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103

Fabien Jourdan


DR INRAE - TOXALIM Unit, Toulouse.
 
Research interests
Food toxicology: some food contaminants, like Bipshenol A, may have impact on Human Health. Our aim is to study potential metabolic effects according to different doses and during critical Human development phases (e.g. pregnancy).

Bioinformatics: developing methods to study genome-scale metabolic networks. These approaches are mainly based on graph models and constraint based models (e.g. FBA). The aim is to use experimental data like metabolomics ones in order to retrieve parts of the organism metabolism affected by genetic or environmental perturbations.
 
Keywords: metabolic networks, metabolomics, information visualization, food toxicology

Affiliations: Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31300 Toulouse, France
MetaboHub, French national infrastructure of metabolomics and fluxomics


Journal articles43 documents

  • Nils Paulhe, Cécile Canlet, Annelaure Damont, Lindsay Peyriga, Stéphanie Durand, et al.. PeakForest: a multi-platform digital infrastructure for interoperable metabolite spectral data and metadata management. Metabolomics, Springer Verlag, 2022, 18 (6), pp.40. ⟨10.1007/s11306-022-01899-3⟩. ⟨hal-03695453⟩
  • Davy Guignard, Cécile Canlet, Marie A Tremblay-Franco, Elodie Chaillou, Roselyne Gautier, et al.. Gestational exposure to bisphenol A induces region-specific changes in brain metabolomic fingerprints in sheep. Environment International, Elsevier, 2022, 165, pp.107336. ⟨10.1016/j.envint.2022.107336⟩. ⟨hal-03701070⟩
  • Blandine Comte, Stéphanie Monnerie, Marion Brandolini-Bunlon, Cécile Canlet, Florence Castelli, et al.. Multiplatform metabolomics for an integrative exploration of metabolic syndrome in older men. EBioMedicine, Elsevier, 2021, 69, ⟨10.1016/j.ebiom.2021.103440⟩. ⟨hal-03283772⟩
  • Julien Boccard, Domitille Schvartz, Santiago Codesido, Mohamed Hanafi, Yoric Gagnebin, et al.. Gaining Insights Into Metabolic Networks Using Chemometrics and Bioinformatics: Chronic Kidney Disease as a Clinical Model. Frontiers in Molecular Biosciences, Frontiers Media, 2021, 8, pp.682559. ⟨10.3389/fmolb.2021.682559⟩. ⟨hal-03318230⟩
  • Maxime Delmas, Olivier Filangi, Nils Paulhe, Florence Vinson, Christophe Duperier, et al.. FORUM: building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases. Bioinformatics, Oxford University Press (OUP), 2021, 37 (21), pp.3896-3904. ⟨10.1093/bioinformatics/btab627⟩. ⟨hal-03361495⟩
  • Marvin Martens, Rob Stierum, Emma Schymanski, Chris Evelo, Reza Aalizadeh, et al.. ELIXIR and Toxicology: a community in development. F1000Research, Faculty of 1000, 2021, 10, pp.1129. ⟨10.12688/f1000research.74502.1⟩. ⟨pasteur-03680151⟩
  • Pablo Rodríguez-Mier, Nathalie Poupin, Carlo de Blasio, Laurent Le Cam, Fabien Jourdan. DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks. PLoS Computational Biology, Public Library of Science, 2021, 17 (2), ⟨10.1371/journal.pcbi.1008730⟩. ⟨hal-03154775⟩
  • Lucille Stuani, Marie Sabatier, Estelle Saland, Guillaume Cognet, Nathalie Poupin, et al.. Mitochondrial metabolism supports resistance to IDH mutant inhibitors in acute myeloid leukemia. Journal of Experimental Medicine, Rockefeller University Press, 2021, 218 (5), pp.e20200924. ⟨10.1084/jem.20200924⟩. ⟨hal-03563454⟩
