir (Centro de Informática, Universidade Federal de Pernambuco); Stefan Roepcke (Dept. of Computational Molecular Biology, Max Planck Institute for Molecular Genetics); Alexander Schliep (Dept. of Computational Molecular Biology, Max Planck Institute for Molecular Genetics);
Short Abstract: Whether to cluster at all, which clustering method to use and how many clusters to choose are pressing questions in bioinformatics. Mostly, decisions are made based on experience guided by benchmarking or indicators for reliability of solutions or model-fit. We use meta-learning to answer these questions with machine learning techniques.
Long Abstract: Click Here

Poster L-34
Modeling Transcription Kinetics with Differential Equations
Pablo R. Freire (National Laboratory for Scientific Computation); Ana Tereza R. Vasconcelos (National Laboratory for Scientific Computation);
Short Abstract: In this work, we propose a model for recovering the time-series expression of a given transcription network. The only input data needed is the time-series expression from global regulators. To test our methodology, we performed simulation and real data cross-validation on a literature-based transcription network.
Long Abstract: Click Here

Poster L-35
Graphical User Interfaces to Microarray Analysis Programs
Keith Satterley (Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research); James Wettenhall (Peter MacCallum Cancer Centre); Ken Simpson (Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research); Gordon K Smyth (Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research);
Short Abstract: Graphical User Interfaces for Microarray Analysis. affylmGUI provides an integrated workflow for Affymetrix microarray data analysis. limmaGUI analyses two-colour spotted microarray experiments. Both packages interface to the limma package. affylmGUI also interfaces to various Affymetrix chip analysis packages. affylmGUI has recently been extended to include extra quality control tools.
Long Abstract: Click Here

Poster L-36
Characterization of gene expression during erytrhoid differentiation by Serial Analysis of Gene Expression (SAGE)
Anderson F Cunha (Universidade Estadual de Campinas- Hemocentro); Ana Flávia Brugnerotto (Universidade Estadual de Campinas- Hemocentro); Adriana S S Duarte (Universidade Estadual de Campinas- Hemocentro); Gustavo G L Costa (Universidade Estadual de Campinas- Hemocentro); Marcelo F Carazolle (Universidade Estadual de Campinas- Instituto de Biologia); Gonçalo A G Pereira (Universidade Estadual de Campinas- Instituto de Biologia); Fernando F Costa (Universidade Estadual de Campinas- Hemocentro);
Short Abstract: SAGE enables the analysis of thousands of genes and a total quantification of each transcript. We used SAGE to quantify expression profiles during the differentiation of human erythroid cells. Results may contribute to the comprehension of erythroid differentiation and identification of new targets genes involved in some erythroid diseases.
Long Abstract: Click Here

Poster L-37
Fuzzy Biclustering of Microarray Data - borrowing ideas from sequence profiles
Stefan Tomiuk ( Miltenyi Biotec GmbH); Michael Brosda ( Miltenyi Biotec GmbH); Corinna Scholz ( Miltenyi Biotec GmbH); Kay Hofmann ( Miltenyi Biotec GmbH);
Short Abstract: We present a novel approach to biclustering that is seeded by a small group of genes known to share a common regulator. The experiments are weighted by their support for the intra-seed similarity, and this weighting gets refined while new members of the group are being added in an iterative process.
Long Abstract: Click Here

Poster L-38
Meta Prediction of Human microRNA Targets
Alal Eran (Children's Hospital Informatics Program, Harvard-MIT Division of Health Sciences and Technology); Alvin Kho (Children's Hospital Informatics Program, Harvard-MIT Division of Health Sciences and Technology); Iris Eisenberg (Howard Hughes Medical Institute, Children's Hospital Boston); Michal Galdzicki (Children's Hospital Informatics Program, Harvard-MIT Division of Health Sciences and Technology); Kamila Naxerova (Children's Hospital Informatics Program, Harvard-MIT Division of Health Sciences and Technology); Marco Ramoni (Children's Hospital Informatics Program, Harvard-MIT Division of Health Sciences and Technology); Louis Kunkel (Howard Hughes Medical Institute, Children's Hospital Boston); Isaac Kohane (Children's Hospital Informatics Program, Harvard-MIT Division of Health Sciences and Technology);
Short Abstract: We present MAMI - MetA Mir:target Inference - a meta-predictor of human microRNA targets based on integrating five widely-used contemporary predictors. We conduct the first head-to-head performance evaluation of these predictors on hundreds of recently validated microRNA-target pairs, and show that MAMI performs significantly better than any single prediction method.
Long Abstract: Click Here

Top

Other

Poster M-1
CUPID: Core and Unique Protein IDentification system
Raja Mazumder (Protein Information Resource, Georgetown University); Darren A. Natale (Protein Information Resource, Georgetown University); Sudhir Murthy (DCWASA- DWT); Rathi Thiagarajan (Protein Information Resource, Georgetown University); Cathy H. Wu (Protein Information Resource, Georgetown University);
Short Abstract: A pipeline using a combination of computational and manual analyses of BLAST results was developed to identify strain-, species-, and genus-specific proteins and to catalog the closest sequenced relative for each protein in a proteome. Such proteins can not only serve as taxon-specific diagnostic targets but also provide insight into the criteria that define an organism.
Long Abstract: Click Here

Poster M-2
Downregulation of anti-apoptotic gene expression by antisense oligonucleotides induces apoptosis and sensitizes head and neck squamous cell carcinoma cells to chemotherapy.
HIMANI SHARMA (DEPT. OF BIOCHEMISTRY, ALL INDIA INSTITUTE OF MEDICAL SCIENCES, ANSARI NAGAR, NEW DELHI. INDIA); NEETA SINGH (DEPT. OF BIOCHEMISTRY, ALL INDIA INSTITUTE OF MEDICAL SCIENCES, ANSARI NAGAR, NEW DELHI. INDIA);
Short Abstract: We addressed the question whether antisense approach towards anti-apoptotic proteins could restore the apoptosis and sensitize the HNSCC cells to chemotherapy. Our results suggest that antisense treatment against these survival factors in combination with lower doses of chemotherapy offers potential as a less toxic chemoadjuvant therapy.
Long Abstract: Click Here

Poster M-3
Synthesis And Selection Of Antibacterials Using Codon-Shuffling As Method For De Novo Protein Design.
Alka Rao (ICGEB, New Delhi); Sidharth Chopra (ICGEB, New Delhi); Geeta Ram (ICGEB, New Delhi); Anand Ranganathan (ICGEB, New Delhi);
Short Abstract: The concept of de novo design and laboratory evolution has gained great importance especially as an invaluable tool in designing novel bioactive molecules. Using codon shuffling as a method of de novo design, five different proteins were generated successfully that proved bacteriostatic on their expression in E. coli.
Long Abstract: Click Here

Poster M-4
Plant Transcription Factors
Diego Mauricio Riano Pachón (Department of Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam); Ingo Dreyer (Department of Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam); Slobodan Ruzicic (Cooperative Research Group, Max Plack Institute of Molecular Plant Physiology); Bernd Mueller-Roeber (Department of Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam);
Short Abstract: Transcription factors (TF) are proteins that play a central role in the regulation of gene expression; usually they are members of gene families. Here we have identified the members of up to 53 TF families of plants whose genome sequences are available (Oryza sativa, Arabidopsis thaliana, Chlamydomonas reinhardtii, Ostreococcus tauri).
Long Abstract: Click Here

Poster M-5
Predicting Chemical Properties of Metabolites
Roman Eisner (University of Alberta); Craig Knox (University of Alberta); Russ Greiner (University of Alberta); David Wishart (University of Alberta);
Short Abstract: We present our efforts in learning to predict chemical properties of metabolites. These properties, such as solubility, are important for completing the annotations in the Human Metabolite Database (http://www.hmdb.ca), and also for facilitating further research on these compounds. This poster evaluates our predictors and discusses the results.
Long Abstract: Click Here

Poster M-6
Identification of Microorganisms Clusters by Using Dynamic Programming to Analyze Antimicrobial Susceptibility Sequences
Braulio RGM Couto (UNI-BH); Ana P Ladeira (UNI-BH); Carlos EF Starling (Hospitais Vera Cruz , Life Center e Baleia);
Short Abstract: Pathogens have their antibiogram inserted in strings of S, R, or U (sensible, resistant or unknown) and analyzed by a dynamic programming algorithm that identifies clusters. Despite the fact that antimicrobial resistance is a phenotype characteristic, the method was capable to identify clusters in absence of automated ribotyping systems.
Long Abstract: Click Here

