Color Key
SIGs/SIG Reports Papers
  AM Tutorials   Posters
  PM Tutorials   Demos
  Opening/Closing Ceremonies/Program Chair Introductions   Social Events
Keynotes
Special Workshop

Thursday, June 23, 2005: SIGS
Ambassador1
Ambassador2
Ambassador3
8:30am
Alternative Splicing
8:30am-6pm
BOSC'2005
8:30am-6pm
Joint Meeting BioPathways and SIGSIM
8:30am-6pm
10:00am

Coffee Break

11:00am
 
12noon
Lunch
1:00pm
     
2:30pm
Coffee Break
3:30pm
 
6:00pm
     

Friday, June 24, 2005: SIGS
Ambassador1
Ambassador2
Ambassador3
LaSalle
Cadillac
Richard
Brule
8:30am
Alternative Splicing
8:30am-6pm
BOSC'2005
8:30am-6pm
Joint Meeting: BioPathways and SIGSM
8:30am-6pm
Automated Function Prediction
8:30am-6pm
Bioinformatics and Disease
8:30am-6pm
BioLINK
8:30am-6pm
Bio-Ontologies
8:30am-6pm
10:00am

Coffee Break

11:00am
   
12noon
Lunch
1:00pm
             
2:30pm
Coffee Break
3:30pm
   
6:00pm              

Saturday, June 25, 2005
Ambassador1 - Level 3
Ambassador2 - Level 3
Cadillac - Level 5
LaSalle - Level 5
Marquette - Level 5
Ambassador3 - Level 3
Nicolet - Level 5
Ontario - Level 5
LaSalle
8:30am
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    
10:00am

Coffee Break

   
11:00am
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    
12noon Poster Session 1: Poster Set up by authors (room not open to delegates)
12noon-5pm
BOF: Retrotransposons and Bioinformatics
Kamal Rawal
12noon-1pm
12:30pm Lunch (lunch on your own)
1pm
 
2:00pm
PM8: 2-6pm PM11: 2-6pm PM13: 2-6pm PM9: 2-6pm PM12: 2-6pm PM10: 2-6pm PM14: 2-6pm  
3:30pm

Coffee Break

 
4:30pm
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  
5pm
   
6:00pm                  

Sunday, June 26, 2005
Room
Renaissance Ballroom
Ambassador Ballroom
Mackinac
Brule
Ontario
Lasalle
Cadillac
Nicolet
Richard
7am
        Poster Session 1: Poster Set up by authors (room not open to delegates)
7-9am
       
8am
Opening Ceremony
8-8:30am
Overflow            
8:30am
Keynote: Howard Cash Biology of Life and Death: Disaster, DNA and the Information Science of Human Identification
8:30-9:20am
             
9am
Poster Session 1: Posters available for viewing by delegates
9am-6pm
9:20am
               
9:30am
AC Intro
9:30-9:45am
Databases: Susan Davidson & Carol Goble
AC Intro
9:30-9:45am
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
9:30-10:30am
Demo
9:30-10:30am
Demo: SynBrowse: A Synteny Browser for Comparative Sequence Analysis
9:30-10:30am
Demo
9:30-10:30am
9:45am
1. Data Integration and Visualization System for Enabling Conceptual Biology
Gopalacharyulu, Lindfors, Bounsaythip, Kivioja, Yetukuri, Hollmen, Oresic
9:45-10:10am
2. A Motif-based Framework for Recognizing Sequence Families
Sharan, Myers
9:45-10:10am
1. Detection of Horizontal Gene Transfer in Whole Metabolic Pathways
Tseng, Aquino, Liu

9:45-10am
 
10am
2. An EM Algorithm for Unambiguous Assignment of Genes to Biochemical Pathways
Popescu, Yona

10-10:15am
10:10am

Coffee Break
10:10-10:40am

Coffee Break
10:10-10:40am
 
10:15am
3. Multiple Knockouts Analysis of Genetic Robustness in the Yeast Metabolic Network
Deutscher, Meilijson, Ruppin
10:15-10:30am
10:30am
    Demo: UCSF Chimera: Molecular Graphics for Research and Analysis
10:30-11:30am
Demo: The Integrated Microbial Genomes (IMG) System
10:30-11:30am
Demo: Friend, an Integrated Analytical Front-end Application for Bioinformatics
10:30-11:30am
Demo: SciTegic: Pipeline Pilot: Providing Informatics Tools and Integration Choicesfor the Life Sciences
10:30-11:30am
10:40am
3. A Procedure for Assessing GO Annotation Consistency
Dolan, Ni, Camon, Blake

