ISMB/ECCB 2007
 
ISMB/ECCB 2007 Full Conference Schedule
(As of May 16, 2007 - Schedule Subject to Change) 		   
         

Wednesday, July 18, 2007
3:00 p.m. -
6:00 p.m.		 Registration: Hilton Vienna Stadtpark Hotel, Foyer
Hilton Vienna Stadtpark
Am Stadtpark 		     
                   

The conference will be held at the Austria Center Vienna.

Thursday, July 19, 2007
Hall E1 Hall E2 Hall F1 Hall F2 Hall N/O Hall M      
7:30 a.m. -
6:00 p.m.		 Registration      
9:00 a.m. -
10:30 a.m.		 3Dsig Satellite Meeting SIG 1 (2 day) BOSC SIG 2 (2 day) BioPathways SIG 3 (2 day) AltSplicing SIG 4 (2 day)
AFP BioSapiens		 SIG 5 (1 day) BioLINK      
10:30 a.m. -
11:00 a.m.		 Coffee Break (available outside meeting rooms)      
11:00 a.m. -
12:00 noon		 3Dsig Satellite Meeting SIG 1 (2 day) SIG 2 (2 day) SIG 3 (2 day) SIG 4 (2 day) SIG 5 (1 day)      
12:00 noon -
1:00 p.m.		 Lunch - Satellite and SIGs      
1:00 p.m. -
3:30 p.m.		 3Dsig Satellite Meeting SIG 1 (2 day) SIG 2 (2 day) SIG 3 (2 day) SIG 4 (2 day) SIG 5 (1 day)      
3:30 p.m. -
4:00 p.m.		 Coffee Break (available outside meeting rooms)      
4:00 p.m. -
6:30 p.m.		 3Dsig Satellite Meeting SIG 1 (2 day) SIG 2 (2 day) SIG 3 (2 day) SIG 4 (2 day) SIG 5 (1 day)      
7:30 p.m. -
10:30 p.m.		 3Dsig Satellite Meeting - Dinner (Ticket holders)
3Dsig Dinner at Hilton Vienna - Stadtpark in the Park Congress Room
(New date and time as of July 9/07)		      

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Friday, July 20, 2007

  
Hall E1 Hall E2 Hall F1 Hall F2 Hall L Hall M Hall N    
7:30 a.m. -
6:00 p.m.		 Registration    
9:00 a.m. -
10:30 a.m.		 3Dsig Satellite Meeting SIG 1 (2 day) BOSC SIG 2 (2 day) BioPathways SIG 3 (2 day) AltSplicing SIG 4 (2 day)
AFP BioSapiens		 SIG 6 (1 day) BioOntologies
 SIG 7 (1 day) Comparative Genomics    
10:30 a.m. -
11:00 a.m.		 Coffee Break (available outside meeting rooms)    
11:00 a.m. -
12:00 noon		 3Dsig Satellite Meeting SIG 1 (2 day) SIG 2 (2 day) SIG 3 (2 day) SIG 4 (2 day) SIG 6 (1 day)
 SIG 7 (1 day)    
12:00 noon -
1:00 p.m.		 Lunch - Satellite and SIGs    
1:00 p.m. -
3:30 p.m.		 3Dsig Satellite Meeting SIG 1 (2 day) SIG 2 (2 day) SIG 3 (2 day) SIG 4 (2 day) SIG 6 (1 day)
 SIG 7 (1 day)    
3:30 p.m. -
4:00 p.m.		 Coffee Break (available outside meeting rooms)    
4:00 p.m. -
6:30 p.m.		 3Dsig Satellite Meeting SIG 1 (2 day) SIG 2 (2 day) SIG 3 (2 day) SIG 4 (2 day) SIG 6 (1 day)
 SIG 7 (1 day)    
5:30 p.m. -
9:30 p.m.		 Board of Directors Meeting (Open to ISCB Board members only)
Location: Hilton Vienna Hotel -- Klimt Ballroom 1		    
7:30 p.m. -
10:30 p.m.		 3Dsig Dinner changed to Thursday, July 19 (as of July 9/07)    

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Saturday, July 21, 2007
Hall E1 Hall E2 Hall F1 Hall F2 Hall L Hall M Hall N Hall O
7:30 a.m. -
6:00 p.m.		 Registration
7:30 a.m. -
5:30 p.m.		 Wireless Internet Available
8:30 a.m. -
10:30 a.m.		 Student Council Symposium (SCS3)

Tutorial AM2
Workflow Approaches to Transcriptomics Analysis

 Tutorial AM7
Genomic data fusion for gene prioritization and function prediction

Tutorial AM5
Genomes, Browsers and Databases: Tools for Integrating Sequence and Annotation Data From Multiple Genomes

Tutorial AM1
Comparative analysis of protein structures: Principles, tools, and applications for establishing evolutionary relationship and predicting function

 Tutorial AM3
Ontologies for Biomedicine – How to make and use them		 Tutorial AM4
Exploring Computational Biology with a Massively Parallel High Performance Computing Environment 		Tutorial AM6
Implementing phylogenetic workflows for comparative genomics using BioPerl
9:00 a.m. -
12:30 p.m.		 Board of Directors Meeting (Open to ISCB Board members only)
Location: Hilton Vienna Hotel -- Klimt Ballroom 1
10:30 a.m. -
10:45 a.m.		 Coffee Break (available outside meeting rooms)
10:45 a.m. -
12:30 p.m.		 SCS3 continued Tutorial AM2 continued Tutorial AM7 continued Tutorial AM5 continued Tutorial AM1 continued Tutorial AM3 continued Tutorial AM4 continued Tutorial AM6 continued
12:30 p.m. -
1:30 p.m.		 Lunch for delegates attending Student Council Symposium, delegates attending 2 tutorials and ticket holders
12:30 p.m. -
1:30 p.m.

