SIGs/SIG Reports Papers AM Tutorials Posters PM Tutorials Demos Opening/Closing Ceremonies/Program Chair Introductions Social Events
Keynotes
Special Workshop
AM1: 8:30am-12:30pm AM2: 8:30am-12:30pm AM3: 8:30am-12:30pm AM4: 8:30am-12:30pm AM5: 8:30am-12:30pm AM6: 8:30am-12:30pm AM7: 8:30am-12:30pm Integration and Analysis of Diverse Genomic Data, Olga Troyanskaya Optimal Design and Analysis of Microarray Experiments, Ernst Wit and John McClure RNA: Algorithms for Structure Prediction and Gene-finders, Peter Clote Developing and Using Special Purpose Hidden Markov Model Databases, Martin Gollery Weighted Finite-State Transducers in Computational Biology, Corinna Cortes and Mehryar Mohri Semantic Aggregation, Integration and Inference of Pathway Data, Joanne Luciano and Jeremy Zucker Attacking Performance Bottlenecks, Ruud van der Pas and Karl V. Steiner Poster Session 1: Poster Set up by authors (room not open to delegates)BOF: Retrotransposons and Bioinformatics PM8: 2-6pm PM11: 2-6pm PM13: 2-6pm PM9: 2-6pm PM12: 2-6pm PM10: 2-6pm PM14: 2-6pm Principles of Ontology Construction, Suzanna Lewis Gene Expression Levels as Traits in Genetic Linkage Analysis, Steffen Möller and Robert Hoffman Computational Geometry of Protein Structure and Function, Iosif Vaisman Introduction to Phylogenetic Networks, Daniel Huson A Bioinformatics Introduction to Cluster Computing, Andrew Boyd and Abhijit Bose Mining the Biomedical Literature: State of the Art, Challenges and Evaluation Issues, Hagit Shatkay A Massively Parallel High Performance Computing Environment for Computational Biology, Gyan Bhanot and Bob Germain
Poster Session 1: Poster Set up by authors (room not open to delegates) Opening Ceremony Overflow Keynote: Howard Cash Biology of Life and Death: Disaster, DNA and the Information Science of Human Identification Poster Session 1: Posters available for viewing by delegates AC Intro Databases: Susan Davidson & Carol Goble AC Intro Sequence Analysis: Des Higgins SC Intro – Trey Ideker 9:30-9:45am Demo: DAMBE is an Integrated Software Package for Data Analysis in Molecular Biology and Evolution Demo Demo: SynBrowse: A Synteny Browser for Comparative Sequence Analysis Demo 1. Data Integration and Visualization System for Enabling Conceptual Biology Gopalacharyulu, Lindfors, Bounsaythip, Kivioja, Yetukuri, Hollmen, Oresic 2. A Motif-based Framework for Recognizing Sequence Families Sharan, Myers 1. Detection of Horizontal Gene Transfer in Whole Metabolic Pathways 2. An EM Algorithm for Unambiguous Assignment of Genes to Biochemical Pathways Coffee Break
Coffee Break 3. Multiple Knockouts Analysis of Genetic Robustness in the Yeast Metabolic Network Deutscher, Meilijson, Ruppin Demo: UCSF Chimera: Molecular Graphics for Research and Analysis Demo: The Integrated Microbial Genomes (IMG) System Demo: Friend, an Integrated Analytical Front-end Application for Bioinformatics Demo: 3. A Procedure for Assessing GO Annotation Consistency 4. An HMM Posterior Decoder for Sequence Feature Prediction that Includes Homology Information Käll, Krogh, Sonnhammer 5. YeastHub: A Semantic Web Use Case for Integrating Data in the Life Sciences Domain Cheung, Yip, Smith, deKnikker, Masiar, Gerstein 6. Self-Organized Clustering Methods for Familial Binding Profiles Mahony, Golden, Smith, Benos Lunch BOF: Application of Bioinformatics in Cancer BOF: x64: is there steak behind the sizzle? Stefan Unger 12noon-1pm BOF: The BioPAX pathway data exchange format Chris Sander 12noon-1pm BOF: Bioinformatics Core Facilities Fran Lewitter 12noon-1pm ISCB Open Business Meeting Demo: Domain-based Small Molecule Binding Site Annotation Demo: The PRIDE Database: Plugging the Hole that is Leaking Proteomics Data Demo: Rapid Determination of Local Structural Features Demo: AC Intro Text Mining: Dietrich Rebholz-Schuhmann Education/Web Workshop