  • Amal Surrati, Evseev Sergey, Fabien Jourdan, Dong-Hyun Kim, Virginie Sottile. Osteogenic Response of Human Mesenchymal Stem Cells Analysed Using Combined Intracellular and Extracellular Metabolomic Monitoring. Cellular Physiology and Biochemistry, Karger, 2021, 55 (3), pp.311-326. ⟨10.33594/000000377⟩. ⟨hal-03312596⟩
  • Bénédict Yanibada, Ulli Hohenester, Mélanie Pétéra, Cécile Canlet, Stéphanie Durand, et al.. Milk metabolome reveals variations on enteric methane emissions from dairy cows fed a specific inhibitor of the methanogenesis pathway. Journal of Dairy Science, inPress, 104 (12), pp.12553-12566. ⟨10.3168/jds.2021-20477⟩. ⟨hal-03351167⟩
  • Cecilia Wieder, Clément Frainay, Nathalie Poupin, Pablo Rodríguez-Mier, Florence Vinson, et al.. Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis. PLoS Computational Biology, Public Library of Science, 2021, 17 (9), ⟨10.1371/journal.pcbi.1009105⟩. ⟨hal-03344682⟩
  • Bénédict Yanibada, Ulli Hohenester, Mélanie Pétéra, Cécile Canlet, Stéphanie Durand, et al.. Inhibition of enteric methanogenesis in dairy cows induces changes in plasma metabolome highlighting metabolic shifts and potential markers of emission. Scientific Reports, Nature Publishing Group, 2020, 10 (1), ⟨10.1038/s41598-020-72145-w⟩. ⟨hal-02949602⟩
  • Nathalie Poupin, Florence Vinson, Arthur Moreau, Aurélie Batut, Maxime Chazalviel, et al.. Improving lipid mapping in Genome Scale Metabolic Networks using ontologies. Metabolomics, Springer Verlag, 2020, 16 (4), ⟨10.1007/s11306-020-01663-5⟩. ⟨hal-02935172⟩
  • Juliette Legler, Daniel Zalko, Fabien Jourdan, Miriam Jacobs, Bernard Fromenty, et al.. The GOLIATH Project: Towards an Internationally Harmonised Approach for Testing Metabolism Disrupting Compounds. International Journal of Molecular Sciences, MDPI, 2020, 21 (10), pp.3480. ⟨10.3390/ijms21103480⟩. ⟨hal-02638423⟩
  • Marie A Tremblay-Franco, Nathalie Poupin, Aurélien Amiel, Cécile Canlet, Didier Remond, et al.. Postprandial NMR-Based Metabolic Exchanges Reflect Impaired Phenotypic Flexibility across Splanchnic Organs in the Obese Yucatan Mini-Pig. Nutrients, MDPI, 2020, 12 (8), pp.2442. ⟨10.3390/nu12082442⟩. ⟨hal-02927174⟩
  • Imourana Alassane-Kpembi, Cecile Canlet, Marie A Tremblay-Franco, Fabien Jourdan, Maxime Chalzaviel, et al.. 1H-NMR metabolomics response to a realistic diet contamination with the mycotoxin deoxynivalenol: Effect of probiotics supplementation. Food and Chemical Toxicology, Elsevier, 2020, 138, pp.111222. ⟨10.1016/j.fct.2020.111222⟩. ⟨hal-03331253⟩
  • Nathalie Poupin, Marie A Tremblay-Franco, Aurélien Amiel, Cécile Canlet, Didier Remond, et al.. Arterio-venous metabolomics exploration reveals major changes across liver and intestine in the obese Yucatan minipig. Scientific Reports, Nature Publishing Group, 2019, 9 (1), ⟨10.1038/s41598-019-48997-2⟩. ⟨hal-02282295⟩
  • Jean Pierre J. P. Cravedi, Fabien Jourdan. Caractérisation des dangers des contaminants alimentaires : ce qui change; conséquences pour la recherche et l’évaluation. Innovations Agronomiques, INRAE, 2019, 73, pp.1-10. ⟨10.15454/ij9z4r⟩. ⟨hal-02275513⟩
