ISMB/ECCB 2004

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Tentative Detailed Agenda for ISMB/ECCB 2004 - Times and running orders of presentations may change

Scroll to view the entire agenda or select an option from the following to jump to a specific day:
[Thursday, 29 July] [Friday, 30 July] [Saturday, 31 July] [Sunday, 1 August] [Monday, 2 August] [Tuesday, 3 August] [Wednesday, 4 August]

Color Key

SIGs/SIG Reports

Long Papers

Tutorials

Short Papers

Opening/Closing Ceremonies/Program Chair Introductions

Demos

Keynotes

Social Events

Thursday, 29 July 2004
	SIG Meeting	SIG Meeting	SIG Meeting	SIG Meeting	SIG Meeting	SIG Meeting
8:00		8:00-19:00 SIG (2 Day): Bioinformatics and Statistical Physics (SECC - Dochart)
8:45						8:45-22:00 SIG (2 Day): 3Dsig: Structural Bioinformatics (SECC - Lomond)
9:00	9:00-17:00 SIG (1 Day): Biolink (Moat House Castle II & III)		9:00-19:00 SIG (2 Day): BioPathways (SECC - Biosdale)	9:00-19:00 SIG (2 Day): BOSC (SECC - Alsh)	9:00-19:00 SIG (2 Day): SIGSIM (Moat House - Argyle Suite 1)
12:00	LUNCH
13:00
17:00
19:00
21:00
22:00

Friday, 30 July 2004
	SIG Meeting	SIG Meeting	SIG Meeting	SIG Meeting	SIG Meeting	SIG Meeting	SIG Meeting	SIG Meeting	SIG Meeting
8:00					8:00-19:00 SIG (2 Day): Bioinformatics and Statistical Physics (SECC - Dochart)
8:30			8:30-17:00 SIG (1 Day): Genome Annotations (SECC - Carron 2)	8:30-17:00 SIG (1 Day): WEB '04 (SECC - Carron 1)
9:00	9:00-18:00 SIG (1 Day): Bioinformatics and Disease (Moat House Island SuitesI)	9:00-19:00 SIG (1 Day): BioOntologies (Moat House Castle II & III)		8:30-17:00 SIG (1 Day): WEB '04 (SECC - Carron 1)		9:00-19:00 SIG (2 Day): BioPathways (SECC - Biosdale)	9:00-19:00 SIG (2 Day): BOSC (SECC - Alsh)	9:00-19:00 SIG (2 Day): SIGSIM (Moat House - Argyle Suite 1)	9:00-18:30 SIG (2 Day): 3Dsig: Structural Bioinformatics (SECC - Lomond)
12:00	LUNCH
13:00
17:00
18:00
18:30
19:00

Saturday, 31 July 2004
	Tutorials	Tutorials	Tutorials	Tutorials	Tutorials	Tutorials	Tutorials
8:30	8:30-12:30 AM1 Tutorial (Lamond): Graph Data Management for Biology (Frank Olken)	8:30-12:30 AM2 Tutorial (Alsh): *Immunoinformatics: Recent Developments and Applications* (Can Kesmir and Ole Lund)	8:30-12:30 AM3 Tutorial (Biosdale) : *Microarray Data-Analysis – Understanding and Application of Modern Methods* (David Kreil and Steven Russell)	8:30-12:30 AM4 Tutorial (Dochart): *Mining the Biomedical Literature: State of the Art, Challenges and Evaluation Issues* (Hagit Shatkay)	8:30-12:30 AM5 Tutorial (Carron) : Computational Methods for the Identification of Regulatory RNA Motifs (Graziano Pesole and Giulio Pavesi)	8:30-12:30 AM6 Tutorial (Forth): In-silico Analysis and Prediction of Protein Function (Yanay Ofran, Macro Punta and Burkhardt Rost)	8:30-12:30 AM7 Tutorial (Gala): *Using Ontologies in Biological Research* (Winston Hide and Janet Kelso)
12:30	12:30-13:30 *Tutorial Luncheon (For Tutorial Registrants Only)*
13:30	13:30-17:30 PM8 Tutorial (Alsh): *The EM Algorithm and Some of its Applications in Molecular Biology* (Frédérique Galisson)	13:30-17:30 PM9 Tutorial: Cancelled	13:30-17:30 PM10 Tutorial (Carron): *Systems Biology of Host-Pathogen and other "Community" Interactions* (Christian Forst)	13:30-17:30 PM11 Tutorial (Biosdale) : *Pattern Discovery* (Laxmi Parida)	13:30-17:30 PM12 Tutorial (Lamond): *Advanced Data Mining for Bioinformatics* (Stefan Kramer)	13:30-17:30 PM13 Tutorial (Gala): *Association Mapping: Fundamental Principles and Applications* (Leif Schauser and Jotun Hein)	13:30-17:30 PM14 Tutorial (Forth): *Computational Methods for Proteomic Analysis* (Michael Giddings and Michael Wisz)
15:00	15:00-17:30 *Orienteering Ice Breaker*
17:30
18:30	18:30-20:00 *ISMB/ECCB 2004 Opening Reception: Glasgow Science Center (Next to Convention Center)*
20:00

