"Towards DNA Sequencing Chips""""

Ohio Supercomputer Center High Performance Computing Seminar

Dr. Pavel Pevzner
Professor, Department of Mathematics
University of Southern California

Sequencing by Hybridization (SBH) is a challenging alternative to the classical DNA sequencing methods. The basic approach is to build an array (Sequencing Chip) of short oligonucleotides, to use hybridization for finding oligonucleotide content of an unknown DNA fragment and to reconstruct the original fragment by a combinatorial algorithm. Several SBH problems must be jointly addressed by biochemists, mathematicians and instrument designers. In this talk I simultaneously address biochemical, mathematical and technological aspects of SBH. I also present a new chip design which might allow significant chip miniaturization without reducing resolving power. The latest advances including positional SBH, PCR-SBH, and optimal codes for VLSIPS photolitographic technique for SBH are discussed. The work on optimal chip design is a joint project with Rob Lipshutz (Affymetrix).

Dr. Pavel Pevzner is currently Professor of Mathematics at the University of Southern California. From 1993-1995, Dr. Pevzner was on faculty at the Pennsylvania State University for the Institutes of Molecular Evolutionary Genetics and Biotechnology. Dr. Pevzner graduated from the Moscow Institute of Physics and Technology in 1988 with a Ph.D. in Mathematics and Physics. He received his M.S. degree in Applied Mathematics from the Moscow Technological Transport Institute in 1979. M.S. thesis (summa cum laude): "Integer Programming and Packing Problems."; Ph.D. thesis: "Combinatorial Methods for Biopolymer Structure Analysis."

Dr. Pevzner has been a member of the Review Board of the Soviet Human Genome Program (Mathematics and computer science), 1989-1990; Member, National Institute of Health Scientific Review Group, Houston, Texas, 1991; Member, DOE Grant Review Panel, Washington, D.C., 1992; National Institute of Health Scientific Review Group, Washington, D.C. 1993; Member, NSF HPCC Grant Review Panel, Washington, D.C., 1993; Member, NIII Human Genome Study Section, Washington, D.C., 1994; Member, DOE Informatics Panel, Washington, D.C., 1994.

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