RECOMB Conference on Regulatory and Systems Genomics,
with Dream Challenges 2014

The full listing of talks can be found below.

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

Title Presenter
Opening Remarks (Thursday)
Opening Remarks (Wednesday)
Reading Lists
RECOMB 2015 Announcement
Future DREAM 9.5 Challenges
RA Challenge Awards
RA Challenge Discussion
SMC Challenge Discussion
Opening Remarks (Tuesday)
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