Sunday, 1 August 2004
	Keynotes & Papers: Clyde Auditorium	Papers: Lomond Auditorium	Industry Poster & Exhibit Hours: Hall 4	Demos: Alsh 1	Demos: Alsh 2	SIG Reports: Carron
8:30	8:30-9:00 Opening Ceremony
9:00	9:00-9:50 Keynote: Leroy Hood - Systems Biology: Strategies for Deciphering Life
9:30				9:30-10:30 DEMO:	9:30-10:30 DEMO: Blueprint SeqHound: A Bioinformatics Application Programming Platform
9:50	9:50-10:10 Program Chair's Introduction: Des Higgins - Sequence Analysis	9:50-10:10 Program Chair's Introduction: Carole Goble - Databases, Ontologies & Text Mining
10:10	10:10-10:40 Long Paper #1 IMGT/JunctionAnalysis: The First Tool for the Analysis of the Immunoglobulin and T Cell Receptor Complex V-J and V-D-J Junctions	10:10-10:40 Long Paper #2 The Gene Ontology Categorizer
10:30		10:10-10:40 Long Paper #2 The Gene Ontology Categorizer		10:30-11:30 DEMO: Bioinformatics Institute WILDFIRE: Distributed, Grid-enabled Workflow Enactment Engine	10:30-11:30 DEMO: Universitat Autònoma de Barcelona PDA: A Pipeline to Explore and Estimate Polymorphism in Large DNA Databases
10:40	COFFEE					COFFEE
11:10	11:10-11:40 Long Paper #3 Tracking Repeats Using Significance and Transitivity	11:10-11:40 Long Paper #4 HyBrow - A Prototype System for Computer-Aided Hypothesis Evaluation				11:10-11:40 SIG Report: WEB '04
11:30				11:30-13:30 DEMO: European Bioinformatics Institute and The Research Collaboratory for Structural Bioinformatics MSD/RCSB PDB Access Tools and Databases	11:30-12:30 DEMO: Japan Biological Information Research Center, AIST H-Invitational Database - A New Human Gene Annotation Database	11:10-11:40 SIG Report: WEB '04
11:40	11:40-12:10 Long Paper #5 Efficient Approximations for Learning Phylogenetic HMM Models from Data	11:40-12:10 Long Paper #6 Mining MEDLINE for Implicit Links between Dietary Substances and Diseases				11:40-12:10 SIG Report: Genome Annotation
12:10	12:10-12:30 Short Paper #7 MUSCLE: Low-complexity Multiple Sequence Alignment with T-Coffee Accuracy	12:10-12:40 Long Paper #8 Protein Names Precisely Peeled Off Free Text
12:30	12:30-12:50 Short Paper #9 PROBCONS: Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences		12:30-20:30 Industry Exhibits		12:30-13:30 DEMO: Bilkent University PATIKA - Pathway Analysis Tool for Integration and Knowledge Acquisition
12:40		12:40-13:00 Short Paper #10 False Annotations of Proteins: Automatic Detection via Keyword-Based Clustering
12:50
13:00	13:00-14:30 LUNCH ISCB/ECCB Open Business Meeting (Hall 1)	LUNCH - Hall 4				BOF Luncheons
13:30		LUNCH - Hall 4		13:30-14:30 DEMO: European Bioinformatics Institute EMBOSS	13:30-14:30 DEMO: Cornell University BIOZON: A System for Unification, Management and Analysis of Heterogeneous Biological Data	BOF Luncheons
14:30	14:30-14:50 Program Chair's Introduction: Win Hide - Applications	14:30-14:50 Program Chair's Introduction: Ying Xu and Gene Myers- Genomes 1		14:30-16:30 DEMO: IBM Graph Data Management for Bioinformatics	14:30-15:30 DEMO: Nanyang Technological University MolStudio - A low end system for VR-enhanced protein visualization
14:50	14:50-15:20 Long Paper #11 Reconstructing Tumor Amplisomes	14:50-15:20 Long Paper #12 Splice Site Identification by idlBNs				14:50-15:20 SIG Report: Bio-link
15:20	15:20-15:50 Long Paper #13 The Cell Graphs of Cancer	15:20-15:50 Long Paper #14 Improved Techniques for the Identification of Pseudogenes				15:20-15:50 SIG Report: Bioinformatics & Statistical Physics
15:30	15:20-15:50 Long Paper #13 The Cell Graphs of Cancer				15:30-16:30 DEMO: Max Planck Institute for Dynamics of Complex Technical Systems Exploring Metabolic Networks Using the FluxAnalyzer
15:50	15:50-16:20 Long Paper #15 Prediction of Class I T-cell Epitopes: Evidence of Presence of Immunological Hot Spots Inside Antigens	15:50-16:20 Long Paper #16 Exploiting Conserved Structure for Faster Annotation of Non-coding RNAs Without Loss of Accuracy				15:50-16:20 SIG Report: BioOntologies
16:20	TEA					TEA
16:30	TEA			16:30-17:30 DEMO: European Bioinformatics Institute Jemboss - the Graphical User Interface to EMBOSS	16:30-17:30 DEMO: European Bioinformatics Institute IntAct - an Open Source Molecular Interaction Database	TEA
16:50	16:50-17:20 Long Paper #17 Exploring Williams-Beuren Syndrome using my Grid	16:50-17:20 Long Paper #18 Functional Inference from Non-random Distributions of Conserved Predicted Transcription Factor Binding Sites
17:20	17:20-18:00 Keynote: Denis Noble - Computational systems biology of the heart
17:30
18:00	18:00-18:10 Introduction to ISMB 2005, Detroit USA	18:00-20:30 Reception & Poster Session 1
18:10				19:30-20:30 DEMO: Accelrys From Genes to Protein Structures Prediction: "A Genome Analysis"	19:30-20:30 DEMO: The Hebrew Univeristy SPRINT – the Side-chain Prediction Inference Toolbox
19:30
20:00
20:30

