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Analyse des systèmes bactériens: une approche in silico pour intégrer les connaissances du vivant

Philippe Bordron 1
1 Combi
LINA - Laboratoire d'Informatique de Nantes Atlantique
Abstract : Nowadays, the emergence of high throughput experiments allows a large number of biological data to be available to biologists, data that they need to structure and analyze. Integrative approaches provide a way to respond to this demand, but the creation of a method that is general and that satisfies the precise requests of biologists is a difficult task. This is the problem of this thesis. We present various approaches that integrate many omic aspects (metabolic, genomic, transcriptomic...) of a bacterial system, and we also propose our own method, called SIPPER, that is both generic and flexible. SIPPER allows us to find consistent biological information between distinct omic aspects by constructing an integrated model and using a distance that is based on given biological properties and hypotheses. We apply SIPPER twice on metabolic and genomic data from E.~coli. The first application tests the hypothesis that "the chains of successive reactions in a metabolic network are catalyzed by enzymes that are products of neighbours genes in the genome", and the second application tests the hypothesis that "the chains of successive reactions in a metabolic network are catalyzed by genes that have a similar expression". These experiments allow us to identify measures that describe some biological entities such as the genomic density that allows us to identify metabolic operons. Integrating different kinds of data into traditional approaches that used only one kind of information is also illustrated in comparative genomics. Thus, we have elaborated M&W-IISCS_M, a method that computes maximum common intervals that have an important omit interest.
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Submitted on : Thursday, October 18, 2012 - 9:39:27 PM
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Philippe Bordron. Analyse des systèmes bactériens: une approche in silico pour intégrer les connaissances du vivant. Bio-informatique [q-bio.QM]. Université de Nantes, 2012. Français. ⟨tel-00743412⟩

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