Centre for Molecular and Biomolecular Informatics Radboud University, Toernooiveld 1, P.O. Box 9010, 6500 GL Nijmegen, +31 (0)24-3653391, postmaster@cmbi.ru.nl

With the sequencing of complete genomes we have the most complete molecular data for the reconstruction of the phylogeny of life. For example, instead of using the sequence similarity between proteins, as is classically done for the reconstruction of phylogenies, we can now use the number of shared genes between genomes. The goal of this project is use these and other types of "complete genome data" in new ways, combining as much of the genome information as possible, to construct phylogenies. Aside from being interesting in themselves, phylogenies are of extreme importance to detect and filter out various types of phylogenetic bias in genomic datasets, and therewith improve our methods for the prediction of protein interactions.

Methodology

This project involves comparing all the presently sequenced genomes with each other, to detect phylogenetically meaningful feaures like the presence of orthologous genes or the presence of conserved gene clusters, and the development of algorithms to turn the sharing of such features into phylogenies. It involves also a lot of "creative thinking" to filter out the effects that lead to the convergence of molecular features, of e.g. horizontal gene transfer or parallel loss of genes.

Required pre-training

It would be useful if the student had some experience in phylogeny detection, and/or in programming.

Keywords: Comparative genomics, genome evolution, phylogeny.

Training period: 6-12 months

Information: Martijn Huynen, huynen@cmbi.kun.nl, tel 024-3653374.