As of June 23, 2008 - Schedule Subject to Change
METRO TORONTO CONVENTION CENTRE (MTCC) CONFERENCE TO BE HELD IN THE SOUTH BUILDING

Thursday	July 17
3:00 p.m.- 6:00 p.m.	Registration: 600 Level (all conference days)

Friday	July 18
7:30 a.m.- 6:00 p.m.	Registration:
	Room: 701A	Room: 714A	Room: 714B	Room: 715A	Room: 716A	Room: 716B	Room: 715B
8:30 a.m.- 10:15 a.m.	3Dsig (2 days)	AltSplicing (2 days)	BioPathways (2 days)	BOSC (2 days)	AFP-BioSapiens (2 days)	BioLINK(1 day)	Student Council Symposium 4
10:15 a.m.- 10:45 a.m.	Coffee Break (PreFunction Level 700)
10:45 a.m.- 12:30 p.m.	3Dsig	AltSplicing	BioPathways	BOSC	AFP-BioSapiens	BioLINK	SCS 4
12:30 p.m.- 1:30 p.m.	Lunch: Hall E
1:30 p.m.- 3:30 p.m.	3Dsig	AltSplicing	BioPathways	BOSC	AFP-BioSapiens	BioLINK	Student Council Symposium 4
3:30 p.m.- 4:00 p.m.	Coffee Break (PreFunction Level 700)
4:00 p.m.- 6:30 p.m.	3Dsig Sessions Ends 6:30 / Dinner at 7:30 p.m. at InterContinental Hotel (ticketed meal)	AltSplicing Ends 6:30	BioPathways Ends 6:30	BOSC Ends 6:30	AFP-BioSapiens Ends 6:30	BioLINK Ends 6:30	SCS4 Ends 8:00

Saturday

July 19

7:30 a.m.- 6:00 p.m.

Registration:

Room: 701A

Room: 714A

Room: 714B

Room: 715A

Room: 716A

Room: 716B

Room: 707

Room: 713A

Room: 713B

Room: 715B

Room: 717A

Room: 717B

8:30 a.m.- 10:15 a.m.

3Dsig (2 days)

AltSplicing (2 days)

BioPathways (2 days)

BOSC (2 days)

AFP-BioSapiens (2 days)

Next-Generation Sequencing (1 day)

Meeting Room - AFP Breakout

Tutorial AM1: PLoS Professional Development, Philip E. Bourne

Tutorial AM2: Computational Analyses and Biological Interpretation of ChIP-chip and ChIP-seq, X. Shirley Liu, Clifford A Meyer

Tutorial AM3: Computational Biology on Multi-Core Computer Systems, Kirk Jordan

Tutorial AM4: Identification of Biomedical Events and Relations in the literature with ontological suppor, Dietrich Rebholz-Schuhmann, Sophia Ananiadou, Jun'ichi Tsujii

Tutorial AM5: Introduction to Molecular Visualization, Conrad Huang, John “Scooter” Morris

10:15 a.m.- 10:45 a.m.

Coffee Break (PreFunction Level 700)

10:45 a.m.- 12:30 p.m.

3Dsig

AltSplicing

BioPathways

BOSC

AFP-BioSapiens

Next-Generation Sequencing

Meeting Room

End 12:30 p.m.

End 12:30 p.m.

End 12:30 p.m.

End 12:30 p.m.

End 12:30 p.m.

12:30 p.m.- 1:30 p.m.

Lunch: Hall E

1:30 p.m.- 3:30 p.m.

3Dsig

AltSplicing

BioPathways

BOSC

AFP-BioSapiens

Next-Generation Sequencing

Meeting Room

Tutorial PM6: Distances, Margins, Kernels: Machine Learning Concepts for Computational Biology, Stefan Kramer, Ulrich Rucker

Tutorial PM7: A structured approach for the engineering of biochemical network models, illustrated for signaling pathways, David Gilbert, Monika Heiner, Rainer Bretling, Robin Donaldson

Tutorial PM8: How to Make Useful Ontologies for Biomedicine, Barry Smith, Nigam Shah

Tutorial PM9: Making informed choices about microarray data analysis, Mark Reimers

Tutorial PM10: Introduction to non-coding RNA gene finding, Jan Gorodkin, Ivo Hofacker

3:30 p.m.- 4:00 p.m.

