AGENDAS - CONFERENCE & DREAM
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| CONFERENCE AGENDA | ||
| Go directly to: [Monday - Nov 7] [Tuesday - Nov 8] | ||
| SUNDAY – DAY 1 – Cytoscape Workshop - November 6, 2016 | ||
| START TIME | END TIME | SESSION TYPE |
| Registration 12:00pm - 5:00pm Location: Anasazi Lobby |
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| 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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| RSG AGENDA | ||
| MONDAY – DAY 2 – November 7, 2016 | ||
| START TIME | END TIME | SESSION TYPE |
| Registration 8:00am - 6:00pm Location: Anasazi Lobby |
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| 8:00 am | 8:45 am | Coffee Break with Pastries and Fruit Location: Kiva Room |
| Keynote 1 Location: Kachina Room |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 | ||
| START TIME | END TIME | SESSION TYPE |
| 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. |
| Registration 8:00am - 6:00pm Location: Anasazi Lobby |
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| 8:00 am | 8:45 am | Coffee Break with Pastries and Fruit Location: Kiva Room |
| Keynote 4 Location: Kachina Room |
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| 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 |
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| 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 |
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| 1:45 pm | 2:30 pm | Keynote - Nicholas Schork Heterogeneity in Large-Scale Biomedical Data Sets |
| Regulatory Genomics: Session 3 Location: Kachina Room |
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| 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 |
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| 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 |
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| START TIME | TALK LENGTH | CATEGORY | EVENT |
| Registration 7:30 am - 6:00pm Location: Anasazi Lobby |
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| 8:30 | 0:20 | DREAM 11: Welcome and Introductory Remarks. Gustavo Stolovitzky |
|
| 9:00 | 0:20 | DRUG COMBO CHALLENGE Chair: 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 | |
| 10:50 | 0:15 | CHALLENGES UPDATES Chair: 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 |
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| 11:50 | 0:40 | Keynote - Isaac Kohane Fake and True Names of Disease: Phenome and/or Genome? |
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| 12:30 | 1:30 | Lunch with Posters | |
| 14:00 | 0:20 | DISEASE MODULE Chair: 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 Chair: 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 |
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| 17:40 | 0:20 | ENCODE CHALLENGE Chair: 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 |
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| 20:30 | Adjourn | ||
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