Poster M-8
An information system to early detect and control plant diseases and other causal agents of damage
Camargo, A. (The University of Liverpool, Department of Electrical Engineering & Electronics, Liverpool, L69 3GJ,); Smith, J. (The University of Liverpool, Department of Electrical Engineering & Electronics, Liverpool, L69 3GJ,);
Short Abstract: The system diagnoses plant disease damages. First with the help of computational techniques the disease visual symptoms are assessed, then an expert system evaluates critical variables that affect the crop year-round, the result produces a diagnosis and the measures to control and eradicate the damage.
Long Abstract: Click Here

Poster M-9
Bioinformatics analysis on ChIP-on-chip data to survey global RNA pol II binding and histone H3 acetylation patterns and the effects induced by HDAC inhibition
Richard Cai (Scientific Computing and Statistics, Genome and Proteome Sciences, NIBRI); Shaowen Wang (Molecular Biology, NIBRI); Darrell Ricke (Scientific Computing and Statistics, Genome and Proteome Sciences, NIBRI); Yan Yan-Neale (Drug Discovery II, Oncology, NIBRI); Richard Young (Whitehead Institute, MIT); Dalia Cohen (Molecular Biology, NIBRI);
Short Abstract: This poster will present our strategy to analyze data from a ChIP-on-chip experiment, a technology to study the binding status of a protein to DNA. The association of acetylated histone H3 and RNA polymerase II to human promoter regions under normal and HDAC inhibitor treated conditions will be reported.
Long Abstract: Click Here

Poster M-11
ASviewer : Visualizing the transcript structure and functional domains of alternatively-spliced genes
Younghee Lee (Ewha Womans University); Wonhyong Chung (National Genome Information Center); Sanghyuk Lee (Ewha Womans University);
Short Abstract: We present a novel viewer named ASviewer that visualizes the transcript structure and functional inference of alternatively spliced genes intuitionally. Key ideas involve in clustering of overlapping exons and representing introns in arbitrary scales. ASviewer is available at http://genome.ewha.ac.kr/ASviewer.
Long Abstract: Click Here

Poster M-12
An open-source software platform for the management and analysis of genotyping data
Corne Schriek (Bioinformatics and Computational Biology Unit, University of Pretoria);
Short Abstract: An open-source web-based genotyping platform for general purpose management, analysis and visualisation of genotyping data such as SNPs, AFLPs and microsatellites. This software ties scattered genotyping technologies and standards together with cutting-edge programming technologies to form one coherent extensible module that slots into a larger functional genomic information management system.
Long Abstract: Click Here

Poster M-13
A Computational Framework for Analysis of Dynamic Social Structures
Tanya Y. Berger-Wolf (Department of Computer Science, University of Illinois at Chicago); Ilya R. Fischhoff (Department of Ecology & Evolutionary Biology, Princeton University); Daniel I. Rubenstein (Department of Ecology & Evolutionary Biology, Princeton University); Jared Saia (Department of Computer Science, University of New Mexico, Albuquerque); Siva Sundaresan (Department of Ecology & Evolutionary Biology, Princeton University);
Short Abstract: Analysis of many processes in animal populations (disease spread, dominance, reproduction) requires analysis of the network of individual interactions. Until now such analysis was essentially aggregate and static. We show that it may produce incorrect answers and propose a novel conceptual and computational framework for analysis of dynamic interaction networks.
Long Abstract: Click Here

Poster M-15
A Numeric Coding Scheme for Amino Acids
Siwo Geoffrey Henry (Dept. Biochemistry, Egerton University);
Short Abstract: This study presents a novel approach of numerically representing amino acids taking into account their biological properties as encoded in the PAM-250 matrix. Representation of amino acids in numerical form could make protein sequence analysis malleable in mathematics, data mining and artificial intelligence.
Long Abstract: Click Here

Poster M-16
DOE Hanford Site Metagenome: A multiple extreme environment that hosts wide diversity of microbes and radiotolerant bacteria
Syed H Mustafa (Argonne National Laboratory); Natalia Maltsev (Argonne National Laboratory); Fred Brockman (Pacific Northwest National Laboratory); Banu Gopalan (Pacific Northwest National Laboratory);
Short Abstract: Metagenome analysis of the microbial community residing in low biomass subsurface sediments beneath a leaking high-level radioactive waste tank at the DOE Hanford Site revealed that it was dominated by representatives of Deinococcus, Actinobacteria and Firmicutes in higher contamination zones, while Proteobacteria and Actinobacteria dominated in lower contamination zones.
Long Abstract: Click Here

Poster M-17
Detecting Cell Cycle Regulated Genes of Schizosaccharomyces pombe by using Non-metric Multidimensional Scaling without Sinusoidal Fitting
Y-h. Taguchi, ( Department of Physics, Chuo University,);
Short Abstract: We applied non-metric multidimensional scaling to cell division cycle microarray of Schizosaccharomyces pombe. Genes turn out to be aligned as circular arrangement whose polar angles are associated with cell cycle phases. One of two gene groups selected by consistency among experiments is associated with known cell cycle regulated genes.
Long Abstract: Click Here

Poster M-18
A Simple Formula for the High Regularisation Limit of SVMs & Ridge Regression with Application to Gene Selection and Classification of Microarrays
Justin Bedo (ANU); Tiberio Caetano (NICTA); Brian Parker (NICTA); Conrad Sanderson (NICTA); Peter Sunehag (NICTA); Adam Kowalczyk (NICTA);
Short Abstract: Microarray experiments typically deliver datasets with few samples of high dimensionality. For Support Vector Machines (SVMs) it has recently been shown that the high amounts of regularisation can lead to better performance. We show that in the high-regularisation limit C->0, SVMS converge to a centroid classifier.
Long Abstract: Click Here

Poster M-19
Quantitative model of the Mdm2-mediated p53 ubiquitination network
Paul Brazhnik (Virginia Tech); Kurt W. Kohn (NCI NIH);
Short Abstract: Stability of the “guardian of the genome” tumor suppressor protein p53 is regulated predominantly through its ubiquitination. Here a data-driven computational dynamic systems model of the Mdm2-mediated p53 ubiquitination network is presented. The model predicts existence of the HAUSP regulated switch from auto- to p53 ubiquitination by Mdm2.
Long Abstract: Click Here

Poster M-20
Optimized Selection of Short Interfering RNA Target Loci
Istvan Ladunga (Center for Biotechnology & Dept. Statistics, University of Nebraska-Lincoln);
Short Abstract: To increase the silencing efficacy of short interfering RNA (siRNA), we developed optimized target selection methods. The constrained optimization, support vector machine and partial least squares methods were trained on 3000 siRNA experiments to predict silencing efficacy with an accuracy of 88 percent in cross-validation and blind-test experiments.
Long Abstract: Click Here

Poster M-22
Choosing the End: Regulation of Alternative 3' Splice Sites
Yael Mandel-Gutfreund (Faculty of Biology, Technion-Israel Institute of Technology); Martin Akerman (Faculty of Biology, Technion-Israel Institute of Technology);
Short Abstract: In this study we apply a Support Vector Machine to identify alternative 3' splice site events. We show that we can distinguish between alternative and constitutive event both for tandem acceptor motifs and for splice sites which are distant apart. Finally, we suggest a possible mechanism of splice site selection.
Long Abstract: Click Here

Poster M-23
GMP-RAM v1.1: A PROPOSED SOFTWARE TOOL TO SUPPORT THE METHOD FOR RISK ASSESSMENT OF GENETICALLY MODIFIED PLANTS
KATIA REGINA EVARISTO DE JESUS (Embrapa Meio Ambiente); FÁBIO DANILO VIEIRA (Embrapa Agriculture Informatics); DENIS UBEDA DE LIMA (Bayer Cropscience Ltda / Bioscience);
Short Abstract: GMP-RAM v1.1: A PROPOSED SOFTWARE TOOL TO SUPPORT THE METHOD FOR RISK ASSESSMENT OF GENETICALLY MODIFIED PLANTS KATIA REGINA EVARISTO DE JESUS1; FÁBIO VIEIRA2; DENIS LIMA3 - 1 - Embrapa Environment, Jaguariúna – SP, Brazil; 2 - Embrapa Agriculture Informatics, Brazil; 3- Bayer Cropscience Ltda / Bioscience, Brazil.
Long Abstract: Click Here

