Tuesday, April 4, 2006
4:30 pm
B17 Upson Hall

Computer Science
Spring 2006

New Life Sciences

Colin Dewey
UC Berkeley

Whole-Genome Alignments and Polytopes for Comparative Genomics

Whole-genome sequencing of many species has presented us with the opportunity to deduce the evolutionary relationships between each and every nucleotide. In this talk, I will present algorithms for this problem, which is that of multiple whole-genome alignment. The sensitivity of whole-genome alignments to parameter values can be ascertained through the use of alignment polytopes, which will be explained. I will also show how whole-genome alignments are used in comparative genomics, including the identification of novel genes, the location of micro-RNA targets, and the elucidation of cis- regulatory element and splicing signal evolution.

Biographical sketch:
Colin Dewey was an undergraduate at the University of California, Berkeley, where he majored in Electrical Engineering and Computer Sciences with an honors breadth area in Molecular Biology. After receiving his B.S. with high honors in 2001, he continued on as a graduate student at Berkeley under the guidance of Lior Pachter. He will receive his Ph.D. in Electrical Engineering and Computer Sciences with a Designated Emphasis in Computational and Genomic Biology in May 2006.

Driven by his interests in molecular evolution and algorithm design, Colin has focused his graduate research on the development of algorithms for comparing multiple whole genome sequences. He has participated in the international sequencing projects for the mouse, rat, and chicken genomes and is currently a member of the ENCODE Consortium, which aims to construct a catalog of all functional elements in the human genome. He has also collaborated with scientists at the National Center for Biotechnology Information.