10:40-11:05am
4. An HMM Posterior Decoder for Sequence Feature Prediction that Includes Homology Information
Käll, Krogh, Sonnhammer
10:40-11:05am
   
11:05am
5. YeastHub: A Semantic Web Use Case for Integrating Data in the Life Sciences Domain
Cheung, Yip, Smith, deKnikker, Masiar, Gerstein
11:05-11:30am
6. Self-Organized Clustering Methods for Familial Binding Profiles
Mahony, Golden, Smith, Benos
11:05-11:30am
   
11:30am     Lunch
11:30am-1:30pm
         
12noon
    BOF: Application of Bioinformatics in Cancer
Kamal Rawal
12noon-1pm
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
12:15pm
  ISCB Open Business Meeting
12:15-1:30pm
1pm
  Demo: Domain-based Small Molecule Binding Site Annotation
1-2pm
Demo: The PRIDE Database: Plugging the Hole that is Leaking Proteomics Data
1-2pm
Demo: Rapid Determination of Local Structural Features
1-2pm
Demo: Ariadne Genomics Inc.: Software for the Analysis of Molecular Networks
1-2pm
1:30pm
AC Intro
1:30-1:45pm
Text Mining: Dietrich Rebholz-Schuhmann
   

Education/Web Workshop
1:30-5pm

1:45pm
7. High-recall Protein Entity Recognition Using a Dictionary
Kou, Cohen, Murphy
1:45-2:10pm
8. Statistics of Local Multiple Alignments
Prakash, Tompa
1:45-2:10pm
 
2pm
 

Demo:The ConSurf Web-Server for the Analysis of Evolutionary Conservation Patterns of Protein Structures
2-3pm

Demo: EMBOSS
2-3pm
Demo: BLASTgres: an Extension of the PostgreSQL Database System to Support Large-scale Bioinformatics Research
2-3pm
Demo
2-3pm
2:10pm
9. Beyond The Clause: Extraction of Phosphorylation Information from Medline Abstracts
Narayanaswamy, Ravikumar, Vijay-Shanker
2:10-2:35pm
10. Computing the P-value of the Information Content from an Alignment of Multiple Sequences
Nagarajan, Jones, Keich
2:10-2:35pm
 
2:30pm
SC Intro – Chris Burge
2:30-2:45pm
2:35pm
AC Intro
2:35-2:50pm
Pathways, Networks and Systems 1: Alfonso Valencia & Vincent Schachter
AC Intro
2:35-2:50pm
Evolution & Phylogeny: Olivier Gascuel & Dannie Durand
2:45pm
4. Regulatory Modules: Identification and Verification
Zhao, Stormo
2:45-3pm
2:50pm
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, Schneider
2:50-3:15pm
12. Identification of Nine Human-specific Frameshift Mutations by Comparative Analysis of the Human and the Chimpanzee Genome Sequences
Hahn, Lee
2:50-3:15pm
3pm
  Demo: WinAgent: Creating and Managing Personal Information Assistants for Biological Data Collection
3-4pm
Demo: The ANNOTATOR Software Suite
3-4pm
Demo: GEOSS: Advanced Microarray Experiment Management and Bioinformatics Analysis
3-4pm
Demo: Using GMOD Tools to Create, Edit, and Browse Genome Features
3-4pm
3:15pm
Coffee Break
3:15-3:45pm
Coffee Break
3:15-3:45pm
 