Top

Late Breaking Posters

Poster LB-1
High affinity and binding specificity of computationally redesigned protein interfaces
Category: Structural Bioinformatics
Vladimir Potapov (Department of Plant Sciences, Weizmann Institute of Science); Dana Reichmann (Department of Biological Chemistry, Weizmann Institute of Science); Vladimir Sobolev (Department of Plant Sciences, Weizmann Institute of Science); Marvin Edelman (Department of Plant Sciences, Weizmann Institute of Science); Gideon Schreiber (Department of Biological Chemistry, Weizmann Institute of Science);
Short Abstract: We demonstrate an approach for computational redesign of protein-protein interfaces combining a scoring function and natural template fragments from resolved structures to produce novel putative complexes. Experimentally validating with the TEM1-BLIP interface, the top-scoring design yielded a complex showing affinity exceeding that of wild type and specific binding.
Long Abstract: Click Here

Poster LB-2
Developing a biorepository database
Category: Databases and Data Integration
Helena Brentani (Hospital do Cancer FAP); Artur Fabri (Hospital do Cancer FAP); Luiz Paulo Camargo (Hospital do Cancer FAP); Diogo F Patrao (Hospital do Cancer FAP); Daniel Simao (Hospital do Cancer FAP); Eduardo Abrantes (Hospital do Cancer FAP); AHJFM Campos (Hospital do Cancer FAP); Fernando Soares (Hospital do Cancer FAP);
Short Abstract: We will present the Hospital do Cancer tumor database and the integration with other institutions to construct a National tumor biorepository
Long Abstract: Click Here

Poster LB-3
Classifiers of the Protein Interactions With Their Substrate/Inhibitors
Category: Structural Bioinformatics
Vera S. Garcia (Unicamp); Paula R. Kuser Falcão (Embrapa);
Short Abstract: Basically all biological processes require protein-ligand identifications. One major challenge to biophysics-chemistry is try to predict these interactions. One step towards solving this mystery is analyzing the structural features involved in the complex formation. A good biological model to start these studies is the cystein-protease family.
Long Abstract: Click Here

Poster LB-4
Proline: The Proteomics Pipeline
Category: Proteomics
Matt Sullivan (UCD); Andreas De Stefani (UCD); Michael Clarke (UCD); Jason Wong (University of Oxford); Gerard Cagney (UCD);
Short Abstract: Proline is a software system that provides complete analysis of proteomics mass spectrometry data. Proline automates the tasks of data conversion, data archiving, process and workflow management, to provide database searching, de novo sequencing, spectral quality assurance, and relative quantification.
Long Abstract: Click Here

Poster LB-5
A survey of data mining methods for linkage disequilibrium mapping
Category: Other
Onkamo Päivi (Department of Biological and Environmental Sciences, University of Helsinki); Toivonen Hannu (HIIT-BRU, Department of Computer Science, University of Helsinki);
Short Abstract: Data mining methods are gaining more interest as potential tools in mapping and identification of complex human disease susceptibility loci. The methods are well suited to large numbers of genetic marker loci, but also might be useful for clarifying the clinical subtypes of disease. We review the current data mining-based methods for genetic association mapping and phenotype analyses.
Long Abstract: Click Here

Poster LB-6
Epitope mapping of monospecific antibodies using cell display
Category: Proteomics
Johan Rockberg (Royal Institute of Technology); John Löfblom (Royal Institute of Technology); Mathias Uhlén (Royal Institute of Technology);
Short Abstract: We describe a novel high throughput method for mapping of antibody epitopes using gene-fragmentation, celldisplay, flowcytometry and Pyrosequencing. Results from epitope mapping of antibodies obtained from the Human Protein Atlas (www.hpa.org) will be shown.
Long Abstract: Click Here

Poster LB-7
Probabilistic Genetic Networks analysis of three Plasmodium falciparum strains from dynamical expression signals
Category: Systems Biology
Junior Barrera (Instituto de Matemática e Estatística - Universidade de São Paulo); Roberto Marcondes Cesar Jr (Instituto de Matemática e Estatística - Universidade de São Paulo); David Corrêa Martins Jr (Instituto de Matemática e Estatística - Universidade de São Paulo); Ricardo Zorzetto Nicoliello Vêncio (Instituto de Matemática e Estatística - Universidade de São Paulo); Carmen Fernández-Becerra (Instituto de Ciências Biomédicas - Universidade de São Paulo); Carlos Alberto de Bragança Pereira (Instituto de Matemática e Estatística - Universidade de São Paulo); Hernando A. del Portillo (Instituto de Ciências Biomédicas - Universidade de São Paulo);
Short Abstract: In this work we present a framework to construct genetic networks from dynamical expression signals. The applicability of this tool for discovering gene networks of the malaria expression regulation system has been validated for simulated and real microarray data. Currently, we are applying the same technique for three malarial strains.
Long Abstract: Click Here

Poster LB-8
A Novel Enzyme-inhibitor Docking Algorithm Based on the Degree of Burial and Conservation of Surface Residues
Category: Structural Bioinformatics
Bingding Huang (Biotec, TU Dresden, Germany); Michael Schroeder (Biotec, TU Dresden, Germany);
Short Abstract: The binding sites of enzyme-inhibitor complexes usually involve a very deep buried pocket and are more conserved than the rest of surface. In our docking approach BDOCK, the degree of burial and conservation of surface residues are taken into account, which significantly improves the performance of traditional FFT docking method.
Long Abstract: Click Here

Poster LB-9
A Global Protein Database Makes Analysis and Comparison of Data Sets Easy
Category: Databases and Data Integration
Morten Bern (Proxeon A/S); Brian Ramsgaard (Proxeon A/S); Søren Schandorff (Proxeon A/S); Hans Jespersen (Proxeon A/S); Ole Vorm (Proxeon A/S); Alexandre Podtelejnikov (Proxeon A/S);
Short Abstract: The generation of vast amounts of data from proteomics studies has become a common practice. We show how an integrated protein database can be used to compare data sets from different laboratories, at protein, fragment and allele level. We also present statistics for the ProteinCenter protein database regarding outdated accessions.
Long Abstract: Click Here

Poster LB-10
Towards structural informatics of biological membranes
Category: Structural Bioinformatics
Andrei Lomize (University of Michigan); Mikhail Lomize (University of Michigan); Irina Pogozheva (University of Michigan);
Short Abstract: Experimental 3D structures are available for thousands of membrane-associated proteins. However, the exact spatial positions of these proteins with respect to the lipid bilayer are unknown. These positions were calculated for 600 proteins, verified against available experimental data, and deposited in the OPM (Orientations of Proteins in Membranes) database http://opm.phar.umich.edu/.
Long Abstract: Click Here

Poster LB-11
IDENTIFICATION OF NOVEL CANCER/TESTIS ANTIGENS BY DATABASE MINING AND mRNA EXPRESSION ANALYSIS.
Category: Transcriptomics
FABIANA BETTONI (LABORATORY OF MOLECULAR BIOLOGY AND GENOMICS, LUDWIG INSTITUTE FOR CANCER RESEARCH); FERNANDO CAMARGO FILHO (LABORATORY OF MOLECULAR BIOLOGY AND GENOMICS, LUDWIG INSTITUTE FOR CANCER RESEARCH); MURILO VIEIRA GERALDO (LABORATORY OF MOLECULAR BIOLOGY AND GENOMICS, LUDWIG INSTITUTE FOR CANCER RESEARCH); PEDRO ALEXANDRE GALANTE (LABORATORY OF COMPUTATIONAL BIOLOGY, LUDWIG INSTITUTE FOR CANCER RESEARCH); RAPHAEL BESSA PARMIGIANI (LABORATORY OF MOLECULAR BIOLOGY AND GENOMICS, LUDWIG INSTITUTE FOR CANCER RESEARCH); SANDRO JOSÉ DE SOUZA (LABORATORY OF COMPUTATIONAL BIOLOGY, LUDWIG INSTITUTE FOR CANCER RESEARCH); HELENA BRENTANI (LABORATORY OF COMPUTATIONAL BIOLOGY, HOSPITAL DO CANCER A.C. CAMARGO); ANAMARIA ARANHA CAMARGO (LABORATORY OF MOLECULAR BIOLOGY AND GENOMICS, LUDWIG INSTITUTE FOR CANCER RESEARCH);
Short Abstract: CT antigens are a subgroup of tumor antigens with restricted expression in normal testis and different types of tumors. In the current study, we used a computational approach followed by experimental validation and identified 5 novel CT antigens. The immunogenicity of these candidates is currently under study. Financial Support: FAPESP and Ludwig Institute for Cancer Research
Long Abstract: Click Here

