| Opening Remarks (Thursday) |
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| Opening Remarks (Wednesday) |
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| Reading Lists |
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| RECOMB 2015 Announcement |
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| Future DREAM 9.5 Challenges |
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| RA Challenge Awards |
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| RA Challenge Discussion |
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| SMC Challenge Discussion |
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| Opening Remarks (Tuesday) |
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| Inferring the genome-wide functional modulatory network: a case study on the NF-κB/RelA transcription factor |
Xueling Li |
| Assessing the impact of non-silent somatic mutations on protein activity |
Mariano Alvarez |
| Elucidating Compound Mechanism of Action by Network Dysregulation Analysis in Perturbed Cells |
Mukesh Bansal |
| A Canonical Correlation Analysis Based Dynamic Bayesian Network Prior to Infer Gene Regulatory Networks from Multiple Types of Biological Data |
Brittany Baur |
| The ICGC-TCGA DREAM Somatic Mutation Calling Challenge: Motivation, Data, Scoring and Results |
Paul Boutros |
| From functional regulatory modules to the genetic determinants of human disease |
Andrea Califano |
| Q & A session: From functional regulatory modules to the genetic determinants of human disease |
Andrea Califano |
| Reconstruction of gene regulatory networks based on repairing sparse low-rank matrices |
Young Hwan Chang |
| Viral and retrotransposon sequences have shaped the preferred contexts for APOBEC-mediated mutagenesis |
Jeffrey Chen |
| novoBreak: robust characterization of structural breakpoints in cancer genomes |
Zechen Chong |
| Mechanistic basis of a causal non-coding FTO obesity variant |
Melina Claussnitzer |
| Regulatory Genomics Keynote: Systems Approaches to Integration of Regulatory Information for Characterizing Genome Variation Affecting Complex Human Traits |
Nancy Cox |
| "Crossing" approach to DREAM AML Outcome prediction |
David Dill |
| PEPPER: Cytoscape app for Protein complex Expansion using Protein-Protein intERaction networks |
Mohamed Elati |
| Identifying Differential Functions Of Cancer Mutations Using A Structurally Resolved Protein Interaction Network |
Hatice Billur Engin |
| Deconvolution of massively-parallel reporter assays tiling 15,000 human regulatory regions reveal activating and repressive regulatory sites at nucleotide-level resolution |
Jason Ernst |
| Network Infusion to infer information sources in networks |
Soheil Feizi |
| ATAC-seq is predictive of chromatin state |
Chuan Sheng Foo |
| Precision Medicine Using Computational Regulatory Models |
Brendan Frey |
| Predicting response to Arthritis treatments: regression-based Gaussian processes on small sets of SNPs |
Javier García-García |
| The Broad-DREAM Gene Essentiality Prediction Challenge: Motivation, Data, Scoring and Results |
Mehmet Gönen |
| Q & A session: The Broad-DREAM Gene Essentiality Prediction Challenge: Motivation, Data, Scoring and Results |
Mehmet Gönen |
| Enhancer poising and regulatory locus complexity shape transcriptional programs in hematopoietic differentiation |
Alvaro Gonzalez |
| Predicting gene essentiality using linear-time greedy feature selection |
Peddinti Gopalacharyulu |
| A strategy to select most informative biomarkers for cancer cell lines, |
Yuanfang Guan |
| The Cyni framework for network inference in Cytoscape |
Oriol Guitart Pla |
| A validated gene regulatory network and GWAS to identify early transcription factors in T-cell associated diseases |
Mika Gustafsson |
| Cell-to-cell variability in overcoming a caspase-8 activity threshold explains fractional killing by TRAIL |
Marc Hafner |
| Systematic interrogation of vulnerabilities in KRAS driven cancers |
William Hahn |
| Single Cell Functional Proteomics: Experimental Methods and Analysis Algorithms that Draw from the Physico-Chemical Laws |
James Heath |
| Genome-wide map of regulatory interactions in the human genome |
Nastaran Heidari |
| Network-based stratification of tumor profiles |
Matan Hofree |
| Master Regulators of Breast Cancer Subtypes |
Archana Iyer |
| Integrative analysis of haplotype-resolved epigenomes across human tissues |
Inkyung Jung |
