Agenda

Please note that what follows below is a tentative schedule and times and speaker assignments may change before the conference. Updates, including presentation titles, additional speakers, and DREAM best performers, will be made here when they become available.


Monday, November 12, 2012 - Regulatory Genomics Day 1

8:15 AM Registration and breakfast
8:45 AM Opening remarks
Manolis Kellis - Massachusetts Institute of Technology
   
  Regulatory Genomics Session 1 - Dissecting Enhancers
9:00 AM Len Pennacchio - DOE Joint Genome Institute (KEYNOTE ADDRESS)
Beyond exomes: noncoding in vivo function and human disease
9:30 AM Michael Beer - Johns Hopkins University
Predicting the fine structure of cis-regulatory elements
9:45 AM Pouya Kheradpour - Massachusetts Institute of Technology
Systematic prediction and validation of enhancer regulatory motifs in ENCODE cell lines
10:00 AM Remo Rohs - University of Southern California
Genome analysis based on the integration of DNA sequence and shape
10:15 AM Antonio Gomes - Boston University
Decoding ChIP-seq with double-binding signal provides site detection with high-resolution and predictions of cooperative interactions
   
10:30 AM Coffee break
   
  Regulatory Genomics Session 2 - Chromatin Structure and Organization
11:00 AM Job Dekker - University of Massachusetts Medical School (KEYNOTE ADDRESS)
Folding principles of genomes
11:30 AM Martin Enge - Karolinska Institute
Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites
11:45 AM Raluca Gordan - Duke University
Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape
12:00 PM Robert Atlas - University of Wisconsin, Madison
A graph-based comparative analysis of three-dimensional organization of chromosomes in yeast and mammals
   
12:15 PM Lunch
Poster Session - Regulatory Genomics

Odd numbered posters
   
  Regulatory Genomics Session 3 - Regulatory Evolution
1:15 PM Angela DePace - Harvard Medical School (KEYNOTE ADDRESS)
Cellular resolution models of enhancer function
1:45 PM David Knowles - University of California, Berkeley
Developing a quantitative, cellular resolution morphology and gene expression atlas for Drosophila embryogenesis: a digital 'Campos-Ortega and Hartenstein’
2:00 PM Nirmala Arul Rayan - Genome Institute of Singapore
Insights from anthropoid-specific functional elements in the human genome
2:15 PM Sheng Zhong - University of California, San Diego
Comparative epigenomic annotation of regulatory DNA
   
2:30 PM Coffee break
   
  Regulatory Genomics Session 4 - Motif Models
3:00 PM Saurabh Sinha - University of Illinois, Urbana-Champaign (KEYNOTE ADDRESS)
Quantitative models of gene expression and TF-DNA binding: two case studies
3:30 PM Yaron Orenstein - Tel Aviv University
RAP: accurate and fast motif finding based on protein binding microarray data
3:45 PM Todd Riley - Columbia University
Building accurate sequence-to-affinity models from protein binding microarray data using FeatureREDUCE
   
4:00 PM Coffee break
   
  Regulatory Genomics Session 5 - RNA Regulation
4:30 PM Howard Chang - Stanford University (KEYNOTE ADDRESS)
Genome regulation by long noncoding RNAs
5:00 PM Leonard Lipovich - Wayne State University
In vivo human brain regulatory networks: lncRNA genes at cis-trans interfaces
5:15 PM Emily Wood - Wayne State University
Cooperative and antagonistic sense-antisense pairs in human breast and skin cancer: emergence of multifunctional primate-specific lncRNA networks
5:30 PM Song Li - Duke University
Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data
5:45 PM Tamir Tuller - Tel Aviv University
Monitoring translation initiation from frame-shifted start codons in S. cerevisiae using fluorescent proteins reveals new translation initiation rules
   
6:00 PM RegGen TopTen Best Paper Awards Presentation
   
6:15 PM RECOMB Regulatory Genomics Social Hour
Posters available for viewing.
   
