RECOMB Conference on Regulatory and Systems Genomics,
with Dream Challenges 2012

The full listing of talks can be found below.

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

Title Presenter
High-resolution mapping of nucleosomes in mammalian T cells allows unbiased identification of functional transcription factor binding sites Tarmo Äijö
Virtual proteomics: inferring global protein activity profiles by network based analysis of gene expression signatures Mariano Alvarez
A non-parametric model-based framework to quantify heterogenous populations in fluorescence activated cell sorting data Benedict Anchang
Changing chasses and inventing elements: developing a combined systems biology and engineering approach to designing complex function in cells Adam Arkin
Genomic Landscape of Anthropoid-Specific Functional Elements Reveals Molecular Correlates of Primate Traits Nirmala Arul Rayan
A graph-based comparative analysis of three-dimensional organization of chromosomes in yeast and mammals Robert Atlas
Patterns of interaction in the genetics of complex human traits and guided discovery from diverse genomic assays Alexis Battle
Predicting the fine structure of cis-regulatory elements Michael Beer
The cis-regulatory landscape of early neocortex development Gill Bejerano
Scoring the Sage Bionetworks-DREAM Breast Cancer Prognosis Challenge Erhan Bilal
Genome regulation by long noncoding RNAs Howard Chang
Breast cancer prognosis model using Attractor Metagenes Wei-Yi Cheng
Results for the NCI-DREAM Drug Sensitivity Challenge James Costello
A Computational Whole-Cell Model of Mycoplasma genitalium Markus Covert
Folding principles of genomes Job Dekker
Cellular resolution models of enhancer function Angela DePace
Turning networks into ontologies of gene function Janusz Dutkowski
Genome-wide analysis of DNA methylation and genotype in 750 individuals reveals global regulatory changes in brain enhancers associated with Alzheimer’s disease Matthew Eaton
Exploring personal and population level epigenome dynamics Joseph Ecker
Cell signaling at the single-cell level Michael Elowitz
Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites Martin Enge
Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types Jason Ernst
Predicting tissue-specific regulatory enhancers by integrating diverse genomic data Genevieve Erwin
Stochastic cytokine expression induces mixed T cell states Miaoqing Fang
Predicting ALS Progression with Bayesian Additive Regression Trees Lilly Fang & Lester Mackey
Network deconvolution: a universal method to distinguish direct dependencies over networks Soheil Feizi
Modeling and predicting oncogene addictio Dean Felsher
Identifying therapeutic targets by using network models to integrate proteomic, transcriptional, and epigenomic data Ernest Fraenkel
Corruption of denial Stephen Friend
Graphical model-based algorithms for inferring the combinatorial regulatory code of transcription factors Audrey Fu
The NCI-DREAM challenge: multiple views of a DREAM and what we learned from them Elisabeth Georgii  & Mehmet Gönen
Identifying a landscape of DNA methylation-driven genes in cancer Olivier Gevaert
The evolution of epigenetic and genetic regulatory mechanisms in primates Yoav Gilad
Decoding ChIP-seq with double-binding signal provides site detection with high-resolution and predictions of cooperative interactions Antonio Gomes
Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape Raluca Gordan
An in vitro system for identification of predictive markers Joe Gray
Introduction to the NCI DREAM7 Challenge Laura Heiser
Transcription factor binding at specific and ubiquitous open chromatin sites across multiple human cell types Martin Hemberg
Systematic prediction and validation of enhancer regulatory motifs in ENCODE cell lines Pouya Kheradpour
Developing a quantitative, cellular resolution morphology and gene expression atlas for Drosophila embryogenesis: a digital 'Campos-Ortega and Hartenstein’ David Knowles
Integrated analyses of drug resistance networks in breast cancer Kakajan Komurov
Scoring the DREAM-Phil Bowen ALS Prediction Prize4Life Robert Küffner
IDBA-MT: de novo assembler for metatranscriptomic data generated from next-generation sequencing technology Henry C.M. Leung
Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data Song Li
The DREAM-Phil Bowen ALS Prediction Prize4Life - Best performer Guang Li  
In vivo human brain regulatory networks: lncRNA genes at cis-trans interfaces Leonard Lipovich
Divide-and-conquer game tree heuristics for iterative network parameter inference Po-Ru Loh
Identifying informative modular features for predictions of breast cancer clinical outcomes Xinghua Lu
A validated global Th17 transcriptional regulatory network derived from integration of multiple genomic data types Aviv Madar
The Sage Bionetworks-DREAM Breast Cancer Prognosis Challenge Adam Margolin
Prediction of cancer cell sensitivity to drugs based on genomic and chemical properties Michael Menden
Scoring the Network Topology and Parameter Inference Challenge Pablo Meyer
Fractal and systems genetics of phenotypic variation and disease risk Joseph Nadeau
Extracting the molecular signature of the cell of origin in acute myeloid leukemia Monica Nicolau
RAP: accurate and fast motif finding based on protein binding microarray data Yaron Orenstein
A genome-scale modelling approach to study inborn errors of liver metabolism: towards an in-silico patient Roberto Pagliarini
Top-down network analysis to drive bottom-up modeling of physiological processes Christopher Poirel
Allele specific gene expression in F1 mice from a reciprocal cross Narayanan Raghupathy
Building accurate sequence-to-affinity models from protein binding microarray data using FeatureREDUCE Todd Riley
Multi-layered stochasticity and paracrine signal propagation shape the type-I interferon response Melanie Rinas
Genome analysis based on the integration of DNA sequence and shape Remo Rohs
The Network Topology and Parameter Inference Challenge Julio Saez-Rodriguez
Inferring small compound mode of action from cell-context specific regulatory networks Yao Shen
Reverse engineering of Alzheimer’s disease neuronal transcriptional networks — Validated targets point to the loss of histone acetylation homeostasis in the disease progression William Shin
Transcription factor target gene identification based on ChIP-seq data Weronika Sikora-Wohlfeld
Quantitative models of gene expression and TF-DNA binding: two case studies Saurabh Sinha
Predictive and integrated systems biology models for malaria drug discovery Geoffrey Siwo
Architecture and dynamics of eukaryotic transcription factor regulatory networks Andrew Stergachis
Optimal sparsity criteria for network inference Andreas Tjärnberg
Monitoring translation initiation from frame-shifted start codons in S. cerevisiae using fluorescent proteins reveals new translation initiation rules Tamir Tuller
Integrative genetic, transcriptional and epigenetic network analysis identifies modulators of chemoresistance in pancreatic cancer Oana Ursu
Monitoring protein synthesis one codon at a time through ribosome profiling Jonathan Weissman
DNase-seq predicts regions of rotational nucleosome stability and suggests sequence asymmetry around the dyad axis Deborah Winter
Functional genomic analysis of mitochondrial RNA processing Ashley Wolf
Cooperative and antagonistic sense-antisense pairs in human breast and skin cancer: emergence of multifunctional primate-specific lncRNA networks Emily Wood
Extensive variation in protein levels and genetic determinants in humans Linfeng Wu
Making a face: what epigenomics can teach us about human development and variation Joanna Wysocka
Predicting synergistic effects of compound combinations using genomics data Yang Xie
Detecting expression modules across species using a spin model Koon-Kiu Yan
A map of the cis-regulatory sequences in the mouse genome Feng Yue
Being PRO-ACTive: using crowdsourcing to catalyze breakthroughs in amyotrophic lateral aclerosis (ALS) - the DREAM-Phil Bowen ALS Prediction Prize4Life Neta Zach
Comparative epigenomic annotation of regulatory DNA Sheng Zhong