INRIA Grenoble – Rhône-Alpes
The IBIS research group at INRIA Grenoble – Rhône-Alpes focuses on the analysis of bacterial regulatory networks through a systems-biology approach, by means of models and experiments. The members of IBIS work on the modeling of large and complex bacterial regulatory networks, the simulation of the network dynamics by means of these models, high-precision and real-time measurements of gene expression and metabolism, the use of these data for model validation and identification, and the control and re-engineering of bacterial regulatory networks.
PIs: Hidde de Jong (project coordinator) and Delphine Ropers
Laboratoire Adaptation et Pathogénie des Microorganismes (LAPM), Université Joseph Fourier and CNRS
The Control of Gene Expression (CEG) group at the Laboratoire Adaptation et Pathogénie des Microorganismes (LAPM) studies genetic regulatory mechanisms in E. coli. The members of CEG have focused these past years on analyzing the dynamics of gene expression, studying different aspects of the regulatory network of E. coli by methods of systems biology and synthetic biology. They have also developed and improved methods for chromosome engineering that allow the efficient creation of desired strains.
N.B. In 2014, the CEG group joined the Laboratoire Interdisciplinaire de Physique (LIPhy).
PI: Johannes Geiselmann
Laboratoire Interdisciplinaire de Physique (LIPhy), Université Joseph Fourier and CNRS
The Biophysics group at the Laboratoire Interdisciplinaire de Physique (LIPhy) has an expertise in studying living matter from the perspective of statistical physics. Its members are concerned with two main topics: (i) the stability and entrainability of the circadian clock in cyanobacteria and (ii) more recently, noise propagation in natural bacterial regulatory networks. The aim is to associate the development of new tools (e.g., quantitative bioluminescence microscopy and microfluidics for long-term monitoring of bacteria) with data analysis, modeling, and numerical simulation.
PI: Irina Mihalcescu
Laboratoire Biologie à Grande Echelle, CEA, Université Joseph Fourier, INSERM and CNRS
The Etude de la Dynamique des Protéomes (EDyP) team at the Laboratoire Biologie à Grande Echelle has a strong expertise in biochemistry and mass spectrometry. This research unit develops new analytical methods in the field of proteomics and offers proteomics services to the community using state-of-the-art instrumentation (including two OrbiTrap and two Q-Trap mass spectrometers). EDyP has been involved in many projects, covering two major themes: the study of the dynamics of cellular and subcellular proteomes and the search for new biomarkers.
PIs: Christophe Bruley and Myriam Ferro
Laboratoire Génétique Végétale du Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech
The Fundamental Quantitative Genetics group at the Laboratoire Génétique Végétale du Moulon performs mathematical and computational studies for complex traits and biological networks, especially gene regulatory networks. The team has been involved in growth models for yeast and E. coli, taking into account metabolism and proteomics data sets. The participants in the project develop mathematical, statistical and computational tools for the in-silico analysis of gene regulatory and metabolic networks, with a stress on optimization algorithms, simulation methods, and network inference.
PI: Olivier Martin
INRIA Sophia-Antipolis – Méditerranée
The aim of the BIOCORE group at INRIA Sophia-Antipolis – Méditerranée is to contribute to environment preservation. In this context, the BIOCORE members design, model, analyze, control and optimize artificial ecosystems. Our tools are developed within the framework of the analysis of applied mathematics: dynamical systems and control theory, which includes (multi-scale) modeling, identification, validation based on experimental measurements, state estimation, control, and optimization. Two applications of particular relevance for the Reset project are biochemical networks (genetic networks, signalling networks) and bioreactors (waste treatment, production of metabolites).
PI: Jean-Luc Gouzé
Metabolic Explorer
Metabolic Explorer is a biological chemistry company specialized in the development of industrial bioprocesses (using renewable, sustainable raw materials), for the production of chemical compounds used in a wide range of everyday products: paints, solvents, textile fibres, animal feed supplements, adhesives, etc. Based on the tried-and-tested principle of industrial fermentation, and with high R&D and industrial assets, Metabolic Explorer designs high-performance microorganisms that can transform plant-derived raw materials into an existing bulk chemical. The company develops and patents innovative, fermentation-based industrial processes opening up new avenues for using natural, sustainable, renewable resources. These environmentally-friendly, economically validated technologies offer industrial businesses a genuine alternative to petrochemicals for producing the bulk chemicals that are used in many everyday products.
PIs: Gwénaëlle Corre