  • Clément Frainay, Sandrine Aros, Maxime Chazalviel, Thomas Garcia, Florence Vinson, et al.. MetaboRank: network-based recommendation system to interpret and enrich metabolomics results. Bioinformatics, Oxford University Press (OUP), 2019, 35 (2), pp.274-283. ⟨10.1093/bioinformatics/bty577⟩. ⟨hal-02627792⟩
  • Nathalie Poupin, Anne Corlu, Nicolas J. Cabaton, Hélène Dubois-Pot-Schneider, Cécile Canlet, et al.. Large-Scale Modeling Approach Reveals Functional Metabolic Shifts during Hepatic Differentiation. Journal of Proteome Research, American Chemical Society, 2019, 18 (1), pp.204-216. ⟨10.1021/acs.jproteome.8b00524⟩. ⟨hal-01937261⟩
  • Robin Mesnage, Martina Biserni, Sucharitha Balu, Clément Frainay, Nathalie Poupin, et al.. Integrated transcriptomics and metabolomics reveal signatures of lipid metabolism dysregulation in HepaRG liver cells exposed to PCB 126. Archives of Toxicology, Springer Verlag, 2018, 92 (8), pp.2533-2547. ⟨10.1007/s00204-018-2235-7⟩. ⟨hal-02621552⟩
  • Maria del Mar Amador, Benoit Colsch, Foudil Lamari, Claude Jardel, Farid Ichou, et al.. Targeted versus untargeted omics — the CAFSA story. Journal of Inherited Metabolic Disease, Springer Verlag, 2018, 41 (3), pp.1-10. ⟨10.1007/s10545-017-0134-3⟩. ⟨hal-01777969⟩
  • Nicolas J. Cabaton, Nathalie Poupin, Cécile Canlet, Marie A Tremblay-Franco, Marc Audebert, et al.. An untargeted metabolomics approach to explore the metabolic modulation of HepG2 cells exposed to low doses of bisphenol A and 17β-estradiol 2. Frontiers in Endocrinology, Frontiers, 2018, 9, ⟨10.3389/fendo.2018.00571⟩. ⟨hal-02618654⟩
  • Maxime Chazalviel, Clément Frainay, Nathalie Poupin, Florence Vinson, Benjamin Merlet, et al.. MetExploreViz: web component for interactive metabolic network visualization. Bioinformatics, Oxford University Press (OUP), 2018, 34 (2), pp.312-313. ⟨10.1093/bioinformatics/btx588⟩. ⟨hal-02621786⟩
  • Ludovic Cottret, Clément Frainay, Maxime Chazalviel, Floréal Cabanettes, Yoann Gloaguen, et al.. MetExplore: collaborative edition and exploration of metabolic networks. Nucleic Acids Research, Oxford University Press, 2018, 46 (W1), 8 p. ⟨10.1093/nar/gky301⟩. ⟨hal-01886470⟩
  • Clément Frainay, Fabien Jourdan. Computational methods to identify metabolic sub-networks based on metabolomic profiles. Briefings in Bioinformatics, Oxford University Press (OUP), 2017, 18 (1), pp.43-56. ⟨10.1093/bib/bbv115⟩. ⟨hal-01608721⟩
  • M. van Rijswijk, C. Beirnaert, C. Caron, M. Cascante, V. Dominguez, et al.. The future of metabolomics in ELIXIR. F1000Research, Faculty of 1000, 2017, 6 (Version 2), ⟨10.12688/f1000research.12342.2⟩. ⟨hal-01630635⟩
  • Sandra Therrien-Laperriere, S. Cherkaoui, G. Boucher, . Igenomed Consortium, Fabien Jourdan, et al.. PathQuant: A bioinformatic tool to quantitatively annotate the relationship between genes and metabolites through metabolic pathway mapping. FASEB Journal, Federation of American Society of Experimental Biology, 2017, 31 (1). ⟨hal-02622661⟩
  • Benjamin Merlet, Nils Paulhe, Florence Vinson, Clément Frainay, Maxime Chazalviel, et al.. A computational solution to automatically map metabolite libraries in the context of genome scale metabolic networks. Frontiers in Molecular Biosciences, Frontiers Media, 2016, 3, ⟨10.3389/fmolb.2016.00002⟩. ⟨hal-02631089⟩
