Génomique comparative

Evolution of photosynthetic functions and Genome dynamics

Nom complet (en toutes lettres)
Evolution of photosynthetic functions and Genome dynamics - Laboratoire Biologie du Chloroplaste et Perception de la Lumière chez les Microalgues - UMR7141 CNRS SU
Adresse

75005 Paris
France

SFBI
N'est pas membre de la SFBI

ComBi

Acronyme ou nom de la structure
Nom complet (en toutes lettres)
Combinatoire et bioinformatique
Adresse

Laboratoire des Sciences du Numérique de Nantes (LS2N CNRS UMR6004)
2, rue de la Houssinière

44322 Nantes
France

Description (English)

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.

English keywords
Comparative genomics, systems biology
SFBI
Membre de la SFBI

GSI

Acronyme ou nom de la structure
Nom complet (en toutes lettres)
Génomique des Systèmes Intégrés
Adresse

Universite Paul Sabatier
CNRS-Laboratoire de Microbiologie et Genetique Moleculaires
BAT. IBCG
118, route de Narbonne

31062 Toulouse CEDEX 9, France  
France

Description (English)

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.

English keywords
Integrated systems, Comparative genomics, Phylogenomics, Bioinformatics, Database, Regularory network modeling
SFBI
Membre de la SFBI

SaAB

Acronyme ou nom de la structure
Nom complet (en toutes lettres)
Statistiques et Algorithmique pour la Biologie
Adresse

Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT)
Inra
Chemin de Borde Rouge
BP 52627

31326 CASTANET-TOLOSAN cedex

France

Téléphone
0561285074
Fax
0561285335
Description (English)

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.     

  • Genetical level A genome is essentially seen through molecular markers whose locations on a chromosome are highly informative in genetics investigation. Localizing these markers on the chromosomes (genetic mapping and radiated hybrid mapping: Carthagène) in order to subsequently locate the regions linked to quantitative traits of interest (disease resistance, yield ...) with respect to those markers (QTL or quantitative trait loci localization by analyzing allelic transmission: MCQTL and by modelling linkage disequilibrium: HAPim). These QTLs can then be used in selecting varieties that combine several desirable traits.
  • Molecular level At the molecular level, the DNA sequence of the genome is directly analyzed to decode and identify functional regions in the sequence. These may be genes coding for proteins (in bacterial genomes and EST cclusters FrameD or in eukaryotic genomes: EuGène) or non coding genes corresponding to functional RNAs (MilPat, DARN!, ApolloRNA, RNAspace). The comparison of genomes of different species and identification of key events that separate them (recombination) can enable the transfer of information between genomes.
  • Gene expression level The use of DNA microarrays allows to partially observe the cellular activity at a given time. It is then possible to establish a link between the contextual conditions of the cell at observation time (disease, polluted environment) and the genes that are over (or under) expressed. This link may help trace the genes related to disease or allow for a diagnosis.

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.

English keywords
genetical and radiated hybrids mapping, QTL mapping, sequence annotation, ncRNA search, inference of gene regulatory network
SFBI
Membre de la SFBI

GEB

Acronyme ou nom de la structure
Nom complet (en toutes lettres)
Genome, Evolution et Bioinformatique
Adresse

Laboratoire de Chimie Bacterienne (LCB)
UMR 7283 AMU CNRS
31 Chemin Joseph Aiguier

13009 Marseille
France

English keywords
Comparative genomics, molecular evolution, bioinformatics
SFBI
Membre de la SFBI