3:45pm
13. Kernel Methods for Predicting Protein-protein Interactions
Ben-Hur, Noble
3:45-4:10pm
14. Maximum Likelihood of Evolutionary Trees: Hardness and Approximation
Tuller, Chor
3:45-4:10pm
6. A Computational Method to Identify Amino Acid Residues Involved in Protein-DNA Interactions
Yan, Terribilini, Wu, Jernigan, Dobbs, Honavar
3:45-4pm
4pm
7. Genome-wide Comparative Analysis of Alternative Splicing in Plants
Wang, Brendel
4-4:15pm
Demo: Reactome - A Knowledgebase of Biological Processes
4-5pm
Demo: Visualizing and Analyzing Biological Network Data in Cytoscape 2.1
4-5pm
Demo: SeqHound: An Open Source Bioinformatics Application-programming Platform
4-5pm
Demo: Apollo: A Genome Annotation Editing Tool
4-5pm
4:10pm
15. Automatic Detection of Subsystem/Pathway Variants in Genome Analysis
Ye, Osterman, Overbeek, Godzik
4:10-4:35pm
16. Detecting Coevolving Amino Acid Sites using Bayesian Mutational Mapping
Dimmic, Hubisz, Bustamante, Nielsen
4:10-4:35pm
4:15pm
8. Inferring Splicing Regulatory Activity of Short Oligonuecleotides from Sequence Neighborhood
Stadler, Yeo, Shomron, Burge
4:15-4:30pm
4:30pm
9. Ab initio Computational Prediction of MicroRNA Genes
Sewer, Pfeffer, Aravin, Landgraf, Tuschl, van Nimwegen, Zavolan
4:30-4:45pm
4:35pm
17. Modeling the Organization of the WUSCHEL Expression Domain in the Shoot Apical Meristem
Jönsson, Heisler, Reddy, Agrawal, Gor, Shapiro, Mjolsness, Meyerowitz
4:35-5pm
18. Efficient Computation of Close Lower and Upper Bounds on the Minimum Number of Recombinations in Biological Sequence Evolution
Song, Wu, Gusfield
4:35-5pm
4:45pm
 
5pm
               
5:10pm
Keynote: Gunnar von Heijne
Membrane Proteins in vivo and in silico - Getting the Best of Two Worlds
5:10-6pm
Overflow            
6pm
        Poster Session 1: Authors Present at their poster
6-8pm
Demo: CREAD: Comprehensive Regulatory Element Analysis and Detection
6-7pm
Demo: INOH Pathway Database
6-7pm
Demo: MiMI: Michigan Molecular Interactions
6-7pm
Demo
6-7pm
7pm
      Demo
7-8pm
Demo: Advanced Micro-array Probe Design Using OligoWiz 2.0
7-8pm
Demo: BioDASH: Demonstration of Semantic Web Application in Life Sciences
7-8pm
Demo
7-8pm

Monday, June 27, 2005
Room
Renaissance Ballroom
Ambassador Ballroom
Mackinac
Ontario
Lasalle
Cadillac
Nicolet
Richard
7am
      Poster Session 2: Poster Set up by authors (room not open to delegates)
7-9am
       
8:30am

Keynote: Jill Mesirov
Gene Expression Analysis: A Knowledge-based Approach
8:30-9:20am

Overflow          
9am
Poster Session 2: Posters available for viewing by delegates
9am-6pm
9:20am
             
9:30am
AC Intro
9:30-9:45am
Proteomics 1: Michal Linial
AC Intro
9:30-9:45am
Transcriptome 1: Martin Vingron
SC Intro – Serafim Batzoglou 9:30-9:45am Demo: BALL (Biochemical ALgorithms Library) and BALLView - A Multiplatform Molecular Viewer and Modeling Tool
9:30-10:30am
Demo: The Pathway Tools Software
9:30-10:30am
Demo: PATIKAweb: A Web Service for Querying, Visualizing and Analyzing
the Graph-based PATIKA Pathway Database

9:30-10:30am
Demo: Biobase Corporation: Pathway analysis with curated protein databases
9:30-10:30am
9:45am
19. Classifying Noisy Protein Sequence Data: A Case study of Immunoglobulin Light Chains
Yu, Zaveljevski, Stevens, Yackovich, Reifman

9:45-10:10am
20. A Statistical Method for Detecting Splice Variation from Expression Data
Cline, Blume, Cawley, Clark, Hu, Lu, Salomonis, Wang, Williams

9:45-10:10am
10. Combining Phylogenetic Data and Network Topology to Identify Regulatory Motifs
Wang, Stormo

9:45-10am
10am
11. Identification of Novel Human Splice Variants Using “- Genomic Fossils”
Shemesh, Novik, Edelheit, Sorek
10-10:15am
10:10am