7:15 PM End of Day One
   

Tuesday, November 13, 2012 - Regulatory Genomics Day 2 & DREAM Day 1

7:45 AM Registration and breakfast
8:15 AM Opening remarks
Gustavo Stolovitzky - IBM Research
Introduction to DREAM7
   
8:30 AM Joe Gray - Oregon Health & Science University (KEYNOTE ADDRESS)
An in vitro system for identification of predictive markers
   
  DREAM Session 1 - The NCI-DREAM Drug Sensitivity Prediction Challenge
9:00 AM Laura Heiser - Oregon Health & Science University
The quest for personalized medicine: a cell line model system for the identification of response-associated aberrations
9:20 AM James Costello - Boston University, Howard Hughes Medical Institute
Results for the NCI-DREAM Drug Sensitivity Challenge
9:40 AM Elisabeth Georgii & Mehmet Gönen - Helsinki Institute for Information Technology, Aalto University
The NCI-DREAM challenge: multiple views of a DREAM and what we learned from them
10:00 AM Yang Xie - University of Texas Southwestern Medical Center
Predicting synergistic effects of compound combinations using genomics data
   
10:20 AM Coffee break
   
  DREAM Session 2 - The DREAM-Phil Bowen ALS Prediction Prize4Life
10:50 AM Neta Zach - Prize4Life, Inc.
Being PRO-ACTive: using crowdsourcing to catalyze breakthroughs in amyotrophic lateral aclerosis (ALS) - the DREAM-Phil Bowen ALS Prediction Prize4Life
11:20 AM Robert Küffner & Johann Hawe - Ludwig Maximilians University Munich
Scoring the DREAM-Phil Bowen ALS Prediction Prize4Life
11:40 AM The DREAM-Phil Bowen ALS Prediction Prize4Life - Best performers to be announced
12:00 PM The DREAM-Phil Bowen ALS Prediction Prize4Life - Best performers to be announced
   
12:20 PM Lunch
Poster Session - Regulatory Genomics

Even numbered posters
   
  Regulatory Genomics Session 6 - Epigenomic Maps
1:30 PM Joanna Wysocka - Stanford University
Making a face: what epigenomics can teach us about human development and variation
2:00 PM Feng Yue - Ludwig Center for Cancer Research
A map of the cis-regulatory sequences in the mouse genome
2:15 PM Deborah Winter - Duke University
DNase-seq predicts regions of rotational nucleosome stability and suggests sequence asymmetry around the dyad axis
2:30 PM Tarmo Äijö - Aalto University of School of Science
High-resolution mapping of nucleosomes in mammalian T cells allows unbiased identification of functional transcription factor binding sites
   
2:45 PM Coffee break
   
  Regulatory Genomics Session 7 - Chromatin Dynamics
3:15 PM Jason Ernst - University of California, Los Angeles
Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types
3:30 PM Martin Hemberg - Boston Children’s Hospital
Transcription factor binding at specific and ubiquitous open chromatin sites across multiple human cell types
3:45 PM Genevieve Erwin - Gladstone Institutes, University of California, San Francisco
Predicting tissue-specific regulatory enhancers by integrating diverse genomic data
   
4:00 PM Coffee break
   
  Regulatory Genomics Session 8 - Variation
4:30 PM Yoav Gilad - University of Chicago (KEYNOTE ADDRESS)
The evolution of epigenetic and genetic regulatory mechanisms in primates
4:45 PM Alexis Battle - Stanford University
Patterns of interaction in the genetics of complex human traits and guided discovery from diverse genomic assays
5:00 PM Matthew Eaton - Massachusetts Institute of Technology
Genome-wide analysis of DNA methylation and genotype in 750 individuals reveals global regulatory changes in brain enhancers associated with Alzheimer’s disease
5:15 PM Linfeng Wu - Stanford University
Extensive variation in protein levels and genetic determinants in humans
5:30 PM Narayanan Raghupathy - The Jackson Laboratory
Allele specific gene expression in F1 mice from a reciprocal cross
   