  • Marie A Tremblay-Franco, Nicolas J. Cabaton, Cécile Canlet, Roselyne Gautier, Cheryl M Schaeberle, et al.. Dynamic metabolic disruption in rats perinatally exposed to low doses of bisphenol-A. PLoS ONE, Public Library of Science, 2015, 10 (10), ⟨10.1371/journal.pone.0141698⟩. ⟨hal-02632321⟩
  • Jean-Charles Martin, Mathieu Maillot, Gerard Mazerolles, Alexandre Verdu, Bernard Lyan, et al.. Can we Trust Untargeted Metabolomics: Results of the Metabo-ring Initiative, a Large-scale Multi-instruments Inter-laboratoire Study. Metabolomics, Springer Verlag, 2015, 11 (4), pp.807-821. ⟨10.1007/s11306-014-0740-0⟩. ⟨hal-01123343⟩
  • Sanu Shameer, Flora J. Logan-Klumpler, Florence Vinson, Ludovic Cottret, Benjamin Merlet, et al.. TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei. Nucleic Acids Research, Oxford University Press, 2015, 43 (D1), pp.D637 - D644. ⟨10.1093/nar/gku944⟩. ⟨hal-02631222⟩
  • Paulo Vieira Milreu, Cecilia Coimbra Klein, Ludovic Cottret, Vicente Acuña, Etienne E. Birmelé, et al.. Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure. Bioinformatics, Oxford University Press (OUP), 2014, 30 (1), pp.61-70. ⟨10.1093/bioinformatics/btt597⟩. ⟨hal-00922567⟩
  • Ricardo R. Silva, Fabien Jourdan, Diego M. Salvanha, Fabien Letisse, Emilien L. Jamin, et al.. ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics. Bioinformatics, Oxford University Press (OUP), 2014, 30 (9), pp.1336 - 1337. ⟨10.1093/bioinformatics/btu019⟩. ⟨hal-01268715⟩
  • Vicente Acuña, Etienne Birmelé, Ludovic Cottret, Pierluigi Crescenzi, Fabien Jourdan, et al.. Telling stories: Enumerating maximal directed acyclic graphs with a constrained set of sources and targets. Theoretical Computer Science, Elsevier, 2012, 457, pp.1--9. ⟨10.1016/j.tcs.2012.07.023⟩. ⟨hal-00764025⟩
  • Amine Ghozlane, Frédéric Bringaud, Hayssam Soueidan, Isabelle Dutour, Fabien Jourdan, et al.. Flux analysis of the Trypanosoma brucei glycolysis based on a multi-objective criteria bioinformatic approach, Advances in Bioinfromatics, 2012, in press. International conference with published acts. Advances in Bioinformatics, Hindawi Publishing Corporation, 2012, 2012, 16 p., Article ID 159423. ⟨10.1155/2012/159423⟩. ⟨hal-00723179⟩
  • Brice Enjalbert, Fabien Jourdan, Jean-Charles Portais. Intuitive Visualization and Analysis of Multi-Omics Dataand Application to Escherichia coli Carbon Metabolism. PLoS ONE, Public Library of Science, 2011, 6 (6), pp.e21318. ⟨10.1371/journal.pone.0021318⟩. ⟨hal-01137055⟩
  • Frédéric Gilbert, Paolo Simonetto, Faraz Zaidi, Fabien Jourdan, Romain Bourqui. Communities and hierarchical structures in dynamic social networks: analysis and visualization. Social Network Analysis and Mining, Springer, 2011, 1 (2), pp.85-95. ⟨10.1007/s13278-010-0002-8⟩. ⟨hal-00520936⟩
  • Fabien Jourdan, Ludovic Cottret, Laurence Huc, David Wildridge, Richard Scheltema, et al.. Use of reconstituted metabolic networks to assist in metabolomic data visualization and mining. Metabolomics, Springer Verlag, 2010, 6 (2), pp.312-321. ⟨10.1007/s11306-009-0196-9⟩. ⟨hal-02662801⟩
  • Ludovic Cottret, Fabien Jourdan. Graph methods for the investigation of metabolic networks in parasitology. Parasitology, Cambridge University Press (CUP), 2010, 137, pp.1393-1407. ⟨10.1017/S0031182010000363⟩. ⟨hal-02661590⟩