Coffee Break
10:10-10:40am

Coffee Break
10:10-10:40am
10:15am 12. A Comparative Genomics Approach to Distinguishing Exon Creation and Loss Events Shows Increased Exon Creation Associated with Alternative Splicing
Alekseyenko, Lee
10:15-10:30am
10:30am
  Demo: M-GCAT: Multiple Genome Comparison and Alignment Tool
10:30-11:30am
Demo: The Protégé Suite of Tools: Accessing, Managing, and Visualizing Biomedical Ontologies
10:30-11:30am
Demo: Automatic Annotation Tool and Browser for Whole-Genome Tiling-Array
Data Analysis

10:30-11:30am
Demo: Apple Computer, Inc.: The Apple Workgroup Cluster
10:30-11:30am
10:40am
21. Protein Function Prediction via Graph Kernels
Borgwardt, Ong, Schoenauer, Vishwanathan, Smola, Kriegel

10:40-11:05am
22. Robust Classification Modeling on Microarray Data Using Misclassification Penalized Posterior
Soukup, Lee

10:40-11:05am
 
11:05am
23. CaSPredictor: A new Computer-based Tool for Caspase Substrate Prediction
Garay-Malpartida, Occhiucci, Alves, Belizário

11:05-11:30am
24. Experimental Design for Three-Color and Four-Color Gene Expression Microarrays
Woo, Krueger, Kaur, Churchill

11:05-11:30am
 
11:30am     Lunch
11:30am-1:30pm
       
12noon
    BOF: Bronchial Asthma, Bioinformatics, and Microarrays
Kamal Rawal
12noon-1pm
BOF: A WIKI on “Methods in bioinformatics”?
Martin Jambon
12noon-1pm
   
12:15pm Interagency Program Workshop
12:15-1:45pm
     
12:45pm
     
1pm
Demo:
1-2pm
Demo: GenDB & The SEED: Two Genome Annotation Systems Integrated
1-2pm
Demo: Estimating Phylogenetic Trees and Networks using SplitsTree 4
1-2pm
Demo: PART 1: Sun Microsystems: Discovery to Development Demos: How to Save Time, Money & Hassels With 6 Solutions
1-2pm
1:30pm
 
1:45pm
25. Families of Membranous Proteins can be Characterized by the Amino Acid Composition of their Transmembrane Domains
Sadka, Linial
1:45-2:10pm
26. A Hidden Markov Model for Analyzing ChIP-chip Experiments on Genome Tiling Arrays and its Application to p53 Binding Sequences
Li, Meyer, Liu
1:45-2:10pm
 
2pm
  Demo: The myGrid/Taverna Toolkit for Workflow Based Bioinformatics
2-3pm
Demo: Protein Homology Detection and Structure Prediction with HHsearch and HHpred
2-3pm
Demo: Development of a Microarray Data Analysis Software (MicroArrayWare) with a Calibration Step for Automatic Selection of Optimal Analysis Methods and Parameters
2-3pm
Demo: CSIRO: GeneRave and New Statistical Algorithms for p>n Data
2-3pm
2:10pm
27. High-Throughput Inference of Protein-Protein Interfaces from Unassigned NMR Data
Mettu, Lilien, Donald

2:10-2:35pm
28. Multi-way Clustering of Microarray Data using Probabilistic Sparse Matrix Factorization
Dueck, Morris, Frey
2:10-2:35pm
 