Coffee Break (PreFunction Level 700)

4:00 p.m.- 6:30 p.m.

3Dsig Ends 6:30

AltSplicing Ends 6:30

BioPathways Ends 6:30

BOSC Ends 6:30

AFP-BioSapiens Ends 6:30

Next-Generation Sequencing Ends 6:30

Meeting Room

Tutorial Ends 6:30

Tutorial Ends 6:30

Tutorial Ends 6:30

Tutorial Ends 6:30

Tutorial Ends 6:30

5:30 p.m.

Orienteering Registration - Room 701B - MTCC, South Building

6:00 p.m.

Orienteering Event

8:00 p.m.- 10:00 p.m.

Opening Reception: InterContinental Toronto Centre - 225 Front Street

Sunday	July 20
7:30 a.m.- 7:30 p.m.	Registration: 600 Level
8:15 a.m.- 8:30 p.m.	Posters on Display - Hall E
	Hall G	Room: 801	Room: 718A	Room: 718B	Room: 701A	Room: 701B	Room: 714	Room: 715	Room: 803
8:45 a.m.- 9:00 a.m.	Opening Welcome - Hall G							SIG TRACK Bio-Ontologies SIG (8:50 a.m.- 6:30 p.m.)	Visual Reflections in Science (VRS)
9:00 a.m.- 10:00 a.m.	Keynote Presentation: Claire M. Fraser-Liggett, University of Maryland School of Medicine Microbial Communities in Health and Disease - Hall G							This SIG requires separate registration to attend
10:00 a.m.- 10:45 a.m.	Coffee Break with Exhibitors - Hall F
Parallel Sessions	Proceedings Track (PT)	Proceedings Track (PT)	Highlights Track (HL)	Highlights Track (HL)	Special Session Track (SST)	Technology Track (TT)	Industry Track (IT)
10:45 a.m.- 11:10 a.m.	PT01: Estimating True Evolutionary Distances under the DCJ Model. Yu Lin	PT02: Differential variability analysis of gene expression and its application to human diseases. Joshua Ho	HL01: Automated learning of generative models for subcellular location. Robert F Murphy, Ting Zhao		Special Session 01: Health and Diseases in our Genomes: Mining Genetic Variation Organizer, Thomas Hudson	TT01: GenoCAD: Computer Assisted Design of genetic constructs. Jean Peccoud	IT01: OpenFreezerTM: an information management system for reagent tracking and workflow automation. Marina Olhovsky	Bio-Ontologies SIG
11:15 a.m.- 11:40 a.m.	PT03: Efficient Inference of Bacterial Strain Trees From Genome-scale Multi-locus Data. Cuong Than	PT04: Selecting anti-HIV Therapies Based on a Variety of Genomic and Clinical Factors. Michal Rosen-Zvi	HL03: Automatic derivation of function prediction from de novo structure prediction for whole genomes. Richard Bonneau			TT02: PredictProtein – Beyond Secondary Structure Prediction. Guy Yachdav, Laszlo Kajan	IT02: OmicsExplorer. Pei Hao
11:45 a.m.- 12:10 p.m.	PT05: The Multiple Gene Duplication Problem Revisited. Mukul S. Bansal	PT06: Reversible Jump MCMC Approach for Peak identification for Stroke SELDI Mass Spectrometry Using Mixture Model. Yuan Wang	HL05: Alternative Splicing and Protein Structure Evolution. Fabian Birzele	HL06: A network-based signaling mechanism of cancer developement and progression. Edwin Wang		TT03: The InterPro Protein Signature Database. Jennifer McDowall
12:15 p.m.- 12:40 p.m.	PT07: Assessment and Improvement of Plasmodium yoelii yoelii Genome Annotation through Comparative Analysis. Xinxia Peng	PT08: Assessing the Functional Structure of Genomic DataI. Curtis Huttenhower	HL07: Local pairwise structural RNA alignments by pruning the dynamical programming matrix. Jan Gorodkin	HL08: Universally Sloppy Parameter Sensitivities in Systems Biology. Christopher R. Myers		TT04: Reactome Pathway Database Demo. Gopal Gopinathrao	IT04: BONDplus – Challenges in Translational Medicine. Eric Andrade, Sam Sgro
