Arnaud Belcour’s PhD defense on “Combining knowledge-based and sequence comparison approaches to elucidate metabolic functions, from pathways to communities” will take place on Friday 21st october 2022 at 14:00, room Métivier at IRISA.
Committee:
- Delphine Ropers, senior researcher, Inria Grenoble
- David Vallenet, senior researcher, CEA Genoscope Évry-Courcouronnes
- Karoline Faust, associate professor, KU Leuven
- Fabien Jourdan, senior researcher, INRAe Toulouse
- Cédric Lhoussaine, professor, Univ. Lille
- Samuel Blanquart, researcher, Inria IRISA Rennes
- Olivier Dameron, professor, Univ. Rennes1, IRISA Rennes
- Anne Siegel, senior researcher, CNRS IRISA Rennes
Abstract:
Metabolism can be modelled and studied at many levels. The first level is the metabolic pathways, which contain a set of chemical transformations leading to the production of compounds of interest. Alternative metabolic pathways were predicted in an alga using a formalism of the metabolic pathway drift and its implementation with constraint programming. The second level is the organism metabolism which contains hundreds of metabolic pathways. A method has been developed to reconstruct homogeneous metabolic networks from heterogeneous public data. The third level is the metabolism of a group of organisms (or taxon) which can be useful to characterize an organism that has not been clearly identified. To achieve this, a method using knowledge engineering and sequence comparison has been created. Finally, the fourth level is the metabolism of a community and the metabolic interaction in this community. A method has been developed to identify the key species among a community.