Monday, 2 August 2004
	Keynotes & Papers: Clyde Auditorium	Papers: Lomond Auditorium	Industry Poster & Exhibit Hours: Hall 4	Demos: Alsh 1	Demos: Alsh 2	SIG Reports: Carron
8:30	8:30-9:20 Keynote: Eric Green - Decoding the Human Genome by Multi-Species Sequence Comparisons
9:20	9:20-9:40 Genomes 2: Short Paper #19 CHAINER: Software for Comparing Genomes	9:20-9:40 Program Chairs' Introduction: Martin Vingron and John Quackenbush: Transcriptomes
9:30				9:30-10:30 DEMO: Kyushu Institute of Technology CADLIVE: A Direct Link of Biochecmial Netoworks to Dynamic Simulations	9:30-10:30 DEMO: EMBL Protein Disorder Prediction
9:40	9:40-10:10 Long Paper #20 Genomic Features in the Breakpoint Regions between Syntenic Blocks	9:40-10:10 Long Paper #21 Predicting Gene Regulation by Sigma Factors in Bacillus subtilis from Genome-wide Data				9:40-10:10 SIG Reports 3D Structural Bioinformatics
10:10	10:10-10:40 Long Paper #22 Using MoBIoS’ Scalable Genome Join to Find Conserved Primer Pair Candidates Between Two Genomes	10:10-10:40 Long Paper #23 Deconvolving Cell Cycle Expression Data with Complementary Information	10:30-20:30 Industry Exhibits and Posters			10:10-10:40 SIG Report Bioinformatics & Disease
10:30				10:30-12:30 DEMO: The MathWorks, Inc. MATLAB for Bioinformatics	10:30-12:30 DEMO: Cold Spring Harbor Laboratory Reactome - A Knowledgebase of Biological Processes	10:10-10:40 SIG Report Bioinformatics & Disease
10:40	COFFEE					COFFEE
11:10	11:10-11:40 Long Paper #24 High Density Linkage Disequilibrium Mapping using Models of Haplotype Block Variation	11:10-11:40 Long Paper #25 Statistical Modeling of Sequencing Errors in SAGE Libraries
11:30
11:40	11:40-12:10 Long Paper #26 Into the Heart of Darkness: Large Scale Clustering of Human Non-Coding DNA	11:40-12:10 Long Paper #27 Optimal Robust Non-Unique Probe Selection Using Integer Linear Programming
11:40
12:00
12:10	12:10-12:30 Short Paper #28 CIS: Compound Importance Sampling Method for Protein-DNA Binding Site p-value Estimation	12:10-12:30 Short Paper #29 TIDE – Terra Incognita Discovery Endeavor: Comprehensive EST Assignment to GeneCards Genes
12:30	LUNCH - Special Session on Funding Opportunities for Bioinformatics Research Hall 5	LUNCH (Hall 4)		12:30-13:30 DEMO: Weizmann Institute of Science The LAMA and CYRCA Protein Profile-to-Profile Alignment and Multiple Profile Alignment Methods	12:30-13:30 DEMO: European Bioinformatics Institute An Introduction to a Number of Web Based Services from the EMBL-European Bioinformatics Institute (EBI)	BOF Luncheons (split 1 and 2)