  • Ludovic Cottret, David Wildridge, Florence Vinson, Michael P Barrett, Hubert Charles, et al.. MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks.. Nucleic Acids Research, Oxford University Press, 2010, 38 (Web Server issue), pp.W132-7. ⟨10.1093/nar/gkq312⟩. ⟨hal-00690651⟩
  • Romain Bourqui, Paolo Simonetto, Fabien Jourdan. Un algorithme stable de décomposition pour l'analyse des réseaux sociaux dynamiques. Revue des Nouvelles Technologies de l'Information, Editions RNTI, 2009, pp.337-348. ⟨hal-00406437⟩
  • Fabien Jourdan, Rainer Breitling, Michael Barrett, Gilbert David. MetaNetter: inference and visualization of high-resolution metabolomic networks. Bioinformatics, Oxford University Press (OUP), 2008, 24 (1), pp.143-145. ⟨10.1093/bioinformatics/btm536⟩. ⟨hal-03318375⟩

Conference papers35 documents

  • Nathalie Poupin, Marie A Tremblay-Franco, Cécile Canlet, Aurélien Amiel, Didier Rémond, et al.. Modelling intrahepatic metabolic rewiring during the onset of obesity using arterio- venous blood metabolomics profiles. European RFMF Metabomeeting 2020, Jan 2020, Toulouse, France. ⟨hal-02948334⟩
  • Bénédict Yanibada, Ulli Hohenester, Mélanie Pétéra, Cécile Canlet, Stéphanie Durand, et al.. Inhibition of enteric methanogenesis in cows induces changes in plasma metabolome highlighting potential emission markers. 7. Greenhouse Gas and Animal Agriculture Conference, Aug 2019, Foz do Iguassu, Brazil. ⟨hal-02788492⟩
  • Laurent Fernando, Lucille Stuani, Tony Lionel Palama, Tony Kaoma, Jean-Emmanuel Sarry, et al.. Modélisation du réseau métabolique des cellules de Leucémies Aiguës Myéloïdes pour comprendre les différences métaboliques liées à la mutation sur IDH1. Congrès de Spectrométrie de Masse, Métabolomique et Fluxomique (SMMAP), Oct 2017, Marne-la-Vallée, France. ⟨hal-02946080⟩
  • Dominique Rolin, Floriant Bellvert, Justine Bertrand-Michel, Cécile Canlet, Richard Cole, et al.. MetaboHUB and RFMF : two tools at the service of metabolomics and fluxomics in France. MERLION Metabolomics Workshop Singapore 2014, Nov 2014, Singapour, Singapore. ⟨hal-02798242⟩
  • Dominique D. Rolin, Alice A. Agasse, Justine Bertrand-Michel, R. R. Cole, B. B. Colsch, et al.. MetaboHUB: a national infrastructure dedicated to metabolomics and fluxomics. 7. Journées scientifiques du Réseau Français de Métabolomique et de Fluxomique (RFMF), Jun 2013, Amiens, France. ⟨hal-01002241⟩
  • Dominique D. Rolin, Alice A. Agasse, Justine Bertrand-Michel, R. R. Cole, B. B. Colsch, et al.. MetaboHUB: une infrastructure nationale au service de la métabolomique. Séance thématique "La métabolomique : son application en recherche pharmaceutique et diagnostique", Académie Nationale de Pharmacie. FRA., Feb 2013, Paris, France. ⟨hal-01002248⟩
  • Dominique D. Rolin, Alice A. Agasse, Justine Bertrand-Michel, R. R. Cole, Sophie S. Colombie, et al.. MetaboHUB: a french infrastructure dedicated to metabolomics and fluxomics. Metabolomics 2013 - 9. Annual conference of the Metabolomics Society, Jul 2013, Glasgow, United Kingdom. ⟨hal-01002247⟩
  • Jonathan Dubois, Ludovic Cottret, Amine Ghozlane, David Auber, Frédéric Bringaud, et al.. Visualization of time-series data in the context of metabolic networks with Systrip Software. Journées Ouvertes Biologie Informatique Mathématiques (JOBIM 2013), Jul 2013, France. ⟨hal-00838725⟩
