RECOMB Conference on Regulatory and Systems Genomics,
with Dream Challenges 2013

The full listing of talks can be found below.

**Not all presenters provided permission to make talks available.

Title Presenter
Discussion: Challenge 2
Discussion: The Future of DREAM
Integrative and Parallel Approaches to Uncover Drivers of Cancer Uri David Akavia
A Computational Platform for the DREAM Whole Cell Parameter Estimation Challenge Brandon Allgood
Dissecting the Regulatory Machinery of Neurodegeneration in an In Vitro Model of ALS Mariano J. Alvarez
Keynote: From Phenotypes to Pathways: Global Exploration of Cellular Networks Using Yeast Functional Genomics Brenda Andrews
BioWheel: A Visualization Tool for Proteomics Amina Ann Qutub
Identifying Drug Mechanism of Action using Network Dysregulation Mukesh Bansal
Keynote: Algorithms in Nature Ziv Bar-Joseph
Chromosome size and centromere function in meiosis: a new link from yeast genomics Anastasia Baryshnikova
Kernel Bilinear Regression for Toxicogenetics Elsa Bernard
The Impact of Natural Genetic Variation on Protein and RNA Networks Andreas Beyer
Future Challenges Paul Boultros
Combinatorial Regulation of Lipoprotein Lipase by MicroRNAs During Mouse Adipogenesis Maria Bouvy-Liivrand
Mapping Functional Transcription Factor Networks from Gene Expression Michael Brent
A Network-based Approach for Drug Synergy Prediction from Gene Expression Data Andrea Califano
Exploring the Dynamic Interplay of Human miRNA-Transcription Factor Regulatory Cycles Daniel Chee
A Crowd-sourced Approach to Whole-cell Model Parameter Estimation Markus Covert
Poly-dA:dT tracts form a Directional Nucleosomal Turnstile In Vivo Carl De Boer
Keynote: From Genome Function to Personalised Omics Emmanouil (Manolis) Dermitzakis
A Computational High-throughput Approach to discover Post-translational Modulators of Transcription Factor Activity from Gene Expression Profiles Diego Di Bernardo
Widespread Evidence for DNA Shape Dependent Transcription-factor Binding Preferences Iris Dror
NIEHS-NCATS-UNC DREAM Toxicogenetics Challenge: Overview and Results Federica Eduati
Informational Requirements for Transcriptional Regulation Ivan Erill
Prediction for Time-Course Proteomics In Vitro Elana Fertig
Next Generation Insight into Signaling Networks: A Systematic Protein-protein Interaction Reporter Assay to Identify Upstream Regulators of Signaling Hubs Marie Filteau
Systematic Detection and Analysis of Epigenomic Changes During Melanoma Cancer Progression Petko Fiziev
Comprehensive Quantification of Transcription Factor Thermodynamics and Kinetics for Both Specific and Nonspecific Binding Modes on a High-Throughput Sequencer Robin Friedman
Novel Trans-eQTL Analysis Demonstrates Effect of Population Genetic Architecture on Detecting and Interpreting Regulatory Associations Terrence Furey
A 13C-based Method for Metabolic Flux Measurement and Prediction in Genome-Scale Models Hector Garcia Martin
Keynote Levi A. Garraway
Using Reporter Synthetic Genetic Array (R-SGA) analysis to explore transcriptional regulatory pathways in budding yeast Hendrikje Goettert
Keynote: The Transcriptome of Drosophila Melanogaster Brenton Graveley
Transcript Level and Sequence Determinants of Protein Abundance and Noise in Escherichia coli Joao Guimaraes
The Functional Potential Score: Integrating Comparative, Population and Functional Genomic Data to Identify Recent Selective Pressure in Noncoding Human DNA Brad Gulko
L1000 Expression Signatures Reveal the Landscape of Ligand and Drug Response in Breast Cancer Cell Lines Marc Hafner
Quantification of Cell-to-cell Variability in Protein Spatial Spread from Fluorescence Microscopy of Unsynchronized Budding Yeast Louis-Francois Handfield
Rational Optimization of Bio-computing Pipelines Nicholas Harding
HPN-DREAM Breast Cancer Network Inference Challenge: Inferring Causal Signaling Networks and Predicting Protein Phosphorylation Dynamics in Cancer Steven Hill
Genome-wide Analysis of Functional and Evolutional Features of Tele-enhancers Di Huang
Keynote: DNA and RNA Binding Motifs for Mapping Gene Regulation Tim Hughes