13:30		LUNCH (Hall 4)		13:30-15:30 DEMO: Synamatix Advantages of a Novel Structured Network Database in Prediction of Biologically Significant Patterns in High-throughput Genomics and Proteomics	13:30-14:30 DEMO: Faculty of Science, University of Zagreb INCA: Synonymous Codon Usage Analysis Software	BOF Luncheons (split 1 and 2)
14:00	14:00-14:20 Program Chairs' Introduction: TBA: Evolution/Phylogeny	14:00-14:20 Short Paper #61 NOTE TIME CHANGE Gene XPress: A Vizualization and Statistical Anaylsis Tool for Gene Expression and Sequence Data
14:20	14:20-14:50 Long Paper #30 Reconstructing Phylogeny by Quadratically Approximated Maximum Likelihood	14:20 -14:50 Transcriptomes 2: Long Paper #31 Finding Disease Specific Alterations in the Co-expression of Genes				14:20-14:50 SIG Reports BioPathways
14:30					14:30-15:30 DEMO: University of California at Berkeley MUSCLE: Faster and More Accurate Multiple Sequence Alignment	14:20-14:50 SIG Reports BioPathways
14:50	14:50-15:20 Long Paper #32 Phylogenomics and the Number of Characters Required for Obtaining an Accurate Phylogeny of Eukaryote Model Species	14:50-15:20 Long Paper #33 Partial Cox Regression Analysis for High-Dimensional Microarray Gene Expression Data				14:50-15:20 SIG Report: BOSC
15:20	15:20-15:40 Short Paper #34 Evolution of Multi-domain Proteins by Gene Fusion and Fission	15:20-15:50 Long Paper #35 Predicting Genetic Regulatory Response Using Classification				15:20-15:50 SIG Report: SIGSIM
15:30				15:30-17:30 DEMO: Sun Microsystems, Inc. Managing Knowledge, Throughput, Visualization, Grids & Data Centers	15:30-17:30 DEMO: University of Leeds Databases and Software Available at Leeds University	15:20-15:50 SIG Report: SIGSIM
15:30
15:50	TEA					TEA
16:20	16:20-16:50 Long Paper #36 *A Nucleotide Substitution Model with Nearest-neighbour Interactions*	16:20-16:50 Long Paper #37 Robust inference of groups in gene expression time-courses using mixtures of HMMs
16:30
16:50	16:50-17:10 Short Paper #38 Transitions at CpG Dinucleotides: are Replication Errors to Blame?	16:50-17:10 Short Paper #39 An Information Theory Approach for Validating Clusters in Microarray Data
17:10	17:10-18:00 Keynote: Svante Pääbo - Evolution of the primate transcriptome
17:30
18:00	18:00-18:10 Introduction to ECCB 2005, Madrid, Spain	18:00-20:30 Reception & Poster Session 2
18:10		18:00-20:30 Reception & Poster Session 2
20:30

