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MAGNOME Research team

Models and Algorithms for the Genome

  • Leader : David Sherman
  • Research center(s) : CRI Bordeaux - Sud-Ouest
  • Field : Digital Health, Biology and Earth
  • Theme : Computational Biology
  • Partner(s) : Université de Bordeaux,CNRS
  • Collaborator(s) : Laboratoire Bordelais de Recherche en Informatique (LaBRI) (UMR5800)

Team presentation

  • The biological sciences ask a number of questions for which informatics can play an important role in finding answers. How genomes evolve? How do gene products cooperate to realize cellular functions? How are biomolecules, genomes, and cells are organized on different scales?
  • Comparative genomics provides an important tool for understanding these questions through the comparison of the completely sequenced genomes of a well-defined set of related species.
  • The organization of gene products into interaction and metabolic networks is an important step towards understanding the dynamic relationships between these components and their influence on cell behavior.
  • These application domains can be addressed by similar informatics tools such as modeling, data-mining, combinatorics, and formal methods, and permit the development of a comprehensive approach to understanding biological phenomena at a systems level.
  • MAGNOME is an interdisciplinary project whose team is composed of computer scientists from the LaBRI and biologists from the CNRS working together towards these goals, whose daily collaboration grew out of work in the Génolevures Consortium and related projects.

Research themes

  • MAGNOME is focused on bioinformatics approaches for comparative genomics of eukaryotic microorganisms, inference of interaction and metabolic networks, and construction of hierarchical stochastic models of cell behavior.
  • We develop novel methods and algorithms for these problems using techniques from data-mining, modeling, combinatorial analysis and formal methods.

International and industrial relations

MAGNOME members are stakeholders in two European projects: ProteomeBinders (FP6) and the Yeast Systems Biology Network (FP6). We are also involved in the HUPO Proteomics Standards Initiative; the international standards developed in this activity have been adopted both by industry and academia. In the Bordeaux region we collaborate with an industrial partner on cellular models of alcohol fermentation for winemaking.

Keywords: Comparative genomics Modeling of biological systems