Poster LB-12
Efficient Morphological Word Variant Discovery: Expanding the recall of biomedical text searches.
Category: Text Mining and Information Extraction
Fabien Campagne (Institute for Computational Biomedicine and Dept. of Physiology and Biophysics; Weill Medical College of Cornell University);
Short Abstract: I will present an alternative to stemming for biomedical text corpora: a scalable and interactive approach to finding words morphologically related to a query word (e.g., ubiquitin, monoubiquitination). The approach can be used for automatic query expansion (i.e., as in http://www.twease.org, our new sentence-level search engine for Medline).
Long Abstract: Click Here

Poster LB-13
EMBnet - World wide collaboration in bioinformatics
Category: Other
Kimmo Mattila (CSC - Scientific Computing Ltd. / EMBnet);
Short Abstract: EMBnet (http://www.embnet.org/) is an international collaboration network that aims to enhance bioinformatics services by bringing together bioinformatics service providers. EMBnet has 35 nodes spread over 27 countries. The nodes support tens of thousands of registered users and even larger number of open-access web users from all over the world.
Long Abstract: Click Here

Poster LB-14
BUILDING BIOINFORMATIC DATABASE SELECTING THE USEFUL CANDIDATE GENES AND RECORDING MEDIUM FOR THE DATABASE
Category: Databases and Data Integration
Young-Joo Seol (National Institute of Agricultural Biotechnology); Man-Jeong Kang (National Institute of Agricultural Biotechnology); Chang-Kug Kim (National Institute of Agricultural Biotechnology); Jang-Ho Hahn (National Institute of Agricultural Biotechnology); Dong-Suk Park (National Institute of Agricultural Biotechnology);
Short Abstract: To search high reliable and useful genes from hypothetical genes in NCBI Database we designed similarity search-based-analysis system and builded the database of useful candidate genes by search for similarities using the BLASTP tool against patent sequence database from NCBI.
Long Abstract: Click Here

Poster LB-15
Genetic Algorithms Help Other Learning Algorithms Answer Whole Protein Questions
Category: Sequence Analysis
Andrew Kernytsky (Department of Biochemistry and Molecular Biophysics, Columbia University); Burkhard Rost (Department of Biochemistry and Molecular Biophysics, Columbia University);
Short Abstract: We have used a genetic algorithm to select the appropriate combinations of local features for use in training another learning algorithm (neural networks or support vector machines) to predict a global protein feature such as its enzymatic activity. The method shows an improvement over using the learning algorithm alone.
Long Abstract: Click Here

Poster LB-16
A model for determining cell-cycle-distributions in synchrony/release experiments
Category: Systems Biology
David Orlando (Duke University); Steven B. Haase (Duke University); Alexander Hartemink (Duke University); Edwin S. Iversen (Duke University); Philip Benfey (Duke University);
Short Abstract: Synchrony/Release protocols are commonly used to examine dynamic processes during the cell cycle. Quantitative time-series measurements are drawn from populations that lose synchrony over time. Each measurement represents a convolution of values over cell cycle states. We describe a model for dynamic population synchrony loss that helps resolve these effects.
Long Abstract: Click Here

Poster LB-17
SNPSTRs: a new tool in population genetics
Category: Evolution and Phylogeny
Ino Agrafioti (Imperial College London); Michael PH Stumpf (Imperial College London);
Short Abstract: A SNPSTR is a relatively new type of compound genetic marker which combines a microsatellite marker with one or more tightly linked SNPs. Here we present SNPSTR datasets from human, mouse, rat, dog and chicken genomes. SNPSTRs have the potential to become a very useful tool in the field of population genetics.
Long Abstract: Click Here

Poster LB-18
Copy Number Variation (CNV): Challenges and Ramifications
Category: Human Health
K. Cara Woodwark (Wellcome Trust Sanger Institute); Tatiana Zerjal (Wellcome Trust Sanger Institute); Donglin Sun (Wellcome Trust Sanger Institute); Yali Xue (Wellcome Trust Sanger Institute); Dan Andrews (Wellcome Trust Sanger Institute); Chris Tyler-Smith (Wellcome Trust Sanger Institute); Nigel Carter (Wellcome Trust Sanger Institute); Hiro Aburatani (University of Tokyo); Charles Lee (Brigham Womens Hospital, Boston); Keith Jones (Affymetrix, Santa Clara); Steve Scherer (The Centre for Applied Genomics, Hospital for Sick Children, Toronto); Matthew E. Hurles (Wellcome Trust Sanger Institute);
Short Abstract: The Genome Structural Variation consortium has produced a CNV map of the human genome based on the 270 HapMap individuals. Using SNP genotyping arrays and comparative genomic hybridisation, 1447 CNVs were discovered, covering 360Mb. A few of the many interesting findings, challenges and far reaching consequences of genomic structural variation, are presented here.
Long Abstract: Click Here

Poster LB-19
Explorations in Environmental and Medical Metagenomics
Category: Comparative Genomics
David Soergel (Biophysics Graduate Group, UC Berkeley); Marcin Joachimiak (Department of Plant and Microbial Biology, University of California, Berkeley); Susan Mashiyama (Department of Plant and Microbial Biology, University of California, Berkeley); Chris van Belle (Department of Molecular and Cellular Biology, UC Berkeley); John-Marc Chandonia (Physical Biosciences Division, Lawrence Berkeley National Laboratory); David Tulga (Department of Bioengineering, UC Berkeley); Daniel H. Present (Division of Gastroenterology, Mount Sinai School of Medicine); Maria Abreu (Division of Gastroenterology, Mount Sinai School of Medicine); Steven Brenner (Biophysics Graduate Group and Departments of Plant and Microbial Biology, Molecular and Cellular Biology, and Bioengineering, UC Berkeley; and Physica);
Short Abstract: Environmental shotgun sequences are accruing at an ever-increasing rate and promise to revolutionize our understanding of microbial community ecology in the environment and medicine. Here we describe our analysis of data from the Global Ocean Survey; discuss possible medical applications of sequencing intestinal microflora; and consider using “genomic signatures” to analyze metagenomic data.
Long Abstract: Click Here

Poster LB-20
Description of atomic burials in compact globular proteins by Fermi-Dirac probability distributions
Category: Structural Bioinformatics
Antonio Luiz Cruz Gomes (Universidade de Brasilia); Julia Rosa de Rezende (Universidade de Brasilia); Antonio F. Pereira de Araujo (Universidade de Brasilia); Eugene I. Shakhnovich (Harvard University);
Short Abstract: We perform a statistical analysis of atomic radial distributions in a non-redundant set of compact globular proteins. Empirical curves are consistent with the volume quadratic increase of spherical shells and a Fermi-Dirac distribution for the atomic density as a function of the distance from the molecular geometrical center.
Long Abstract: Click Here

Poster LB-21
High-throughput identification and gene expression analysis of novel antisense transcripts using MPSS
Category: Transcriptomics
Daniel O. Vidal (Laboratory of Molecular Biology and Genomics - Ludwig Intitute for Cancer Research, Sao Paulo Branch, Brazil); Pedro A. F. Galante (Laboratory of Computational Biology - Ludwig Intitute for Cancer Research, Sao Paulo Branch, Brazil); Lilian C. Pires (Laboratory of Molecular Biology and Genomics - Ludwig Intitute for Cancer Research, Sao Paulo Branch, Brazil); Jorge E. de Souza (Laboratory of Computational Biology - Ludwig Intitute for Cancer Research, Sao Paulo Branch, Brazil); Anamaria A. Camargo (Laboratory of Molecular Biology and Genomics - Ludwig Intitute for Cancer Research, Sao Paulo Branch, Brazil); Sandro J. de Souza (Laboratory of Computational Biology - Ludwig Intitute for Cancer Research, Sao Paulo Branch, Brazil);
Short Abstract: NATs are RNA messages presenting complementarity to other endogenous RNA. In the current study, using a computational approach and MPSS data we identified 4308 new NATs exclusively represented by MPSS tags. 27 of 96 tags selected were confirmed as antisense transcripts by GLGI. Validation using strand-specific RT-PCR is currently underway.
Long Abstract: Click Here

