modélisation de réseaux de régulation

Dyliss

Acronyme ou nom de la structure
Nom complet (en toutes lettres)
DYnamics, Logics and Inference for biological Systems and Sequences
Adresse

IRISA & INRIA Rennes
Bat 12A
Campus de Beaulieu

35042 Rennes cedex
France

Téléphone
0299847100
Description (English)

Dyliss is a research team in bioinformatics. We focus on sequence analysis and systems biology. We use qualitative formal systems to characterize genetic actors from non model species, such as algae or mining baceria, that control phenotypic answers when challenged by their environment.

  • Methods: constraint logic programming, symbolic dynamics, machine learning, formal systems.
  • Expertise: functional characterization, non-model species, multi-scale integration.
  • Application domains: marine biology, micro-environmental biology...

The main computational challenge is to face lacks and incompleteness in both expert knowledge and experimental observations. Our strategy relies on three main points.

  • We focus on a targeted functional characterization rather than on a complete understanding of the species.
  • We rely on knowledge rather than on amounts of experimentations.
  • We use model-species to validate methods.

We use qualitative formal systems for knowledge acquisition and integration. All our methods aim at identifying the space of all models that are consistent with both knowledge and observations. Then we provide tools to navigate in this space in order to investigate which properties are shared by a large proportion of the space.

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

IBIS

Acronyme ou nom de la structure
Nom complet (en toutes lettres)
IBIS
Adresse


655 avenue de l'Europe, Montbonnot,

38334 Saint Ismier CEDEX, France

France

Description (English)

Modeling, simulation, measurement, and control of bacterial regulatory networks

English keywords
bioinformatics, systems biology, microbiology, molecular biology, modeling of regulatory networks, dynamical systems, systems identification
SFBI
Membre de la SFBI