7. High-recall Protein Entity Recognition Using a Dictionary Kou, Cohen, Murphy 8. Statistics of Local Multiple Alignments Prakash, Tompa Demo:The ConSurf Web-Server for the Analysis of Evolutionary Conservation Patterns of Protein Structures
Demo: EMBOSS Demo: BLASTgres: an Extension of the PostgreSQL Database System to Support Large-scale Bioinformatics Research Demo 9. Beyond The Clause: Extraction of Phosphorylation Information from Medline Abstracts Narayanaswamy, Ravikumar, Vijay-Shanker 10. Computing the P-value of the Information Content from an Alignment of Multiple Sequences Nagarajan, Jones, Keich SC Intro – Chris Burge AC Intro Pathways, Networks and Systems 1: Alfonso Valencia & Vincent Schachter AC Intro Evolution & Phylogeny: Olivier Gascuel & Dannie Durand 4. Regulatory Modules: Identification and Verification Zhao, Stormo 11. Validation of Qualitative Models of Genetic Regulatory Networks by Model Checking: Analysis of the Nutritional Stress Response in Escherichia coli Batt, Ropers, de Jong, Geiselmann, Mateescu, Page, Schneide r12. Identification of Nine Human-specific Frameshift Mutations by Comparative Analysis of the Human and the Chimpanzee Genome Sequences Hahn, Lee Demo: WinAgent: Creating and Managing Personal Information Assistants for Biological Data Collection Demo: The ANNOTATOR Software Suite Demo: GEOSS: Advanced Microarray Experiment Management and Bioinformatics Analysis Demo: Using GMOD Tools to Create, Edit, and Browse Genome Features Coffee Break Coffee Break 13. Kernel Methods for Predicting Protein-protein Interactions Ben-Hur, Noble 14. Maximum Likelihood of Evolutionary Trees: Hardness and Approximation Tuller, Chor 6. A Computational Method to Identify Amino Acid Residues Involved in Protein-DNA Interactions Yan, Terribilini, Wu, Jernigan, Dobbs, Honavar 7. Genome-wide Comparative Analysis of Alternative Splicing in Plants Wang, Brendel Demo: Reactome - A Knowledgebase of Biological Processes Demo: Visualizing and Analyzing Biological Network Data in Cytoscape 2.1 Demo: SeqHound: An Open Source Bioinformatics Application-programming Platform Demo: Apollo: A Genome Annotation Editing Tool 15. Automatic Detection of Subsystem/Pathway Variants in Genome Analysis Ye, Osterman, Overbeek, Godzik 16. Detecting Coevolving Amino Acid Sites using Bayesian Mutational Mapping Dimmic, Hubisz, Bustamante, Nielsen 8. Inferring Splicing Regulatory Activity of Short Oligonuecleotides from Sequence Neighborhood Stadler, Yeo, Shomron, Burge 9. Ab initio Computational Prediction of MicroRNA GenesSewer, Pfeffer, Aravin, Landgraf, Tuschl, van Nimwegen, Zavolan 17. Modeling the Organization of the WUSCHEL Expression Domain in the Shoot Apical Meristem Jönsson, Heisler, Reddy, Agrawal, Gor, Shapiro, Mjolsness, Meyerowitz 18. Efficient Computation of Close Lower and Upper Bounds on the Minimum Number of Recombinations in Biological Sequence Evolution Song, Wu, Gusfield Keynote: Gunnar von Heijne Membrane Proteins in vivo and in silico - Getting the Best of Two Worlds Overflow Poster Session 1: Authors Present at their poster Demo: CREAD: Comprehensive Regulatory Element Analysis and Detection Demo: INOH Pathway Database Demo: MiMI: Michigan Molecular Interactions Demo Demo Demo: Advanced Micro-array Probe Design Using OligoWiz 2.0 Demo: BioDASH: Demonstration of Semantic Web Application in Life Sciences Demo
Poster Session 2: Poster Set up by authors (room not open to delegates) Keynote: Jill Mesirov Gene Expression Analysis: A Knowledge-based Approach
