Génomique évolutive des microbes
28 Rue Dr Roux
75724 Paris cedex 15
Laboratoire des Sciences du Numérique de Nantes (LS2N CNRS UMR6004)
2, rue de la Houssinière
The ComBi team at LINA aims at developping original algorithmic and mathematics methods for studying problems issued from biology. Its main research topics focus on comparative genomics and systems biology.
Universite Paul Sabatier
CNRS-Laboratoire de Microbiologie et Genetique Moleculaires
118, route de Narbonne
31062 Toulouse CEDEX 9, France
Systematic sequencing genome projects generate large amounts of data that must be annotated for their biological exploitation. If the first annotation step may allow the identification of single genes/gene products, a complementary level of annotation consists in taking into account interactions of the proteins involved in the same supra-molecular system and/or biological process. These interactions can be stable, or transient, and either physical or functional. The cellular functions that emerge from these complex systems are not only an addition of the individual protein properties but result also from the interactions between the proteins. Biological systems result also from a complex evolutionary history, in a sense that partners and/or relationships between them can have been added, removed or replaced along the evolutionary history, with two extreme consequences, the loss or the duplication of systems in a phylogenetic clade. In general, duplicated systems do not conserve the same cellular function. Such a complex evolutionary scenario occurs when partners are encoded by multigenic families. In this framework, our group has focused its activity on two main research axes: i) development of strategies in order to identify, reconstruct and classify, from the genomic sequences, functional supra-molecular assemblies whose members belong to multigenic families and ii) phylogenomics analyses involving also the development of approaches to identify orthologous genes/proteins. ABC systems were initially chosen as a model because they form one of the largest ubiquitous families of paralogous systems that have arisen early in evolution and are involved in many essential physiological processes. The developed strategies lead to the creation and maintenance of a public database dedicated to ABC systems (ABCdb). Since then, we have extended our expertise in phylogenomics analyses on different gene families and systems through collaborations. To address the dynamics of the interaction between biological entities, we started to implement systems biology approaches focused on the modeling of the regulatory pathway of natural genetic transformation in streptococcal species.
75230 PARIS CEDEX 05
Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT)
Chemin de Borde Rouge
31326 CASTANET-TOLOSAN cedex
The team develops mathematical, statistical and computational methods to address life science research problems. These methods are usually directly made available to biologists through dedicated software.
Bioinformatics problems addressed
The topics addressed in the team concern the localization and identification of functional elements in bacterial, plant and animal genomes. Three investigation levels are considered.
To go beyond the localization of isolated functional elements, we are are now increasingly interested in approaches aiming at the inference of gene regulatory networks. We are currently studying the simultaneous analysis of expression data and polymorphism data (such as SNP) on a collection of individuals. This allows to observe different perturbated modes of operation of the network to better infer gene network structures.
Laboratoire de Chimie Bacterienne (LCB)
UMR 7283 AMU CNRS
31 Chemin Joseph Aiguier