S. Cenk Sahinalp, Canada Research Chair in Computational Genomics
School Of Computing Science
Date: Oct 15, 2009
Recent studies show that along with single nucleotide polymorphisms and small indels, larger structural variants among human individuals are common. The Human Genome Structural Variation Project aims to identify and classify deletions, insertions, and inversions (>5 Kbp) in a small number of normal individuals with a fosmid-based paired-end sequencing approach using traditional sequencing technologies. The realization of new ultra-high-throughput sequencing platforms now makes it feasible to detect the full spectrum of genomic variation among many individual genomes, including cancer patients and others suffering from diseases of genomic origin. Unfortunately, existing algorithms for identifying structural variation (SV) among individuals have not been designed to handle the short read lengths and the errors implied by the "next-gen" sequencing (NGS) technologies. In this talk we will describe combinatorial formulations for the SV detection between a reference genome sequence and a next-gen-based, paired-end, whole genome shotgun-sequenced individual. We will provide efficient algorithms for each of the formulations we give, which all turn out to be fast and quite reliable; they are also applicable to all next-gen sequencing methods (Illumina, 454 Life Sciences, SOLiD, etc.) and traditional capillary sequencing technology.
Cenk Sahinalp is a Professor of Computing Science at Simon Fraser University, Burnaby BC, Canada where he directs the Lab for Computational Biology and co-leads the program on Bioinformatics for Combating Infectious Diseases. He is also an associate faculty at the Department of Molecular Biology and Biochemistry and a visiting scientist at the Department of Genome Sciences, University of Washington. Cenk's research focuses on problems in sequence alignment, and search, biomolecular sequence analysis and in particular search and analysis of genome wide structural variations through the use of high throughput sequencing, RNA structure and interaction prediction, biomolecular network analysis and small molecule bioinformatics. Cenk received a B.S. in Electrical Engineering from Bilkent University. His Ph.D. was in Computer Science with Uzi Vishkin from University of Maryland, College Park. He was then a postdoc with Yossi Matias at Bell Labs, Murray Hill, and subsequently a research associate with Chris Overton, at the first lab ever established for Bioinformatics in the University of Pennsylvania. During this time he also held a faculty position at the University of Warwick and was a frequent visitor to DIMACS and AT&T Research. Before moving to SFU in 2003 he was a faculty member at Case Western Reserve University where he had co-founded the Case Center for Computational Genomics. Cenk has published over 75 refereed full length papers in some of the flagship venues in computer science, computational biology and genomics. He has received an NSF Career Award, a Glennan Teaching Award from CWRU, a BC Advanced Systems Institute Fellowship a Michael Smith Foundation Scholarship.