Keynote: Turning Networks Into Ontologies: Towards A Data-driven Gene Ontology Trey Ideker
Keynote: Building Protein Networks to Understand Human Disease: Ciliopathies Explain Stanford University School of Medicine, United States Peter Jackson
Primate Transcript and Protein Expression Levels Evolve under Compensatory Selection Pressures Zia Khan
Discovering Latent Cancer Characteristics Predictive of Drug Sensitivity David A. Knowles
Parameter Estimation for Huge Systems Clemens Kreutz
Mapping Trigenic Interactions of Whole Genome Duplicates in Yeast Elena Kuzmin
Integrating gene expression and sequence data with existing biological knowledge to model context-specific gene regulation Sofia Kyriazopoulou-Panagiotopoulou
Keynote: Encoding Cellular Information through p53 Dynamics in Individual Cells Galit Lahav
Chemogenomic Profiling Reveals a Network of the Cellular Responses to Small Molecules Anna Lee
System Wide Analyses have Underestimated Transcriptional Importance in Animals Jingyi Jessica Li
Keynote: Reduce, Reuse, Recycle: The Dynamics of Regulatory Information Usage in Development Jason D. Lieb
Elucidating Influenza Inhibition Pathways via Network Reconstruction Arnon Mazza
A Nutrient-responsive Pathway that Determines M Phase Timing Through Control of B-cyclin mRNA Stability Vincent Messier
Parameter Estimation Challenge Introduction & Overall results Pablo Meyer
Localized Enzymes Reflect Cellular metabolic state Pablo Meyer Rojas
Validation of Vertebrate Developmental Phenotype Predictions using Zebrafish Gabe Musso
Evolution After Whole-genome Duplication: A Network Perspective Luay Nakhleh
Keynote: Predictive Uses of Metabolic Reconstructions Bernhard Palsson
Dynamic Analysis of Cellular Differentiation and Drug Mode of Action Using Large-scale, Real time 3D Living Cell Arrays Beatriz Penalver Bernabe
Gata3 and Runx3 Binding Underlies Differential Nucleosome Organization in Helper and Cytolytic T Cells Matthew E. Pipkin
Analysis of Non-coding Genetic Variants Impact on Gene Regulation and Complex Traits Roger Pique-Regi
Keynote Olivier Pourquié
Distinct and Predictive Histone Lysine Acetylation Patterns at Promoters, Enhancers and Gene Bodies Nisha Rajagopal
Keynote: Reconstructing Regulatory Circuits Aviv Regev
The Mutational landscape of Phosphorylation Signaling in Cancer Juri Reimand
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
Analysis of C2H2 Transcription Factor Binding Sites Using a High-throughput ChIP-seq Approach Frank Schmitges
Finding Alternative eQTLs by Exploring Sparse Model Space Xinghua Shi
The Regulatory Landscape of Human Fetal Development Kyle Siebenthall
Prophetic Granger Causality and the Role of a Biological Prior Artem Sokolov
Keynote Peter Sorger
Keynote: Genome-wide Analysis of Protein-DNA Interactions Jussi Taipale
Condition-specific Binding of the Glucocorticoid Receptor Morgane Thomas-Chollier
Understanding the Synonymous Information Encoded in Transcripts via Evolutionary Systems Biology and Synthetic Biology Approaches Tamir Tuller
Ensemble Inference and Inferability of Gene Regulatory Networks Minhaz Ud-Dean
Linking Signaling Pathways To Transcriptional Response In Breast Cancer Hatice Ulku Osmanbeyoglu
The Accessible Chromatin Landscape of the Mouse Genome Reveals a Core Mammalian Regulon Jeff Vierstra
Estimating Population-scale Toxicities for Environmental Chemicals from Genomic and Chemical Information Tao Wang
Cardiac Enhancers Harbor Undiscovered Genetic Variants Associated with Heart Contraction Traits Xinchen Wang
Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity Matt Weirauch
A massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks Michael White
Parameter Fitting as Statistical Inference: an outsider's perspective Alex Williams
Conserved Combinatorial Transcription Factor Binding Identifies Regulatory Variants in Human Disease Pathways Michael D. Wilson
Awards Challenge 2 Rick Woychik
Tony Pawson and Modular Biology: From Domains to Cell Signalling Systems Jeff Wrana
Systematic Exploration of Autonomous Modules in Noisy MicroRNA-target Networks for Testing the Generality of the ceRNA Hypothesis Kevin Y Yip