12:40 p.m.- 2:15 p.m.	Lunch - Hall E							Lunch - Hall E
12:40 p.m.- 2:00 p.m.	ISCB Open Business Meeting (lunch provided at meeting)- Room 801 Download Agenda Here
1:00 p.m.- 2:15 p.m.			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
Parallel Sessions	Proceedings Track (PT)	Proceedings Track (PT)	Highlights Track (HL)	Highlights Track (HL)	Special Session Track (SST)	Technology Track (TT)	Industry Track (IT)	SIG TRACK Bio-Ontologies SIG	Visual Reflections in Science
2:15 p.m.- 2:40 p.m.	PT09: MACHOS: Markov Clusters of Homologous Subsequences. Simon Wong	PT10: Identifying Functional Modules in Protein-Protein Interaction Networks: An Integrated Exact Approach. Gunnar W. Klau	HL09: Computational Approaches for the Analysis of Immunoglobulin Gene Rearrangement. Bruno A Gaeta	HL10: Heat Shock Response in CHO Mammalian Cells Is Controlled by a Nonlinear Stochastic Process. Ovidiu Lipan	Special Session 2: Frontiers in cell imaging: Automated image analysis Organizer: Robert F. Murphy	TT05: EMBRACE-Enabling Data Integration. Syed Haider	IT05: Next Generation of Selected Bioinformatics Applications: Using Massively Parallel Supercomputers. Carlos P. Sosa	Bio-Ontologies SIG Concluding at 6:30 p.m.
2:45 p.m.- 3:10 p.m.	PT11: Classification and Feature Selection Algorithms for Multi-class CGH DataI. Jun Liu	PT12: Prediction of Drug-target Interaction Networks from the Integration of Chemical and Genomic Spaces. Yoshihiro Yamanishi	HL11: Predicting Protein Function with Hierarchical Phylogenetic Profiles. Corin Yeats			TT06: PIR Resources for Protein Knowledge Discovery. Zhang-Zhi Hu, Anastasia Nikolskaya	IT06: Beyond Next Gen Sequencing: Applying Bioinformatics to Obtain Biological Answers. Arif Anwar
3:15 p.m.- 3:40 p.m.	PT13: A High Accurate Model of the Individual Haplotyping Problem Based on Weighted SNP Fragments and Genotype with Errors. Minzhu Xie	PT14: Biomolecular Network Motif Counting and Discovery by Color Coding. Iman Hajirasouliha	HL13: Automated Protein Subfamily Identification and Classification. Kimmen Sjolander	HL14: De Novo identification of in Vivo Binding Sites from ChIP-chip Data. Victor X Jin		TT07: Fiesta: An Interactive Sequence Management and Analysis Framework. Kannan Vijayan and Dustin Cram	IT07: Drug Discovery. Greg Tucker-Kellogg
3:45 p.m.- 4:10 p.m.	PT15: Guided Genome Halving: Hardness, Heuristics and the History of the Hemiascomycetes. Chunfang Zheng	PT16: Protein Complex Identification by Supervised Graph Local Clustering. Yanjun Qi		HL16: SherLoc: High-accuracy Prediction of Protein Subcellular Localization by Integrating Text and Protein Sequence Data. Hagit Shatkay		TT08: VisANT: an integrative platform for multiple-scale visualization and  modeling of biological networks/pathways. Zhenjun Hu
4:15 p.m.- 4:45 p.m.	Coffee Break with Exhibitors - Hall F
4:45 p.m.- 5:45 p.m.	Keynote Presentation: David Jaffe, Broad Institute of MIT and Harvard Tiny bits and pieces: new sequencing technologies and what they can do for you
5:45 p.m.- 8:30 p.m.	Poster Session with Authors (Odd Numbers) & Reception - Hall E