Board of Directors Lunch (Open to ISCB Board members only)
Location: Hilton Vienna Hotel -- Klimt Ballroom 1
1:30 p.m. -
3:30 p.m.		 SCS3 continued

Tutorial PM12
Comprehensive analysis of Affymetrix Exon expression data using BioConductor

Tutorial PM10
Reverse engineering mammalian transcriptional regulatory circuits

 Tutorial PM8
Gene and Protein Networks

Tutorial PM9
Automatic text analysis based on Web services

Tutorial PM11
Systems Biology of Host-Pathogen Interactions and Microbial Communities		 Tutorial PM13
Introduction to Phylogenetic Networks		 Tutorial PM14
An introduction to bioinformatics for glycomics research
3:30 p.m. -
3:45 p.m.		 Coffee Break (available outside meeting rooms)
3:45 p.m. -
5:30 p.m.		 SCS3 continued Tutorial PM12 continued Tutorial PM10 continued Tutorial PM8 continued Tutorial PM9 continued Tutorial PM11 continued Tutorial PM13 continued Tutorial PM14 continued
5:30 p.m. Orienteering Registration Location: TBD
6:00 p.m Orienteering Event at Unterer Prater Park
8:00 p.m. -
10:00 p.m.		 Opening Reception at Vienna City Hall

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Sunday, July 22, 2007
Hall A Hall B
 Hall C
 Hall E1
 Hall F1
 Hall NO
 Hall L
 Hall M
7:30 a.m. -
7:30 p.m.		 Registration
7:30 a.m. -
9:00 p.m.		 Wireless Internet Available
8:15 a.m. -
8:00 p.m.		 Posters on display
8:15 a.m. -
8:30 a.m.		 Opening Welcome and Introduction of Keynote 1: Erin K. O'Shea, Howard Hughes Medical Institute & Harvard University
8:30 a.m. -
9:20 a.m.		 Keynote 1: Erin K. O'Shea:
Dissecting Transcriptional Network Structure and Function
9:30 a.m. -
5:30 p.m.		 Exhibits Open
Paper Track Paper Track Highlights Track Highlights Track Special Session Track

PLoS Track

 Demonstrations Track SIG & Satellite Presentations
9:30 a.m. -
9:55 a.m.		 Paper 1:
A physical model for tiling array analysis - Ho-Ryun Chung, Dennis Kostka and Martin Vingron		 Paper 2:
SPIN: SPIN: A Framework for Signaling - Regulatory Pathway Inference from Cause-Effect Experiments - Oved Ourfali, Tomer Shlomi, Trey Ideker, Eytan Ruppin and Roded Sharan		 Highlights 1:
The Inferelator: learning predictive dynamic regulatory networks from heterogeneous data - Richard Bonneau		 Highlight 2:
What made us human? - Katherine Pollard

Special
Session 1: Private fears in public places? Ethical and regulatory concerns regarding human genomic databases

Organizers: David Gurwitz & Barbara Prainsack (session ends at 12:30 p.m.)

 PLoS 1:
Computational Neuroscience for Computational Biologists: A Brief Tour - Lyle J. Graham		 Demo 1:
geWorkbench: An Open-Source Platform for Integrated Genomics 		3Dsig:
Structural Bioinformatics & Computational Biophysics Satellite Meeting
(Update Session)
10:00 a.m. - 10:25 a.m. Paper 3:
Genomic Characterization of Perturbation Sensitivity - Jung Hun Ohn, Jihun Kim and Ju Han Kim 		Paper 4:
Annotating Gene Function by Combining Expression Data with a Modular Gene Network - Motoki Shiga, Ichigaku Takigawa and Hiroshi Mamitsuka		 Highlight 3:
Redefining nodes and edges: Relating three-dimensional structures to protein networks provides evolutionary insights - Philip Kim 		Highlight 4:
Expansion of protein domain repeats - Asa K Bjoerklund		 PLoS 2:
New methods for tracing the flow of information and computational operations in cortical networks of neurons - Wolfgang Maass		 Demo 2:
Demonstration of The Pathway Tools Software

SIG 1:
Alternative Splicing (AS-SIG)?
(Update Session)
10:25 a.m. - 10:50 a.m. Coffee Break with Exhibitors Coffee Break with Exhibitors
10:50 a.m. - 11:15 a.m. Paper 5:
Nested Effects Models for High -Dimensional Phenotyping Screens - Florian Markowetz, Dennis Kostka, Olga Troyanskaya and Rainer Spang		 Paper 6: Identification of Functional Modules from Conserved Ancestral Protein-Protein Interactions - Janusz Dutkowski and Jerzy Tiuryn Highlight 5:
From phenome-genome networks to disease - Atul Butte		 Highlight 6:
Simulation - Emergent dynamics of thymocyte - Sol Efroni		 PLoS 3:
Semantics for Integrating Forest Structure Data - Judith Cushing		 Demo 3:
SpotRobot

SIG 2:
Bioinformatics Open Source Conference (BOSC)?
(Update Session)
11:20 a.m. - 11:45 a.m. Paper 7:
Biases induced by pooling samples in microarray experiments - Tristan Mary-Huard, JeanJacques Daudin, Michela Baccini, Annibale Biggeri and Avner Bar-Hen		 Paper 8:
Functional Annotation of Regulatory Pathways - Jayesh Pandey, Mehmet Koyuturk, Yohan Kim, Wojciech Szpankowski, Shankar Subramaniam and Ananth Grama		 Highlight 7:
Network motif identification in stochastic networks - Fengzhu Sun		 Highlight 8:
Evolutionary origin of the peroxisome - Toni Gabaldon		 PLoS 4:
An ontology for the semantic modelling of natural systems - Gary Johnson		 Demo 4:
The Phylogeny Cafe

SIG 3:
BioLINK
(Update Session)
11:50 a.m. - 12:15 p.m. Paper 9:
Nucleotide variation of regulatory motifs may lead to distinct expression patterns - Liat Segal, Michal Lapidot, Zach Solan, Eytan Ruppin, Yitzhak Pilpel and David Horn		 Paper 10:
Supervised reconstruction of biological networks with local models - Kevin Bleakley, Gérard Biau and Jean-Phlippe Vert		 Highlight 9:
Sense-antisense pairs: functional/ evolutionary considerations - Sandro de Souza		 Highlight 10:
A first look at ARFome: novel dual-coding genes conserved in mammalian - Wen-Yu Chung		 PLoS 5:
Nested Systems Modeling: A Hierarchical Approach to Individual Based Models - Bert van der Werf		 Demo 5:
ENDEAVOUR, an application to prioritize candidate disease genes

SIG 4:
Bio-Ontologies
(Update Session)
12:15 p.m. -
1:30 p.m.

