Go directly to: [Tuesday - November 17] [Wednesday - November 18]

*Schedule subject to change.

SUNDAY – DAY 1 – November 15, 2015
2:00 pm 5:00 pm Registration On site
Location: Independence Lobby
3:15 pm 3:30 pm Welcome & Announcements
Room: Independence A & B
3:30 pm 3:50 pm Invited Presentation:
Project Data Sphere® initiative overview
Liz Zhou
Room: Independence A & B
Room: Independence A & B
3:50 pm 4:10 pm Introduction to the DREAM Prostate Cancer Challenge - Jim Costello
4:10 pm 4:20 pm Presentation of Certificates
4:20 pm 4:40 pm Best Performer SC1
Predicting patient survival in the DREAM 9.5 mCRPC challenge
- Teemu D. Laajala, Suleiman Khan, Antti Airola, Tuomas Mirtti, Tapio Pahikkala, Peddinti Gopalacharyulu, Tero Aittokallio
4:40 pm 5:00 pm- Best Performer SC2
Docetaxel adverse event prediction: a boosting method application
Fatemeh Seyednasrollah, Mehrad Mahmoudian, Outi Hirvonen, Sirkku Jyrkkiö, and Laura L. Elo
5:00 pm 5:20 pm Best Performer SC3
Predicting discontinuation due to adverse effect in mCRPC
- Yuanfang Guan
5:20 pm 5:30 pm NCI contracts for Best performers:
Dan Gallahan
5:30 pm 6:00 pm Preparation for the Hackathon
6:00 pm 9:00 pm DREAM Hackathon
For pre-registration go to
Room: Independence C & D
9:00 pm Adjourn
MONDAY – DAY 2 – November 16, 2015
8:00 am 6:00 pm Registration On site
Location: Independence Lobby
8:45 am 9:00 am Morning Welcome & Announcements
Room: Independence A & B
9:00 am 9:45 am Keynote: Leslie Vosshall
The Known and Unknown of Human Smell
Room: Independence A & B
Room: Independence A & B
9:45 am 10:05 am Introduction to the DREAM Olfaction Challenge
Andreas Keller
10:05 am 10:15 am Presentation of Certificates
10:15 am 10:35 am Best Performer SC1: Guanlab
Predicting olfaction response for each individual - Yuanfang Guan
10:35 am 10:55 am Best Performer SC2: IKW Allstars
From Shape to Smell: Predicting Olfactory Perceptual Descriptors using Molecular Structural Information
- Richard C. Gerkin
10:55 am 11:15 am DREAM Olfaction Prediction Challenge Lessons Learned - Amit Dhurandhar
11:15 am 11:45 am Coffee Break with Posters
Room: Liberty AB
Room: Independence A & B
11:45 am 12:05 pm Using the Power of Crowdsourcing to Catalyze Breakthroughs in Amyotrophic Lateral Sclerosis
- Neta Zach
12:05 pm 12:15 pm Presentation of Certificates
12:15 pm 12:35 pm Best Performer SC1:
A Boosting Approach to Predicting ALSFRS Slope for the PRO-ACT Database, Wen-Chieh Fang
12:35 pm 12:55 pm Best Performer SC2 & SC4
Predicting ALS survival through complete ranking of censored data, Yuanfang Guan
12:55 pm 1:15 pm Best Performer SC3: Using aggregated weights along paths across random forest to select important features and predict ALS progression, Jinfeng Xiao
1:15 pm 2:15 pm Lunch with Posters
2:15 pm 3:00 pm Keynote: Steve Quake
Single Cell Genomics
3:00 pm 3:05 pm NCI Cancer Systems Biology Consortium - Dan Gallahan
DREAM SMC CHALLENGE, Paul Boutros, Chair
Room: Independence A & B
3:05 pm 3:25 pm The ICGC-TCGA DREAM Somatic Mutation Calling Challenge: benchmarking somatic variant detection - Josh Stuart
3:25 pm 3:30 pm Presentation of Certificates
3:30 pm 3:50 pm Best Performer SV:
novoBreak: a k-mer targeted assembly algorithm for breakpoint detection in cancer genomes - Zechen Chong
3:50 pm 4:10 pm Best Performer SC3:
Strategies for SNV and Indel Detection in the DREAM Challenges
Team WashU, R. Jay Mashl
4:10 pm 4:30 pm Lessons from the SMC-DNA IS Challenges & Looking Forward
- Paul Boutros
4:30 pm 5:00 pm Coffee Break with Posters
Room: Liberty AB
Room: Independence A & B
5:00 pm 5:20 pm Crowdsourcing combinatorial therapies: The AZ-Sanger DREAM synergy prediction challenge
- Michael Menden
5:20 pm 5:40 pm Preventing data-leakage in leaderboard evaluations: the Ladder and LadderBoot algorithms
- Elias Chaibub Neto
5:40 pm 5:50 pm The DREAM Challenges channel: open science publishing for all participating DREAMers - Michael Markie
5:50 pm 6:00 pm DREAM Brainstorm
6:00 pm 7:30 pm DREAM Posters on Display
Room: Liberty AB
7:35pm   DREAM Poster presenters:
Please remove posters.
6:30 pm 9:30 pm DREAM Hackathon
Room: Independence C & D
9:30 pm Adjourn
TUESDAY – DAY 3 – November 17, 2015
8:00 am 6:00 pm Registration On site
Location: Independence Lobby
8:45 am 9:00 am Morning Welcome & Announcements
Room: Independence A & B
9:00 am 9:45 am Keynote: Bonnie Berger
Scaling with Compressive Algorithms
Room: Independence A & B
C & D
A & B
9:50 am 10:05 am SB Oral Talk 01
MiSL: a method for mining synthetic lethal partners of recurrent cancer mutations uncovers novel mutation-specific therapeutic targets

