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)
12noon-5pm
BOF: Retrotransposons
and Bioinformatics
Kamal Rawal
12noon-1pm
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)
7-9am
Opening Ceremony
8-8:30am
Overflow
Keynote: Howard
Cash Biology of Life and Death: Disaster, DNA and
the Information Science of Human Identification
8:30-9:20am
Poster Session 1:
Posters available for viewing by delegates
9am-6pm
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
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
2. An
EM Algorithm for Unambiguous Assignment of Genes to Biochemical Pathways
Popescu, Yona
10-10:15am
Coffee Break
10:10-10:40am
Coffee Break
10:10-10:40am
3. Multiple Knockouts
Analysis of Genetic Robustness in the Yeast Metabolic Network
Deutscher, Meilijson, Ruppin
10:15-10:30am
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:
10:30-11:30am
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
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
Lunch
11:30am-1:30pm
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
ISCB Open Business
Meeting
12:15-1:30pm
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:
1-2pm
AC Intro
1:30-1:45pm Text Mining: Dietrich Rebholz-Schuhmann
Education/Web
Workshop
1:30-5pm
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
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
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
SC Intro – Chris
Burge
2:30-2:45pm
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
4. Regulatory Modules:
Identification and Verification
Zhao, Stormo
2:45-3pm
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 r
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
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
Coffee Break
3:15-3:45pm
Coffee Break
3:15-3:45pm
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
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
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
8. Inferring Splicing Regulatory
Activity of Short Oligonuecleotides from Sequence Neighborhood
Stadler, Yeo, Shomron, Burge
4:15-4:30pm
9. Ab initio Computational
Prediction of MicroRNA Genes
Sewer, Pfeffer, Aravin, Landgraf, Tuschl, van Nimwegen, Zavolan
4:30-4:45pm
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
Keynote: Gunnar
von Heijne
Membrane Proteins in vivo and in silico -
Getting the Best of Two Worlds
5:10-6pm
Overflow
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
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
Poster Session 2: Poster
Set up by authors (room not open to delegates)
7-9am
Keynote:
Jill Mesirov
Gene Expression Analysis: A Knowledge-based Approach
8:30-9:20am
Overflow
Poster Session 2:
Posters available for viewing by delegates
9am-6pm
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
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
11. Identification
of Novel Human Splice Variants Using “- Genomic Fossils”
Shemesh, Novik, Edelheit, Sorek
10-10:15am
Coffee Break
10:10-10:40am
Coffee Break
10:10-10:40am
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
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
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
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
Lunch
11:30am-1:30pm
BOF: Bronchial Asthma,
Bioinformatics, and Microarrays
Kamal Rawal
12noon-1pm
BOF: A WIKI on “Methods
in bioinformatics”?
Martin Jambon
12noon-1pm
Interagency
Program Workshop
12:15-1:45pm
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
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
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
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
13. A Gamma Mixture
Model Better Accounts for Among Site Rate Heterogeneity Mayrose,
Friedman, Pupko
2:30-2:45pm
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
14. Evidence of
a Large-scale Functional Organization of Mammalian Chromosomes
Graber, Churchill, DiPetrillo, King, Petkov, Paigen
2:45-3pm
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
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
Coffee Break
3:15-3:45pm
Coffee Break
3:15-3:45pm
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
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
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
17. Enzyme Mechanism Annotation
and Classification Almonacid, Holliday, Murray-Rust, Thornton,
Mitchell
4:15-4:30pm
18. A Novel Approach
to Structural Alignment using Realistic Structural and Environmental Information
Chen, Crippen
4:30-4:45pm
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
19. On the Importance of Being
Left-handed Novotny, Kleywegt
4:45-5pm
Keynote: Pavel
Pevzner
Transforming Men into Mice: Fragile versus Random Breakage
Models of Chromosome Evolution
5:10-6pm
Overflow
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
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
Poster Session 3 (PLoS
CB Latebreaking Posters): Poster Set up by authors (room
not open to delegates)
7-9am
Keynote: Peter
Hunter
Computational Physiology and the IUPS Physiome Project
8:30-9:20am
Overflow
Poster Session 3
(PLoS CB Latebreaking Posters): Posters available for viewing
by delegates
9am-5:20pm
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
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
21. Feasibility of
Genome-wide Recognition of Mutant Single Nucleotide Polymorphisms (SNPs)
with Effects on Constitutive mRNA Splicing
Rogan, Nalla
10-10:15am
Coffee Break
10:10-10:40am
Coffee Break
10:10-10:40am
22. Transcriptional Reprogramming
in Genetic Backup Circuits
Kafri, Pilpel
10:15-10:30am
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
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
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
Lunch
11:30am-1:30pm
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
Federal Agencies (organized by Marc Rigas, NIH)
12:15-1:45pm
NSF Workshop
12:15-1:45pm
TENTATIVE
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
43. Clustering
Short Time Series Gene Expression Data Ernst, Nau,
Bar-Joseph
1 :20-1:45pm
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
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
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
Coffee Break
2:35-3:05pm
Coffee Break
2:35-3:05pm
SC Intro – Mark
Musen
2:50-3:05pm
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
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
24. Ontological Visualization
of Protein-Protein Interactions Using the Gene Ontologies
Drabkin, Hollenbeck, Hill, Dolan, Kadin, Blake
3:20-3:35pm
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
26. BioPAX - Biological
Pathway Data Exchange Format
Cary, BioPAX Workgroup, Bader, and Sander
3:50-4:05pm
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
27. Hubs of Knowledge: Using
the Functional Link Structure in Biozon to Mine for Biologically Significant
Entities
Shafer, Isganitis, Yona
4:05-4:20pm
Keynote: Satoru
Miyano Computational Challenges for Gene Networks
4:30-5:20pm
Overflow
Poster Session 3 (PLoS CB Latebreaking
Posters): Authors
Present at their poster
5:20-6:30pm
Off
Site Gala Dinner: The Detroit Princess Riverboat Cruise
6:30-10:30pm
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
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:
9:30-10:30am
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
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
55.
Bayesian Neural Network Approaches
to Ovarian Cancer Identification from High-resolution Mass Spectrometry
Data
Yu, Chen
10:10-10:35am
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
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
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
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
Coffee Break
11:00-11:30am
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
BOF: Can we look for Breast
cancer markers which are commercially viable?
Kamal Rawal
12noon-1pm
Closing/Awards Ceremony
12:20-1:00pm
Overflow
Overflow
Overflow
Overflow