RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges
AGENDA
Please note that this schedule is tentative and is subject to change without notice. Any updates will be posted on this page as soon as possible. (Last update: November 10, 2013)
All talks will be held in the Appel Salon at the Toronto Reference Library
(789 Yonge Street, Toronto). >>Click here<< for the map.
| --> FRIDAY, NOVEMBER 08, 2013 | ||
| Links within this page: Saturday | Sunday | Monday | Tuesday | ||
| 08:00 AM | Registration | |
| 08:45 AM | Opening Remarks: Gustavo Stolovitzky (IBM) | |
| Chair: Julio Saez-Rodriguez (EBI) | 09:00 AM - 09:20 AM | Challenge 1: HPN-DREAM Breast Cancer Network Inference Challenge: Inferring Causal Signaling Networks and Predicting Protein Phosphorylation Dynamics in Cancer, Laura Heiser (OHSU) and Steven Hill (NKI) |
| 09:20 AM - 09:30 AM | Awards Challenge 1. Presenters: Mark Wagar, President of Heritage Medical Systems (HPN) and Dan Gallahan, Deputy Director, Div. Cancer Biology (NCI) |
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| 09:30 AM - 09:50 AM | Ch1.1A Best Performer*: Team DC_TDC. Prophetic Granger Causality and the Role of a Biological Prior, Artem Sokolov (UC Santa Cruz) | |
| 09:50 AM - 10:10 AM | Ch1.2A Best Performer**: Team StochasticChaos. Prediction for Time-Course Proteomics In Vitro, Elana Fertig (JHU) | |
| 10:10 AM - 10:30 AM | Ch1.3 Best Performer: Team ABCD. BioWheel: A Visualization Tool for Proteomics, Amina Ann Qutub (Rice University) | |
| 10:30 AM - 10:40 AM | Challenge 1 discussion | |
| 10:40 AM - 11:10 AM | Coffee Break & Poster Session | |
| 11:10 AM - 11:40 AM | Keynote: Turning Networks Into Ontologies: Towards A Data-driven Gene Ontology, Trey Ideker, University of California, San Diego, United States | |
| Chair: Rick Woychik (NIEHS) |
11:40 AM - 12:00 PM | Challenge 2: NIEHS-NCATS-UNC DREAM Toxicogenetics Challenge: Overview and Results, Federica Eduati (EBI) and Fred Wright (NCSU) |
| 12:00 PM - 12:10 PM | Awards Challenge 2. Presenter: Rick Woychik, Deputy Director (NIEHS) | |
| 12:10 PM - 12:30 PM | Ch2.1/Ch2.2 Best Performer: Teams YangLab/QBRC. Estimating Population-scale Toxicities for Environmental Chemicals from Genomic and Chemical Information, Tao Wang and Hao Tang (UTSW) | |
| 12:30 PM - 12:50 PM | Ch2.1 Second Best Performer: Team Cassis. Kernel Bilinear Regression for Toxicogenetics, Elsa Bernard (Inst. Curie) | |
| 12:50 PM - 13:00 PM | Challenge 2 discussion | |
| 13:00 PM - 14:30 PM | Lunch & Poster Session | |
| 14:30 PM - 15:00 PM | Keynote: DNA and RNA Binding Motifs for Mapping Gene Regulation, Tim Hughes, University of Toronto, Canada | |
| Chair: Markus Covert (Stanford University) |
15:00 PM - 15:20 PM | Challenge 3: A Crowd-sourced Approach to Whole-cell Model Parameter Estimation, Markus Covert (Stanford Univ) and Pablo Meyer (IBM) |
| 15:20 PM - 15:30 PM | A Computational Platform for the DREAM Whole Cell Parameter Estimation Challenge, Brandon Allgood (Numerate Inc.) | |
| 15:40 PM - 15:40 PM | Awards Challenge 3. Presenter: Pablo Meyer (IBM Research) |
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| 15:40 PM - 16:00 PM | Ch3.1 Best Performer: Team Crux. Parameter Estimation for Huge Systems, Clemens Kreutz (University of Freiburg) |
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| 16:00 PM - 16:20 PM | Ch3.2 Best Performer: Team Whole-Sale Modelers. Parameter Fitting as Statistical Inference: An Outsider's Perspective, Alex H Williams (Brandeis Univ.) | |
| 16:20 PM - 16:30 PM | Challenge 3 discussion | |
| 16:30 PM - 17:00 PM | Coffee Break & Poster Session | |
| 17:00 PM - 17:20 PM | Future Challenges: Paul Boutros (OICR) and Gustavo Stolovitzky (IBM Research) | |
| 17:20 PM - 18:00 PM | Discussion: The Future of DREAM (All) | |