Monday	July 21
7:30 a.m.- 7:30 p.m.	Registration: 600 Level
8:15 a.m.- 8:30 p.m.	Posters on Display - Hall E
	Hall G	Room: 801	Room: 718A	Room: 718B	Room: 701A	Room: 701B	Room: 714	Room: 715	Room: 803
8:45 a.m.- 9:00 a.m.	Morning Welcome, ISMB/ECCB 2009 Promotion - Hall G								Visual Reflections in Science
9:00 a.m.- 9:10 a.m.	Keynote Presentation: Eugene W. Myers, HHMI Janelia Farm Research Campus, Imaging Bioinformatics - Hall G
10:00 a.m.- 10:45 a.m.	Coffee Break with Exhibitors - Hall F							SIG TRACK Post Encode SIG (10:10 AM - 5:00 PM) This SIG requires separate registration to attend
Parallel Sessions	Proceedings Track (PT)	Proceedings Track (PT)	Highlights Track (HL)	Highlights Track (HL)	Special Session Track (SST)	Technology Track (TT)	Technology Track (TT)		Visual Reflections in Science
10:45 a.m.- 11:10 a.m.	PT17: Annotation-based Inference of Transporter Function. Peter Karp	PT18: HMM PSSM Compostion-specific gap Position-specific Gap . Yi-Kuo Yu	HL17: Towards Ontology-driven Navigation of the Lipid Bibliosphere and Mutation Literature. Christopher J. O. Baker	HL18: The Utilization of Redundancy by Genetic Networks. Ran Kafri	Special Session 3: Interaction Networks and Disease Organizers: Shoshana Wodak, Gary Bader	TT09: The Subcellular Location Image Finder - Extracting Information from Text and Images in Biological Journal Articles. Robert F. Murphy	TT10: Dominating the Next Generation Sequencing Data Analysis Challenge, Thomas Knudsen (session to 11:40 a.m.)
11:15 a.m.- 11:40 a.m.	PT19: Detection of IUPAC and IUPAC-like Chemical Names. Roman Klinger	PT20: ProSOM: Core Promoter Prediction Based on Unsupervised Clustering of DNA Physical Profiles. Thomas Abeel	HL19: Toward the Demise of the Highest Scoring Paradigm. Charles E. Lawrence	HL20: Casting a Net for Kinases - Systematic Discovery of Cellular Phosphorylation Networks. Rune Linding		TT11: CiteXplore, Whatizit et al: Latest Innovations in EBI's Literature Infrastructure. Dietrich Rebholz-Schuhmann, M. Rijnbeek
11:45 a.m.- 12:10 p.m.	PT21: Identifying Gene-Disease Associations Using Centrality on a Literature Mined Gene Interaction Network. Arzucan Ozgur	PT22: Optimal pooling for Genome Re-sequencing with Ultra-high-throughput Short-read Ttechnologies. Fereydoun Hormozdiari	HL21: Modelling Ion Channel Kinetics Using Voltage-Clamp Recordings and a Genetic Algorithm. Meron Gurkiewicz	HL22: A Systems Biology Analysis of the Drosophila Phagosome. Joel Bader		TT13: CAMERA: Tools and Data for Metagenomics. Iddo Friedberg, Weizhong Li	TT14: BONDplus, BINDplus and GENESEQ. Eric Andrade and Sam Sgro (session to 12:40 p.m.)
12:15 p.m.- 12:40 p.m.	PT23: Integrating High Dimensional Bi-directional Parsing Models for Gene Mention Tagging. Chun-Nan Hsu	PT24: POIMs: Positional Oligomer Importance Matrices --- Understanding Support Vector Machine Based Signal Detectors Sequence Analysis and Alignment. Soeren Sonnenburg	HL23: Qualitative Biological Ontologies. Thomas Bittner	HL24: eQED: an Efficient Method for Interpreting eQTL Associations Using Protein Networks. Andreas Beyer		TT15: InterMine – Open Source Data Warehouse and Query Interface. Richard Smith