Poster LB-22
Global DNA Methylation Analysis in Breast Tumors Using Promoter Microarray
Category: Other
Anna Christina de Matos Salim (Ludwig Institute for Cancer Research); Luiz Paulo Camargo (Hospital do Câncer); Diogo Ferreira da Costa Patrão (Hospital do Câncer); Yipeng Wang (Sidney Kimmel Cancer Center); Helena Paula Brentani (Hospital do Câncer); Michael McClelland (Sidney Kimmel Cancer Center); Dirce Maria Carraro (Ludwig Institute for Cancer Research); Anamaria Aranha Camargo (Ludwig Institute for Cancer Research);
Short Abstract: Aberrant DNA methylation of CpG sites in promoter regions is among the most frequent alterations in tumors and is emerging as an important molecular marker for disease diagnosis and prognosis. In this study we have been using promoter microarray to identify methylation differences between four groups of breast tumors patients.
Long Abstract: Click Here

Poster LB-23
“Functional role of a novel tandem repeat polymorphism (VNTR) of the human Dopamine Transporter gene (SLC6A3) and positive association with general cognitive abilities”
Category: Human Health
Fabio Miyajima (Capes - CIGMR/University of Manchester); Kate Haddley (University of Liverpool); Jill Bubb (University of Liverpool); Neil Pendleton (University of Manchester); Mike Horan (University of Manchester); JF William Deakin (University of Manchester); John Quinn (University of Liverpool); Antony Payton (University of Manchester); William Ollier (University of Manchester);
Short Abstract: Dysregulation of dopamine in the synaptic cleft is thought to account for cognitive dysfunction. In non-demented individuals dopamine levels also tend to decline from adulthood through to death. Hence the dopamine transporter gene (SLC6A3) is a natural candidate for cognition studies. Here we have characterised and investigated the functional role of a novel intragenic VNTR-polymorphism and its association with general cognitive abilities(n=684)
Long Abstract: Click Here

Poster LB-24
National Cancer Imaging Archive (NCIA): An Integrative Approach in Cancer Research and Clinical Trial Image Management
Category: Databases and Data Integration
James Luo (Science Applications International Corporation (SAIC)); Sharon Settnek (Science Applications International Corporation (SAIC)); Jon Dietrich (Science Applications International Corporation (SAIC)); Andrew Shinohara (Science Applications International Corporation (SAIC)); Jin Chen (Science Applications International Corporation (SAIC)); Derek Kong (Science Applications International Corporation (SAIC)); Thai Le (Science Applications International Corporation (SAIC)); Qinyan Pan (Science Applications International Corporation (SAIC)); Rona Zhou (Science Applications International Corporation (SAIC)); Durga Addepalli (Science Applications International Corporation (SAIC)); Ye Wu (Science Applications International Corporation (SAIC)); David Kupferschmid (Northern Taiga Ventures Incorporated); Carl Jaffe (Cancer Imaging Program, U.S. National Cancer Institute); John Freymann (SAIC-Frederick, Inc.); Laurence Clarke (Cancer Imaging Program, U.S. National Cancer Institute); John Perry (Radiological Society of North America); Eliot Siegel (Department of Diagnostic Radiology, University of Maryland; VA Maryland Healthcare System and Radiological Society of North America); Daniel Sullivan (Cancer Imaging Program, U.S. National Cancer Institute); Anand Basu (Center for Bioinformatics, National Cancer Institute); Sichen Liu (Center for Bioinformatics, National Cancer Institute); Peter Covitz (Center for Bioinformatics, National Cancer Institute); Ken Buetow (Center for Bioinformatics, National Cancer Institute);
Short Abstract: The National Cancer Imaging Archive (NCIA) is a searchable repository of in vivo cancer images. The system provides the cancer research community with public access to images in DICOM format as well as rich metadata, annotations and markup to be used in the development and validation of analytical software tools.
Long Abstract: Click Here

Poster LB-25
Computational Implementation of Whole-Part Graphs
Category: Systems Biology
Marcelo Trindade dos Santos (LNCC); Mauricio Vieira Kritz (LNCC); Liliane Paiva de Souza (LNCC); Paulo Sérgio Rodrigues (LNCC);
Short Abstract: We present an OO computational model and its implementation for whole-part graphs, constructing a framework for systemic biological analysis. We show that this construct is adequate for representing the modular and hierarchical nature of metabolic networks.
Long Abstract: Click Here

Poster LB-26
Quantitative Proteomic Analysis of the Mouse Photoreceptor Sensory Cilium Reveals a Highly Complex Organelle
Category: Proteomics
Qin Liu (University of Pennsylvania School of Medicine); Glenn Tan (The Wistar Institute); Natasha Levenkova (The Wistar Institute); John J. Rux (The Wistar Institute); David Speicher (The Wistar Institute); Eric Pierce (University of Pennsylvania School of Medicine);
Short Abstract: The complete mouse photoreceptor sensory cilium (PSC) proteome identified by 2 or more peptides contains 1975 proteins, making it the most complex organelle whose proteome has been reported. It contains the majority of PSC proteins produced by retinal degeneration disease genes, and many novel photoreceptor and cilium proteins.
Long Abstract: Click Here

Poster LB-27
Classification of Protein-DNA Complexes Based on Structural Descriptors
Category: Structural Bioinformatics
Ponraj Prabakaran (NCI, NIH, USA); Joerg G. Siebers (Dept. of Biosci. Bioinf., Kyushu Inst. of Tech.); Shandar Ahmad (Dept. of Biosci., Jamia Millia Islamia Univ., India); Michael Gromiha (Comp. Biol. Res. Cent., AIST Japan); Maria G. Singarayan (SAIC-Frederick, Inc., NCI, USA); Akinori Sarai (Dept. of Biosci. Bioinf., Kyushu Inst. of Tech.);
Short Abstract: We attempt to classify a unique set of 62 protein-DNA complexes using a set of descriptors, mainly characterizing protein-DNA interactions, and identified 7 distinct clusters. The results are distinct from the traditional motif-based classification. The present classification may help to identify common properties and rules that govern protein-DNA recognition.
Long Abstract: Click Here

Poster LB-28
In vitro Molecular Evolution of Bean alpha-Amylase Inhibitors to Investigate Specificty of Binding to alpha-Amylases
Category: Structural Bioinformatics
Maria Cristina Mattar da Silva (Embrapa Recursos Genéticos e Biotecnologia); Fabíola Rodrigues Teixeira (Embrapa Recursos Genéticos e Biotecnologia); Cleiton C. M da Cruz (Embrapa Recursos Genéticos e Biotecnologia); Roberto C. Togawa (Embrapa Recursos Genéticos e Biotecnologia); Goran Neshich (Embrapa Recursos GEnéticos e Biotecnologia); Maria Fátima Grossi de Sa (Embrapa Recursos Genéticos e Biotecnologia);
Short Abstract: Combined DNA shuffling and Phage-display are important techniques to generate large number of alpha-amylase inhibitor mutants in vitro in order to identify new molecules with improved activities towards specific insects. We present new mutants and discuss possible repercussion of mutations on protein stability and function. We also introduced the STING parameter
Long Abstract: Click Here

Poster LB-29
Indexing with Uniprot
Category: Text Mining and Information Extraction
Sylvain Gaudan (EBI); Miguel Arregui (EBI); Harald Kirsch (EBI); Vivian Lee (EBI); Dietrich Rebholz-Schuhmann (EBI);
Short Abstract: Retrieving all the publications related to a protein can be tricky. Omitting synonyms results in missing publications whereas ambiguous protein names produce unwanted results. Furthermore, filtering publications related to a specific model organism is laborious. We present the creation of a search engine index that has been expanded to include Protein Accession Numbers from UniProtKB. To this end, the protein names and their synonyms from UniProtKB are automatically identified, disambiguated and linked to the organism mentioned in the document. Finally the PANs are integrated into the Medline index to allow retrieving publications based on PANs instead of protein names.
Long Abstract: Click Here

Poster LB-30
Semantic Abstraction based WSD for Text Mining of Coarse-grained Corpus
Category: Text Mining and Information Extraction
Sa-kwang Song (Electronics and Telecommunications Research Institute); Sunghee Park (Electronics and Telecommunications Research Institute); Soo jun Park (Electronics and Telecommunications Research Institute);
Short Abstract: We propose a Word Sense Disambiguation method in coarse-grained biomedical documents such as patient’s records which have many different characteristics compared to fine-grained ones like Medline abstracts. In addition to POS and UMLS tagging, we utilize semantic abstraction of frequently used patterns including stopwords like numeric terms and symbols.
Long Abstract: Click Here

