Algorithms for Cancer Genomics

Speaker: Ben Raphael , Brown University

Date: Wednesday, April 08, 2015

Time: 11:30 AM to 1:00 PM Note: all times are in the Eastern Time Zone

Refreshments: 11:15 AM

Public: Yes

Location: 32-G575

Event Type:

Room Description:

Host: Bonnie Berger

Contact: Patrice Macaluso, 617-253-3037,

Relevant URL:

Speaker URL: None

Speaker Photo:

Reminders to:,,

Reminder Subject: TALK: Algorithms for Cancer Genomics

Recent advances in DNA sequencing technology now enable large-scale measurement of the molecular alterations that occur in cancer cells. Translating this information into deeper insights about processes that drive cancer development demands novel computational approaches.

In this talk, I will describe algorithms to address two key problems in cancer genomics. First, I will describe techniques to identify combinations of mutations that perturb cellular signaling and regulatory networks. One algorithm employs a heat diffusion process to identify subnetworks of a genome-scale interaction network that are recurrently altered across samples. A second algorithm finds combinations of mutations that optimize a statistical measure of mutual exclusivity. Second, I discuss approaches to deconvolve DNA sequencing data from a single tumor and derive subpopulations of cancer cells harboring different mutations. These algorithms exploit integrality constraints on copy number aberrations and phylogenetic tree constraints that relate subpopulations. I will illustrate applications of these approaches to multiple cancer types in The Cancer Genome Atlas (TCGA), including a recent Pan-Cancer study of >3000 samples from 12 cancer types.

Research Areas:

Impact Areas:

See other events that are part of the Bioinformatics Seminar Series 2015.

Created by Patrice Macaluso Email at Monday, April 06, 2015 at 11:17 AM.