12:40 p.m.- 2:15 p.m.	Lunch - Hall E
12:40 p.m.- 2:00 p.m.	ISCB Student Council Open Meeting - Room 801 (lunch should be brought to the room by attending delegates)
1:00 p.m.- 2:15 p.m.			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	Lunch - Hall E
Parallel Sessions	Proceedings Track (PT)	Proceedings Track (PT)	Highlights Track (HL)	Highlights Track (HL)	Special Session Track (SST)	Technology Track (TT)	Technology Track (TT)	SIG TRACK Post-Encode SIG	Visual Reflections in Science
2:15 p.m.- 2:40 p.m.	PT25: The EXACT Description of Biomedical Protocols. Wayne Aubrey	PT26: Efficient Algorithms for Exact Hierarchical Clustering of Huge Datasets: Tackling the Entire Protein Space. Yaniv Loewenstein	HL25: High-confidence Prediction of Global Interactomes Based on Genome-wide Coevolutionary Networks. David Juan	HL26: Growth-specific Programs of Gene Expression. Curtis Huttenhower	Special Session 4: Structural Bioinformatics: Deciphering the proteome, Organizers: Igor Jurisica, Ryan Lilien	TT16: Multiplierz and the mzAPI: A Common API and Desktop Environment for Mass Spectrometry Based Proteomics. Manor Askenazi	TT17: Working with the NCBC’s: Integration Tools and Data, NCIBI Suite of Tools. James Cavalcoli
2:45 p.m.- 3:10 p.m.	PT27: Towards the use of Argumentation in Bioinformatics: A Gene Expression Case Study. Kenneth McLeod	PT28: MiRNA Prediction with a Novel Ranking Algorithm Based on Random Walks. Xuefeng Zhou	HL27: Using Conserved Protein Interactions Across Eukaryotes to Construct a Predicted Plant Interactome. Matt Geisler	HL28: Allostery: Absence of a Change in Shape Does not Imply That Allostery is Not at Play. Antonio del Sol		TT18: How to use Bio2RDF with a Virtuoso Server. François Belleau	TT19: MAGNet: Integrating Tools and Data. Aris Floratos
3:15 p.m.- 3:40 p.m.	PT29: The Ontology of Biological Taxa. Stefan Schulz	PT30 A Robust Framework for Detecting Structural Variations in a GenomeI. Seunghak Lee	HL29: Off Targets for Some Major Pharmaceuticals and Their Implications. Philip Bourne	HL30: Binding Site Sequence Does not Determine Function – but Position Can Help. John L Spouge		TT20: Pathway Tools Software: Regulatory Networks and Recent Developments. Peter Karp	TT21: Simbios: Fast Molecular Dynamics Calculations on your Laptop. Jeanette Schmidt
3:45 p.m.- 4:10 p.m.	PT31: GenoQuery: A New Querying Module for Functional Annotation in a Genomic Warehouse. Frederic Lemoine	PT32: A Max-margin Model for Efficient Simultaneous Alignment and Folding of RNA Sequences. Chuong Do	HL31: Evolution of Cellular Interaction Networks. Pedro Beltrao	HL32: A Nucleosome-Guided Map of Transcription Factor Binding Sites in Yeast. Raluca M Gordan		TT22: Chipster - User Friendly Analysis Tool for DNA Microarray Data. Eija Korpelainen	TT23: i2b2	Post-Encode SIG
4:15 p.m.- 4:45 p.m.	Coffee Break with Exhibitors - Hall F
4:45 p.m.- 5:45 p.m.	Introduction of Keynote 4: ISCB Overton Prize Lecture: Aviv Regev, Broad Institute of MIT and Harvard - Hall G
5:45 p.m.- 8:30 p.m.	Poster Session with Authors (Even Numbers) & Reception - Hall E

