Joint Colloquium Distinguished Lecture Series

Robust Alignment for Drosophila Genomics

blank image Wednesday, October 5th
HP Auditorium, Soda Hall
4:00

Lior Pachter
University of California, Berkeley
Math Department

Abstract:

The Drosophila Genome Project is a large scale research effort whose aim is to sequence, compare and contrast 12 Drosophila genomes with the goal of significantly advancing comparative genomics methods. We will provide an overview of our recent work on annotation and alignment of the genomes, which focuses on the related problems of transposable element identification, gene finding and multiple sequence alignment. In particular, we emphasize the importance of robust alignment methods, and their relevance for identifying functional elements in genomes. A key concept is the alignment polytope, which will be explained and illustrated.

Biography:

Lior Pachter was born in Ramat Gan, Israel, and grew up in Pretoria, South Africa where he attended Pretoria Boys High School. After receiving a B.S. in Mathematics from Caltech in 1994, he left for MIT where he was awarded a PhD in applied mathematics in 1999. He then moved to the University of California at Berkeley where he was a postdoctoral researcher (1999-2001), assistant professor (2001-2005) and is currently associate professor of mathematics.

His research interests span the mathematical and biological sciences, and he has authored over 50 research articles in the areas of algorithms, combinatorics, comparative genomics, algebraic statistics, molecular biology and evolution. His honors include a National Science Foundation CAREER award, a Sloan Research Fellowship, and the Federal Laboratory Consortium award for the development of widely used sequence alignment software.

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