Workshops

Spring 2016

Computational Cancer Biology

Feb 1, 2016 to Feb 5, 2016

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Click on the titles of individual talks for abstract, slides and archived video.

Monday, February 1st, 2016
8:45 am–9:05 am		Coffee & Check-In
9:05 am–9:15 am		Opening Remarks
9:15 am–9:45 am		The Current State of Mutation Detection and Prospects for Long Read Sequencing Jared Simpson (Ontario Institute for Cancer Research)
9:45 am–10:15 am		Modeling Cancer Evolution from Genomic Data Niko Beerenwinkel (ETH Zürich)
10:15 am–11:00 am		Break
11:00 am–11:30 am		Interaction-based Methods for Uncovering Genes Functionally Important in Cancers Mona Singh (Princeton University)
11:30 am–12:00 pm		Joint Analysis of Multiple Cancer Types for Revealing Disease-Specific Genomic Events Ron Shamir (Tel Aviv University) & David Amar (Tel Aviv University)
12:00 pm–2:00 pm		Lunch
2:00 pm–2:30 pm		Somatic Mutations that Alter RNA Splicing in Human Cancers Angela Brooks (UC Santa Cruz)
2:30 pm–3:00 pm		Algorithms for Population Genomics and Cancer Genomics Serafim Batzoglou (Stanford University)
3:00 pm–3:30 pm		Break
3:30 pm–4:00 pm		Mechanisms of Amplification in Tumor Genomes Vineet Bafna (UC San Diego)
4:00 pm–5:00 pm		Afternoon Discussion
5:00 pm–6:00 pm		Reception

Tuesday, February 2nd, 2016
8:30 am–9:00 am		Coffee & Check-In
9:00 am–9:30 pm		Challenges and Opportunities in Intelligent Molecular Medicine Igor Jurisica (University of Toronto)
9:30 am–9:45 am		Fast and Scalable Inference of Cancer Cell Lineages Using Multi-sample Deep Sequencing Somatic SNVs Victoria Popic (Stanford University)
9:45 am–10:15 am		Molecular Data Integration for Precision Medicine in Breast Cancer Laura Van 'T Veer (UCSF)
10:15 am–11:00 am		Break
11:00 am–11:40 am		Molecular Characterization for Diagnoses and Treatment David Haussler (UC Santa Cruz)
11:40 am–11:55 am		CoMEt: A Statistical Approach to Identify Combinations of Mutually Exclusive Alterations in Cancer Max Leiserson, Brown University
12:00 pm–2:00 pm		Lunch
2:00 pm–2:30 pm		Finding Mutated Subnetworks Associated with Survival in Cancer Fabio Vandin (University of Padova)
2:30 pm–3:00 pm		Diverse High Throughput Technologies in Cancer Research and Synthetic Biology Zohar Yakhini (Agilent Technologies and Technion)
3:00 pm–3:30 pm		Break
3:30 pm–3:45 pm		The Copy Number Transformation Problem Meirav Zehavi (Technion Israel Institute of Technology)
3:45 pm–4:00 pm		Inferring Selective Advantage Relationships to Reconstruct Cancer Progression Models Marco Antoniotti (Università degli Studi di Milano Bicocca)
4:00 pm–5:00 pm		Afternoon Discussion

Wednesday, February 3rd, 2016
8:30 am–9:00 am		Coffee & Check-In
9:00 am–9:30 am		Toward Pathway-and Pancancer-Guided Interpretation of an Individual’s Cancer Genome Josh Stuart (UC Santa Cruz)
9:30 am–9:45 am		Somatic Structural Variation Discovery in Multiple Cancer Genomes Iman Hajirasouliha (Stanford University)
9:45 am–10:15 am		Towards Inference of Fitness Landscapes in Human Cancer Sohrab Shah (BC Cancer Research Agency)
10:15 am–11:00 am		Break
11:00 am–11:40 am		Tumor Evolution - Simplicity and Constraints Paul Spellman (Oregon Health and Science University)
11:40 am–11:55 am		Inference of Personalized Drug Targets via Network Propagation Dana Silverbush (Tel Aviv University)
12:00 pm–2:00 pm		Lunch
2:00 pm–2:30 pm		Quantifying the Evolutionary Dynamics of Human Tumor Growth and Progression Christina Curtis (Stanford University)
2:30 pm–3:00 pm		Complexity Issues in Rearrangement Evolution Chris Greenman (University of East Anglia)
3:00 pm–3:30 pm		Break
3:30 pm–4:00 pm		Inferring Evolution by Copy Number Variations in Tumor Cell Populations Russell Schwartz (Carnegie Mellon University)
4:00 pm–5:00 pm		Afternoon Discussion

Thursday, February 4th, 2016
8:30 am–9:00 am		Coffee & Check-In
9:00 am–9:30 am		Interpreting Cancer Genomes with Network Knowledge Trey Ideker (UC San Diego)
9:30 am–9:45 am		Multi-State Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing Mohammed El Kebir, Brown University
9:45 am–10:15 am		Optimizing Combination Cancer Therapy Based on Single Cell Analysis Sylvia Plevritis (Stanford University)
10:15 am–11:00 am		Break
11:00 am–11:40 am		Synthetic Rescue Determinants of Resistance and Response to Cancer Therapy Eytan Ruppin (University of Maryland)
11:40 am–11:55 am		Survival Time Prediction from Mutation Profiles Using Gene Networks Marine Le Morvan (Mines ParisTech)
12:00 pm–2:00 pm		Lunch
2:00 pm–2:30 pm		Modeling Mutational Patterns in Tumor Genomic Data Ewa Szczurek (ETH Zürich)
2:30 pm–3:00 pm		Insights To Treatment Resistance and Precision Therapy In Prostate Cancer Colin Collins (Vancouver Prostate Center)
3:00 pm–3:30 pm		Break
3:30 pm–4:00 pm		Mutual Exclusivity of Mutations Across Different Cancer Types - A Molecular Network Perspective Teresa Przytycka (National Institutes of Health)
4:00 pm–5:00 pm		Afternoon Discussion

Friday, February 5th, 2016
8:30 am–9:00 am		Coffee & Check-In
9:00 am–9:30 am		Detection and Systems Level Identification of Expressed, Clone Specific Structural Alterations that Drive the Tumor Phenotype Cenk Sahinalp (Indiana University)
9:30 am–9:45 am		BitPhylogeny: A Probabilistic Framework for Reconstructing Intra-tumor Phylogenies Thomas Sakoparnig (University of Basel, Biozentrum)
9:45 am–10:15 am		Expression Analysis of Tumors Based on Patterns in Alternative Splicing Elizabeth Purdom, UC Berkeley
10:15 am–11:00 am		Break
11:00 am–11:30 am		Modeling the Impact of Somatic Alterations in Human Cancers Hatice Ulku Osmanbeyoglu, Memorial Sloan Kettering Cancer Center
11:30 am–12:00 pm		Rank-Based Representations to Learn from Omics Data Jean-Philippe Vert (MINES ParisTech)
12:00 pm–12:15 pm		Closing Discussion