ISCB Open Business Meeting - Hall C
All ISMB/ECCB Conference delegates are invited to participate in the ISCB Business Meeting

Lunch

 Birds of a Feather Flock Together
 Birds of a Feather Flock Together
 Birds of a Feather Flock Together
 Birds of a Feather Flock Together
 Birds of a Feather Flock Together
1:30 p.m. -
1:35 p.m.		 Introduction of Keynote 2: Søren Brunak, Technical University of Denmark
1:35 p.m. -
2:25 p.m.		 Keynote 2: Søren Brunak:
Understanding interactomes by data integration
Paper Track Paper Track Highlights Track Highlights Track Special Session Track

PLoS Track

 Demonstrations Track SIG & Satellite Presentations
2:30 p.m. -
2:55 p.m.		 Paper 11:
Optimized Design and Assessment of Whole Genome Tiling Arrays - Stefan Graf, Fiona G.G. Nielsen, Stefan Kurtz, Martijn A. Huynen, Ewan Birney, Henk Stunnenberg and Paul Flicek		 Paper 12:
An Ensemble Framework for Clustering Protein - Protein Interaction Networks - Sitaram Asur, Srinivasan Parthasarathy and Duygu Ucar		 Highlight 11:
Computational Inference of Neural Information Flow Networks - Alexander Hartemink		 No Presentation Special
Session 2: Cheminformatics

Organizer: Matthias Rarey		 PLoS 6:
Statistics of network connectivity optimizing information storage - Nicolas Brunel		 Demo 6:
CADLIVE: Computer- Aided Design of Living Systems		 SIG 5:
Joint AFP-Biosapiens SIG
(Update Session)
3:00 p.m. -
3:25 p.m.		 Paper 13:
Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks - Wei Keat Lim, Kai Wang, Celine Lefebvre and Andrea Califano 		Paper 14:
Computational Modeling of C. elegans Vulval Induction - Xiaoyun Sun and Pengyu Hong		 Highlight 13:
A metabolic network in the evolutionary context: Multiscale structure and modularity - Leonid Mirny 		Highlight 14:
Comparative analysis of 22 coronavirus HKU1 genomes reveals a novel genotype and evidence of natural recombination in coronavirus HKU1 - Yi Huang		 PLoS 7:
Cortical Network Dynamics - Ad Aersten		 Demo 7:
Reactome		 Industry 1:
Scientific Workflow Driven Solutions for Life Sciences: The Next Frontier
3:25 p.m. -
3:50 p.m.		 Coffee Break with Exhibitors Coffee Break with Exhibitors
3:50 p.m. -
4:15 p.m.		 Paper 15:
Continuous Hidden Process Model for Time Series Expression Experiments - Yanxin Shi, Michael Klutstein, Itamar Simon, Tom Mitchell and Ziv Bar-Joseph		 Paper 16:
Prediction of DNA binding residues from sequence - Yanay Ofran, Venkatesh Mysore and Burkhard Rost		 Highlight 15:
Reconstructing Dynamic Regulatory Maps - Jason Ernst		 Highlight 16:
Who lives Where - Taxonomic Assessment of Microbial Communities in the Wild - Christian von Mering		 PLoS 8:
Comparative Analysis of Primate Alternative Splicing using Exon Arrays - Augix Xu		 Demo 8:
The European Molecular Biology Open Software Suite (EMBOSS)		 Industry 2:
New insights from expression profiling of P. falciparum genome
4:20 p.m. -
4:45 p.m.		 Paper 17:
RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors - Xiaoyu Chen, Timothy Hughes and Quaid Morris 		Paper 18:
Automated Image Analysis of Protein Localization in Budding Yeast - Shann-Ching Chen, Ting Zhao, Geoffrey Gordon and Robert Murphy		 Highlight 17:
A genome-wide analysis in Saccharomyces cerevisiae demonstrates the influence of chromatin modifiers on transcription - Israel Steinfeld		 Highlight 18:
Comparative Genomics of translation regulation in yeast - Pilpel Yitzhak		 PLoS 9:
The Human Phylome - Jaime Huerat-Cepas		 Demo 9:
Exploring Ensembl beyond the Genome Browser		 Industry 3:
Fast laptopsequence analysisusinghi- performance computing
4:50 p.m. -
5:15 p.m.		 Paper 19:
A graph-based approach to systematically reconstruct human transcriptional regulatory modules - Xifeng Yan, Michael Mehan, Yu Huang, Michael Waterman, Philip Yu and Jasmine Zhou		 Paper 20:
Using genome context data to identify specific types of functional associations in pathway / genome databases - Michelle Green and Peter Karp		 Highlight 19:
Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites - Timothy Reddy		 Highlight 20:
Bringing automatic curation to an automatic world - Raul Rodriguez-Esteban		 PLoS 10:
Origin of bacterial transmembrane beta-barrels by duplication of a beta-beta hairpin - Johannes Soeding		 Demo 10:
MADMAX- MicroArray Database Management and Analysis of eXperiments		 Industry 4:
Project Prospect: Life Science Informatics at Royal Society of Chemistry Publishing
5:20 p.m. -
5:45 p.m.		 Paper 21:
Connecting Quantitative Regulatory-Network Models to genome - Yue Pan, Timothy Durfee, Joseph Bockhorst and Mark Craven		 Paper 22:
Systematic Discovery of Functional Modules and Context - Specific Functional Annotation of Human Genome - Yu Huang, Haifeng Li, Haiyan Hu, Xifeng Yan, Michael Waterman, Haiyan Huang and Jasmine Zhou		 Highlight 21:
Dynomics era: How information on conformational dynamics can be used to gain a deeper understanding of biological events at the molecular level? - Lee Yang		 Highlight 22:
The implications of alternative splicing in the ENCODE protein complement - Michael Tress		 PLoS 11:
Inferring ancestral states of the bZIP transcription factor interaction network - John Pinney		 Demo 11:
The EMBL Nucleotide Sequence Database (EMBL-Bank): Submission methods to the repository, data curation and innovative solutions to the handling of large datasets.		 Industry 5:
WISDOM: a grid-enabled virtual screening initiative
5:50 p.m. -
5:55 p.m.		 Introduction of Keynote 3: Michael Eisen, University of California, Berkeley
5:55 p.m. -
6:45 p.m.		 Keynote 3: Michael Eisen:
Understanding and exploiting the evolution of the sequences that control gene expression
6:45 p.m. -
8:00 p.m.		 Poster Session with Authors (Odd Numbers) & Reception
ISCB Open Committee Meetings
All ISMB/ECCB conference delegates are invited to participate in the ISCB Open Committee Meetings as listed below:

Sunday, July 22
4:30 p.m. - 5:30 p.m.
SIG Coordinators Meeting (Open Meeting) -- Room: 02 A353

6:45 p.m. - 7:45 p.m.
Affiliates (Open Meeting) -- Room: 02 A353
Finance & Business Development (Open Meeting) -- Room: 02 A355

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Monday, July 23, 2007
Hall A Hall B Hall C Hall E1 Hall F1 Hall NO Hall L Hall M
7:30 a.m. -
7:30 p.m.		 Registration
7:30 a.m. -
9:00 p.m.		 Wireless Internet Available
8:15 a.m. -
8:00 p.m.		 Posters on display
8:15 a.m. -
8:30 a.m.		 Morning Welcome, ISMB 2008 Promotion and Introduction of Keynote 4: Anne-Claude Gavin, European Molecular Biology Laboratory
8:30 a.m. -
9:20 a.m.		 Keynote 4: Anne-Claude Gavin:
Interaction Networks Probed by Mass Spectrometry
9:30 a.m. -
5:30 p.m.		 Exhibits Open
Paper Track Paper Track Highlights Track Highlights Track Special Session Track

PLoS Track

 Demonstrations Track Industry Track
9:30 a.m. -
9:55 a.m.		 Paper 23: Spectrum: Joint Bayesian Inference of Population Structure and Recombination Event - Kyung-Ah Sohn and Eric P. Xing Paper 24:
Cotranslational protein folding – fact or fiction? - Charlotte M. Deane, Mingqiang Dong, Fabien Huard, Braddon K. Lance and Graham R. Wood		 Highlight 23: Folding upon binding: why folding instability has only a small effect on binding affinity - Carlos Camacho Highlight 24:
Computational biology of membrane proteins: From structure-based alignment to function of complex molecular machines - Harel Weinstein

Special
Session 3: Genetic networks: Inferring pathways by combinatorial perturbation

Organizer: Frederick ‘Fritz’ Roth
(session ends at 12:30 p.m.)

 PLoS 12:
Visual Tools for Managing Taxonomic Concepts in Ecological and Biodiversity Research -Jessie Kennedy		 Demo 12/13:
Improving Scientific Intelligence through Integration		 Industry 6:
A Novel Approach for Rapid Mapping and Analysis of Second Generation Sequence Reads
10:00 a.m. - 10:25 a.m. Paper 25: Locomotif: From Graphical Motif Description to RNA Motif Search - Janina Reeder, Jens Reeder and Robert Giegerich Paper 26:
Different mechanistic requirements for prokaryotic and eukaryotic chaperonins: a lattice study - Etai Jacob, Amnon Horovitz and Ron Unger		 Highlight 25: Domain-domain interactions are evolutionary conserved - Zohar Itzhaki Highlight 26:
A View from the EVEREST: Insights on Evolutionary Conserved Domains in Protein Sequences - Michal Linial		 PLoS 13:
Computable Field Guides: Time and Place Dependent Species Identification and Reporting - Robert Morris		 Industry 7:
An Algorithm for Automatic 2D Depiction of Molecules
10:25 a.m. - 10:50 a.m. Coffee Break with Exhibitors Coffee Break with Exhibitors
10:50 a.m. - 11:15 a.m. Paper 27:
SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation - Frank Panitz, Henrik Stengaard, Henrik Hornshøj, Jan Gorodkin, Jakob Hedegaard, Susanna Cirera, Bo Thomsen, Lone B. Madsen, Anette Høj, Rikke K. Vingborg, Bujie Zahn, Xuegang Wang, Xuefei Wang, Rasmus Wernersson, Claus B. Jørgensen, Karsten Scheibye-Knudsen, Troels Arvin, Steen Lumholdt, Milena Sawera, Trine Green, Bente J. Nielsen, Jakob H. Havgaard, Søren Brunak, Merete Fredholm and Christian Bendixen		 Paper 28:
Anisotropic Fluctuations of Amino Acids in Protein Structures: Insights from X-Ray Crystallography and Elastic Network Models - Eran Eyal, Chakra Chennubhotla, Lee-Wey Yang and Ivet Bahar		 Highlight 27:
Local structural disorder imparts plasticity on linear motifs - Istvan Simon		 Highlight 28:
GRID Deployment of Legacy Bioinformatics Applications with Transparent Data Access - Christophe Blanchet		 PLoS 14:
Changing patterns of selective pressure in Human Influenza H3 - Richard Goldstein		 Demo 14/16:
Genomics Acceleration using the FPGA based BLAST appliance by SGI and Mitrionics.		 Demo 15:
Pedro: A Model Driven Data Entry Tool for Bioinformatics
11:20 a.m. - 11:45 a.m. Paper 29:
Translation initiation site prediction on a genomic scale: beauty in simplicity - Yvan Saeys, Thomas Abeel, Sven Degroeve and Yves Van de Peer		 Paper 30:
Adaptive Torsion-Angle Quasi-Statics: a General Simulation Method with Applications to Protein Structure Analysis and Design - Romain Rossi, Mathieu Isorce, Sandy Morin, Julien Flocard, Karthik Arumugam, Serge Crouzy, Michel Vivaudou and Stephane Redon		 Highlight 29:
The diversity and evolution of interface geometry - Wan Kyu Kim		 Highlight 30:
Network robustness and modularity of protein structures in the identification of key residues for the allosteric communications - Antonio del Sol		 PLoS 15:
Comparative docking on protein structure models from ten tropical disease genomes - Marc Marti-Renom		 Demo 17:
Semantic Web for Healthcare and Life Sciences
11:50 a.m. - 12:15 p.m. Paper 31:
A Statistical Method for Alignment- free Comparison of Regulatory Sequences - Miriam R. Kantorovitz, Gene E. Robinson and Saurabh Sinha		 Paper 32:
Dead-End Elimination with Backbone Flexibility - Ivelin Georgiev and Bruce Randall Donald		 Highlight 31:
Computational Design of Peptides that Target Transmembrane Helices - Joanna Slusky		 Highlight 32:
Evaluation of coarse-grained models of protein dynamics using large sets of crystallographic data - Dmitry Kondrashov		 PLoS 16:
Genome wide identification of off-site protein targets for major pharmaceuticals using functiaonl site similarity and protein-ligand docking - Daniel Goodman		 Demo 18:
beta.uniprot.org: a preview of the new Web site of the UniProt consortium 		Demo 19:
BioModels Database, a curated resource of annotated published models
12:15 p.m. -
1:30 p.m.