| 18:00 PM | Adjourn | |
| * Due to Agenda Constraints, Team NMSUSongLab (the best performer in Ch1.1B and the most consistent performer through Ch1.1A and Ch1.1B) will be presenting their contribution in a Poster Presentation DREAM Poster 09). Presenters: Yang Zhang and Joe Song (NMSU) | ||
| ** Due to Visa Issues the originally scheduled presentation by Team GuanLab (the co-best performer in Ch1.2A): Network Time-Course Projection Using Truncated SVD, Fan Zhu (University of Michigan) has been cancelled, and replaced with the presentation by Team StochchasticChaos. | ||
| ** Due to Agenda Constraints, Team CGR (the best performer in Ch1.2B will be presenting their contribution in a Poster Presentation (DREAM Poster 08). Presenter: Chunhua Yan | ||
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| -->SATURDAY, NOVEMBER 09, 2013 - SYSTEMS BIOLOGY | ||
| 08:00 AM | Registration | |
| 08:45 AM | Opening Remarks | |
| Chair: Andrea Califano (Columbia University) |
09:00 AM - 09:30 AM | Keynote: Building Protein Networks to Understand Human Disease: Ciliopathies Explain Retinal Degeneration, Obesity, and Cancer, Peter Jackson, Stanford University School of Medicine, United States |
| 09:35 AM - 09:50 AM | Evolution After Whole-genome Duplication: A Network Perspective, Luay Nakhleh, Rice University, United States | |
| 09:50 AM - 10:05 AM | Rational Optimization of Computational Biology Pipelines, Nicholas Harding, OICR, Canada |
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| 10:05 AM - 10:20 AM | Global Linkage Map Connects Meiotic Centromere Function to Chromosome Size in Budding Yeast, Anastasia Baryshnikova, Princeton University, United States | |
| 10:20 AM - 10:35 AM | Mapping Trigenic Interactions of Whole Genome Duplicates in Yeast, Elena Kuzmin , University of Toronto | |
| 10:35 AM - 11:00 AM | Coffee Break | |
| Chair: Trey Ideker (UC, San Diego) |
11:00 AM - 11:30 AM | Keynote: Peter Sorger,Harvard Medical School, United States |
| 11:30 AM - 11:45 AM | Systematic Exploration of Autonomous Modules in Noisy MicroRNA-target Networks for Testing the Generality of the ceRNA Hypothesis, Kevin Y. Yip, The Chinese University of Hong Kong | |
| 11:45 AM - 12:00 PM | Ensemble Inference and Inferability of Gene Regulatory Networks, S M Minhaz Ud-Dean, ETH Zurich, Switzerland | |
| 12:00 PM - 12:15 PM | A Nutrient-responsive Pathway that Determines M Phase Timing Through Control of B-cyclin mRNA Stability, Vincent Messier, CCBR, Canada | |
| 12:15 PM - 13:30 PM | Lunch & Poster Session | |
| Chair: Gustavo Stolovitsky (IBM Research) |
13:30 PM - 14:00 PM | Keynote: Tony Pawson and Modular Biology: From Domains to Cell Signalling Systems by Dr. Jeff Wrana, Mount Sinai Hospital, Canada |
| 14:05 PM - 14:20 PM | A Computational High-throughput Approach to discover Post-translational Modulators of Transcription Factor Activity from Gene Expression Profiles, Diego Di Bernardo, Telethon Institute of Genetics and Medicine, Italy | |
| 14:20 PM - 14:35 PM | Exploring the Dynamic Interplay of Human miRNA-Transcription Factor Regulatory Cycles, Daniel Chee, University of Washington, United States | |
| 14:35 PM - 14:50 PM | Localized Enzymes Reflect Cellular metabolic state, Pablo Meyer, IBM, United States | |
| 14:50 PM - 15:05 PM | Next Generation Insight into Signaling Networks: A Systematic Protein-protein Interaction Reporter Assay to Identify Upstream Regulators of Signaling Hubs, Marie Filteau, Laval University, Canada | |
| 15:05 PM - 15:30 PM | Coffee Break | |
| Chair: Laura Heiser (Oregon Health and Science University) |
15:30 PM - 15:45 PM | The Mutational landscape of Phosphorylation Signaling in Cancer, Juri Reimand, University of Toronto, Canada |