Overflow Poster Session 2: Posters available for viewing by delegates AC Intro Proteomics 1: Michal Linial AC Intro Transcriptome 1: Martin Vingron SC Intro – Serafim Batzoglou 9:30-9:45amDemo: BALL (Biochemical ALgorithms Library) and BALLView - A Multiplatform Molecular Viewer and Modeling Tool Demo: The Pathway Tools Software Demo: PATIKAweb: A Web Service for Querying, Visualizing and Analyzing Demo: Biobase Corporation: Pathway analysis with curated protein databases 19. Classifying Noisy Protein Sequence Data: A Case study of Immunoglobulin Light Chains Yu, Zaveljevski, Stevens, Yackovich, Reifman 20. A Statistical Method for Detecting Splice Variation from Expression Data Cline, Blume, Cawley, Clark, Hu, Lu, Salomonis, Wang, Williams 10. Combining Phylogenetic Data and Network Topology to Identify Regulatory Motifs 11. Identification of Novel Human Splice Variants Using “- Genomic Fossils” Shemesh, Novik, Edelheit, Sorek Coffee Break
Coffee Break 12. A Comparative Genomics Approach to Distinguishing Exon Creation and Loss Events Shows Increased Exon Creation Associated with Alternative Splicing Alekseyenko, Lee Demo: M-GCAT: Multiple Genome Comparison and Alignment Tool Demo: The Protégé Suite of Tools: Accessing, Managing, and Visualizing Biomedical Ontologies Demo: Automatic Annotation Tool and Browser for Whole-Genome Tiling-Array Demo: Apple Computer, Inc.: The Apple Workgroup Cluster 21. Protein Function Prediction via Graph Kernels Borgwardt, Ong, Schoenauer, Vishwanathan, Smola, Kriegel 22. Robust Classification Modeling on Microarray Data Using Misclassification Penalized Posterior Soukup, Lee 23. CaSPredictor: A new Computer-based Tool for Caspase Substrate Prediction Garay-Malpartida, Occhiucci, Alves, Belizário 24. Experimental Design for Three-Color and Four-Color Gene Expression Microarrays Woo, Krueger, Kaur, Churchill Lunch BOF: Bronchial Asthma, Bioinformatics, and Microarrays BOF: A WIKI on “Methods in bioinformatics”? Interagency Program Workshop Demo: Demo: GenDB & The SEED: Two Genome Annotation Systems Integrated Demo: Estimating Phylogenetic Trees and Networks using SplitsTree 4 Demo: PART 1: Discovery to Development Demos: How to Save Time, Money & Hassels With 6 Solutions 25. Families of Membranous Proteins can be Characterized by the Amino Acid Composition of their Transmembrane Domains Sadka, Linial 26. A Hidden Markov Model for Analyzing ChIP-chip Experiments on Genome Tiling Arrays and its Application to p53 Binding Sequences Li, Meyer, Liu Demo: The myGrid/Taverna Toolkit for Workflow Based Bioinformatics Demo: Protein Homology Detection and Structure Prediction with HHsearch and HHpred Demo: Development of a Microarray Data Analysis Software (MicroArrayWare) with a Calibration Step for Automatic Selection of Optimal Analysis Methods and Parameters Demo: CSIRO: GeneRave and New Statistical Algorithms for p>n Data 27. High-Throughput Inference of Protein-Protein Interfaces from Unassigned NMR Data Mettu, Lilien, Donald 28. Multi-way Clustering of Microarray Data using Probabilistic Sparse Matrix Factorization Dueck, Morris, Frey 13. A Gamma Mixture Model Better Accounts for Among Site Rate Heterogeneity Mayrose, Friedman, Pupko AC Intro Genomes 1: Ying Xu & Steven Salzberg AC Intro Structural Bioinformatics: Nir Ben-Tal & Ramanathan Sowdhamini 14. Evidence of a Large-scale Functional Organization of Mammalian Chromosomes Graber, Churchill, DiPetrillo, King, Petkov, Paigen 29. Tag SNP Selection in Genotype Data for Maximizing SNP Prediction Accuracy Halperin, Kimmel, Shamir Paper 30. Three-Stage