ISCB Student Council Open Meeting -- Hall C

Lunch

 Birds of a Feather Flock Together
 Birds of a Feather Flock Together
 Birds of a Feather Flock Together
 Birds of a Feather Flock Together
 Birds of a Feather Flock Together
1:30 p.m. -
1:35 p.m.		 Introduction of Keynote 5: ISCB Overton Prize Lecture: Eran Segal, Weizmann Institute of Science
1:35 p.m. -
2:25 p.m.		 Keynote 5: Eran Segal:
Quantitative Models for Chromatin and Transcription Regulation
Paper Track Paper Track Highlights Track Highlights Track Special Session Track

PLoS Track

 Demonstrations Track Industry Presentations
2:30 p.m. -
2:55 p.m.		 Paper 33:
Inferring protein-DNA dependencies using motif alignments and mutual information - Shaun Mahony, Philip Auron and Panayiotis Benos		 Paper 34:
Kinetics Analysis Methods For Approximate Folding Landscapes - Lydia Tapia, Xinyu Tang, Shawna Thomas and Nancy Amato		 Highlight 33:
The relationship among sequence diversity, coevolution, and specificity in protein interactions - Simon Lovell		 Highlight 34:
Predicting the Arabidopsis calmodulin interaction network from protein microarray data - George Popescu

Special
Session 4: Computational epigenetics and chromatin regulation

Organizer: Michael Zhang

 PLoS 17: Systems-level Exploration of the Breast and Colorectal Cancer Genomes - Jimmy Cheng-Ho Lin Demo 20/21:
Pattern Discovery in Bioinformatics: Theory and Algorithms		 Industry 8:
Heuristic rule based protein function prediction for genome scale data sets
3:00 p.m. -
3:25 p.m.		 Paper 35:
Efficient parameter estimation for RNA secondary structure prediction - Mirela Andronescu, Anne Condon, Holger Hoos, David H. Mathews and Kevin P. Murphy		 Paper 36:
Learning to Extract Relations For Protein Annotation - Jee-Hyub Kim, Alex Mitchell, Teresa Attwood and Melanie Hilario		 Highlight 35:
The dynamic personality of proteins: Connecting internal protein dynamics and enzyme catalysis - Pratul Agarwal		 Highlight 36:
Quantitative proteomic approach to study subcellular localization of membrane proteins - Pawel Sadowski		 PLoS 18:
A Conserved Network of Human MAPK Interactions - Trey Ideker		 Industry 9:
Accelerating Metagenomics and Next-Generation Genomics using FPGAs
3:25 p.m. -
3:50 p.m.		 Coffee Break with Exhibitors Coffee Break with Exhibitors
3:50 p.m. -
4:15 p.m.		 Paper 37:
Homology Search for Genes Using Biased HMMs - Xuefeng Cui, Tomas Vinar, Brona Brejova, Dennis Shasha and Ming Li		 Paper 38:
Negation of protein - protein interactions: analysis and extraction - Olivia Sanchez-Graillet and Massimo Poesio		 Highlight 37:
Gene prioritization through genomic data fusion - Peter Van Loo		 Highlight 38:
Large-scale mapping of human protein - protein interactions by
mass spectrometry -.
Thodoros Topaloglou		 PLoS 19:
Identification of new AP-2alpha regulated genes: a biological and bioinformatic approach - Davide Cora		 Demo 22:
E-Cell Simulation Environment and E-Cell 3D visualization front-end 		Industry 10:
ARTS - Apple Research & Technology Support
4:20 p.m. -
4:45 p.m.		 Paper 39:
Computing multiple sequence alignments by aligning alignments - Travis Wheeler and John Kececioglu		 Paper 40:
Identification of New Drug Classification Terms in Textual Resources - Corinna Kolarik, Martin Hofmann, Marc Zimmermann and Juliane Fluck		 Highlight 39:
From Fit to Fat and Back: Computational Discovery of Mechanisms of Insulin Resistance - Andre Ptitsyn		 Highlight 40:
Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution - Soile V Keraenen		 PLoS 20:
Subtle donor splice variation at the verge of regulation - Ralf Bortfeldt		 Demo 23:
Visualisation and Analysis of Molecular Sequences, Alignments and Structures Software Demo: Interoperable analysis applications 		Industry 11:
Improving Scientific Intelligence through Integration
4:50 p.m. -
5:40 p.m.		 Poster Session with Authors (Even Numbers) Poster Session with Authors (Even Numbers)
5:45 p.m. -
5:50 p.m.		 Introduction of Keynote 6: John Mattick, University of Queensland
5:50 p.m. -
6:40 p.m.		 Keynote 6: John Mattick:
The majority of the genome of complex organisms is devoted to an RNA regulatory system that directs differentiation and development
6:40 p.m. -
8:00 p.m.		 Poster Session with Authors (Even Numbers) & Reception
ISCB Open Committee Meetings
All ISMB/ECCB conference delegates are invited to participate in the ISCB Open Committee Meetings as listed below:

Monday, July 23
6:45 p.m. - 7:45 p.m.
Conferences (Open Meeting) -- Room: 02 A353
Public Affairs & Policies (Open Meeting) -- Room: 02 A355

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Tuesday, July 24, 2007
Hall A Hall B Hall C Hall E1 Hall F1 Hall NO Hall L Hall M
7:30 a.m. -
6:00 p.m.		 Registration
7:30 a.m. -
6:00 p.m.		 Wireless Internet Available
8:15 a.m. -
8:00 p.m.		 Posters on display
8:15 a.m. -
8:30 a.m.		 Morning Welcome, ECCB 2008 Promotion and Introduction of Keynote 7: Stephen K. Burley, SGX Pharmaceuticals, Inc.
8:30 a.m. -
9:20 a.m.		 Keynote 7: Stephen K. Burley:
Fragment-based discovery of BCR-ABL inhibitors for treatment of chronic myelogenous leukemia
9:30 a.m. -
4:30 p.m.		 Exhibits Open
Paper Track Paper Track Highlights Track Highlights Track Special Session
Track

PLoS Track

PLoS Track

 Demonstration Track
9:30 a.m. -
9:55 a.m.		 Paper 41:
Automatic genome-wide reconstruction of phylogenetic gene trees - Ilan Wapinski, Avi Pfeffer, Nir Friedman and Aviv Regev		 Paper 42:
Semiparametric Functional Mapping of Quantitative Trait Loci Governing Long-term HIV Dynamics - Song Wu, Jie Yang and Rongling Wu		 No Presentation Highlight 42:
Identication of Hot Spots within Druggable Binding Pockets by Computational Solvent Mapping - Melissa Landon

Special
Session 5: Computational Approaches to the Modern RNA World

Organizer:
Ivo Hofacker

 PLoS 21:
Novel toxin-like proteins in non-venomous tissues of mammals and insects - Noam Kaplan		 PLoS 22:
Spatially- resolved, multiscale modeling permits detailed simulation of eukaryotic chemosensing that predicts the importance of local regulatory signaling mechanisms - Martin Meier-Schellersheim		 Demo 24/25:
Apple Workgroup Server for Next-Generation Sequencing
10:00 a.m. - 10:25 a.m. Paper 43:
In search of lost introns - Miklos Csuros, J. Andrew Holey and Igor Rogozin		 Paper 44:
Choosing where to look next in a mutation sequence space: Active Learning of informative p53 cancer rescue mutants - Samuel A. Danziger, Jue Zeng, Ying Wang, Rainer Brachmann and Richard H. Lathrop		 Highlight 43:
Pathway and gene-set activation measurement from mRNA expression data: the tissue distribution of human pathways - John Castle		 Highlight 44:
Function Driven Target Selection for Structural Genomics - Iddo Friedberg		 PLoS 23:
Tandem Block Signatures Are Shared Across Multiple Bacterial Genomes - Stephen Beckstrom-Sternberg		 PLoS 24:
Patterns of Mesenchymal Condensation in a Multiscale, Quasi-3D Discrete Stochastic Model - Mark Alber
10:25 a.m. - 10:50 a.m. Coffee Break with Exhibitors Coffee Break with Exhibitors
10:50 a.m. - 11:15 a.m. Paper 45:
Reconstruction of Highly Heterogeneous Gene-Content Evolution across the Three Domains of Life - Wataru Iwasaki and Toshihisa Takagi		 Paper 46:
Exploring the lipoprotein composition using Bayesian regression on serum lipidomic profiles - Marko Tapani Sysi-Aho, Aki Vehtari, Vidya Velagapudi, Jukka Westerbacka, Laxman Yetukuri, Robert Bergholm, Marja-Riitta Taskinen, Hannele Yki-Järvinen and Matej Oresic		 Highlight 45:
Bioinformatics of protein regulatory modules: predicting cyclin dependent kinase targets based on clustering of consensus motifs - Alan Moses		 Highlight 46:
Using electron density in structural bioinformatics - Roland Dunbrack		 PLoS 25:
Predictive Modeling of Signaling Crosstalk during C. elegans Vulval Development - Jasmin Fisher 		PLoS 26:
Recombination and linkage disequilibrium in Arabidopsis thaliana - Magnus Nordborg		 Demo 26/27:
Exploring Ensembl beyond the Genome Browser
11:20 a.m. - 11:45 a.m. Paper 47:
Towards realistic codon models: among site variability and de-pendency of synonymous and nonsynonymous rates - Itay Mayrose, Adi Doron-Faigenboim, Eran Bacharach and Tal Pupko		 Paper 48:
Kernel-based data fusion for gene prioritization - Tijl De Bie, Leon-Charles Tranchevent, Liesbeth van Oeffelen and Yves Moreau		 Highlight 47:
Genome scan for cis-regulatory DNA motifs associated with social behavior in honey bees - Saurabh Sinha		 Highlight 48:
Modeling the structure of the EmrE multidrug transporter: when two x-ray structures are not enough - Nir Ben-Tal		 PLoS 27:
S. cerevisiae Mitochondria: Validating Predictions from Microarray Integration - Curtis Huttenhower		 PLoS 28:
A novel graphical model approach for identifying host mediated selection pressure on viral evolution reveals the surprisingly strong influence of HLA class I alleles on HIV-1 evolution - Jonathan Carlson
11:50 a.m. - 12:15 p.m. Paper 49:
Reconstructing Sibling Relationships in Wild Populations - Tanya Berger-Wolf, Saad Sheikh, Bhaskar DasGupta, Mary Ashley, Isabel C. Caballero and Satya Lahari Putrevu		 Paper 50:
Structural templates predict novel proteins interactions and targets from pancreas tumour gene expression data - Gihan Dawelbait, Christof Winter, Yanju Zhang, Christian Pilarsky, Robert Grützmann, Jörg-Christian Heinrich and Michael Schroeder		 Highlight 49:
Genomic Regulatory Blocks and Conservation of Synteny - Boris Lenhard		 Highlight 50:
Protein Structures: New Rules for Old Games - Manfred Sippl		 PLoS 29:
Integrating computational methods and high-throughput technology to map the global yeast genetic interaction network - Chad Myers		 PLoS 30:
Saccharomyces yeasts as a model organism for finding Dobzhansky-Muller determinants - Katy Kao		 Demo 28:
ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform
12:15 p.m. -
1:30 p.m.		 Lunch Birds of a Feather Flock Together
 Birds of a Feather Flock Together
 Birds of a Feather Flock Together
 Birds of a Feather Flock Together
 Birds of a Feather Flock Together
Paper Track Paper Track Highlights Track Highlights Track Special Session
Track