5:45 PM Dean Felsher - Stanford University School of Medicine (KEYNOTE ADDRESS)
Modeling and predicting oncogene addiction
   
6:15 PM End of Day Two
   

Wednesday, November 14, 2012 - Systems Biology Day 1 & DREAM Day 2

8:15 AM Registration and breakfast
8:45 AM Opening remarks
Andrea Califano - Columbia University
   
  Systems Biology Session 1 - Modeling, from Theory to Experiments I
9:00 AM Jonathan Weissman - University of California, San Francisco (KEYNOTE ADDRESS)
Monitoring protein synthesis one codon at a time through ribosome profiling
9:30 AM Michael Menden - EMBL: European Bioinformatics Institute
Prediction of cancer cell sensitivity to drugs based on genomic and chemical properties
9:45 AM Mariano Alvarez - Columbia University
Virtual proteomics: inferring global protein activity profiles by network based analysis of gene expression signatures
10:00 AM Yao Shen - Columbia University
Inferring small compound mode of action from cell-context specific regulatory networks
10:15 AM Oana Ursu - MIT and Stanford University School of Medicine
Integrative genetic, transcriptional and epigenetic network analysis identifies modulators of chemoresistance in pancreatic cancer
   
10:30 AM Coffee break
   
  Systems Biology Session 2 - Modeling, from Theory to Experiments II
11:00 AM Michael Elowitz - Caltech (KEYNOTE ADDRESS)
Cell signaling at the single-cell level
11:30 AM Geoffrey Siwo - University of Notre Dame
Predictive and integrated systems biology models for malaria drug discovery
11:45 AM Melanie Rinas - German Cancer Research Center
Multi-layered stochasticity and paracrine signal propagation shape the type-I interferon response
12:00 PM Kakajan Komurov - Cincinnati Children's Hospital
Integrated analyses of drug resistance networks in breast cancer
   
12:15 PM Lunch
Poster Session - Systems Biology

Odd numbered posters
   
  DREAM Session 3 - The Network Topology and Parameter Inference Challenge
1:30 PM Julio Saez-Rodriguez - European Bioinformatics Institute
The Network Topology and Parameter Inference Challenge
1:50 PM Pablo Meyer - IBM Research
Scoring the Network Topology and Parameter Inference Challenge
2:10 PM Po-Ru Loh - Massachusetts Institute of Technology
Divide-and-conquer game tree heuristics for iterative network parameter inference
2:30 PM Bernhard Steiert - Freiburg University
Solving the DREAM7 network topology and parameter inference challenge
   
2:50 PM Coffee break
   
  DREAM Session 4 - The Sage Bionetworks-DREAM Breast Cancer Prognosis Challenge
3:20 PM Stephen Friend - Sage Bionetworks (KEYNOTE ADDRESS)
Corruption of denial
3:50 PM Adam Margolin - Sage Bionetworks
The Sage Bionetworks-DREAM Breast Cancer Prognosis Challenge
4:10 PM Erhan Bilal - IBM Research
Scoring the Sage Bionetworks-DREAM Breast Cancer Prognosis Challenge
4:30 PM Wei-Yi Cheng - Columbia University
Breast cancer prognosis model using Attractor Metagenes
4:50 PM Xinhua Lu - University of Pittsburgh
Identifying informative modular features for predictions of breast cancer clinical outcomes
5:10 PM Future challenges for DREAM (ROUND TABLE)
   
6:00 PM RECOMB Systems Biology Social Hour
Posters available for viewing.
   