2:30pm
13. A Gamma Mixture Model Better Accounts for Among Site Rate Heterogeneity
Mayrose, Friedman, Pupko
2:30-2:45pm
2:35pm
AC Intro
2:35-2:50pm
Genomes 1: Ying Xu & Steven Salzberg
AC Intro
9:30-9:45am
Structural Bioinformatics: Nir Ben-Tal & Ramanathan Sowdhamini
2:45pm
14. Evidence of a Large-scale Functional Organization of Mammalian Chromosomes
Graber, Churchill, DiPetrillo, King, Petkov, Paigen
2:45-3pm
2:50pm
29. Tag SNP Selection in Genotype Data for Maximizing SNP Prediction Accuracy
Halperin, Kimmel, Shamir Paper
2:50-3:15pm
30. Three-Stage Prediction of Protein Beta-Sheets by Neural Networks, Alignments, and Graph Algorithms
Cheng, Baldi
2:50-3:15pm
3pm
15. Trees and Forests: A Genome-wide Reconstruction of Orthologous Gene Groups in Fungi
Wapinski, Friedman, Regev, Pfeffer
3-3:15pm
Demo: Integrating Text Mining into Bioinformatics Workflows
3-4pm
Demo: STING - A Web Server for Comprehensive Analysis of Protein Structure and Sequence
3-4pm
Demo: Atomic Reconstruction of Metabolism: Metabolic Map Editor
3-4pm
Demo: IBM: From Biological Networks to Web Services: The Latest IBM Technologies for Querying Biological Data
3-5pm
3:15pm
Coffee Break
3:15-3:45pm
Coffee Break
3:15-3:45pm
 
3:45pm
31. Mining ChIP-chip Data for Transcription Factor and Cofactor Binding Sites
Smith, Sumazin, Das, Zhang
3:45-4:10pm
32. Improving Protein Structure Prediction With Model-Based Search
Brunette, Brock
3:45-4:10pm
SC Intro – Michael Zuker
3:45-4pm
4pm
16. A Conserved Sparse Dicodon Framework Which Correlates Sequence and Structure: Implications for Gene Finding
Halitsky, Lesk, Fresco

4-4:15pm
Demo: LARALink: A Web Application for Cytogenetic Linkage Analysis
4-5pm
Demo: Data Integration in the Comparative Toxicogenomics Database (CTD)
4-5pm
Demo: MSight: An LC-MS Image Analysis Software
4-5pm
4:10pm
33. GenXHC: A Probabilistic Generative Model for Cross-hybridization Compensation in High-density Genome-wide Microarray Data
Huang, Morris, Frey Paper

4:10-4:35pm
34. Prediction of Active Sites for Protein Structures from Computed Chemical Properties
Ko, Murga, Ondrechen
4:10-4:35pm
4:15pm
17. Enzyme Mechanism Annotation and Classification
Almonacid, Holliday, Murray-Rust, Thornton, Mitchell
4:15-4:30pm
4:30pm
18. A Novel Approach to Structural Alignment using Realistic Structural and Environmental Information
Chen, Crippen
4:30-4:45pm
4:35pm
35. RASE: Recognition of Alternatively Spliced Exons in C. elegans
Raetsch, Sonnenburg, Schoelkopf

4:35-5pm
36. In silico Identification of Functional Regions in Proteins
Nimrod, Glaser, Steinberg, Ben-Tal, Pupko
4:35-5pm
4:45pm
19. On the Importance of Being Left-handed
Novotny, Kleywegt
4:45-5pm
5pm
             
5:10pm
Keynote: Pavel Pevzner
Transforming Men into Mice: Fragile versus Random Breakage Models of Chromosome Evolution
5:10-6pm
Overflow          
6:00pm
      Poster Session 2: Authors Present at their poster
6-8pm
Demo: Using GEMS for Cancer Diagnosis and Biomarker Discovery from Microarray Gene Expression Data
6-7pm
Demo: The Oncology Thinking Cap
6-7pm
Demo: GeneNotes - A Novel Information Management Software for Biologists
6-7pm
Demo
6-7pm
7:00pm
      Demo: Vigyaan: An Integrated Software Workbench for Bioinformatics and Computational Biology
7-8pm
Demo: PUMA2 - A Grid Technology Based Computational Environment for High-throughput Genetic Sequence Analysis and Evolutionary Analysis of Metabolism
7-8pm
Demo
7-8pm
Demo
7-8pm

Tuesday, June 28, 2005
Room
Renaissance Ballroom
Ambassador Ballroom
Mackinac
Ontario
Lasalle
Cadillac
Nicolet
Richard
Brule
7am
      Poster Session 3 (PLoS CB Latebreaking Posters): Poster Set up by authors (room not open to delegates)
7-9am
         
8:30am

Keynote: Peter Hunter
Computational Physiology and the IUPS Physiome Project
8:30-9:20am

Overflow            
9am
Poster Session 3 (PLoS CB Latebreaking Posters): Posters available for viewing by delegates
9am-5:20pm
9:20am
               