Poster LB-31
Semantic Abstraction based WSD for Text Mining of Coarse-grained Biomedical Corpus
Category: Text Mining and Information Extraction
Sa-kwang Song (Electronics and Telecommunications Research Institute); Sunghee Park (Electronics and Telecommunications Research Institute); Soo jun Park (Electronics and Telecommunications Research Institute);
Short Abstract: We propose a Word Sense Disambiguation method in coarse-grained biomedical documents such as patient’s records which have many different characteristics compared to fine-grained ones like Medline abstracts. In addition to POS and UMLS tagging, we utilize semantic abstraction of frequently used patterns including stopwords like numeric terms and symbols.
Long Abstract: Click Here

Poster LB-32
Development of a Software For Filtering Contaminant Masses From Peptide Mass Spectra
Category: Proteomics
Barreto,Sérgio (UNB - Universidade de Brasília); Cunha, Karina (UNB - Universidade de Brasília); Castro, Mariana S (UNB - Universidade de Brasília); Fontes,Wagner (UNB - Universidade de Brasília);
Short Abstract: During the experimental procedures, contaminants can be introduced in the sample averting its identification. The objective of the work is to present an application in the WEB that eliminates contaminants masses from the list of peptide masses. A key to successful peptide-mass searching is employing the highest mass accuracy available
Long Abstract: Click Here

Poster LB-33
Building three-dimensional complex structures automatically from binary interacting components
Category: Structural Bioinformatics
Matthieu Pichaud (EMBL); Robert B. Russell (EMBL);
Short Abstract: Interacting structures can serve as templates to predict structures for protein complexes. The number of possible templates makes predictions involving three or more proteins problematic. We present a procedure for making such predictions. Structures are generated using an interaction template library, and experimental constraints.
Long Abstract: Click Here

Poster LB-35
Localization of binding sites in protein structures by optimization of a composite scoring function
Category: Structural Bioinformatics
Andrea Rossi (UCSF); Marc Marti-Renom (Prince Felipe Research Center, Spain); Andrej Sali (UCSF);
Short Abstract: We describe a method for predicting the location of a binding site of a given type on a target protein structure. The method relies on a composite scoring function optimized by a Monte Carlo Simulated Annealing to find a good scoring patch on the protein surface.
Long Abstract: Click Here

Poster LB-36
Prediction of Transmembrane Region Adjacencies in Membrane Proteins
Category: Structural Bioinformatics
Roberto C. Togawa (Embrapa/Cenargen); John F. Antoniw (Rothansted Research); Jonathan G.L. Mullins (University of Wales, Swansea);
Short Abstract: We report a reliable approach for predicting the packing arrangements of transmembrane regions directly from amino acid sequence. The approach utilises residue pair association matrices from determined structures, and buried / exposed propensity scales, applied in a permutation based rotational algorithm to predicting adjacencies of transmembrane regions with high accuracy.
Long Abstract: Click Here

Poster LB-37
Finding the Needle from the Haystack: Definitional Question Answering
Category: Text Mining and Information Extraction
Hong Yu (University of Wisconsin-Milwaukee); Minsuk Lee (University of Wisconsin-Milwaukee);
Short Abstract: We developed a question answering system BioQA that automatically analyzes thousands of documents and then identifies short texts to specifically answer questions posed by biologists.
Long Abstract: Click Here

Poster LB-38
Using different softwares in a proteomic analysis of 2D-gels of plasmas from patients with dengue hemorrhagic fever and from healthy donors.
Category: Proteomics
Monique R. O. Trugilho (Lab. Toxinologia, IOC, FIOCRUZ); Lidiane M. Albuquerque (Lab. Toxinologia, IOC, FIOCRUZ); Ana Gisele C. Neves-Ferreira (Lab. Toxinologia, IOC, FIOCRUZ); Alexander Chapeaurouge (Lab. Toxinologia, IOC, FIOCRUZ); Hugo C. Castro-Faria-Neto (Lab. Imunofarmacologia, IOC, FIOCRUZ); Patrícia T. Bozza (Lab. Imunofarmacologia, IOC, FIOCRUZ); Fernando Bozza (IPEC, FIOCRUZ); Jonas Perales (Lab. Toxinologia, IOC, FIOCRUZ);
Short Abstract: We compared 2-D electrophoresis profiles of plasmas from patients with dengue and from healthy donors using the multiplex analysis by 2-D DIGE and the DeCyder software. After reducing the experimental variability, we have detected several differentially expressed proteins (p< 0.01) that may contribute for a better understanding of the disease.
Long Abstract: Click Here

Poster LB-39
Serine Proteases analysis based on phylogenetics trees constructed from the sequence and structure alignments
Category: Structural Bioinformatics
Cristina Ribeiro (UFMG); Francisco P. Lobo (UFMG); Marcelo M. Santoro (UFMG); Goran Neshich (EMBRAPA-CNPTIA);
Short Abstract: This work is to compare two different approaches to construct phylogenetic trees from a set of non-redundant serine proteases with deciphered 3D structure. The first one the sequence alignment generates a phylogenetic tree, and the other one is based on a sequence alignment strictly following the structure alignment. The differences between the two are discussed.
Long Abstract: Click Here

Poster LB-40
Molecular modeling of Phoneutria nigriventer spider toxins Tx2-1, Tx2-5, Tx2-6 and Tx2-9, using cysteine pattern
Category: Structural Bioinformatics
Cécile Fleury (UFMG ICB); Franck Molina (CPBS CNRS UMR 5160); Paulo S. L. Beirão (UFMG ICB);
Short Abstract: The three-dimensional structure of four cysteine-rich neurotoxic polypeptides (Tx2-1, Tx2-5, Tx2-6 and Tx2-9), purified in 1992 by Cordeiro et al. from the venom of the Brazilian ‘armed’ spider Phoneutria nigriventer, were modeled using homology molecular modeling method. The templates were chosen according to their cysteine pattern in the new spider neurotoxin classification proposed by Koslov et al. in 2005.
Long Abstract: Click Here

Poster LB-41
Oxidative modification of neurogranin by nitric oxide and its role in the activation of CaMKII: a computational model
Category: Other
Gabriela Antunes (Lab. of Neural Systems, FFCLRP, USP); Antonio Carlos Roque (Lab. of Neural Systems, FFCLRP, USP);
Short Abstract: We did a computational model containing the CaM-binding protein RC3, the calcium/CaM-binding proteins CaMKII and NOS, enzyme that produces NO. We verified that the oxidative modification of RC3 by NO alters its ability to accelerate the release of calcium from CaM/CaMKII only to high frequencies of calcium stimulation.
Long Abstract: Click Here

Poster LB-42
Javaprot: a three-dimensional visualization and processing tool of protein sequences
Category: Proteomics
Medrado,R. G. (Departamento de Ciências Exatas e da Terra, Universidade Estadual de Santa Cruz,Brasil); Corrêa,R.X. (Departamento de Ciências Biológicas,Universidade Estadual de Santa Cruz,Brasil); Bertoldi,M.M.D. (Departamento de Ciências Exatas e da Terra,Universidade Estadual de Santa Cruz,Brasil);
Short Abstract: A visualization software of proteomics structures was modeled and documented , using the modeling language UML (Unified Modelling Language) and implemented in the programming language Java , on the basis of two APIs (Application Program Interface): BIOJAVA and JAVA 3D.
Long Abstract: Click Here

Poster LB-43
Characterization of CRISPR repeat elements
Category: Comparative Genomics
Victor Kunin (DOE-JGI); Rotem Sorek (DOE-JGI); Philip Hugenholtz (DOE-JGI);
Short Abstract: We analyze the recently identified bacterial antiviral defense system called CRISPR in 267 microorganisms. We identify distinct families of CRISPR repeat sequences, and show that RNA secondary structures, spacer lengths and associated protein machineries differ between families. These features are likely to play crucial role in this antiviral defense system.
Long Abstract: Click Here

Poster LB-44
Semantic Abstraction based Word Sense Disambiguation for Text Mining of Coarse-grained Biomedical Corpus
Category: Text Mining and Information Extraction
Sa-kwang Song (Electronics and Telecommunications Research Institute); Jaewon Jang (Electronics and Telecommunications Research Institute); Soojun Park (Electronics and Telecommunications Research Institute);
Short Abstract: We propose a Word Sense Disambiguation method in coarse-grained biomedical documents such as patient’s records which have many different characteristics compared to fine-grained ones like Medline abstracts. In addition to POS and UMLS tagging, we utilize semantic abstraction of frequently used patterns including stopwords like numeric terms and symbols.
Long Abstract: Click Here

