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RSG with DREAM & Cytoscape Workshop | November 6 - 9, 2016 | Phoenix, AZ |Agendas


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*Proposed Programs. Agendas subject to change.

Go directly to: [Monday - Nov 7] [Tuesday - Nov 8]
SUNDAY – DAY 1 – Cytoscape Workshop - November 6, 2016
12:00pm - 5:00pm
Location: Anasazi Lobby
1:00 pm 3:00 pm Cytoscape Workshop
Location: Kachina Room
3:00 pm 3:30 pm Break
3:30 pm 5:00 pm Cytoscape Workshop (continued) - Location: Kachina Room
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MONDAY – DAY 2 – November 7, 2016
8:00am - 6:00pm
Location: Anasazi Lobby
8:00 am 8:45 am Coffee Break with Pastries and Fruit
Location: Kiva Room
Keynote 1
Location: Kachina Room
9:00 am 9:45 am Keynote - Gordon B. Mills
Systems approach to rational drug combinations
9:45 am 10:00 am Coffee Break
Location: Kiva Room
Regulatory Genomics: Session 1
Location: Kachina Room
10:00 am 10:15 am Alexendar Perez, Yuri Pritykin, Joana Vidigal, Sagar Chhangawala, Lee Zamparo, Christina Leslie and Andrea Ventura
GuideScan: a comprehensive and customizable guide RNA design tool
10:15 am 10:30 am Istvan Ladunga, Avi Knecht, Adam Caprez, Timothy Bailey, Tao Liu, Pedro Madrigal and David Swanson
ChIPathlon: community-wide performance assessment of tools for mapping transcription factor binding sites and histone modifications
10:30 am 10:45 am Alberto Giaretta, Barbara Di Camillo, Luisa Barzon, Gianna Maria Toffolo and Timothy Charles Elston
Stochastic modeling of HPV early promoter gene regulation
10:45 am 11:00 am Alireza Fotuhi Siahpirani and Sushmita Roy
A prior-based integrative framework for functional transcriptional regulatory network inference
11:00 am 11:15 am Buffer for Q&A
11:15 am 11:30 am Coffee Break
Location: Kiva Room
Regulatory Genomics: Session 2
Location: Kachina Room
11:30 am 11:45 am Lingfei Wang and Tom Michoel
Scalable causal gene network inference from genetics of gene expression data
11:45 am 12:00 pm Allison Richards, Athma Pai, Daniel Kurtz, Gregory Moyerbrailean, Omar Davis, Chris Harvey, Adnan Alazizi, Yoram Sorokin, Nancy Hauff, Xiaoquan Wen, Roger Pique-Regi and Francesca Luca
Gene expression and splicing responses to environmental perturbations across 250 cellular conditions
12:00 pm 12:15 pm H. Tomas Rube, Chaitanya Rastogi and Harmen J. Bussemaker
Revisiting the relationship between DNA shape, base sequence, and transcription factor binding
12:15 pm 12:30 pm Cynthia Kalita, Gregory Moyerbrailean, Christopher Brown, Francesca Luca and Roger Pique-Regi
A novel allele-specific data analysis method for high-throughput reporter assays
12:30 pm 1:45 pm Lunch On Own
Poster Viewing in the Kiva Room
Keynote 2
Location: Kachina Room
1:45 pm 2:30 pm Keynote - Christopher Burge
Protein-RNA interactions and function of alternative 3’ UTRs
Systems Biology: Session 1
Location: Kachina Room
2:30 pm 2:45 pm Yuval Itan, Laurent Abel and Jean-Laurent Casanova
Finding a needle in a haystack: new approaches to select disease-causing mutations in patients’ genomes
2:45 pm 3:00 pm Janhavi Moharil, Daniel Gaile, Paul May and Rachael Hageman Blair
Probabilistic reasoning in genotype-phenotype networks
3:00 pm 3:15 pm Heeju Noh, Ziyi Hua and Rudiyanto Gunawan
Inferring molecular targets and mechanism of action from time course expression data
3:15 pm 3:30 pm Hatice Osmanbeyoglu, Eneda Toska, Carmen Chan, Jose Baselga and Christina Leslie
Modeling the impact of somatic alterations on signaling pathways and transcriptional programs in human cancers
3:30 pm 3:45 pm Joseph J. Muldoon, Yishan Chuang, Neda Bagheri and Joshua N. Leonard
A dynamical model for the regulation of heterogeneous macrophage activation by apparent quorum sensing
3:45 pm 4:00 pm Brian Ross and James Costello
Modeling heterogeneous cell populations using Boolean networks
4:00 pm 4:10 pm Buffer for Q&A
4:10 pm 4:30 pm Tech Talk
Presenter:  Blake Borgeson

