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 To this end, the genome sequence and annotation of an as yet unpublished Ciona savignyi assembly was compared to that of Ciona intestinalis using comparative genomics approaches and a number of interested findings were identified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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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%).
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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)
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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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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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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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.
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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.
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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.
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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.
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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.
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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.
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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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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
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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).
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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
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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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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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/
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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

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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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
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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.
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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.
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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).
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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).
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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