  • Laurent Debrauwer, Emilien L. Jamin, Isabelle Jouanin, Sylvie S. Chevolleau, Marlène Z. Lacroix, et al.. Metabolomics for food and environmental toxicology : from targeted to global integrative approaches. LC-MS Montreux Symposium 2012, Nov 2012, Montreux, Switzerland. ⟨hal-02745532⟩
  • Jonathan Dubois, Ludovic Cottret, Amine Ghozlane, David Auber, Frédéric Bringaud, et al.. Systrip: a visual environment for the investigation of time-series data in the context of metabolic networks. 16th International Conference on Information Visualization (IV'12), Jul 2012, Montpellier, France. pp.4771a204. ⟨hal-00742176⟩
  • Alexandre Verdu, Bernard Lyan, Carole Migné, Catherine Defoort, Cécile Canlet, et al.. Peut-on faire confiance à la métabolomique: résultats de l'initiative MetaboRing. 6. Journées Scientifiques du Réseau Français de Métabolomique et Fluxomique (RFMF), May 2012, Nantes, France. ⟨hal-01594993⟩
  • Alexandre Verdu, Bernard Lyan, Carole Migné, Catherine Defoort, Cécile Canlet, et al.. Can we trust untargeted metabolomics: results of the metabo-ring study. 2. African-European Conference on Chemometrics - Afrodata 2012, Nov 2012, Stellenbosch, South Africa. ⟨hal-01595486⟩
  • Fabien Jourdan. Use of reconstituted metabolic networks to assist in metabolomic data visualization and mining. Metabolomics 2011, Saisissez le nom du laboratoire, du service ou du département., Ville service., Jun 2011, Cairns, Australia. ⟨hal-02802559⟩
  • Fabien Jourdan. Extraction d'"histoires métaboliques" dans les réseaux métaboliques à partir de données métabolomiques. 5eme journées du RFMF, Saisissez le nom du laboratoire, du service ou du département., Ville service., May 2011, Paris, France. ⟨hal-02803297⟩
  • Daniel Zalko, Nicolas J. Cabaton, Cécile Canlet, Marie A Tremblay-Franco, Fabien Jourdan. Approche métabonomique pour l'étude in vivo, in vitro et in silico de la toxicologie des faibles doses. . 5emes Journées scientifiques TOXALIM, Ville service., Dec 2011, Toulouse, France. ⟨hal-02811476⟩
  • Emilien L. Jamin, Cécile Canlet, Maria-Helena Meireles, Marc Dubois, Marie A Tremblay-Franco, et al.. Development of metabolomics method associating NMR and UPLC-HRMS. SMAP 2011, Saisissez le nom du laboratoire, du service ou du département., Ville service., Sep 2011, Avignon, France. ⟨hal-02804072⟩
  • Romain Bourqui, Helen Purchase, Fabien Jourdan. Domain specific vs Generic Network Visualization: an evaluation with metabolic networks. Australasian Conference on User Interface, Jan 2011, Australia. pp.9-18. ⟨hal-00579230⟩
  • Fabien Jourdan. Computing "metabolic stories" in genome scale metabolic networks based on metabolomics data.(2011). Metabolomics 2011, Ville service., Jun 2011, Cairns, Australia. ⟨hal-02803877⟩
  • Vicente Acuña, Etienne Birmele, Ludovic Cottret, Pierluigi Crescenzi, Fabien Jourdan, et al.. Telling Stories. ICALP 2011 satellite workshop: Graph Algorithms and Applications (GA), 2011, Zurich, Switzerland. ⟨10.1016/j.tcs.2012.07.023⟩. ⟨hal-00748788⟩
  • Amine Ghozlane, Frédéric Bringaud, Fabien Jourdan, Patricia Thebault. Metaboflux : a method to analyze flux distribution in metabolic networks. Workshop Metabolomics2010, AmsterdamRAI, the Netherlands, 2010, Amsterdam, Netherlands. ⟨hal-00648759⟩