Prediction of Protein Beta-Sheets by Neural Networks, Alignments, and Graph Algorithms Cheng, Baldi 15. Trees and Forests: A Genome-wide Reconstruction of Orthologous Gene Groups in Fungi Wapinski, Friedman, Regev, Pfeffer Demo: Integrating Text Mining into Bioinformatics Workflows Demo: STING - A Web Server for Comprehensive Analysis of Protein Structure and Sequence Demo: Atomic Reconstruction of Metabolism: Metabolic Map Editor Demo: IBM: From Biological Networks to Web Services: The Latest IBM Technologies for Querying Biological Data Coffee Break Coffee Break 31. Mining ChIP-chip Data for Transcription Factor and Cofactor Binding Sites Smith, Sumazin, Das, Zhang 32. Improving Protein Structure Prediction With Model-Based Search Brunette, Brock SC Intro – Michael Zuker 3:45-4pm 16. A Conserved Sparse Dicodon Framework Which Correlates Sequence and Structure: Implications for Gene Finding Demo: LARALink: A Web Application for Cytogenetic Linkage Analysis Demo: Data Integration in the Comparative Toxicogenomics Database (CTD) Demo: MSight: An LC-MS Image Analysis Software 33. GenXHC: A Probabilistic Generative Model for Cross-hybridization Compensation in High-density Genome-wide Microarray Data Huang, Morris, Frey Paper 34. Prediction of Active Sites for Protein Structures from Computed Chemical Properties Ko, Murga, Ondrechen 17. Enzyme Mechanism Annotation and Classification Almonacid, Holliday, Murray-Rust, Thornton, Mitchell 18. A Novel Approach to Structural Alignment using Realistic Structural and Environmental Information Chen, Crippen 35. RASE: Recognition of Alternatively Spliced Exons in C. elegans Raetsch, Sonnenburg, Schoelkopf 36. In silico Identification of Functional Regions in Proteins Nimrod, Glaser, Steinberg, Ben-Tal, Pupko 19. On the Importance of Being Left-handed Novotny, Kleywegt Keynote: Pavel Pevzner Transforming Men into Mice: Fragile versus Random Breakage Models of Chromosome Evolution Overflow Poster Session 2: Authors Present at their poster Demo: Using GEMS for Cancer Diagnosis and Biomarker Discovery from Microarray Gene Expression Data Demo: The Oncology Thinking Cap Demo: GeneNotes - A Novel Information Management Software for Biologists Demo Demo: Vigyaan: An Integrated Software Workbench for Bioinformatics and Computational Biology Demo: PUMA2 - A Grid Technology Based Computational Environment for High-throughput Genetic Sequence Analysis and Evolutionary Analysis of Metabolism Demo Demo
Poster Session 3 (PLoS CB Latebreaking Posters): Poster Set up by authors (room not open to delegates) Keynote: Peter Hunter Computational Physiology and the IUPS Physiome Project
Overflow Poster Session 3 (PLoS CB Latebreaking Posters): Posters available for viewing by delegates SC Intro – Michael Eisen Demo: BioNavigation: Selecting Optimum Paths Through Resources to Evaluate Scientific Queries Demo: GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences Demo: Immunological Web Tools Demo: Synamatix: Applications of a Novel Structured Network Database in Ultra-high-throughput Genomics Analysis 37. Enhanced Position Weight Matrices using Mixture Models Hannenhalli, Wang 38. How Old is Your Fold? Winstanley, Abeln, Deane 20. TEPC: Total Evidence Phylogenetic Correlation of Microbial Phenotypes and Genotypes Sarkar, Planet, DeSalle 21. Feasibility of Genome-wide Recognition of Mutant Single Nucleotide Polymorphisms (SNPs) with Effects on Constitutive mRNA Splicing Coffee Break