Poster LB-45
Construction of Suicidal Plasmids to put out Encoding Virulence Genes of Brucella abortus
Category: Systems Biology
Grácia Maria Soares Rosinha (Embrapa Beef Catlle); Fabiane Gonçalves de Souza (Embrapa Beef Cattle); Flábio Ribeiro de Araújo (Embrapa Beef Cattle); Cleber Oliveira Soares (Embrapa Beef Cattle); Cláudio Roberto Madruga (Embrapa Beef Cattle); Carina Elisei de Oliveira (Embrapa Beef Cattle); Bárbara Csordas (Embrapa Beef Cattle);
Short Abstract: Construction of Suicidal Plasmids to put out Encoding Virulence Genes of Brucella abortus Rosinha, G. M. S. (1); Souza, F. G. (1); Araújo, F. R. (1); Soares, C. O. (1); Madruga, C. R. (1); Elisei, C. (1); Csordas, B. G.(1). (1) Embrapa Beef Cattle, MS-Brazil. Brucella spp. are found in association with a large number of wild and domesticated animal and also may affect humans. The objective of this work was the construction of suicidal plasmids that could be used to put out of genes of Brucella that codify molecules related to virulence of Brucella abortus.
Long Abstract: Click Here

Poster LB-46
Identifying natively unstructured proteins using residue contact predictions
Category: Structural Bioinformatics
Avner Schlessinger (Department of Biochemistry and Molecular Biophysics, Columbia University); Marco Punta (Department of Biochemistry and Molecular Biophysics, Columbia University); Burkhard Rost (Department of Biochemistry and Molecular Biophysics, Columbia University);
Short Abstract: Recently, increasing attention has been drawn to the study of ‘natively unstructured’ proteins. Here, we combine a position specific contact propensity predictor with an average pairwise energy-like matrix to estimate the energetic contribution of each residue of the protein sequence to the protein foldability. Our novel approach outperforms competing methods.
Long Abstract: Click Here

Poster LB-47
GARSA Next Generation: towards a fully integrated annotation system
Category: Comparative Genomics
Glauber Wagner (Instituto Oswaldo Cruz); Luciana Matos (Coppe-Universidade Federal do Rio de Janeiro); Kele Belloze (Instituto Militar de Engenharia); Henrique Jucá (Instituto Oswaldo Cruz); Jean Ngomo (Instituto Oswaldo Cruz); Maria Luiza M. Campos (DCC, Universidade Federal do Rio de Janeiro); Marta Mattoso (COPPE-Universidade Federal do Rio de Janeiro); Maria C. Reis Cavalcanti (Instituto Militar de Engenharia); Edmundo C. Grisard (Universidade Federal de Santa Catarina); Alberto M. R. Dávila (Instituto Oswaldo Cruz);
Short Abstract: GARSA workflow has been conceived to facilitate the tasks of integrating, analyzing and presenting genomic information from several bioinformatics tools, in a flexible and user friendly web-based system. GARSA-Next Generation will incorporate the PolyBayes, OrthoMCL, Probcons, Mafft, Phyml softwares, predicted ORFs by similarity-based gene detection and protein analyses.
Long Abstract: Click Here

Poster LB-48
Title: BLAST on Virtual Clusters, Affordable High Performance Computing
Category: Other
Inus Scheepers (NBN); Dan Jacobson (NBN);
Short Abstract: Short Abstract: BLAST has been deployed on a virtual cluster architecture. This provides a rapid and cost affective method for doing high throughput sequence similarity searches on demand on and as-needed basis, without the high cost of deploying and maintaining large compute clusters in-house.
Long Abstract: Click Here

Poster LB-49
A Framework for Promoter Recognition in Mycoplasmas
Category: Sequence Analysis
João Valiati (Instituto de Informática - UFRGS); Paulo Martins Engel (Instituto de Informática - UFRGS);
Short Abstract: This work proposes of a framework based on connectionist approaches that explore intergenic regions, to be applied for promoter recognition in Mycoplasmas. The framework consists of three main tasks: the acquisition of sequences from the repositories; pre-processing of the sequences in Genbank format; and the construction of connectionist models
Long Abstract: Click Here

Poster LB-50
Bioinformatics analyses of Schistosoma mansoni ESTs generated from trans-spliced enriched cDNA libraries
Category: Transcriptomics
Marina M Mourão (UFMG); Francisco P Lobo (UFMG); Francisco Prosdocimi (UFMG); Gloria R Franco (UFMG);
Short Abstract: We analyzed a possible enrichment of GO terms in trans-spliced transcripts of Schistosoma mansoni by comparing 2644 GO-annotated trans-spliced ESTs against 1500 random-chosen, non trans-spliced and non-annotated ones. Our results indicate enrichment of terms related to rRNA and mRNA metabolism, notably GOs associated to splicing and ribonucleoprotein complex formation
Long Abstract: Click Here

Poster LB-51
SWAMI: the Next Generation Biology Workbench
Category: Databases and Data Integration
Rami Rifaieh (San Diego Supercomputer Center);
Short Abstract: Currently biology students and researchers have to spend an extensive amount of time in order to collect the data that they are interested in. In this respect, the Swami project helps users to reduce the task of collecting, storing, and manipulating data. It provides an accessible portal that offers a subset of the public genomics databases, a user storage space, and a set of tools to manipulate and annotate biological data.
Long Abstract: Click Here

Poster LB-52
BNDb - Biomolecules Nucleus Database: An Integrated Proteomics and Transcriptomics Database
Category: Databases and Data Integration
Faria-Campos, A. C. (Department of Biochemistry and Immunology, Federal Universtity of Minas Gerais); Gomes, R. R. (Department of Biochemistry and Immunology, Federal Universtity of Minas Gerais); Moratelli, F. S. (Department of Biochemistry and Immunology, Federal Universtity of Minas Gerais); Rausch-Fernandes, H. (Department of Biochemistry and Immunology, Federal Universtity of Minas Gerais); Rolla, A. F. M. (Tribunal de Justiça de Minas Gerais); Pena, S. D. J. (Department of Biochemistry and Immunology, Federal Universtity of Minas Gerais); Franco, G. R. (Department of Biochemistry and Immunology, Federal Universtity of Minas Gerais); Campos, S. V. A. (Department of Computer Science, Federal University of Minas Gerais);
Short Abstract: This work proposes an integrated proteomics and transcriptomics database harboring both raw and processed data and related publications. It uses a MySQL server and stores proteomics data from Schistosoma mansoni, Tittyus serrulatus and Phoneutria nigriventer, together with transcriptomics data associated to the identifications performed in new samples.
Long Abstract: Click Here

Poster LB-53
Understanding Condition-Dependent Transcription Factor Targeting
Category: Sequence Analysis
Kenzie D. MacIsaac (Department of Electrical Engineering and Computer Science, MIT); Ernest Fraenkel (Biological Engineering Division, MIT);
Short Abstract: We present an algorithm for analyzing ChIP-chip data for a transcription factor in multiple conditions that jointly learns the protein’s binding specificity, its condition-specific targets, and assesses whether binding differences between conditions are better explained by changes in transcription factor concentration, or by condition-specific changes in binding specificity.
Long Abstract: Click Here

Poster LB-54
Likeness of human tissues may be revealed by sets of highly expressed genes
Category: Transcriptomics
Saulo Paula Pinto (UFMG); J Miguel Ortega (UFMG);
Short Abstract: Gene expression changes from tissue to tissue in the human body. Each tissue has a set of genes that are more expressed in it as in other tissues. In a similar way, each tissue has a set of genes that are expressed in lower rates in it than in other tissues. Here we analyzed the number of the most expressed genes that are shared by pairs of human tissues to verify whether or not this measure can be used to group tissues developmentally related. A dataset composed of microarray gene expression data from 36 different human tissues was analyzed. Overall, our analyses show that 75% to 87% of the most expressed genes are shared between pairs of tissues for the topmost 30 pairs. On the order hand, only 22% to 33% of the most expressed genes are shared between the 30 pairs of tissues that share fewer genes. So, our initial analysis shows that the pattern of highly expressed genes seems to depict related tissues.
Long Abstract: Click Here

