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Combinatorial Algorithms for Tree-Based Haplotype Inference

Algebra & Discrete Mathematics

Speaker: Prof. Dan Gusfield, Dept. of CS UC Davis
Location: 693 Kerr
Start time: Thu, Oct 24 2002, 12:10PM

The next high-priority phase of human genomics will involve the development of a full Haplotype Map of the human genome. It will be used in large-scale screens of populations to associate specific haplotypes with specific complex genetic-influenced diseases. However, most studies will collect genotype data rather than haplotype data, requiring the deduction of haplotype information from genotype data. How to deduce haplotype information from genotype data was a nice quite research problem, but with the Haplotype Map Project, it has recently become "hot". Over the last several years, I have developed several distinct combinatorial algorithms for the haplotyping problem. I will talk about my most recent approach, based on viewing the haplotyping problem in the context of the perfect phylogeny problem. I will fully explain any needed biology in this talk, so no background in biology (or matroids) is needed.