| 15:45 PM - 16:00 PM | A 13C-based Method for Metabolic Flux Measurement and Prediction in Genome-Scale Models, Hector Garcia Martin, Lawrence Berkeley National Laboratory, United States | |
| 16:00 PM - 16:30 PM | Keynote: Predictive Uses of Metabolic Reconstructions, Berhnard Palsson,University of California, San Diego, United States | |
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| -->SUNDAY, NOVEMBER 10, 2013 - SYSTEMS BIOLOGY | ||
| 08:00 AM | Registration | |
| 08:45 AM | Opening Remarks | |
| Chair: Brenda Andrews (University of Toronto) |
09:00 AM - 09:30 AM | Keynote: Olivier Pourquié, Université de Strasbourg, France |
| 09:35 AM - 9:50 AM | Elucidating Influenza Inhibition Pathways via Network Reconstruction, Arnon Mazza, Tel Aviv University, Israel | |
| 09:30 AM - 10:05 AM | Quantification of Cell-to-cell Variability in Protein Spatial Spread from Fluorescence Microscopy of Unsynchronized Budding Yeast, Louis-Francois Handfield, University of Toronto, Canada | |
| 10:05 AM - 10:20 AM | Validation of Vertebrate Developmental Phenotype Predictions using Zebrafish, Garbiel Musso, Brigham and Women's Hospital / Harvard Medical School, United States | |
| 10:20 AM - 10:35 AM | The Regulatory Landscape of Human Fetal Development, Kyle Siebenthall, University of Washington, United States | |
| 10:35 AM - 11:00 AM | Coffee Break | |
| Chair: Michael White (Washington University School of Medicine) |
11:00 AM - 11:30 AM | Keynote: From Phenotypes to Pathways: Global Exploration of Cellular Networks Using Yeast Functional Genomics, Brenda Andrews,University of Toronto, Canada |
| 11:30 AM - 11:45 AM | Transcript Level and Sequence Determinants of Protein Abundance and Noise in Escherichia coli, Joao C. Guimaraes, University of California, Berkeley, United States | |
| 11:45 AM - 12:00 PM | Dissecting the Regulatory Machinery of Neurodegeneration in an In Vitro Model of ALS, Mariano J. Alvarez, Columbia University, United States | |
| 12:00 PM - 12:15 PM | Combinatorial Regulation of Lipoprotein Lipase by MicroRNAs During Mouse Adipogenesis, Maria Bouvy-Liivrand, University of Luxembourg | |
| 12:15 PM - 13:30 PM | Lunch & Poster Session | |
| Chair: Josh Stuart (UC, Santa Cruz) |
13:30 PM - 14:00 PM | Keynote: Levi A. Garraway, Dana-Farber Cancer Institute and the Broad Institute, United States |
| 14:05 PM - 14:20 PM | A Network-based Approach for Drug Synergy Prediction from Gene Expression Data, Andrea Califano, Columbia University, United States | |
| 14:20 PM - 14:35 PM | Identifying Drug Mechanism of Action using Network Dysregulation, Mukesh Bansal, Columbia University, United States | |
| 14:35 PM - 14:50 PM | Dynamic Analysis of Cellular Differentiation and Drug Mode of Action Using Large-scale, Real time 3D Living Cell Arrays, Beatriz Penalver Bernabe, Northwestern University, United States | |
| 14:50 PM - 15:05 PM | Chemogenomic Profiling Reveals a Network of the Cellular Responses to Small Molecules, Anna Y Lee, University of Toronto, Canada | |
| 15:05 PM - 15:30 PM | Coffee Break | |
| Chair: Jason Enst (UCLA) |
15:30 PM - 15:45 PM | Discovering Latent Cancer Characteristics Predictive of Drug Sensitivity, David A. Knowles, Stanford University, United States |
| 15:45 PM - 16:00 PM | Integrated Profiling of p53 Wild-type Cell Lines Identifies Differentially Responsive Populations and a Gene Expression Signature that Predicts Sensitivity to SAR299155, a Potent and Selective Disruptor of the p53-MDM2 Interaction, Stephen Rowley, Sanofi, United States | |
| 16:00 PM - 16:15 PM | L1000 Expression Signatures Reveal the Landscape of Ligand and Drug Response in Breast Cancer Cell Lines, Marc Hafner, Harvard Medical School, United States | |
| 16:15 PM - 16:45 PM | Keynote: Reconstructing Regulatory Circuits: Lessons from Immune Cells, Aviv Regev, Broad Institute, United States | |