| A pooling-based approach to mapping genetic variants associated with DNA methylation |
Irene Kaplow |
| Learning kernel-based feature representation for gene essentiality prediction |
Masayuki Karasuyama |
| Variability in B-vitamin dependencies in the human microbiome genomes |
Matvei Khoroshkin |
| Synthesizing signaling pathways from temporal phosphoproteomic data |
Ali Sinan Koksal |
| A first truly systems level mechanistic model – unravelling the gene regulation of Th2 differentiation |
Mattias Köpsén |
| The Dream AML Outcome Prediction Challenge: Motivation, Data, Scoring & Results |
Steven Kornblau |
| Understanding multicellular function and disease with human tissue-specific networks |
Arjun Krishnan |
| Enhancer RNAs reveal widespread chromatin reorganization in prostate cancer cell lines |
Ville Kytölä |
| Comparison of D. melanogaster, C. elegans Developmental Stages, Tissues, Cells by modENCODE RNA-Seq data |
Jingyi (Jessica) Li |
| Evolution-informed Modeling to Predict AML Outcomes |
Li Liu |
| WikiPathways App |
Samad Lotia |
| Context-specific regulation by miR-155 through ApA-dependent and independent mechanisms |
Yuheng Lu |
| Epigenomics of the mammalian brain |
Chongyuan Luo |
| Ensemble-based Design of Experiments for Gene Regulatory Networks |
Erica Manesso |
| The DREAM Rheumatoid Arthritis Responder Challenge: Motivation, Data, Scoring and Results |
Lara Mangravite |
| Multi-species network inference improves gene regulatory network reconstruction for early embryonic development in Drosophila |
Tom Michoel |
| A Cytoscape App for NCBI's Conserved Domain Database |
John "Scooter" Morris |
| Are all genetic variants in DNase I sensitivity regions functional? |
Gregory Moyerbrailean |
| Integrated omics analysis pipeline for model organism with Cytoscape |
Kozo Nishida |
| High Parameter Single Cell Analysis define a Structured Immune System & Cancer Hierarchies |
Garry Nolan |
| A scalable method for molecular network reconstruction identifies properties of targets and mutations in acute myeloid leukemia |
Giovanni Paternostro |
| Computational dissection of phenotypic and functional heterogeneity in cancer |
Dana Pe'er |
| Identifying genetic and environmental determinants of gene expression |
Roger Pique-Regi |
| Accessing NDEx from Cytoscape |
Dexter Pratt |
| Cell type-specific regulatory networks reveal common pathways of disease variants |
Gerald Quon |
| Acute Myeloid Leukemia Outcome Prediction Challenge |
Amina Qutub |
| Fast-SL: An efficient algorithm to identify synthetic lethal reaction/gene sets in metabolic networks |
Karthik Raman |
| Pathways on demand: automated reconstruction of human signaling networks |
Anna Ritz |
| Trafficking and Signaling Interplay Modeling After Serotonin Receptor Activation |
Aurélien Rizk |
| Quantitative Modeling of Transcription Factor Binding Specificities using DNA Shape |
Remo Rohs |
| Genome-wide transcriptional machinery of a cell-fate choice: the early T-cell pathway |
Ellen Rothenberg |
| Pathway-based biomarkers specifically and robustly classify diverse multiple diseases |
Ron Shamir |
| Regulatory Genomics Keynote: Next Generation Functional Analysis of Genetic Variants |
Jay Shendure |
| Systems Biology Keynote: Integrative Analysis of Data from The Cancer Genome Atlas |
Ilya Shmulevich |
| The Future of Genomic Databases |
Lincoln Stein |
| Q & A session: The Future of Genomic Databases |
Lincoln Stein |
| Network modeling reveals key features of epithelial-to-mesenchymal transition dynamics in liver cancer invasion |
Steven Steinway |
| cyNeo4j - Connecting Neo4j and Cytoscape |
Georg Summer |
| Regulatory Genomics Keynote: Inferring Gene Regulation in the Single Cell Era |
Amos Tanay |
| Systematic study of synthetic transcript features in S. cerevisiae exposes gene-expression determinants |
Tamir Tuller |
| Simulation predicts IGFBP2-HIF1α interaction drives glioblastoma growth |
Ka Wai Lin |
| Dissecting germ cell metabolism through network modeling |
Leanne Whitmore |
| cDREM: Inferring dynamic combinatorial gene regulation |
Aaron Wise |
| Disease gene prioritization using network and feature |
Bingqing Xie |
| Regulatory Genomics Keynote: Insights from transcriptome-wide RNA binding protein-RNA networks |
Gene Yeo |
| Joint learning over drugs improves prediction of cancer drug response |
Han Yuan |
| A generic method for predicting clinical outcomes and drug response |
Fan Zhu |