Tuesday, 3 August 2004
	Keynotes & Papers: Clyde Auditorium	Papers: Lomond Auditorium	Industry Poster & Exhibit Hours: Hall 4	Demos: Alsh 1	Demos: Alsh 2	Carron
8:30	8:30-9:20 Keynote: Matthias Mann - Organellar and time resolved proteomics
9:20	9:20-9:40 Program Chairs' Introduction: Michal Linial and Michael Gribskov - Proteomes
9:30		9:30-9:40 Program Chairs' Introduction: Burkhard Rost - Structural bioinformatics		9:30-11:30 DEMO: Vanderbilt University Medical Center Metaclinic Database System	9:30-10:30 DEMO: Baylor College of Medicine Analysis of Intermediate Resolution Structures
9:40	9:40-10:10 Long Paper #40 *Analysis of Domain Correlations in Yeast Protein Complexes*	9:40-10:10 Structures 2: Long Paper #41 A Neural Network-Based Method for Predicting Protein Stability Changes upon Single Point Mutations
10:10	10:10-10:40 Long Paper #42 *Predicting Protein-protein Interactions Via a Network-Based Motif Sampler*	10:10-10:40 Long Paper #43 Mining Frequent Patterns in Protein Structures: A Study of Protease Families
10:30			10:30-16:30 Industry Exhibits and Posters		10:30-12:30 DEMO: UniProt UniProt (Universal Protein Resource): A Comprehensive Catalog of Information on Proteins	10:30-11:30 Special session on bioinformatics in industry, chaired by Nick Stuart, Partnership Sourcing Ltd
10:40	COFFEE
11:10	11:10-11:40 Long Paper #44 Automatic Quality Assessment of Peptide Tandem Mass Spectra	11:10-11:40 Long Paper #45 Striped Sheets and Protein Contact Prediction
11:30				11:30-12:30 DEMO: Apple Computer Xgrid and Mac OS X: A Platform for Distributed Scientific Computing
11:40	11:40-12:00 Short Paper #46 MSMS Peak Identification and its Applications	11:40-12:10 Long Paper #47 SCOPEC: a Database of Protein Catalytic Domains
12:00	12:00-12:20 Short Paper #48 Cross-species Protein Identification in Proteomics via Protein Profiles
12:10
12:20
12:30	12:30-14:00 LUNCH - ISCB Open Student Council Meeting(Hall 1)	LUNCH (Hall 4)		12:30-13:30 DEMO: Apple Computer Blending Power with Simplicity in Life Science Clustering: iNquiry and the Apple Workgroup Cluster	12:30-13:30 DEMO: CNRG Genoscope YIB: A Tool for Biological Network Motif Analysis
13:30				13:30-15:30 DEMO: Scottish Enterprise The Scottish Bioinformatics Forum - Demonstrating Bioinformatics Excellence in Scotland	13:30-14:30 DEMO: University of Georgia MAGIC Database: A Tool for Gene Discovery and Expression
14:00		14:00-14:20 Program Chairs' Introduction: Minoru Kanehisa and Alfonso Valencia, Pathways, networks and systems
14:10	14:10-14:20 Program Chairs' Introduction: Program Chair’s introduction part 2: R. Sowdhamini, Structural Bioinformatics
14:20	14:20-14:50 Long Paper #49 Assigning Transmembrane Segments to Helices in Intermediate-Resolution Structures	14:20-14:50 Long Paper #50 Learning Kernels from Biological Networks by Maximizing Entropy
14:30					14:30-15:30 DEMO:
14:50	14:50-15:20 Long Paper #51 Predicting Protein Folding Pathways	14:50-15:20 Long Paper #52 Protein Network Inference from Multiple Genomic Data: A Supervised Approach
15:20	15:20-15:50 Long Paper #53 A Two-stage Classifier for Identification of Protein-Protein Interface Residues	15:20-15:50 Long Paper #54 Inferring Quantitative Models of Regulatory Networks from Expression Data
15:30				15:30-16:30 DEMO: SciTegic Private Demo by invitation	15:30-16:30 DEMO: European Bioinformatics Institute The HUPO PSI Object Model and the mzData format
15:50	TEA
16:20	16:20-16:50 Long Paper #55 Application of a New Probabilistic Model for Recognizing Complex Patterns in Glycans	16:20-16:50 Long Paper #56 TraitMap: An XML-based Genetic-map Database Combining Multigenic Loci and Biomolecular Networks
16:30				16:30-17:30 DEMO: SciTegic A Graphical Pipelining Environment for the Integration of Bioinformatics Data and Tools: Pipeline Pilot™	16:30-17:30 DEMO: Rat Genome Database Rat Genome Database
16:50	16:50-17:10 Short Paper #57 Centrality of Weak Interhelical H-bonds in Membrane Protein Functional Assembly and Conformational Gating	16:50-17:10 Short Paper #58 Divergent Evolutionary Drift Contradicts Power Law
17:00
17:10	17:10-18:00 Keynote: Anna Tramontano - Progress, assessment and perspectives in protein structure prediction
17:30
18:00
19:00	19:00 Gala Dinner
20:30