Tuesday	July 22
7:30 a.m.- 6:00 p.m.	Registration: 600 Level
8:15 a.m.- 5:00 p.m.	Posters on Display - Hall E
	Hall G	Room: 801	Room: 718A	Room: 718B	Room: 701A	Room: 701B	Room 714	Room: 803
8:45 a.m.- 9:00 a.m.	Morning Welcome - Hall G							Visual Reflections in Science
9:00 a.m.- 10:00 a.m.	Keynote Presentation: Morag Park, McGill Unviersity, Profiling the Breast Tumor Microenvironment
10:00 a.m.- 10:45 a.m.	Coffee Break with Exhibitors - Hall F
Parallel Sessions	Proceedings Track (PT)	Proceedings Track (PT)	Highlights Track (HL)	Highlights Track (HL)	Special Session Track (SST)	Technology Track (TT)	Technology Track (TT)	Visual Reflections in Science
10:45 a.m.- 11:10 a.m.	PT33: Designing Succinct Structural Alphabets. Shuai Cheng Li	PT34: Alignment and Classification of Time Series Gene Expression in Clinical Studies. Tien-ho Lin	HL33: Structural Reorganisation and Potential Toxicity of Oligomeric Species Formed during the Assembly of Amyloid Fibrils. Giorgio Favrin		Special Session 5: Sequencing thousands of human genomes - perspectives, challenges, and analysis, Organizers: Francisco De La Vega, Gabor Marth	TT24: NMPDR: National Microbial Pathogen Data Resource. Leslie McNeil	TT32: Pathway Ontology for Analysis of High-throughput Data: Anton Yuryev, Ariadne Genomics, US
11:15 a.m.- 11:40 a.m.	PT35: Predicting Protein Thermostability Changes from Sequence Upon Multiple Mutations. Ludovica Montanucci	PT36: Inferring Differentiation Pathways from Gene Expression. Ivan Gesteira Costa	HL35: Pathway-based Diagnosis of Cancer and Metastasis. Han-Yu Chuang	HL36: Association Analysis-based Transformations for Protein Interaction Networks: A Function Prediction Case Study. Gaurav Pandey		TT25: MG-RAST Rapid Meta-genome Annotation Server. Leslie McNeil
11:45 a.m.- 12:10 p.m.	PT37: Algorithm for Backrub Motions in Protein Design. Ivelin Georgiev	PT38: Predicting functional transcription factor binding through alignment-free, affinity-based analysis of orthologous promoter sequences. Lucas Ward	HL37: Integration of Genome-wide Experiments to Find Genes Associated with Complex Polygenic Disorders: Fighting Back Against the Limitations of GWAS. Atul Butte	HL38: Unraveling Protein Networks with Power Graph Analysis. Loïc Alain Royer		TT26: RAST Rapid Microbial Genome Annotation server. Leslie McNeil	TT33: EB-eye – The EMBL-EBI search engine, Franck Valentin
12:15 p.m.- 12:40 p.m.	PT39: A Computational Framework to Empower Probabilistic Protein Design. Menachem Fromer	PT40: Combinatorial Influence of Environmental Parameters on Transcription Factor Activity. Theo Knijnenburg	HL39: Combined Analysis Reveals a Core Set of Cycling Genes. Yong Lu	HL40: A Global Analysis of Genetic Interactions in Caenorhabditis Elegans. Matthew T. Weirauch		TT27: A database of Chemical Entities of Biological Interest. Ana Paula de Matos	TT34: Chimera. Scooter Morris