PLoS Track

 PLoS Track Demonstration Track
1:30 p.m. -
1:55 p.m.		 Paper 51:
Polyploids, Genome Halving and Phylogeny - David Sankoff, Chunfang Zheng and Qian Zhu		 Paper 52:
Co-occurrence Analysis of Insertional Mutagenesis Data Reveals Cooperating Oncogenes - Jeroen de Ridder, Jaap Kool, Anthony Uren, Jan Bot, Lodewyk Wessels and Marcel J.T. Reinders		 Highlight 51:
The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families - Adam Godzik		 Highlight 52:
Evolution of alternative splicing - Mikhail Gelfand		 Special
Session 5 continued		 PLoS 31:
Bayesian gene networks predict regulators of apoptosis and inflammation - Cristin Print		 PLoS 32:
Population Genetic Analysis of Tiled DNA Data - Innes Hellman		 Demo 29:
The Next Generation Biology Workbench
2:00 p.m. -
2:25 p.m.		 Paper 53:
Inferring Missing Genotypes in Large SNP Panels Using Fast Nearest-Neighbor Searches Over Sliding Windows - Adam Roberts, Leonard McMillan, Wei Wang, Joel Parker, Ivan Rusyn and David Threadgill		 Paper 54:
GPDTI: A Genetic Programming Decision Tree Induction method to find epistatic effects in common complex diseases - Jesus K. Estrada-Gil, Juan C. Fernandez-Lopez, Enrique Hernadez-Lemus, Irma Silva-Zolezzi, Alfredo Hidalgo-Miranda, Gerardo Jimenez-Sanchez and Edgar E. Vallejo		 Highlight 53:
Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements - Steven Brenner		 Highlight 54:
RNA structures in genomic regions of low sequence similarity between human and mouse - Jan Gorodkin		 PLoS 33:
Influence Flow: Integrating Pathway-specific RNAi data and Protein Interaction Data - Rohit Singh		 PLoS 34:
Maximum likelihood methods to infer the recent demographic and adaptive history of Drosophila melanogaster from chromosome-wide SNP data - Haipeng Li		 Demo 30:
Symphony: An Open Source Framework for Lab Information and Data Management
2:30 p.m. -
2:55 p.m.		 Paper 55:
Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes - Gerton Lunter		 Paper 56:
Bayesian association of haplotypes and non-genetic factors to regulatory and phenotypic variation in human populations - Jim Huang, Anitha Kannan and John Winn		 PLoS 35:
Inferring the ancestral vertebrate transcriptome: investigating the evolution of vertebrate gene expression and regulation - Esther Chan		 PLoS 36:
Structural Bioinformatics Reveals Probably Biological Interfaces in Protein Crystals - Roland Dunbrack		 PLoS 37:
Beyond Epistasis Analysis: Combinatorial Perturbation Analysis by Dynamic Modeling - Sven Nelander 		PLoS 38:
Widespread Positive Selection in Synonymous Sites of Mammalian Genes - Alissa Resch		 Demo 31:
My BioAID: personalised text mining with web services from the AIDA toolbox
3:00 p.m. -
3:25 p.m.		 Coffee Break with Exhibitors
3:25 p.m. -
4:55 p.m.		 Poster Session with Authors
3:30 p.m. -
4:30 p.m.		  
4:55 p.m. -
5:00 p.m.		 Introduction of Keynote 8: Terry Speed, University of California at Berkeley and Walter & Eliza Hall Institute of Medical Research
5:00 p.m. -
5:50 p.m.		 Keynote 8: Terry Speed:
Genome-wide genotyping: the great classification challenge
6:00 p.m. Offsite event - shuttles to Heurigen: TBD
ISCB Open Committee Meetings
All ISMB/ECCB conference delegates are invited to participate in the ISCB Open Committee Meetings as listed below:

Tuesday, July 24
3:30 p.m. - 4:30 p.m.
Education (Open Meeting) -- Room: 02 A353
Publications (Open Meeting) -- Room: 02 A355