9:30am
    SC Intro – Michael Eisen
9:30-9:45am
Demo: BioNavigation: Selecting Optimum Paths Through Resources to Evaluate Scientific Queries
9:30-10:30am
Demo: GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences
9:30-10:30am
Demo: Immunological Web Tools
9:30-10:30am
Demo: Synamatix: Applications of a Novel Structured Network Database in Ultra-high-throughput Genomics Analysis
9:30-10:30am
 
9:45am 37. Enhanced Position Weight Matrices using Mixture Models
Hannenhalli, Wang
9:45-10:10am
38. How Old is Your Fold?
Winstanley, Abeln, Deane
9:45-10:10am
20. TEPC: Total Evidence Phylogenetic Correlation of Microbial Phenotypes and Genotypes
Sarkar, Planet, DeSalle
9:45-10am
 
10am
21. Feasibility of Genome-wide Recognition of Mutant Single Nucleotide Polymorphisms (SNPs) with Effects on Constitutive mRNA Splicing
Rogan, Nalla

10-10:15am
 
10:10am

Coffee Break
10:10-10:40am

Coffee Break
10:10-10:40am
 
10:15am 22. Transcriptional Reprogramming in Genetic Backup Circuits
Kafri, Pilpel

10:15-10:30am
 
10:30am
  Demo: Protein Modeling with POSE: Protein Optimization Steering Environment
10:30-11:30am
Demo: PIR: A Comprehensive Resource for Functional Analysis of Protein Sequences and Families
10:30-11:30am
Demo: The Short Time-series Expression Miner (STEM)
10:30-11:30am
Demo: Apple Computer, Inc.: Mac OS X v10.4 'Tiger' for the Life Sciences
10:30-11:30am
 
10:40am
39. De Novo Identification of Repeat Families in Large Genomes
Price, Jones, Pevzner
10:40-11:05am
40. Search for Folding Nuclei in Native Protein Structures
Shmygelska
10:40-11:05am
 
 
11:05am
41. Automatic Interpretation of MS/MS Spectra of Oligosaccharides
Tang, Mechref, Novotny

11:05-11:30am
42. A Path Planning Approach for Computing Large-Amplitude Motions of Flexible Molecules
Cortes, Simeon, Ruiz de Angulo, Guieysse, Remaud-Simeon, Tran
11:05-11:30am
 
 
11:30am
    Lunch
11:30am-1:30pm
         
12noon
BOF: Semantic Web for Life Sciences
Eric Neumann
12noon-1pm
BOF: Automated Function Prediction
Iddo Friedberg
12noon-1pm
12:15pm
NIH Workshop
Getting the Grant: Tips on Writing Grants Applications to
Federal Agencies (organized by Marc Rigas, NIH)

12:15-1:45pm
      NSF Workshop
12:15-1:45pm
TENTATIVE
1pm
  Demo: INDUS: A System for Information Integration and Knowledge Acquisition from Autonomous, Distributed, and Semantically Heterogeneous Data Sources
1-2pm
Demo: Using the Biozon System for Search and Analysis of Heterogeneous Interrelated Biological Data
1-2pm
Demo: VitaPad: A Tool for Visualizing Pathways
1-2pm
Demo: Hewlett Packard: Build and Execute Genomics Pipelines with HP and TimeLogic
1-2pm
1:20pm
43. Clustering Short Time Series Gene Expression Data
Ernst, Nau, Bar-Joseph
1 :20-1:45pm
1:30pm
 
1:45pm
44. PILER: Identification and Classification of Genomic Repeats
Edgar, Myers

1:45-2:10pm
45. Predicting the in vivo Signature of Human Gene Regulatory Sequences
Noble, Kuehn, Thurman, Yu, Stamatoyannopoulos
1:45-2:10pm
   
2pm
  Demo: SNP-VISTA: An Interactive SNPs Visualization Tool
2-3pm
Demo: Notung 2.0: Putting the Macroevolution Back in Phylogenetics
2-3pm
Demo: Rat Genome Database: A Database for Comparative Genomics using the Rat Model Organism
2-3pm
Demo: Gene Logic Inc.: Biomarker Discovery Using an Extensive Clinical Microarray Gene Expression Database
2-3pm
 
