Computational Cancer Biology

Program

Algorithmic Challenges in Genomics

Location

Calvin Lab Auditorium

Date

Monday, Feb. 1 – Friday, Feb. 5, 2016

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

8:45 – 9:05 a.m.

Coffee & Check-In

9:05 – 9:15 a.m.

Opening Remarks

9:15 – 9:45 a.m.

The Current State of Mutation Detection and Prospects for Long Read Sequencing

Jared Simpson (Ontario Institute for Cancer Research)

9:45 – 10:15 a.m.

Modeling Cancer Evolution from Genomic Data

Niko Beerenwinkel (ETH Zürich)

10:15 – 11 a.m.

Break

11 – 11:30 a.m.

Interaction-based Methods for Uncovering Genes Functionally Important in Cancers

Mona Singh (Princeton University)

11:30 a.m. – 12 p.m.

Joint Analysis of Multiple Cancer Types for Revealing Disease-Specific Genomic Events

Ron Shamir (Tel Aviv University) & David Amar (Tel Aviv University)

12 – 2 p.m.

Lunch

2 – 2:30 p.m.

Somatic Mutations that Alter RNA Splicing in Human Cancers

Angela Brooks (UC Santa Cruz)

2:30 – 3 p.m.

Algorithms for Population Genomics and Cancer Genomics

Serafim Batzoglou (Stanford University)

3 – 3:30 p.m.

Break

3:30 – 4 p.m.

Mechanisms of Amplification in Tumor Genomes

Vineet Bafna (UC San Diego)

4 – 5 p.m.

Afternoon Discussion

5 – 6 p.m.

Reception

8:30 – 9 a.m.

Coffee & Check-In

9 a.m. – 9:30 p.m.

Challenges and Opportunities in Intelligent Molecular Medicine

Igor Jurisica (University of Toronto)

9:30 – 9:45 a.m.

Fast and Scalable Inference of Cancer Cell Lineages Using Multi-sample Deep Sequencing Somatic SNVs

Victoria Popic (Stanford University)

9:45 – 10:15 a.m.

Molecular Data Integration for Precision Medicine in Breast Cancer

Laura Van 'T Veer (UCSF)

10:15 – 11 a.m.

Break

11 – 11:40 a.m.

Molecular Characterization for Diagnoses and Treatment

David Haussler (UC Santa Cruz)

11:40 – 11:55 a.m.

CoMEt: A Statistical Approach to Identify Combinations of Mutually Exclusive Alterations in Cancer

Max Leiserson, Brown University

12 – 2 p.m.

Lunch

2 – 2:30 p.m.

Finding Mutated Subnetworks Associated with Survival in Cancer

Fabio Vandin (University of Padova)

2:30 – 3 p.m.

Diverse High Throughput Technologies in Cancer Research and Synthetic Biology

Zohar Yakhini (Agilent Technologies and Technion)

3 – 3:30 p.m.

Break

3:30 – 3:45 p.m.

The Copy Number Transformation Problem

Meirav Zehavi (Technion Israel Institute of Technology)

3:45 – 4 p.m.

Inferring Selective Advantage Relationships to Reconstruct Cancer Progression Models

Marco Antoniotti (Università degli Studi di Milano Bicocca)

4 – 5 p.m.

Afternoon Discussion

8:30 – 9 a.m.

Coffee & Check-In

9 – 9:30 a.m.

Toward Pathway-and Pancancer-Guided Interpretation of an Individual’s Cancer Genome

Josh Stuart (UC Santa Cruz)

9:30 – 9:45 a.m.

Somatic Structural Variation Discovery in Multiple Cancer Genomes

Iman Hajirasouliha (Stanford University)

9:45 – 10:15 a.m.

Towards Inference of Fitness Landscapes in Human Cancer

Sohrab Shah (BC Cancer Research Agency)

10:15 – 11 a.m.

Break

11 – 11:40 a.m.

Tumor Evolution - Simplicity and Constraints

Paul Spellman (Oregon Health and Science University)

11:40 – 11:55 a.m.

Inference of Personalized Drug Targets via Network Propagation

Dana Silverbush (Tel Aviv University)

12 – 2 p.m.

Lunch

2 – 2:30 p.m.

Quantifying the Evolutionary Dynamics of Human Tumor Growth and Progression

Christina Curtis (Stanford University)

2:30 – 3 p.m.

Complexity Issues in Rearrangement Evolution

Chris Greenman (University of East Anglia)

3 – 3:30 p.m.

Break

3:30 – 4 p.m.

Inferring Evolution by Copy Number Variations in Tumor Cell Populations

Russell Schwartz (Carnegie Mellon University)

4 – 5 p.m.

Afternoon Discussion

8:30 – 9 a.m.

Coffee & Check-In

9 – 9:30 a.m.

Interpreting Cancer Genomes with Network Knowledge

Trey Ideker (UC San Diego)

9:30 – 9:45 a.m.

Multi-State Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing

Mohammed El Kebir, Brown University

9:45 – 10:15 a.m.

Optimizing Combination Cancer Therapy Based on Single Cell Analysis

Sylvia Plevritis (Stanford University)

10:15 – 11 a.m.

Break

11 – 11:40 a.m.

Synthetic Rescue Determinants of Resistance and Response to Cancer Therapy

Eytan Ruppin (University of Maryland)

11:40 – 11:55 a.m.

Survival Time Prediction from Mutation Profiles Using Gene Networks

Marine Le Morvan (Mines ParisTech)

12 – 2 p.m.

Lunch

2 – 2:30 p.m.

Modeling Mutational Patterns in Tumor Genomic Data

Ewa Szczurek (ETH Zürich)

2:30 – 3 p.m.

Insights To Treatment Resistance and Precision Therapy In Prostate Cancer

Colin Collins (Vancouver Prostate Center)

3 – 3:30 p.m.

Break

3:30 – 4 p.m.

Mutual Exclusivity of Mutations Across Different Cancer Types - A Molecular Network Perspective

Teresa Przytycka (National Institutes of Health)

4 – 5 p.m.

Afternoon Discussion

8:30 – 9 a.m.

Coffee & Check-In

9 – 9:30 a.m.

Detection and Systems Level Identification of Expressed, Clone Specific Structural Alterations that Drive the Tumor Phenotype

Cenk Sahinalp (Indiana University)

9:30 – 9:45 a.m.

BitPhylogeny: A Probabilistic Framework for Reconstructing Intra-tumor Phylogenies

Thomas Sakoparnig (University of Basel, Biozentrum)

9:45 – 10:15 a.m.

Expression Analysis of Tumors Based on Patterns in Alternative Splicing

Elizabeth Purdom, UC Berkeley

10:15 – 11 a.m.

Break

11 – 11:30 a.m.

Modeling the Impact of Somatic Alterations in Human Cancers

Hatice Ulku Osmanbeyoglu, Memorial Sloan Kettering Cancer Center

11:30 a.m. – 12 p.m.

Rank-Based Representations to Learn from Omics Data

Jean-Philippe Vert (MINES ParisTech)

12 – 12:15 p.m.

Closing Discussion