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
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