Subarna Sinha
RG Oral Talk 01
Transcription factor binding site prediction in vivo using DNA sequence and shape features

Anthony Mathelier

10:05 am 10:20 am SB Oral Talk 02
The germline genetic component of drug sensitivity in cancer cell lines

Michael Menden
RG Oral Talk 02
A PBM-based glossary for motif discovery in regulatory regions

Luca Mariani
10:20 am 10:45 am Coffee Break with Posters
Room: Liberty AB
C & D
A & B
10:45 am 11:00 am SB Oral Talk 03
Estimating the Number and Diversity of Cancer Mutations In the Overall Population from 5,319 Complete Cancer Genomes

Prathik Naidu
RG Oral Talk 03
Distinct specificities of the androgen and glucocorticoid receptors revealed using feature-based recognition model analysis of SELEX data

Harmen J. Bussemaker
11:00 am 11:15 am SB Oral Talk 04
From phenotypic to molecular synergy: A transcriptional study of the dynamics of drug combinations based on single drug responses

Mehmet Eren Ahsen
RG Oral Talk 04
How do closely related transcription factors recognize distinct genomic targets?

Raluca Gordan
11:15 am 11:30 am SB Oral Talk 05
RG Oral Talk 05
Quantitative modeling of gene expression from sequence, using DNA shape-based model of binding sites

Pei-Chen Peng
11:30 am 12:45 pm Lunch with Posters (odd)
Room: Liberty AB
12:45 pm 1:30 pm Keynote: Tuuli Lappalainen
Functional Variation in the Human Genome: Lessons from the Transcriptome
Room: Independence A & B
C & D
A & B
1:35 pm 1:50 pm SB Oral Talk 06
Large-scale models of signal propagation derived from phosphoproteomic data to study kinase inhibitors

Julio Saez-Rodriguez
RG Oral Talk 06
Tracking the Evolution of 3D Gene Organization

Alon Diament

1:50 pm 2:05 pm SB Oral Talk 07
Global chromatin defects and spurious transcription defines a novel subset of human cancers

Kakajan Komurov
RG Oral Talk 07
Three-dimensional analysis of regulatory features reveals functional enhancer-associated loops

Yao Wang
2:05 pm 2:20 pm SB Oral Talk 08
Network Maximal Correlation to Infer Nonlinear Gene Modules in Cancer

Soheil Feizi
RG Oral Talk 08
An integrated model for detecting significant chromatin interactions from high-resolution Hi-C data

Mark Carty
2:20 pm 2:35 pm SB Oral Talk 09
Integrating single cell transcriptional signatures and cell-cell interaction network models to study multiscale control of liver regeneration dynamics

Raj Vadigepalli
RG Oral Talk 09
Visualizing three-dimensional organization and long-range interactions of the mammalian genome with the 3D Genome Browser

Yanli Wang
2:35 pm 3:00 pm Coffee Break with Posters
Room: Liberty AB
3:00 pm 3:45 pm Keynote: James (Jay) Bradner
Targeting Cancer Core Regulatory Circuitry
Room: Independence A & B
C & D
A & B
3:50 pm 4:05 pm SB Oral Talk 10
Understanding Breast Cancer Heterogeneity through Personalized Drosophila Models

Jennifer EL Diaz
RG Oral Talk 10
Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet

Coby Viner
4:05 pm 4:20 pm SB Oral Talk 11
A linear time-invariant model of phenotype dynamics in breast cancer cell populations

Margaret P. Chapman
RG Oral Talk 11
Genome-wide mapping of histone marks at single-nucleosome resolution

Marcelo Rivas-Astroza
4:20 pm 4:35 pm SB Oral Talk 12
Precision drug rescue and drug repurposing using structural systems pharmacology

