phylogénie

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

SMILE

Acronyme ou nom de la structure
Nom complet (en toutes lettres)
Stochastic Models for the Inference of Life Evolution
Adresse

Stochastic Models for the Inference of Life Evolution
CIRB - Collège de France
11 place Marcelin Berthelot

75005 Paris

France

Téléphone
+33144271391
SFBI
N'est pas 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