Current group
Fabien JOURDAN (INRA DR, Senior Research scientist). @metexplore
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).@LudoCottret
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) @NathaliePoupin
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) @vinson6431
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 (INRAE CR, Research scientist)
Clément joined the group in 2019 to develop computational solutions for predictive toxicology. Prior to that Clément did a PhD at INRA on graph based analysis of metabolic networks and their usage for metabolomics data intepretation. He then moved to Imperial College to work on epidemiological data.
keywords: genome scale models, chemoinformatics, predictive toxicology
Pablo RODRIGUEZ MIER (INCA project, Post-doc, network modelling) @PabloRMier
Pablo works on genome scale modelling of cancer metabolism in particular the impact of P53 tumor suppressor on cell metabolism.
keywords: cancer metabolism, flux modelling, machine learning
Maxime DELMAS (PhD, INRAE-H2020, Data Mining)
During his PhD, Maxime is working creating and exploiting knowledge resources on metabolic profiles of diseases and exposition to Food Contaminants. He is using metabolic network to better classify metabolic fingerprints.
Supervisors: Clément Frainay and Fabien Jourdan.
keywords: data mining, metabolic fingerprints, metabolic networks
Juliette COOKE (PhD, network modelling)
Julette works on using human genome scale metabolic network to create metabolic fingerprints. The aim is to link molecular initiating events which could happen during exposition to Metabolic Disrupting Compounds (MDCs) with observable metabolic modulations.
Keywods: flux modelling, biomarkers
Louison FRESNAIS (PhD, INRAE-L'Oréal, Cellular metabolism modelling)
Louison is developping computational solutions to study genome scale metabolic networks modulations using omics data produced in vitro.
Supervisors: Fabien Jourdan, Olivier Perin (L'Oréal)
Keywords, metabolic networks, flux modelling
Alumni
These great people helped us developing our projects. It was a pleasure and those staying in the academic field are still active collaborators.Amina works on MetExploreViz. She is developping methods and web tools to allow abstractions in metabolic network visualisation. Amina is supervised by Maxime Chazalviel.
Keywords: visualisation, web
Maxime worked on software development for clinical metabolomics data analysis. He was engineer at MedDay pharmaceutical company, hosted in our team. He was in charge of MetExploreViz development.
Jeanne studied the topology of metabolic networks of human gut microbiota. She developped graph based methods and implemented them in JAVA.
During is master internship, Adrien wass 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
During is master internship, Arthur was working on lipid mapping in metabolic networks.
Etienne was 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
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.
During is master internship, Arthur was working on lipid mapping in metabolic networks.
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 work on pathway enrichment calculation and result visualisaiton. Maxime is under the supervision of Maxime Chazalviel and Florence Vinson.
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 worked on method and software development to retrieve biological information on biomarker lists using publicly available resources.
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
Cerys JENKINS post-doc at the University of Edinburgh, Cerys is specialised in IR spectroscopy with application to biomarker discovery in cancer. Cerys joined the group 4 weeks to process LC-MS data using workflow4metabolomics and MetExplore.
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.
