Algorithms for detecting structural variation in genomes
EECS Distinguished Seminar Series
Dr. Vineet Bafna
Friday, March 28, 2008
11:00AM ~ 12:00PM, Harris Center 101
Abstract
Many of the available technologies do well for detecting copy number variation, but other variation, like inversions and translocations remain hard to detect. Here, I will describe a number of computational approaches to identify these variations, focusing in particular on the identification of copy neutral variations. This includes mining of genotype data to detect inversions, the use of 'older' technologies like multiplex PCR, and BAC end-sequencing to detect fusion events, and algorithms for 'haplotype assembly' as a prelude to detecting structural variation.
Short Bio
Vineet Bafna is an Associate Professor in the Computer Science Department at UCSD. Prior to joining UCSD in 2003, he spent seven years in the bio-science industry. From 1996-99, Dr. Bafna was a senior investigator at SmithKline Beecham, conducting research on DNA signaling, target discovery and EST assembly. From 1999 to 2002, he worked at Celera Genomics, ultimately as Director of Informatics Research. At Celera, he participated in the human genome pro ject, designing novel tools for gene discovery, and leading the analysis of mass spectrometry data for identifying cancer bio-markers. His current research focus is on computational problems arising in mass spectrometric data analysis, populations genetics, non-coding genes, and cancer genomics. He is an Associate Editor for JBCB, IEEE TCBB, and Biology Direct, and has served on the program committees of ISMB, RECOMB, and other conferences. He has co-authored over sixty research articles in refereed journals and conference proceedings.