| 16:45 PM - 19:00 PM | Reception at Appel Salon – Sponsored by the University of Toronto’s Donnelly Center | |
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| -->MONDAY, NOVEMBER 11, 2013 - REGULATORY GENOMICS | ||
| 08:00 AM | Registration | |
| 08:45 AM | Opening remarks | |
| Chair: Tim Hughes, (University of Toronto) |
09:00 AM - 09:30 AM | Keynote: Algorithms in Nature, Ziv Bar-Joseph, Carnegie Mellon University, United States |
| 09:35 AM - 09:50 AM | Understanding the Synonymous Information Encoded in Transcripts via Evolutionary Systems Biology and Synthetic Biology Approaches, Tamir Tuller, Tel Aviv University, Israel | |
| 09:50 AM - 10:05 AM | The Functional Potential Score: Integrating Comparative, Population and Functional Genomic Data to Identify Recent Selective Pressure in Noncoding Human DNA, Brad Gulko, Cornell University, United States | |
| 10:05 AM - 10:20 AM | Primate Transcript and Protein Expression Levels Evolve under Compensatory Selection Pressures, Zia Khan, University of Chicago, United States | |
| 10:20 AM - 10:35 AM | The Accessible Chromatin Landscape of the Mouse Genome Reveals a Core Mammalian Regulon, Jeff Vierstra, University of Washington-Seattle, United States | |
| 10:35 AM - 11:00 AM | Coffee Break | |
| Chair: Ziv Bar-Joseph (Carnegie Mellon University) |
11:00 AM - 11:30 AM | Keynote: Encoding Cellular Information Through p53 Dynamics in Individual Cells, Galit Lahav, Harvard Medical School, United States |
| 11:30 AM - 11:45 AM | Linking Signaling Pathways To Transcriptional Response In Breast Cancer, Hatice Ulku Osmanbeyoglu, Memorial Sloan–Kettering Cancer Center, United States | |
| 11:45 AM - 12:00 PM | Systematic Detection and Analysis of Epigenomic Changes During Melanoma Cancer Progression, Petko Fiziev, University of California, Los Angeles, United States | |
| 12:00 PM - 12:15 PM | Gata3 and Runx3 Binding Underlies Differential Nucleosome Organization in Helper and Cytolytic T Cells, Matthew E. Pipkin, The Scripps Research Institute, United States | |
| 12:15 PM - 13:30 PM | Lunch & Poster Session | |
| Chair: Jason Ernst (UCLA) |
13:30 PM - 14:00 PM | Keynote: Reduce, Reuse, Recycle: The Dynamics of Regulatory Information Usage in Development, Jason D. Lieb, Princeton University, United States |
| 14:05 PM - 14:20 PM | Distinct and Predictive Histone Lysine Acetylation Patterns at Promoters, Enhancers and Gene Bodies, Nisha Rajagopal, University of California, San Diego, United States | |
| 14:20 PM - 14:35 PM | Poly-dA:dT tracts form a Directional Nucleosomal Turnstile In Vivo, Carl de Boer, University of Toronto, Canada | |
| 14:35 PM - 14:50 PM | Condition-specific Binding of the Glucocorticoid Receptor, Morgane Thomas-Chollier, Institut de Biologie de l'Ecole Normale Supérieure, France | |
| 14:50 PM - 15:05 PM | Genome-wide Analysis of Functional and Evolutional Features of Tele-enhancers, Huang Di, National Institutes of Health, United States | |
| 15:05 PM - 15:30 PM | Coffee Break | |
| Chair: Terry Furey (University of North Carolina at Chapel Hill) |
15:30 PM - 15:45 PM | Integrative and Parallel Approaches to Uncover Drivers of Cancer, Uri David Akavia, McGill University, Canada |
| 15:45 PM - 16:00 PM | Cardiac Enhancers Harbor Undiscovered Genetic Variants Associated with Heart Contraction Traits, Xinchen Wang, Massachusetts Institute of Technology, United States | |
| 16:00 PM - 16:15 PM | Conserved Combinatorial Transcription Factor Binding Identifies Regulatory Variants in Human Disease Pathways, Michael D. Wilson, SickKids Research Institute, Canada | |
| 16:15 PM - 16:45 PM | Mentoring Session: Regulatory Genomics and Systems Biology in Industry: Opportunities and Challenges. Presenters: Monica Boyle, Dart NeuroScience LLC; Andrea Califano, Columbia University; Boris Hayete, GNS; Raquel Norel, IBM Research; Ravi Pandya, Microsoft Research; Stephen Rowley, Sanofi | |