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Wednesday, July 25, 2007
Hall A Hall B Hall C Hall E1 Hall F1 Hall NO Hall L Hall M
7:30 a.m. -
4:00 p.m.		 Registration
7:30 a.m. -
2:00 p.m.		 Wireless Internet Available
8:30 a.m. -
3:00 p.m.		 Posters on display
8:30 a.m. -
8:45 a.m.		 Morning Welcome and Introduction of Keynote 9: Renée Schroeder, University of Vienna
8:45 a.m. -
9:35 a.m.		 Keynote 9: Renée Schroeder:
Genomic SELEX for the identification of novel non-coding RNAs independent of their expression level
9:30 a.m. -
2:00 p.m.		 Exhibits Open
Paper Track Paper Track Highlights Track Highlights Track Special Session Track

PLoS Track

Demonstration Track

 Demonstration Track
9:45 a.m. -
10:10 a.m.		 Paper 57:
Using Dynamic Programming to Create Isotopic Distribution Maps from Mass Spectra - Sean McIlwain, David Page, Edward Huttlin and Michael Sussman 		Paper 58:
From protein microarrays to diagnostic antigen discovery: A study of the pathogen Francisella tularensis - Suman Sundaresh, Arlo Randall, Berkay Unal, Jeannine M. Petersen, John T. Belisle, M. Gill Hartley, Melanie Duffield, Richard W. Titball, D. Huw Davies, Philip L. Felgner and Pierre Baldi		 Highlight 55:
Co-evolution of transcriptional and post-translational cell-cycle regulation - Lars Jensen		 Highlight 56:
Modeling AAA+ ring complexes from monomeric structures - Alexander Diemand

Special
Session 6:
Dry work in a wet world: Improving methodology and access of computational methods in Systems Biology

Organizer:
Ewan Birney

 PLoS 39: Unbiased Discovery of Common Histone Modification Patterns In The Human ENCODE Regions - Gary Hon Demo 32:
NCIBI Suite of Tools 		Demo 33/35:
ExPlain(TM): ExPlaining Gene Expression Data
10:15 a.m. - 10:40 a.m. Paper 59:
A Geometric Approach for the Alignment of Liquid Chromatography - Mass Spectrometry Data - Eva Lange, Clemens Gröpl, Ole Schulz-Trieglaff and Knut Reinert		 Paper 60:
Computational Prediction of Host-Pathogen Protein-Protein Interactions - Matthew D. Dyer, T. M. Murali and Bruno W. Sobral 		No Presentation Highlight 58:
RNA findings raise questions about direct optimization based predictions - Charles Lawrence
 PLoS 40:
Markov chain-based promoter structure modeling - Alexis Vandenbon		 Demo 34:
GALAXY: a simple web application for the analysis of enormous datasets
10:40 a.m. - 11:10 a.m. Coffee Break with Exhibitors Coffee Break with Exhibitors
11:10 a.m. - 11:35 a.m. Paper 61:
Manual curation is not sufficient for annotation of genomic databases - William Baumgartner, Lynne Fox, George Acquaah-Mensah, K. Bretonnel Cohen and Lawrence Hunter 		Paper 62:
Multiway Analysis of Epilepsy Tensors - Evrim Acar Ataman, Canan Aykut-Bingol, Haluk Bingol, Bulent Yener and Rasmus Bro		 Highlight 59:
An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits - Yves Lussier		 Highlight 60:
Machineprose: Encoding Knowledge for Humans & Machines - Deendayal Dinakarpandian		 PLoS 41:
Computational design of a thioredoxin protein with esterase activity - Pablo Tortosa 		Demo 36:
Effortless integration of tools into simple, scalable, multiuser, pythonic framework 		Demo 37:
Multi-Scale Cellular Modeling with Simmune
11:40 a.m. - 12:05 p.m. Paper 63:
Information Theory Applied to the Sparse Gene Ontology Annotation Network to Predict Novel Gene Function - Ying Tao, Lee Sam, Jianrong Li, Carol Friedman and Yves A. Lussier		 Paper 64:
Gene Selection via the BAHSIC Family of Algorithms - Le Song, Justin Bedo, Karsten Borgwardt, Arthur Gretton and Alex Smola		 Highlight 61:
Pre- steady- state decoding of the Bicoid morphogen gradient - Sven Bergmann		 Highlight 62:
Improving catalytic function by ProSAR- driven enzyme evolution - Richard Fox		 PLoS 42:
Predicting activated conformations of substrates in enzyme binding sites - Joannis Apostolakis		 Demo 38:
AMAP–Fast and accurate multiple alignment using posterior decoding and sequence annealing 		Demo 39:
Revised Title: YASARA View – free molecular modeling environment – now in Python!
12:10 p.m. - 12:35 p.m. Paper 65:
A Chado Case Study: An Ontology - based Modular Schema for Representing Genome - Associated Biological Information - Christopher J Mungall, David B Emmert, Suzanna Lewis and The FlyBase Consortium		 Paper 66:
Modeling recurrent DNA copy number alterations in array CGH data - Sohrab P. Shah, Wan L. Lam, Raymond T. Ng and Kevin P. Murphy		 Highlight 63:
Simulating Normal and Dysregulated In Vitro Epithelical Cell Morphogenisis - Anthony Hunt		 PLoS 43:
SimShiftDB: Chemical - Shift - Based Homology Modeling - Simon Ginzinger		 PLoS 44:
Identification of druggable binding sites of proteins by computational fragment mapping using novel FFT correlation based algorithm - Dima Kozakov		 Demo 40:
H-Invitational Database:an integrated database of all human genes and transcripts 		Demo 41:
Online Resource Center for Biodefense Proteomics Research
12:35 p.m. -
1:45 p.m.		 Lunch Birds of a Feather Flock Together
 Special
Session 6
(continues until 12:45 p.m.)
 Birds of a Feather Flock Together
 Birds of a Feather Flock Together
 Birds of a Feather Flock Together
1:45 p.m. -
1:50 p.m.		 Introduction of Keynote 10: ISCB Senior Scientist Accomplishment Award, Temple F. Smith, Boston University
1:50 p.m. -
2:40 p.m.		 Keynote 10: Temple F. Smith
2:40 p.m. -
3:00 p.m.		 Conference Awards and Closing

back to Conference Schedule

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