Extracting the biology of a hundred diseases from a million images
Recursion Pharmaceuticals
4:30 pm 5:00 pm Coffee Break with light snacks
Location: Kiva Room
Keynote 3
Location: Kachina Room
5:00 pm 5:45 pm Keynote - Réka Albert
Control and Damage Mitigation in Regulatory Networks
6:00 pm 8:00 pm Wine and Cheese Reception
with Poster Viewing
Location: Kiva Room
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TUESDAY – DAY 3 – November 8, 2016
6:45 am 8:00 am Sunrise Networking Hike - Meet-up location is of South Pointe Lobby.
Leaving lobby at 6:45 to begin the hike.

Hiking trail map is available here.
8:00am - 6:00pm
Location: Anasazi Lobby
8:00 am 8:45 am Coffee Break with Pastries and Fruit
Location: Kiva Room
Keynote 4
Location: Kachina Room
9:00 am 9:45 am Keynote - Jill Mesirov
Signature and Integrative Computational Approaches to Genomic Medicine
9:45 am 10:00 am Coffee Break
Location: Kiva Room
Systems Biology: Session 2
Location: Kachina Room
10:00 am 10:15 am Xuewei Wang, Zhifu Sun, Jean-Pierre Kocher and Burgrim Andrej
Pathway-based approach to predict drug response of cancer cells
10:15 am 10:30 am Pooya Zakeri, Jaak Simm, Adam Arany, Sarah Elshal and Yves Moreau
Towards a Bayesian Data Fusion Model for Hunting Disease Candidate Genes
10:30 am 10:45 am Anasuya Pal, Jia Zeng, Laura Gonzalez-Malerva, Seron Eaton, Jin Park and Joshua Labaer
Integrated pathway analysis on phenotypic and molecular alterations induced by different missense mutant p53 proteins in mammary epithelial cells
10:45 am 11:00 am Yungil Kim, Xin Li, Emily Tsang, Joe Davis, Farhan Damani and Colby Chiang
The impact of rare variation on gene expression across tissues
11:00 am 11:10 am Buffer for Q&A
11:10 am 11:30 am Coffee Break
Location: Kiva Room
11:30 am 11:45 am Robert Vogel, Mehmet Eren Ahsen and Gustavo Stolovitzky
Unsupervised aggregation of rank predictions for binary classification in translational systems biology tasks
11:45 am 12:00 pm Laura Heiser, James Korkola, Mark Dane, Elmar Bucher, David Kilburn, Rebecca Smith, Wallace Thompson, Sean Gross, Damir Sudar, Michel Nederlof and Joe Gray
Elucidating the role of the microenvironment in modulating cellular phenotypes
12:00 pm 12:15 pm Casey Hanson, Junmei Cairns, Liewei Wang and Saurabh Sinha
A Probabilistic Graphical Model integrates genotype, gene expression and ChIP-seq data to identify transcription factors associated with drug response variation
12:15 pm 12:30 pm Aditya Pratapa, Neil Adames, Pavel Kraikivski, John Tyson, Jean Peccoud and T. M. Murali
Systematic Planning of Genetic Crosses to Validate Mathematical Models
12:30 pm 1:45 pm Grab N' Go Lunch
Includes: sandwich or salad, chips, cookie or whole fruit and a drink
Poster Viewing in the Kiva Room
Keynote 5
Location: Kachina Room
1:45 pm 2:30 pm Keynote - Nicholas Schork
Heterogeneity in Large-Scale Biomedical Data Sets
Regulatory Genomics: Session 3
Location: Kachina Room
2:30 pm 2:45 pm Beibei Xin and Remo Rohs
Protein family-specific relationship between histone modifications and transcription factor binding
2:45 pm 3:00 pm Mark Grimes, Nicolas Fernandez, Neil Clark, Avi Ma’ayan, Klarisa Rikova and Peter Hornbeck
Tandem Mass Tag Data Analysis Reveals Post-translational Modification Signaling Pathways in Lung Cancer Cell Lines
3:00 pm 3:15 pm Alon Diament and Tamir Tuller
Inter-organismal analysis of Hi-C data demonstrates a relation between phenotypic divergence and gene re-organization
3:15 pm 3:30 pm Yaron Orenstein and Bonnie Berger
Structural analysis of the compendium of RNA-binding proteins
3:30 pm 3:45 pm Oana Ursu, Nathan Boley, Maryna Taranova, Rachel Wang and Anshul Kundaje
A graph diffusion framework for multi-scale reproducibility and differential analysis of 3D chromatin contact maps
3:45 pm 4:00 pm Jingkang Zhao, Dongshunyi Li, Andrew Allen and Raluca Gordan
Quantifying the impact of non-coding variants on TF-DNA binding
4:00 pm 4:15 pm Michaela Willi and Lothar Hennighausen
Super-enhancers and CTCF in the regulation of mammary-specific genes
4:15 pm 4:30 pm Buffer for Q&A
4:20 pm 5:00 pm Coffee Break with light snacks
Location: Kiva Room
Keynote 6
Location: Kachina Room
5:00 pm 5:45 pm Keynote - Martha Bulyk
Genetic variation in human transcription factors
6:00 pm 7:00 pm Sponsored Talk
Presenter: Chris Cheadle PhD
Sponsor: Elsevier
Hands-on workshop with Pathway Studio, a high content, molecular modeling software tool
Location: Kachina Room
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DREAM AGENDA - WEDNESDAY – November 9, 2016
7:30 am - 6:00pm
Location: Anasazi Lobby
8:30 0:20 DREAM 11: Welcome and Introductory Remarks.
Gustavo Stolovitzky
9:00 0:20 DRUG COMBO