Wednesday, 4 August 2004
	Keynotes & Papers: Clyde Auditorium	Papers: Lomond Auditorium	Industry Poster & Exhibit Hours: Hall 4	Demos: Alsh 1	Demos: Alsh 2
8:30	8:30-9:20 Keynote: Overton Prize Lecture: Uri Alon - Simplicity in complex biological networks
9:20	9:20-9:40 Pathways 2: Short Paper #59 Constraint-Based Modelling Of Perturbed Organisms: A ROOM for improvement	9:20-9:40 Program Chairs' Introduction: Phil Bourne - Databases
9:30				9:30-10:30 DEMO: Université Libre de Bruxelles-SCMBB A Snow/aMAZE Demo	9:30-10:30 DEMO: European Bioinformatics Institute Taverna - a Bioinformatics Workflow Tool
9:40	9:40-10:10 Long Paper #60 Filling gaps in a metabolic network using expression information	9:40-10:10 Long Paper #63 Filtering Erroneous Protein Annotation
10:10	10:10-10:40 Long Paper #62 An Efficient Algorithm for Detecting Frequent Subgraphs in Biological Networks
10:30			10:30-14:00 Industry Exhibits	10:30-11:30 DEMO: Gene Ontology Consortium The DAG-Edit Ontology Development System	10:30-11:30 DEMO: European Bioinformatics Institute BioMart: A Family of Tools to Facilitate Rapid Querys Against Large Volumes of Biological Data
10:40	COFFEE
11:10	11:10-11:40 Long Paper #64 A Knowledge Based Approach for Representing and Reasoning about Signaling Networks	11:10-11:40 Long Paper #65 Selecting Biomedical Data Sources according to User Preferences
11:30				11:30-12:30 DEMO: Center for Applied Computer Science, University of Cologne and Max Planck Institute for Molecular Genetics, Berlin GQL - A comprehensive tool for gene expression time course analysis	11:30-12:30 DEMO: Heriot-Watt University, Edinburgh University XSPAN - A Cross-Species Anatomy Network
11:40		11:40-12:10 Short Paper #66 Integration of Biological Data From Web Resources : Management of Multiple Answers Through Metadata Retrieval
12:00
12:10		12:10-12:30 Short Paper #67 Criticality-Based Task Composition in Distributed Bioinformatics Systems
12:30	LUNCH			12:30-13:30 DEMO: NESC Bridges Project	12:30-13:30 DEMO: San Diego Supercomputer Center The Encyclopedia of Life
13:30	LUNCH			13:30-14:30 DEMO: Fraunhofer FIT Biozoom	13:30-14:30 DEMO: European Bioinformatics Institute ArrayExpress, MIAMExpress, Expression Profiler Tools for Microarray Annotation, Storage and Analysis
14:00	14:00-14:50 Keynote: ISCB Senior Scientist Accomplishment Award Lecture: David Lipman - Message and meaning in sequence comparison: is systems biology possible?
14:20
14:30
14:50	*Closing Ceremony*
15:20