RECOMB Conference on Regulatory and Systems Genomics,
with Dream Challenges 2015

The full listing of talks can be found below.

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

Title Presenter
Welcome & Announcements -
DREAM Hackathon -
From phenotypic to molecular synergy: A transcriptional study of the dynamics of drug combinations based on single drug responses Mehmet Eren Ahsen
Comparison of Methods to Predict Impact of Regulatory Variants Michael Beer
Feature-based analysis of SELEX-seq data reveals distinct specificities of the androgen and glucocorticoid receptors Harmen Bussemaker
A linear time-invariant model of phenotype dynamics in breast cancer cell populations Margaret P Chapman
Integrating transcriptomic and proteomic data with predictive regulatory network models of host response to pathogens Deborah Chasman
novoBreak: a k-mer targeted assembly algorithm for breakpoint detection in cancer genomes Zechen Chong
DREAM Olfaction Prediction Challenge Lessons Learned Amit Dhurandhar
Tracking the Evolution of 3D Gene Organization Alon Diament
A Boosting Approach to Predicting ALSFRS Slope for the PRO-ACT Database Wen-Chieh Fang
From Shape to Smell: Predicting Olfactory Perceptual Descriptors using Molecular Structural Information Richard C Gerkin
How do closely related transcription factors recognize distinct genomic targets? Raluca Gordan
tRNA-derived fragments in Drosophila and their potential targets Andrey Grigoriev
Predicting discontinuation due to adverse effect in mCRPC Yuanfang Guan
Predicting olfaction response for each individual Yuanfang Guan
Predicting ALS survival through complete ranking of censored data Yuanfang Guan
Introduction to the DREAM Olfaction Challenge Andreas Keller
Multi-omics learning and optimal experimental design for microbial organisms Minseung Kim
Predicting patient survival in the DREAM 9.5 mCRPC challenge Teemu Daniel Laajala
Creating a library of genome-wide chromatin state patterns during B lymphopoiesis Mark Maienschein-Cline
A PBM-based glossary for motif discovery in regulatory regions Luca Mariani
Transcription factor binding site prediction in vivo using DNA sequence and shape features Anthony Mathelier
Crowdsourcing combinatorial therapies: The AZ-Sanger DREAM synergy prediction challenge Michael Menden
The germline genetic component of drug sensitivity in cancer cell lines. Michael Menden
Transcriptional regulatory network inference for rare immune cell populations from gene expression and chromatin accessibility measurements Emily Miraldi
High-throughput allele-specific expression across 250 environmental conditions Gregory Moyerbrailean
Microbes are STICKY – Large‐scale Inference and Topological Analysis of Microbial Interaction Networks Christian Mueller
Gene Regulation in 3D William Noble
AEF: Amethodology based on Assortativity of Epigenetic Features in promoter centered chromatin interaction networks identifies Polycomb and RNA polymerase as main players Vera Pancaldi
Quantitative modeling of gene expression from sequence, using DNA shape-based model of binding sites Pei-Chen Peng
Transcription and differential DNA repair underlies promoter mutation hotspots in cancer genomes Dilmi Perera
Single Cell Genomics Stephen Quake
Genome-wide mapping of histone marks at single-nucleosome resolution Marcelo Rivas-Astroza
Large-scale models of signal propagation derived from phosphoproteomic data to study kinase inhibitors Julio Saez Rodriguez
Predicting the adverse event of docetaxel in mCRP patients Fatemeh Seyednasrollah
Evaluating Genetic Variation Impact on Transcription Factor Binding Sites Wenqiang Shi
MiSL: a method for mining synthetic lethal partners of recurrent cancer mutations uncovers novel mutation‐specific therapeutic targets Subarna Sinha
Network model of normal gene expression predicts gene perturbation fold changes Sudhir Varma
Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet Coby Viner
The known and unknown of human smell Leslie Vosshall
Visualizing three-dimensional organization and long-range interactions of the mammalian genome with the 3D Genome Browser Yanli Wang
Using aggregated weights along paths across random forest to select important features and predict ALS progression Jinfeng Xiao
Precision drug rescue and drug repurposing using structural systems pharmacology Lei Xie
Combinatorial Regulation of Enhancers during Drosophila Development Julia Zeitlinger
Project Data Sphere Initiative & the Making of Prostate Cancer DREAM Challenge Fang Zhou