Justin Guinney
Invited Talk: Why AstraZeneca decided to DREAM about better cancer drug combinations. Jonathan Dry
9:20 0:20 Challenge Overview Talk: Community analysis to predict therapeutic synergy within the AstraZeneca-Sanger Drug Combination Challenge.
Michael Menden
9:40 0:20 Best Performer Talk: Boosted Tree Based Prediction of Drug Synergisms in the AstraZeneca-Sanger Drug Combination Prediction DREAM Challenge. Tin Nguyen and Bence Szalai
10:00 0:20 Best Performer Talk: Drug Synergy Prediction using High Performance Computing and Support Vector Regression. Minji Jeon
10:20 0:30 Coffee Break with Posters

Lara Mangravite
Challenge Update. Respiratory Viral DREAM Challenge: Discovering dynamic molecular signatures in response to viral exposure. Solly Sieberts
11:05 0:15 Challenge Update. Update SMC-RNA. Paul Boutros
11:20 0:15 Challenge Update. The Digital Mammography Challenge Update. Justin Guinney
11:35 0:15 Upcoming DREAM Challenges.
Gustavo Stolovitzky
11:50 0:40 Keynote - Isaac Kohane
Fake and True Names of Disease: Phenome and/or Genome?
12:30 1:30 Lunch with Posters

Gustavo Stolovitzky
Challenge Overview Talk. The Disease Module Identification DREAM Challenge. D. Marbach and S. Schoobdar
14:20 0:20 Best Performer Talk: A double spectral approach to the DREAM module identification challenge. Jake Crawford and Lenore Cowen
14:40 0:20 Best Performer Talk: Strategies for discovering disease-associated modules in integrated biological networks.
A. Lysenko and P. Kamola
15:00 0:30 Coffee Break with Posters
15:30 0:20 SMC-HET

Pablo Meyer
Challenge Overview Talk.
SMC-Het Challenge: Understanding the subclonality of tumours.
Paul Boutros
15:50 0:20 Best Performer Talk: Subclonal reconstruction from tumor genomic variation data using a cascade ensemble model. Kaiyi Zhu
16:10 0:20 Best Performer Talk:  An ultra-fast tumour heterogeneity inference method using density-based infinite mixture model. Hongjiu Zhang
16:30 0:30 Coffee Break with Posters
17:00 0:40 Keynote - Zhiping Weng
Expanding the ENCODE Encyclopedia: Applications for Annotating Non-coding Variants

Laura Heiser
Challenge Overview Talk.
The ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge.
Anshul Kundaje
18:00 0:20 Best Performer Talk: Discriminative learning using iterative background data set complementation. Jens Keilwagen
18:20 0:20 Best Performer Talk: Preselection of training cell types improves prediction of transcription factor binding sites.
Andrey S. Lando
18:40 1:50 DREAM Reception and Posters
20:30   Adjourn
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