Coffee Break 22. Transcriptional Reprogramming in Genetic Backup Circuits Demo: Protein Modeling with POSE: Protein Optimization Steering Environment Demo: PIR: A Comprehensive Resource for Functional Analysis of Protein Sequences and Families Demo: The Short Time-series Expression Miner (STEM) Demo: Apple Computer, Inc.: Mac OS X v10.4 'Tiger' for the Life Sciences 39. De Novo Identification of Repeat Families in Large Genomes Price, Jones, Pevzner 40. Search for Folding Nuclei in Native Protein Structures Shmygelska 41. Automatic Interpretation of MS/MS Spectra of Oligosaccharides Tang, Mechref, Novotny 42. A Path Planning Approach for Computing Large-Amplitude Motions of Flexible Molecules Cortes, Simeon, Ruiz de Angulo, Guieysse, Remaud-Simeon, Tran Lunch BOF: Semantic Web for Life Sciences Eric Neumann 12noon-1pm BOF: Automated Function Prediction Iddo Friedberg 12noon-1pm NIH Workshop Getting the Grant: Tips on Writing Grants Applications to NSF Workshop Demo: INDUS: A System for Information Integration and Knowledge Acquisition from Autonomous, Distributed, and Semantically Heterogeneous Data Sources Demo: Using the Biozon System for Search and Analysis of Heterogeneous Interrelated Biological Data Demo: VitaPad: A Tool for Visualizing Pathways Demo: Hewlett Packard: Build and Execute Genomics Pipelines with HP and TimeLogic 43. Clustering Short Time Series Gene Expression Data Ernst, Nau, Bar-Joseph 44. PILER: Identification and Classification of Genomic Repeats Edgar, Myers 45. Predicting the in vivo Signature of Human Gene Regulatory Sequences Noble, Kuehn, Thurman, Yu, Stamatoyannopoulos Demo: SNP-VISTA: An Interactive SNPs Visualization Tool Demo: Notung 2.0: Putting the Macroevolution Back in Phylogenetics Demo: Rat Genome Database: A Database for Comparative Genomics using the Rat Model Organism Demo: Gene Logic Inc.: Biomarker Discovery Using an Extensive Clinical Microarray Gene Expression Database 46. The Precise Positioning of Genomic Landmarks Can Aid in the Identification of Regulatory Elements Tharakaraman, Marino-Ramirez, Sheetlin, Landsman, Spouge 47. Predicting Protein-Protein Interaction by Searching Evolutionary Tree Automorphism Space Jothi, Kann, Przytycka Coffee Break Coffee Break SC Intro – Mark Musen Demo: REMBRANDT: Empowering Translational Research Demo: VisANT: Integrative Visual Analysis Tool for Biological Networks, Pathways and Modules Demo: CDTree: A Tool to Analyze and Annotate Protein Subfamily Hierarchies Demo: PART 2: Discovery to Development Demos: How to Save Time, Money & Hassels With 6 Solutions 48. Reversal Distance for Partially Ordered Genomes Zheng, Lenert, Sankoff 49. Supervised Enzyme Network Inference from the Integration of Genomic Data and Chemical Information Yamanishi, Vert, Kanehisa 23. Where do we GO next? Refining the Content of the Gene Ontology Harris 24. Ontological Visualization of Protein-Protein Interactions Using the Gene Ontologies 50. ExonHunter: A Comprehensive Approach to Gene Finding Brejova, Brown, Li, Vinar 51. Whole-proteome Prediction of Protein Function via Graph-theoretic Analysis of Interaction Maps Nabieva, Jim, Agarwal, Chazelle, Singh 26. BioPAX - Biological Pathway Data Exchange Format Cary, BioPAX Workgroup, Bader, and Sander 52. Conservative Extraction of Over-represented Extensible Motifs Apostolico, Comin, Parida 53. Mining Coherent Dense Subgraphs Across Massive Biological Networks for Functional Discovery Hu, Yan, Huang, Han, Zhou 27. Hubs of Knowledge: Using the Functional Link Structure in Biozon to Mine for Biologically Significant Entities Keynote: Satoru Miyano Computational Challenges for Gene Networks Overflow Poster Session 3 (PLoS CB Latebreaking Posters): Authors Present at their poster Off Site Gala Dinner: The Detroit Princess Riverboat Cruise 6:30-10:30pm
