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COMPUTER SCIENCE COLLOQUIUM

Algorithmics and Optimization for Complex Biological Systems

Daniel Merkle
Department of Computer Science
University of Leipzig
Germany

Monday, January 21, 2008, at 10:15
IMADA's Seminar Room

ABSTRACT

In this talk recent research results for difficult optimization problems with the focus on problems that arise in computational biology are presented. In the first part a state-of-the-art particle swarm algorithm for solving the molecular docking problem is investigated, i.e., to find a good position and orientation for a small molecule that has to be docked to a larger receptor molecule. In the second part a powerful approach to infer the phylogenetic relationship of gene orders representing different species is presented. Given the gene orders and the phylogenetic relationship of a set of taxa, the problem of finding a plausible and parsimonious assignment of genomic rearrangement events to the edges of the given phylogenetic tree, is studied. For such events an efficient tree data-structure, that represents the common gene orders of a set of taxa, is introduced. This so-called strong common interval tree is furthermore applied to solve the NP-complete problem of finding an ancestral gene order for a set of three given taxa, such that the common gene orders of the input taxa are not destroyed --- a basic operation to infer phylogenetic trees. In the third part of the talk a dynamic programming based method and a corresponding tool for studying the coevolutionary history of two groups of species, like hosts and their parasites or plants and insects, will be presented.


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Joan Boyar (joan@imada.sdu.dk)

 


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