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| -->TUESDAY, NOVEMBER 12, 2013 - REGULATORY GENOMICS | ||
| 08:00 AM | Registration | |
| 08:45 AM | Opening Remarks | |
| Chair: Manolis Kellis (MIT) |
09:00 AM - 09:30 AM | Keynote: From Genome Function to Personalised Omics, Emmanouil (Manolis) Dermitzakis, University of Geneva Medical School, Switzerland |
| 09:35 AM - 09:50 AM | Analysis of Non-coding Genetic Variants Impact on Gene Regulation and Complex Traits, Roger Pique-Regi, Wayne State University, United States | |
| 09:50 AM - 10:05 AM | Finding Alternative eQTLs by Exploring Sparse Model Space, Xinghua Shi, University of North Carolina at Charlotte, United States | |
| 10:05 AM - 10:20 AM | The Impact of Natural Genetic Variation on Protein and RNA Networks, Andreas Beyer, University of Cologne, Germany | |
| 10:20 AM - 10:35 AM | Novel Trans-eQTL Analysis Demonstrates Effect of Population Genetic Architecture on Detecting and Interpreting Regulatory Associations, Terrence Furey, University of North Carolina at Chapel Hill, United States | |
| 10:35 AM - 11:00 AM | Coffee Break | |
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Chair: Christina Leslie (MSKCC) |
11:00 AM - 11:30 AM | Keynote: Genome-wide Analysis of Protein-DNA Interactions, Jussi Taipale, Karolinska Institutet, Sweden |
| 11:30 AM - 11:45 AM | System Wide Analyses have Underestimated Transcriptional Importance in Animals, Jingyi Jessica Li, University of California, Los Angeles, United States | |
| 11:45 AM - 12:00 PM | Mapping Functional Transcription Factor Networks from Gene Expression Data, Michael R. Brent, Washington University, United States | |
| 12:00 PM - 12:15 PM | Integrating Gene Expression and Sequence Data with Existing Biological Knowledge to Model Context-specific Gene Regulation, Sofia Kyriazopoulou-Panagiotopoulou, Stanford University, United States | |
| 12:15 PM - 13:30 PM | Lunch & Poster Session | |
| Chair: Roger Pique-Regi (Wayne State University) |
13:30 PM - 14:00 PM | Keynote: The Transcriptome of Drosophila Melanogaster, Brenton R. Graveley, University of Connecticut Health Center, United States |
| 14:00 PM - 14:20 PM | Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity, Matt Weirauch, Cincinnati Children's Hospital, United States | |
| 14:20 PM - 14:35 PM | Informational Requirements for Transcriptional Regulation, Ivan Erill, University of Maryland Baltimore County, United States | |
| 14:35 PM - 14:50 PM | Widespread Evidence for DNA Shape Dependent Transcription-factor Binding Preferences, Iris Dror, Technion, Israel | |
| 14:50 PM - 15:05 PM | Analysis of C2H2 Transcription Factor Binding Sites Using a High-throughput ChIP-seq Approach, Frank W. Schmitges, University of Toronto, Canada | |
| 15:05 PM - 15:30 PM | Coffee Break | |
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Chair: |
15:30 PM - 15:45 PM | Comprehensive Quantification of Transcription Factor Thermodynamics and Kinetics for Both Specific and Nonspecific Binding Modes on a High-Throughput Sequencer, Robin Friedman, Institut Pasteur, France |
| 15:45 PM - 16:00 PM | Using Reporter Synthetic Genetic Array (R-SGA) Analysis to Explore Transcriptional Regulatory Pathways in Budding Yeast, Hendrikje Goettert, University of Toronto, Canada | |
| 16:00 PM - 16:15 PM | A Massively Parallel In Vivo Enhancer Assay Reveals that Highly Local Features Determine the Cis-regulatory Function of ChIP-seq Peaks, Michael A. White, Washington University, United States | |
| 16:15 PM - 16:45 PM | Conference Wrap-up, Top 10 Announcements, Survey Results |
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