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Algebraic structure of computational problems in haplotype inferenceOptimization
|Speaker: ||Prof. Daniel Brown, U. of Waterloo|
|Location: ||2112 MSB|
|Start time: ||Fri, May 26 2006, 12:10PM|
Haplotype inference is a field that results from a technological
limitation: it is expensive to separate the paternal and maternal
chromosomes of an organism. However, being able to do so would be useful,
particuarly when one tries to identify genetic variations partly
responsible for common diseases. Haplotype inference is the computation
problem of inferring these different chromosome sequences, by optimizing
some combinatorial or statistical requirement.
What makes haplotype inference attractive to computer scientists is that
one can very quickly abstract away many biological details, and focus on
the underlying mathematical structure of the various problems in the field.
Moreover, in many cases, this structure is attractive, making this an
appealing area in which to do research.
We will discuss a few of these different problems and their properties, and
for one problem, the Haplotype Inference by Pure Parsimony problem, focus
on some of the mathematical structure that we have discovered.
This is joint work with PhD student Ian Harrower.