2:10pm
46. The Precise Positioning of Genomic Landmarks Can Aid in the Identification of Regulatory Elements
Tharakaraman, Marino-Ramirez, Sheetlin, Landsman, Spouge
2:10-2:35pm
47. Predicting Protein-Protein Interaction by Searching Evolutionary Tree Automorphism Space
Jothi, Kann, Przytycka
2:10-2:35pm
   
2:35pm
Coffee Break
2:35-3:05pm
Coffee Break
2:35-3:05pm
   
2:50pm
SC Intro – Mark Musen
2:50-3:05pm
 
3pm
Demo: REMBRANDT: Empowering Translational Research
3-4pm
Demo: VisANT: Integrative Visual Analysis Tool for Biological Networks, Pathways and Modules
3-4pm
Demo: CDTree: A Tool to Analyze and Annotate Protein Subfamily Hierarchies
3-4pm
Demo: PART 2: Sun Microsystems: Discovery to Development Demos: How to Save Time, Money & Hassels With 6 Solutions
3-4pm
 
3:05pm
48. Reversal Distance for Partially Ordered Genomes
Zheng, Lenert, Sankoff
3:05-3:30pm
49. Supervised Enzyme Network Inference from the Integration of Genomic Data and Chemical Information
Yamanishi, Vert, Kanehisa
3:05-3:30pm
23. Where do we GO next? Refining the Content of the Gene Ontology
Harris
3:05-3:20pm
 
3:20pm
24. Ontological Visualization of Protein-Protein Interactions Using the Gene Ontologies
Drabkin, Hollenbeck, Hill, Dolan, Kadin, Blake

3:20-3:35pm
3:30pm
50. ExonHunter: A Comprehensive Approach to Gene Finding
Brejova, Brown, Li, Vinar
3:30-3:55pm
51. Whole-proteome Prediction of Protein Function via Graph-theoretic Analysis of Interaction Maps
Nabieva, Jim, Agarwal, Chazelle, Singh
3:30-3:55pm
 
3:35pm
 
3:50pm
26. BioPAX - Biological Pathway Data Exchange Format
Cary, BioPAX Workgroup, Bader, and Sander
3:50-4:05pm
3:55pm
52. Conservative Extraction of Over-represented Extensible Motifs
Apostolico, Comin, Parida
3:55-4:20pm
53. Mining Coherent Dense Subgraphs Across Massive Biological Networks for Functional Discovery
Hu, Yan, Huang, Han, Zhou
3:55-4:20pm
 
4pm
         
4:05pm
27. Hubs of Knowledge: Using the Functional Link Structure in Biozon to Mine for Biologically Significant Entities
Shafer, Isganitis, Yona

4:05-4:20pm
4:20pm
               
4:30pm
Keynote: Satoru Miyano
Computational Challenges for Gene Networks
4:30-5:20pm
Overflow            
5:20pm
      Poster Session 3 (PLoS CB Latebreaking Posters): Authors Present at their poster
5:20-6:30pm
         
6:30pm
Off Site Gala Dinner: The Detroit Princess Riverboat Cruise
6:30-10:30pm
10:30pm
                 

Wednesday, June 29, 2005
Room
Renaissance Ballroom
Ambassador 1
Ambassador 2
Ambassador 3
Mackinac
Ontario
LaSalle
Cadillac
Nicolet
Richard
8:30am
Keynote: ISCB Overton Prize Winner Ewan Birney
Genomes to Systems Biology
8:30-9:20am
Overflow Overflow Overflow Overflow

Poster Session 3 (PLoS CB Latebreaking Posters): Authors Present at their poster
10:30-11:30am

       
9:20am
                 
9:30am
AC Intro
9:30-9:45am
Bioinformatics Applications: Phil Bourne

28. Route as Trees: The Parsing View on Protein Folding
Hockenmaier, Joshi, Dill
9:30-9:45am

 

29. Dynamic Complex formation During the Yeast Cell Cycle
de Lichtenberg, Jensen, Brunak, Bork
9:30-9:45am

30. Literature Data Mining and Protein Ontology Development at the Protein Information Resource (PIR)
Hu, Mani, Liu, Shanker, Hermoso, Nikolskaya, Natale, Wu
9:30-9:45am

