<html><body>Colloquium Speaker<br>Ben Raphael, Brown University<br>Monday, January 12, 4:30pm<br>Computer Science 105<br><div id="9fa6274a-1b34-4f45-893b-c0a3fda3060b"><br><br><span name="x"></span>Understanding the molecular alterations that cause cancer is one of the
greatest challenges in biology and medicine. Recent advances in DNA
sequencing technology now enable large-scale measurement of mutations in
cancer genomes and provide an unprecedented opportunity to address this
challenge. However, translating this information into deeper insight
about the mutational process that drives cancer demands novel
computational approaches. <br><br>
<p>In this talk, I will describe algorithms that we have developed to
address key problems in cancer genomics. First, I will discuss
algorithms that deconvolve DNA sequencing data from a single tumor and
determine subpopulations of cancer cells harboring different mutations.
These algorithms exploit integrality constraints on copy number
aberrations and phylogenetic tree constraints that relate
subpopulations. Next, I will describe algorithms 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
mutated across samples. A second algorithm finds combinations of
mutations that optimize a measure of mutual exclusivity across samples.
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.</p><p><br></p>
<p>Ben Raphael is an Associate Professor in the Department of Computer
Science and Director of the Center for Computational Molecular Biology
(CCMB) at Brown University. His research focuses on the design of
algorithms for genome sequencing and interpretation. Recent interests
include structural variation in human and cancer genomes, and
network/pathway analysis of genetic variants. He received an S.B. in
Mathematics from MIT, a Ph.D. in Mathematics from the University of
California, San Diego (UCSD), and completed postdoctoral training in
Bioinformatics and Computer Science at UCSD. He is the recipient of an
NSF CAREER award, a Career Award from the Burroughs Wellcome Fund, and a
Sloan Research Fellowship.</p></div><br></body></html>