Combinatorial models and algorithms for comparative genomics

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The research program I propose focuses on the development of  non-trivial combinatorial  models and efficient algorithms for genomic data comparison and analysis. The main aspect of this project deals with the comparison, in terms of gene order, of whole genomes. In particular, I will study two aspects: (1) using the information given by the conservation of combinatorial structures, (2) extending the existing models to the case of genomes with multigenes families. In both problems, I will concentrate my efforts on the notion of common intervals. The precise problems that will be studied in a first time are the detection of rearranged gene clusters, the assignment of plausible evolutionary relations in multigenes families, and the computation of evolution scenarios. The resulting algorithms will be implemented and used to analyse several datasets of genomes, including prokaryotic genomes - essentially bacterial genomes, that are of primary importance from a biomedical point of view - and eukaryotic genomes - yeasts and vertebrates. I also plan to work on biological networks, in particuliar gene regulation networks. I will study the notion of conserved structures among a set of several networks and the reconstruction of possible ancestral networks. Finally, I am interested in the developement of algorithms for the analysis of noncoding RNA genes. In particular, I will study how to compare such structures by decomposing them into simple stem-loops substructures.