Current group

Fabien JOURDAN (INRA DR, Senior Research scientist)
Fabien Jourdan is a research scientist at INRA (the French National Research Institute for Agricultural Research). He is developing bioinformatics methods to study genome-scale metabolic networks aiming at, based on experimental data like metabolomics ones, retrieving parts of the organism metabolism affected by genetic or environmental perturbations. Fabien Jourdan is leading the development of MetExplore web server which is used by more than 400 users and developed by a group of 10 computational biologists. Fabien Jourdan is member of the board of the French National infrastructure for metabolomics and fluxomics, MetaboHub. Since 2015, he is president of the French-speaking Metabolomics and Fluxomics Network (RFMF).

Ludovic COTTRET (INRA IR, Research Engineer)

Ludovic is in charge of the operational coordination of MetExplore webserver. Ludovic is specialist in genome scale metabolic network reconstruction and omics data analysis in the context of these networks. His scientific interests are focused on plant-microorganisms interactions.

Nathalie POUPIN (INRA CR, Research scientist)
Nathalie joined the team in 2013. She studies the effects of low doses of food contaminants on the human metabolic network. She is specialized in the mathematical modelling of metabolic systems, using approaches based on constraint based modelling and flux analysis. She has particularly been involved in developing specific in silico models of the metabolic network of human cells in order to identify the cellular metabolic modulations that are linked to particular pathophysiological, nutritional or environmental conditions.
keywords: constraint based modelling, genome scale models, food contaminants and metabolic impacts
Florence VINSON (INRA IE, bioinformatics engineer)
Florence has a background in biology and is now a computer scientist engineer of INRA. She is involved in national (ANR ExpoMatPest) and international projects (ANR Systryp). She is in charge of MetExplore and metabolic annotation projects.
keywords: Meta-analysis, databases,web 2.0
Clément FRAINAY (INRA CR, Currently at Imperial College)
Clément works on taking into account chemical structure of molecules while computing metabolic stories between biomarkers identified in metabolomics. This work is done on Human genome scale metabolic network.
PhD title : "Système de recommandation basé sur les réseaux pour l'interprétation de résultats de métabolomique."
keywords: genome scale models, chemoinformatics
Maxime CHAZALVIEL(MedDay IE, Bioinformatics engineer)
Maxime works on software development for clinical metabolomics data analysis. He is engineer at MedDay pharmaceutical company, hosted in our team. He is in charge of MetExploreViz development.
keywords: web development, visualization
Etienne CAMENEN (H2020 IE, Bioinformatics engineer)
Etienne is involved in PhenoMeNal H2020 project aiming at proposing a Virtual Research Environment for clinical phenotypic data. He is in charge of proposing network analysis in docker containers.
keywords: cloud computing, docker
Arthur MOREAU (M2, Bioinformatics)
During is master internship, Arthur is working on lipid mapping in metabolic networks.
Adrien ROHAN (M2, Bioinformatics)
During is master internship, Adrien is working on metabolic network visualisation within MetExploreViz project. His aim is to make representation more similar to the ones which can be found in text books.

Alumni

These great people helped us developing our projects. It was a pleasure and those staying in the academic field are still active collaborators.

Benjamin MERLET (IE, bioinformatics engineer) MetaboHub
Benjamin was in charge of the system administration of the MetExplore web server. Within the framework of the MetaboHub project, he contributed to strengthen the platform service. He was then involved in PhenoMeNal European project.

Maxime DELMAS (Undergraduate, 1st year Master student, Université de Rouen, 2017)
Maxime work on pathway enrichment calculation and result visualisaiton. Maxime is under the supervision of Maxime Chazalviel and Florence Vinson.
Laurent FERNANDO (Undergraduate, 2nd year Master student, Université de Toulouse)
Laurent works on the identification of active metabolism in cancerous cells. This work is achieved in collaboration with Toulouse Cancer Research Centre. Laurent is under the supervision of Nathalie Poupin.
Thomas GARCIA (Undergraduate, 1st and 2nd year Master student, Université de Toulouse, 2016-17)
Thomas worked on method and software development to retrieve biological information on biomarker lists using publicly available resources.
Sanu SHAMEER (PhD student, systems biology 2013-16)
Sanu has a bioinformatics background (master at the University of Manchester). He worked  in the framework of the European project Paramet on kinetoplastid metabolism. He was in charge of model reconstruction and flux modeling of Trypanosoma brucei.
PhD title: "
Genome-scale metabolic reconstruction and the analysis of Trypanosoma brucei from a Systems Biology perspective"
Sanu is currently postdoc at the University of Oxford.
Florence MAURIER (IE, bioinformatics engieneer 12months 2015/16) MetaboHub
Florence developed algorithms to identify functional modules in genome scale metabolic networks. She also works on the metabolic network reconstruction of Tomato fruit.
 
Paula NUNES
MSc student in Bioinformatics (Toulouse, Master de Bioinformatique et de biologie des systèmes) february-august 2012 (6 months)
Now informatics engineer in Capgemini

Marianne DUSSART MSc student in Bioinformatics (Bordeaux, Master de Bioinformatique de Bordeaux) february-august 2011 (6 months)

Marc DUBOIS MSc student in Bioinformatics (Bordeaux, Master de Bioinformatique de Bordeaux) february-august 2009 (6 months) then software engineer 12 months 2010-2011
Now engineer in Toulouse proteomics facility  / CEO and co-founder of omics-services

Visiting Researchers

 

Sandra THERRIEN-LAPIERRE master student at the University of Montreal visited us from july 18th to july 29th 2016. Sandra is working with Pr. Christine Des Rosiers on the integration of mGWAS data in the context of metabolic networks.

David RENAULT senior lecturer in ecology, University of Rennes. He came for a one week training in April 2016 to analyze metabolomics data obtained on insects leaving in Kerguelen islands. Funding: CNRS.

Helen PURCHASE senior lecturer in computer science at the University of Glasgow from October 5th to October 9th 2015. Working on evaluation of metabolic drawings. Funding: PhenoMeNal.

Audrey LE GOUELLEC researcher at Grenoble hospital. One week from September 21st to September 25th 2015. Working on mapping metabolomics data on tryptophane catabolism.

Elisabete CARVALHO postodc at the Royal Holloway University, London. One week September 29th to October 3rd 2014. Topic: interpretation of plant metabolomics data using MetExplore. Funding: COST action.

Karl BURGESS Head of metabolomics facility in Glasgow Polyomics. Two weeks in 2014. Topic: bioinformatics for MS data analysis. Funding:  SULSA.

Florence MONDEGUER Researcher at IFREMER Nantes. One week in 2009. Topic: training in XCMS data treatment of MS data.