12:40 p.m.- 2:15 p.m.	Lunch - Hall E
1:00 p.m.- 2:15 p.m.		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
Parallel Sessions	Proceedings Track (PT)	Proceedings Track (PT)	Highlights Track (HL)	Highlights Track (HL)	Special Session Track (SST)	Technology Track (TT)
2:15 p.m.- 2:40 p.m.	PT41: Nucleosome Positioning from Tiling Microarray Data. Moran Yassour	PT42: A Maximum Common Substructure-Based Algorithm for Searching and Predicting Drug-Like Compounds. Yiqun Cao	HL41: Organization and Evolution of Primate Centromeric DNA from Whole Genome Shotgun Sequence Data. Can Alkan	HL42: Life Works on AC Power. Andrey Ptitsyn	Special Session 6: Computational Challenges and Opportunities in Host-Pathogen Systems Biology, Organizers: T. M. Murali, Matthew D. Dyer	TT28: Designing, Executing, Reusing and Sharing Workflows: Taverna and myExperiment Supporting the in silico Experiment Life Cycle. Katy Wolstencroft
2:45 p.m.- 3:10 p.m.	PT43: Multi-Spectra Peptide Sequencing and its Applications to Multistage Mass Spectrometry. Nuno Bandeira	PT44: Contact Replacement for NMR Resonance AssignmentI. Fei Xiong	HL43: Graph-theory Meets Evolutionary Biology: Reticulate Classification of Prokaryotic Mobile Genetic Elements. Gipsi Lima-Mendez	HL44: A Systems Approach to Delineate Functions of Paralogous Transcription FactorsI. Kai Tan		TT29: EBI Web Services APIs for Data-retrieval and Analysis. Franck Valentin
3:15 p.m.- 3:40 p.m.	PT45: Modelling peptide fragmentation with dynamic Bayesian networks for peptide identification. Aaron Klammer	PT46: Classification of arrayCGH Data Using a Fused SVM. Franck Rapaport	HL45: Discovering Common Sequence Variation in Arabidopsis thalianaI. Ratsch Gunnar	HL46: Genome-wide Transcriptional Analysis of the Human Cell Cycle Identifies Genes Differentially Regulated in Normal and Cancer Cells. Ziv Bar-Joseph		TT30: Galaxy Workflows: Enabling Complex Computational Analysis For Experimental Biologists. James Taylor
3:45 p.m.- 4:10 p.m.	PT47: BLASTing Small Molecules - Statistics and Extreme Statistics of Chemical Similarity Scores. Pierre Baldi	PT48: Matching Isotopic Distributions from Metabolically Labeled Samples. Sean McIlwain	HL47: A Phylogenomic Study of Human, Dog and Mouse. Gina M. Cannarozzi	HL48: High-resolution Timing of Cell Cycle-regulated Gene Expression. Andrzej S. Kudlicki		TT31: New GALAXY Tools. Anton Nekrutenko
4:15 p.m.- 4:45 p.m.	Coffee Break with Exhibitors - Hall F
4:45 p.m.- 5:45 p.m.	Keynote Presentation: Bernhard Ø. Palsson, University of California, Systems Biology: an era of reconstruction and interrogation - Hall G
6:00 p.m.	Offsite event - Departs MTCC - South Building Ground Level entrance to Liberty Grand Venue

