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Metabolic Networks

Metabolic Networks
Thanks to the functional annotation of genomes and advances in metabolomics, it is now possible to study the metabolic network of an organism as a whole. Bioinformatics makes an indispensable contribution to each step leading to the overall analysis of a metabolic network, automated rebuilding of it in developing new algorithms and dedicated tools..

Application field: some food contaminants like Bipshenol A may have impact on Human Health. Our aim is to study potential metabolic impacts of these compounds according to different doses and during critical Human development phases (e.g. pregnancy).
developing methods to study genome-scale metabolic networks. These approaches are mainly based on graph models and constraint based modelling. The aim is, based on experimental data like metabolomics ones, to retrieve parts of the organism metabolism affected by genetic or environmental perturbations.

MetabolicNetworkJourdan

For a more complete presentation, please visit this page.

Software and web servers:

Title

Aim

URL

Publication

MetExplore

Webserver for genome scale analysis of metabolic networks.

www.metexplore.fr

Cottret Ludovic, Frainay Clément, Chazalviel Maxime, Cabanettes Floréal, Gloaguen Yoann, Camenen Etienne, Merlet Benjamin, Portais Jean-Charles, Heux Stéphanie, Poupin Nathalie, Vinson Florence and Jourdan Fabien. MetExplore: Manage and Explore metabolic networks. (2018) Nucelic Acids Research. In press.

Modam

A Cytoscape plug-in to facilitate multilayer data interpretation

https://sites.google.com/site/modamplugin/

Enjalbert et al. Intuitive visualization and analysis of multi-omics data and application to Escherichia coli carbon metabolism (2011) Plos One. 6(6).

Metanetter

ab initio reconstruction of metabolic networks

http://compbio.dcs.gla.ac.uk/fabien/abinitio/abinitio.html

Jourdan et al. MetaNetter: inference and visualization of high-resolution metabolomic networks. (2008) Bioinformatics, 24, 143-145.

People involved:

  • Fabien Jourdan (DR INRA)
  • Nathalie Poupin (CR INRA)
  • Florence Vinson (IE INRA)

Collaborations :

MetaSys, INRIA Toulouse : Jean-Charles Portais, Fabien Letisse, Stéphanie Heux

Bordeaux 1 (LaBRI)- MabioVis team : Pr. Guy Melançon, David Auber, Romain Bourqui, Jonathan Dubois

INRIA Bamboo team : Marie-France Sagot, Vincent Lacroix

University of Glasgow : Pr Michael P. Barrett, Yoann Gloaguen, Karl Burgess

CEA Saclay : Christophe Junot