Lei Xie
RG Oral Talk 12
Creating a library of genome-wide chromatin state patterns during B lymphopoiesis

Mark Maienschein-Cline
4:35 pm 4:50 pm SB Oral Talk 13
Bringing big genomic data into focus for studying complex diseases in specific biological contexts

Arjun Krishnan
RG Oral Talk 13
AEF: A methodology based on Assortativity of Epigenetic Features in promoter centered chromatin interaction networks identifies Polycomb and RNA Polymerase as main players

Vera Pancaldi
4:50 pm 5:35 pm Keynote: William Stafford Noble
Gene Regulation in 3D
Room: Independence A & B
5:35 pm 7:00 pm Poster Reception - SB and RG
Room: Liberty AB
WEDNESDAY – DAY 4 – November 18, 2015
8:00 am 11:00 am Registration On site
Location: Independence Lobby
8:45 am 9:00 am Morning Welcome & Announcements
Room: Independence A & B
9:00 am 9:45 am Keynote: Michael Shen
Systems Analyses of Prostate Development and Cancer

Room: Independence A & B
C & D
A & B
9:50 am 10:05 am SB Oral Talk 14
Integrating transcriptomic and proteomic data with predictive regulatory network models of host response to pathogens

Deborah Chasman
RG Oral Talk 14
Nucleotide Sequence Composition Adjacent to Intronic Splice Sites Improves Splicing Efficiency and Reduces Translation Costs in Fungi

Tamir Tuller
10:05 am 10:20 am SB Oral Talk 15
Microbes are STICKY – Large-scale Inference and Topological Analysis of Microbial Interaction Networks

Christian L. Müller
RG Oral Talk 15
Lobular Scale Spatio-temporal Modeling of Calcium Signal Propagation in the Liver

Aalap Verma
10:20 am 10:35 am SB Oral Talk 16
Multi-omics learning and optimal experimental design for microbial organisms

Minseung Kim
RG Oral Talk 16
Dysregulated transcription factor networks and clusters in breast cancer subtypes, identified by coexpression and cistromic data integration

Qian Zhu
10:35 am 11:00 am Coffee Break with Posters
Room: Liberty AB
11:00 am 11:45 am Keynote: Julia Zeitlinger
Combinatorial Regulation of Enhancers during Drosophila Development
Room: Independence A & B
C & D
A & B
11:50 am 12:05 pm RG Oral Talk 17
Transcription and differential DNA repair underlies promoter mutation hotspots in cancer genomes

Dilmi Perera

RG Oral Talk 18
The regulation of distal enhancers and silencers from the Cebpa locus during hematopoiesis, inferred using a transcriptional model

12:05 pm 12:20 pm RG Oral Talk 19
Comparison of Methods to Predict Impact of Regulatory Variants

Michael Beer
RG Oral Talk 20
Super-enhancers delineate disease-associated regulatory nodes in T cells

Golnaz Vahedi
12:20 pm 12:35 pm RG Oral Talk 21
Evaluating Genetic Variation Impact on Transcription Factor Binding Sites

Wenqiang Shi
RG Oral Talk 22
Identifying condition specific transcription factor binding with ATAC-seq

Roger Pique-Regi
12:35 pm 1:30 pm Lunch with Posters (even)
Room: Liberty AB
1:30 pm 2:15 pm Keynote: Andre Levchenko
How Noisy is Noise? Analysis and Interpretation of Variability in Signaling Networks
Room: Independence A & B
C & D
A & B
2:20 pm 2:35 pm SB Oral Talk 17
tRNA-derived fragments in Drosophila and their potential targets

Andrey Grigoriev
RG Oral Talk 23
An Experimentally Supported Model of the Bacillus subtilis Global Transcriptional Regulatory Network

Mario L. Arrieta
2:35 pm 2:50 pm SB Oral Talk 18
High-throughput allele-specific expression across 250 environmental conditions

Gregory Moyerbrailean
RG Oral Talk 24
Transcriptional regulatory network inference for rare immune cell populations from gene expression and chromatin accessibility measurements

Emily Miraldi
2:50 pm 3:05 pm SB Oral Talk 19
DREISS: dynamics of gene expression driven by external and internal regulatory networks based on state space model

Daifeng Wang
RG Oral Talk 25
Network model of normal gene expression predicts gene perturbation fold changes

Sudhir Varma
3:05 pm 3:20 pm SB Oral Talk 20
SplashRNA: accurate prediction of potent shRNAs with a sequential classification strategy

Lauren Fairchild
3:20 pm 4:05 pm Keynote: Olga Troyanskaya
From Piles of Data to Understanding Human Disease
Room: Independence A & B
4:05 pm 4:20 pm Conference Closing Comments
Room: Independence A & B