Keynote: ISCB Overton Prize Winner Ewan Birney Genomes to Systems Biology Overflow Overflow Overflow Overflow Poster Session 3 (PLoS CB Latebreaking Posters): Authors Present at their poster
AC Intro Bioinformatics Applications: Phil Bourne 28. Route as Trees: The Parsing View on Protein Folding Hockenmaier, Joshi, Dill
29. Dynamic Complex formation During the Yeast Cell Cycle de Lichtenberg, Jensen, Brunak, Bork
30. Literature Data Mining and Protein Ontology Development at the Protein Information Resource (PIR) Hu, Mani, Liu, Shanker, Hermoso, Nikolskaya, Natale, Wu
Demo: FUZEBASE: An Online Platform for Exploration and Information Fusion of Biomedical Informatics Data Demo: The MAPPER Platform for the Computational Identification of Transcription Factor Binding Sites Demo: Pygr: A Python Graph Database Framework for Bioinformatics Demo: 54. A Systematic Approach for Comprehensive T-cell Epitope Discovery Using Peptide Libraries Beissbarth, Tye-Din, Smyth, Speed, Anderson 31. All-Atom Modeling of RNA Conformational Changes Mathews, Case 32. Genome-wide Transcription Regulatory Circuits Controlling Cellular Malignant Tabach, Milyavsky, Zuk, Yitzhaki, Polak, Domany, Rotter, Pilpel 33. CGHGate: Array-CGH, Case Reports, Phenotypes and Biomedical Literature for Human Genome Annotation Van Vooren, Maas, Vermeesch, Moreau, De Moor 9:45-10am 34. A Novel Covariance Model Based RNA Motif Finding Algorithm Yao, Ruzzo 35. Structure Prediction and Analysis of Remote Homology Relations for Proteins in Complete Genomes Sadreyev, Grishin 36. Conserved Protein Domain Interactions from Structure data: A Modeling Resource for Novel Protein Interactions Shoemaker, Bryant 37. Text-mining Challenges for Protein Family Database Annotation Divoli, Attwood 55. Bayesian Neural Network Approaches to Ovarian Cancer Identification from High-resolution Mass Spectrometry Data Yu, Chen
38. ncRNA Genefinding in C. elegans Stricklin, Reinke, Stolc, Eddy 39. The Canonical Representation of Proteins: Application to Remote Homology Recognition Ku, Yona 40. A Probabilistic Functional Gene Network of Yeast - Version 2.0 Lee, Marcotte 10:15-10:30am 41. A Transcriptome Atlas of the Mouse Brain at Cellular Resolution Carson, Ju, Lu, Thaller, Bello, Kakadiaris, Eichele, Warren, Chiu 42. Isostericity Matrices: Tools for Analyzing Recurrent Motifs and Structurally Aligning Homologous RNAs Leontis, Westhof, Craig, Mokdad, Stombaugh, Sarver 43. Domain-based Protein Hierarchy and Detection of Semantically Significant Domain Architectures Ku, Yona 44. New Machine Learning Approaches for Classification of Mass Spectrometry Database Search Results Ulintz, Zhu, Andrews, Qin 45. Are Antisense Transcripts prone to A-to-I RNA Editing? Neeman, Dahary, Eisenberg, Levanon, Sorek Demo: BioArrayMiner: A Software Package for Integrative Analysis of Cross-platform and Cross-species Microarray Data Demo: caArray Data Management and Analysis Tools at the National Cancer Institute (NCI) Center for Bioinformatics Demo: Genome Visualization and Analysis with S-plot Demo 56. Kernels for Small Molecules and the Prediction of Mutagenicity, Toxicity, and Anti-Cancer Activity Ralaivola, Chen, Phung, Bruand, Swamidass, Baldi 46. Pattern-based Phylogenetic Distance Estimation and Tree Reconstruction Hoehl, Rigoutsos, Ragan 47. Clustering 2D mRNA Expression Patterns of Drosophila Embryos Peng, Long, Eisen, Myers Coffee Break Keynote: 2005 ISCB Senior Scientist Accomplishment Award Janet Thornton From Proteins to Life - Old and New Challenges Overflow Overflow Overflow Overflow BOF: Can we look for Breast cancer markers which are commercially viable? Closing/Awards Ceremony Overflow Overflow Overflow Overflow