Demo: FUZEBASE: An Online Platform for Exploration and Information Fusion of Biomedical Informatics Data
9:30-10:30am
Demo: The MAPPER Platform for the Computational Identification of Transcription Factor Binding Sites
9:30-10:30am
Demo: Pygr: A Python Graph Database Framework for Bioinformatics
9:30-10:30am
Demo: Accelrys, Inc.: DS GCG a Boinformatics Solution
9:30-10:30am
9:45am
54. A Systematic Approach for Comprehensive T-cell Epitope Discovery Using Peptide Libraries
Beissbarth, Tye-Din, Smyth, Speed, Anderson
9:45-10:10am
31. All-Atom Modeling of RNA Conformational Changes
Mathews, Case
9:45-10am
  32. Genome-wide Transcription Regulatory Circuits Controlling Cellular Malignant
Tabach, Milyavsky, Zuk, Yitzhaki, Polak, Domany, Rotter, Pilpel
9:45-10am
33. CGHGate: Array-CGH, Case Reports, Phenotypes and Biomedical Literature for Human Genome Annotation
Van Vooren, Maas, Vermeesch, Moreau, De Moor 9:45-10am
10am
34. A Novel Covariance Model Based RNA Motif Finding Algorithm
Yao, Ruzzo
10-10:15am
35. Structure Prediction and Analysis of Remote Homology Relations for Proteins in Complete Genomes
Sadreyev, Grishin
10-10:15am
36. Conserved Protein Domain Interactions from Structure data: A Modeling Resource for Novel Protein Interactions
Shoemaker, Bryant
10-10:15am
37. Text-mining Challenges for Protein Family Database Annotation
Divoli, Attwood 10-10:15am
10:10am

55. Bayesian Neural Network Approaches to Ovarian Cancer Identification from High-resolution Mass Spectrometry Data
Yu, Chen
10:10-10:35am

10:15am 38. ncRNA Genefinding in C. elegans
Stricklin, Reinke, Stolc, Eddy
10:15-10:30am
39. The Canonical Representation of Proteins: Application to Remote Homology Recognition
Ku, Yona
10:15-10:30am
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
10:15-10:30am
10:30am
42. Isostericity Matrices: Tools for Analyzing Recurrent Motifs and Structurally Aligning Homologous RNAs
Leontis, Westhof, Craig, Mokdad, Stombaugh, Sarver
10:30-10:45am
43. Domain-based Protein Hierarchy and Detection of Semantically Significant Domain Architectures
Ku, Yona
10:30-10:45am
44. New Machine Learning Approaches for Classification of Mass Spectrometry Database Search Results
Ulintz, Zhu, Andrews, Qin
10:30-10:45am
45. Are Antisense Transcripts prone to A-to-I RNA Editing?
Neeman, Dahary, Eisenberg, Levanon, Sorek
10:30-10:45am
Demo: BioArrayMiner: A Software Package for Integrative Analysis of Cross-platform and Cross-species Microarray Data
10:30-11:30am
Demo: caArray Data Management and Analysis Tools at the National Cancer Institute (NCI) Center for Bioinformatics
10:30-11:30am
Demo: Genome Visualization and Analysis with S-plot
10:30-11:30am
Demo
10:30-11:30am
10:35am
56. Kernels for Small Molecules and the Prediction of Mutagenicity, Toxicity, and Anti-Cancer Activity
Ralaivola, Chen, Phung, Bruand, Swamidass, Baldi
10:35-11:00am
10:45am
  46. Pattern-based Phylogenetic Distance Estimation and Tree Reconstruction
Hoehl, Rigoutsos, Ragan
10:45-11am
47. Clustering 2D mRNA Expression Patterns of Drosophila Embryos
Peng, Long, Eisen, Myers
10:45-11am
11am
Coffee Break
11:00-11:30am
       
11:30am
Keynote: 2005 ISCB Senior Scientist Accomplishment Award Janet Thornton
From Proteins to Life - Old and New Challenges
11:30am-12:20pm
Overflow Overflow Overflow Overflow          
12noon BOF: Can we look for Breast cancer markers which are commercially viable?
Kamal Rawal
12noon-1pm
12:20pm
Closing/Awards Ceremony
12:20-1:00pm
Overflow Overflow Overflow Overflow        
1:00pm