Wednesday	July 23
7:30 a.m.- 3:30 p.m.	Registration: 600 Level
8:15 a.m.- 2:30 p.m.	Posters on Display - Hall E
	Hall G	Room: 801	Room: 718A	Room: 718B	Room: 701A	Room: 701B	Room: 714	Room: 715	Room: 802	Room: 803
8:45 a.m.- 9:00 a.m.	Morning Welcome - Hall G
9:00 a.m.- 10:00 a.m.	Keynote Presentation: Hanah Margalit, The Hebrew University of Jerusalem, Intriguing roles for small non-coding RNAs in the cellular regulatory networks
10:00 a.m.- 10:45 a.m.	Coffee Break with Exhibitors - Hall F							Workshop Workshop 2: CytoScape Workshop, Gary Bader, Shoshana Wodak 10:00am-11:15am Cytoscape: An Open-Source Platform for Network Analysis and Visualization 11:15am-11:30am A Cytoscape Plugin to Access the MiMI Molecular Interactions 11:30am-11:45am GenePro: a Cytoscape Plug-in for Advanced Visualization and Analysis of Interaction Network 11:45am-12:00pm Interactive analysis of metabolic pathways, their enzymes and metabolites
Parallel Sessions	Highlights Track (HL)	Highlights Track (HL)	Highlights Track (HL)	Highlights Track (HL)	Special Session Track (SST)	Funding Opportunities & Activities Session	Workshop		Workshop	Visual Reflections in Science
10:45 a.m.- 11:10 a.m.	HL49: Transducers: a Unified Framework for Alignment, Phylogeny, Annotation, Reconstruction, Parameter Estimation and Simulating Evolution. Ian Holmes	HL50: Accurate Multiple Sequence and Structural Alignment of Distantly Related Proteins. Jimin Pei	HL51: Signal Propagation in Proteins and Relation to Equilibrium Fluctuations. Chakra S. Chennubhotla	HL52: Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites. Boris E Shakhnovich	Special Session 7: Future of Scientific Publishing, Organizer: Scott Markel	FS1:  Funding Opportunities & Activities of the US NIH/NIGMS, Karin Remington	Workshop 1: GenePattern Workshop, Ted Liefeld (10:45 a.m. - 12:40 p.m.)		Workshop 3: Ensembl/UCSC Genome Browser Workshop - Hiram Clawson (10:45 a.m. - 11:40 a.m.), Michael Schuster (11:45 a.m - 12:40 p.m.) **Please note Laptop Computer required for this workshop**
11:15 a.m.- 11:40 a.m.	HL53: Detecting Coevolution in and Among Protein Domains. Chen-Hsiang Yeang	HL54: Local Flexibility Aids Protein Multiple Structure Alignment. Lenore J Cowen	HL55: Transient mediated fate-determination in HIV (why bistability in unnecessary). Leor S Weinberger	HL04: A Systems Biology Approach for Steady State Analysis of Signaling Pathways. Sorin Draghici		FS2: Funding Opportunities & Activities of the US NSF, Frank Olken
11:45 a.m.- 12:10 p.m.	HL56: Nucleosome Positioning Signals in Yeast and Human Genomic DNA. William S Noble	HL57: Directed Search of Large Microarray Compendia. Matthew A Hibbs	HL58: Semi-supervised Learning for Peptide Identification from Shotgun Proteomics Datasets. Lukas Käll			FS3: Funding Opportunities & Activities of the US DOE, Susan Guerick
12:15 p.m.- 12:40 p.m.	HL59: Inferring Non-Coding RNA Families by Genome-Scale Structure-Based Clustering. Rolf Backofen	HL60: Exploring Interaction Space of Multiple Retroviral Proteases and Their Substrates. Aleksejs Kontijevskis				FS4: Elixir: Changing the Panorama of Grant Applciations in Europe, Andrew Lyall
12:40 p.m.- 2:00 p.m.	Lunch - Hall E					FS5 12:45 - 1:10 Funding Opportunities & Activities in Canada (CIHR, NSERC & Genome Canada) Gregory Huyer, CIHR
1:15 p.m.- 2:00 p.m.						FS6 1:15 - 1:40 p.m. Funding Opportunities & Activities in Ontario. Mima Vulovic
2:00 p.m. - 3:00 p.m.	Keynote Presentation - ISCB Senior Scientist Accomplishment Award, David Haussler, Hall G
3:00 p.m.- 3:30 p.m.	Conference Awards and Closing - Hall G