Poster LB-55
Survey of Leishmania chagasi transcriptome
Category: Transcriptomics
Andrade, P.P. (UFPE); Andrade, C.R. (UFPE); Araújo, D.A.M. (UFPB); Balbino, V.Q. (UFPE); Barbosa, M.H.N. (UFMA); Barbosa-da-Silva, A. (UFPE); Benko-Iseppon, A.M. (UFPE); Cananéa, I.C. (UFPE); Cassilhas, A.P.P. (UFPE); Castro, J.A.F. (UFPI); Costa, R.B. (UECE); Da Silva, E.C. (UFPE); De Paula, M.F. (IPA); Do Carmo, H.V. (UFPE); Ferreira, F.L. (UFMA); Galdino, M.L. (UFPE); Gomes-Filho, M.J.A. (UFPE); Grisi, T.C.S.L. (UFPB); Guerra, M.C. (UFPE); Jucá, M.H.C. (UFPE); Kido, E.A. (UFPE); Kido, L.M.H. (UFPE); Lima, M.A. (UFPE); Maciel, D.B. (IPA); Maggioni, R. (UECE); Marcelino, A.M.S. (IPA); Melo, M.A. (UFCG); Mesquita, E.R.L. (UFMA); Montarroyos, A.V.V. (IPA); Monte, S.J.H. (UFPI); Montenegro, M.M.A. (UFPE); Morais, D.A.L. (UFPE); Moura, P.V.S. (UFPE); Nhani Jr, A. (UFPE); Oliveira, D.M. (UECE); Ortega, J.M. (UFMG); Pereira, P.V.S. (UFMA); Queiroz, R.A. (UFPE); Santos, C.F. (UFPB); Santos, E.O. (IPA); Santos, E.S.C. (UFPE); Silva, F.F. (UFMA); Silva, R.N. (UFPI); Torquato, G.N. (UFPE); Viana, A.M.H.A (UFMA);
Short Abstract: The first 10,000 EST sequences comprising the Leishmania chagasi transcriptoma were produced and analyzed. In total, 6,041unique transcript sequences were obtained, 1,022 being clusters. The transcriptome was distributed over the 36 chromosomes. KOG categories J, O, R, Z, T and C were the most common; genes exclusive from trypanosomatids were identified.
Long Abstract: Click Here

Poster LB-56
Divergent paralogous in Uniref50 enriched- COG clusters depicted by Phylip neighbor trees rooted with Taxbrowser tables
Category: Evolution and Phylogeny
Daniela V. C. Barnosa (UFMG); J. Miguel Ortega (UFMG); Sérgio V. A. Campos (UFMG); Alessandra C. Faria-Campos (UFMG); Maurício A. Mudado (UFMG);
Short Abstract: A challenge in molecular biology is the identification of genome differences between closely related species that may account for different fenotype. For example, two strains of H. pylori that are the cause of either gastritis (26695) or ulcer (J99) had their genomes sequenced and their paralogous and orthologous proteins classified in COG database (NCBI). Knowing what differs between them might make the treatment of such illnesses more effective. These differences are codified in the genome of the species, but identifying them is a complex task. In this work we propose to assist in this task by comparing the complete proteome set of the different species by identifying which genes are common to both species and which ones are different. A automated procedure based on Uniref50 enriched- COG clusters depicted by Phylip neighbor trees rooted with Taxbrowser tables was developed and able to depict divergent paralogous genes.
Long Abstract: Click Here

Poster LB-57
Evaluation of KEGG Orthology (KO) as a source for annotation using ESTs from Model Organisms
Category: Databases and Data Integration
Gabriel R Fernandes (ICB UFMG); Maurício A Mudado (ICB UFMG); J Miguel Ortega (ICB UFMG);
Short Abstract: Secondary databases consist of sequences of gene products organized under functional categories. Devised or not as a repository of groups of orthologous, such databases will tend to cluster under well defined strings those sequences that represent the same functional product in diverse organisms. One such database consist of the dataset from KEGG know as Kegg Orthology (KO). We analyzed the performance of KO as a source for annotation using all entries in KO for seven prominent organisms: C. familiaris (Cfa), M. musculus (Mmu), R. norvegicus (Rno), A. thaliana (Ath), C. elegans (Cel), D. melanogaster (Dme) and H. sapiens (Has), totalizing 25,060 proteins clustered under 17,056 distinct KO entries. Secondary databases composed of clusters of orthologous proteins present high accuracy when used as source for annotarion. Such annotation procedure might either be used under the automated scope, or alternatively coupled with manual inspection although conducted in a reverse way, since categorized pathways and biological processes are prompted to work as check lists guiding gene discovery approaches.
Long Abstract: Click Here

Poster LB-58
Codon usage and protein hydrophobicity for three major Leishmania chagasi antigens
Category: Sequence Analysis
De Sousa, N.G.F.B.R (Universidade de Aveiro); Ramos, C.P.S. (UFPE); Nhani Jr, A. (UFPE); Melo, M.A. (UFCG); Andrade, P.P. (UFPE);
Short Abstract: The genes for three major Leishmania antigens, their paralogs and chromosomes were investigated for codon usage and hydrophobicity using correspondence analysis. All three antigens were highly hydrophilic and displayed an optimized codon usage, suggesting that these intrinsic features may be a clue to understand B cell antigenicity in Leishmania and in other pathogens.
Long Abstract: Click Here

Poster LB-59
Discriminative analysis of microRNAs
Category: Sequence Analysis
Niels Tolstrup (Exiqon); Mette Jørgensen (Exiqon); Niels Bonde Jensen (Exiqon); Jacob Bunk Nielsen (Exiqon); Bing Zang (Exiqon);
Short Abstract: MicroRNAs are a new class of small non-coding RNAs, which have been shown to play an important role in cell differentiation and the development of cancer. The detection and analysis of microRNAs requires special software tools. We present new web based design tools for integrated microRNA analysis at www.exiqon.com.
Long Abstract: Click Here

Poster LB-60
Self- similar models for biological system and process
Category: Systems Biology
Manjunath (Freelancer);
Short Abstract: Self-similar models play an important role in understanding biological systems and processes. It reasons out the intention behind various biological processes. The self-similarity originates as a result of differential feedback in the system. The system or process also follows other interesting properties that originate as a result of differential feedback.
Long Abstract: Click Here

Poster LB-61
Associative Browsing of the Biomedical Literature
Category: Text Mining and Information Extraction
Kieran O'Neill (National Bioinformatics Network (South Africa) Central Node); Fernando Martinez (National Bioinformatics Network (South Africa) Central Node); Darren Otgaar (National Bioinformatics Network (South Africa) Central Node); Junaid Gamieldien (National Bioinformatics Network (South Africa) Central Node); Daniel Jacobson (National Bioinformatics Network (South Africa) Central Node);
Short Abstract: Digr is being applied to the MeSH ontology, enabling associative browsing for MeSH terms related by articles. This enables researchers to find focused sets of related MeSH terms, and the literature specific to those sets.
Long Abstract: Click Here

Poster LB-62
Predicting of Protein Structure Using Genetic Algorithms and Rotamer Library
Category: Structural Bioinformatics
Luis Paulo Scott (Unifev/Ibilce); Jorge Chahine (Unesp/Ibilce); José Roberto Ruggiero (Unesp/Ibilce);
Short Abstract: In this work, genetic algorithms concepts along with a rotamer library for proteins side chains are used to optimize the tertiary structure of the hydrophobic core starting from the known PDB structure of its backbone which is kept fixed
Long Abstract: Click Here

Poster LB-63
MINING HIGH CONTENT DATA FROM A PROTEIN BIOMARKER DISCOVERY PLATFORM
Category: Proteomics
Luc Krols (Peakadilly); Gregoire Thomas (Peakadilly); Sven Degroeve (Peakadilly); Christine Labeur (Peakadilly); Koen De Cremer (Peakadilly); Lies Vanneste (Peakadilly); Filip D'hondt (Peakadilly); Koen Kas (Peakadilly);
Short Abstract: We will show the discriminative power of our novel approach applying it to serum of different patient groups and the methods used for mining through the vast amounts of data that is generated in these proteomic experiments. We will show that, using state of the art bioinformatics and data mining techniques that we are able to discriminate between patient who will respond to drug therapy and those who won't respond to drug therap prior to drug treatment.
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Poster LB-65
A Simple Genetic Algorithm for Multiple Sequence Alignment
Category: Other
Cedric Gondro (University of New England); Brian Kinghorn (University of New England);
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Poster LB-66
Protein hydrophobicity and codon usage patterns in Chromobacterium violaceum
Category: Comparative Genomics
Catarina Ramos (Universidade Federal de Pernambuco); Tetsuo Tashiro (Universidade Federal de Pernambuco); Enivaldo Rocha (Universidade Federal de Pernambuco); Valdir Balbino (Universidade Federal de Pernambuco); Paulo Andrade (Universidade Federal de Pernambuco);
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