UCLA Bioinformatics Program

Speaker: Ben Raphael, Dept. of Computer Science & Center for Computational Molecular Biology, Brown Univ.

When: Mon, Mar 10, 2008

Where: CNSI Auditorium

Abstract:
Every time a cell divides, it makes a copy of its DNA. Errors in this process lead to mutations, which can be single letter changes in the DNA sequence or rearrangements, gains, or losses of large pieces of DNA. In this talk, I will describe algorithms to study these genome rearrangements and copy number changes, focusing on two biological contexts. The first context is somatic mutations in cancer. Recent genome sequencing techniques have shown that some cancer genomes have a complicated organization resulting from numerous, overlapping rearrangements and duplications. The second context is segmental duplications that are common in mammalian evolution. Many of these segmental duplications are complex mosaics of fragments of other segmental duplications, and determining the history of these genomic regions is a challenging problem. In both of these contexts, the algorithms I will describe are based on finding a parsimonious sequence of rearrangement and duplication operations that transform one genomic sequence into another sequence.

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