7:00 PM End of Day Three
   

Thursday, November 15, 2012 - Systems Biology Day 2

8:15 AM Registration and breakfast
8:45 AM Opening remarks
Andrea Califano - Columbia University
   
  Systems Biology Session 3 - Reconstruction and Analysis of Regulatory Networks
9:00 AM Joseph Nadeau - Pacific Northwest Research Institute (KEYNOTE ADDRESS)
Fractal and systems genetics of phenotypic variation and disease risk
9:30 AM William Shin - Columbia University
Reverse engineering of Alzheimer’s disease neuronal transcriptional networks — Validated targets point to the loss of histone acetylation homeostasis in the disease progression
9:45 AM Aviv Madar - New York University
A validated global Th17 transcriptional regulatory network derived from integration of multiple genomic data types
10:00 AM Miaoqing Fang - Massachusetts Institute of Technology
Stochastic cytokine expression induces mixed T cell states
10:15 AM Monica Nicolau - Stanford University
Extracting the molecular signature of the cell of origin in acute myeloid leukemia
10:30 AM Henry C.M. Leung - University of Hong Kong
IDBA-MT: de novo assembler for metatranscriptomic data generated from next-generation sequencing technology
   
10:45 AM Coffee break
   
  Systems Biology Session 4 - Systems Biology of Development and Disease I
11:15 AM Markus Covert - Stanford University (KEYNOTE ADDRESS)
A whole-cell computational model predicts phenotype from genotype
11:45 AM Gill Bejerano - Stanford University
The cis-regulatory landscape of early neocortex development
12:00 PM Andreas Tjärnberg - Stockholm Bioinformatics Centre, Science for Life Laboratory
Optimal sparsity criteria for network inference
12:15 PM Audrey Fu - University of Chicago
Graphical model-based algorithms for inferring the combinatorial regulatory code of transcription factors
12:30 PM Weronika Sikora-Wohlfeld - Biotec TU Dresden
Transcription factor target gene identification based on ChIP-seq data
   
12:45 PM Lunch
Poster Session - Systems Biology

Even numbered posters
   
  Systems Biology Session 5 - Systems Biology of Development and Disease II
1:45 PM Ernest Fraenkel - Massachusetts Institute of Technology (KEYNOTE ADDRESS)
Identifying therapeutic targets by using network models to integrate proteomic, transcriptional, and epigenomic data
2:15 PM Ashley Wolf - Harvard University
Functional genomic analysis of mitochondrial RNA processing
2:30 PM Andrew Stergachis - University of Washington
Architecture and dynamics of eukaryotic transcription factor regulatory networks
2:45 PM Soheil Feizi - Massachusetts Institute of Technology
Network deconvolution: a universal method to distinguish direct dependencies over networks
3:00 PM Olivier Gevaert - Stanford University
Identifying a landscape of DNA methylation-driven genes in cancer
3:15 PM Janusz Dutkowski - University of California, San Diego
Turning networks into ontologies of gene function
   
3:30 PM ISCB Regulatory Genomics SIG – Best Poster Award Presented
   
3:45 PM Coffee break
   
  Systems Biology Session 6 - Elucidating Drug Activity and Sensitivity
4:15 PM Adam Arkin - Lawrence Berkeley National Laboratory (KEYNOTE ADDRESS)
Changing chasses and inventing elements: developing a combined systems biology and engineering approach to designing complex function in cells
4:45 PM Christopher Poirel - Virginia Tech
Top-down network analysis to drive bottom-up modeling of physiological processes
5:00 PM Hillel Kugler - Microsoft Research
A model of stem cell population dynamics: in silico analysis and in vivo validation
5:15 PM Roberto Pagliarini - Telethon Institute of Genetics and Medicine
A genome-scale modelling approach to study inborn errors of liver metabolism: towards an in-silico patient
5:30 PM Benedict Anchang - Stanford University
A non-parametric model-based framework to quantify heterogenous populations in fluorescence activated cell sorting data
5:45 PM Koon-Kiu Yan - Yale University
Detecting expression modules across species using a spin model
   
6:00 PM Closing Remarks