  • Romain Bourqui, Frédéric Gilbert, Paolo Simonetto, Faraz Zaidi, Umang Sharan, et al.. Detecting structural changes and command hierarchies in dynamic social networks. Advances in Social Network Analysis and Data Mining, 2009, Greece. pp.83-88. ⟨hal-00406240⟩
  • Romain Bourqui, Fabien Jourdan. Revealing subnetwork roles using contextual visualization: comparison of metabolic networks. 12th International Conference on Information Visualisation, Jul 2008, London, United Kingdom. pp.638-643. ⟨hal-00343889⟩
  • Romain Bourqui, Fabien Jourdan. Comparaison Visuelle de Réseaux Métaboliques. 8èmes Journées Ouvertes Biologie Informatique Mathématiques, 2007, France. pp.285-286. ⟨hal-00306674⟩
  • Fabien Jourdan, Alain Paris, Pierre-Yves Koenig, Guy Melançon. Multiscale scatterplot matrix for visual and interactive exploration of metabonomic data. 1st Visual Information Expert Workshop (VIEW), Apr 2006, Paris, France. ⟨hal-02751211⟩
  • Fabien Jourdan, Alain Paris, Pierre-Yves Koenig, Guy Melançon. Multiscale scatterplot matrix for visual and interactive exploration of metabonomics data. Visual Information Expert Workshop, Apr 2006, Paris, France. pp.202-215, ⟨10.1007/978-3-540-71027-1_18⟩. ⟨lirmm-00091360⟩
  • Romain Bourqui, David Auber, Vincent Lacroix, Fabien Jourdan. Un Algorithme Contraint de Dessin de Graphe Planaire pour la Visualisation de Réseaux Métaboliques. Quatrième édition du congrés francophone de doctorants en STIC, MajecSTIC, 2006, France. pp.électronique. ⟨hal-00306673⟩
  • Romain Bourqui, David Auber, Vincent Lacroix, Fabien Jourdan. Metabolic network visualization using constraint planar graph drawing Algorithm. IV 06: Proceedings of the 10 International Conference on Information Visualisation (IV06), 2006, United States. pp.489 - 496. ⟨hal-00306676⟩
  • Fabien Jourdan, Guy Melançon, Christophe Douy, Alexandre Gasne. Une Approche MDS Hybride pour l'Exploration Visuelle Interactive. Conférence Francophone sur l'Interaction Homme-Machine, Sep 2005, Toulouse, France. ⟨lirmm-00106468⟩
  • Yves Chiricota, Fabien Jourdan, Guy Melançon. Metric-Based Network Exploration and Multiscale Scatterplot. InfoVis: Information Visualization, Oct 2004, Austin, United States. pp.135-142, ⟨10.1109/INFVIS.2004.47⟩. ⟨lirmm-00108871⟩
  • Fabien Jourdan. Drawing, Clustering and Visualization of Biological Pathways. International Symposium on Networks in Bio-Informatics, Mar 2004, Paris, France. ⟨lirmm-00109131⟩
  • Fabien Jourdan, Guy Melançon. Multiscale hybrid MDS. IV: Information Visualization, Jul 2004, London, United Kingdom. pp.388-393, ⟨10.1109/IV.2004.1320173⟩. ⟨lirmm-00108864⟩
  • Yves Chiricota, Fabien Jourdan, Guy Melançon. Software Components Capture using Graph Clustering. IEEE International Workshop on Program Comprehension, 2003, Portland, Oregon, United States. pp.217-226. ⟨lirmm-00191947⟩
  • Yves Chiricota, Fabien Jourdan, Guy Melançon. Software Components Capture using Graph Clustering. IEEE International Workshop on Program Comprehension, 2003, Portland, Oregon, United States. pp.217-226. ⟨lirmm-00269464⟩
  • Fabien Jourdan, Guy Melançon. A Tool for Metabolic and Regolatory Pathways Visual Analysis. Conference on Visualization and Data Analysis, Jan 2003, Santa Clara, United States. pp.46-55. ⟨lirmm-00269772⟩
  • David Auber, Yves Chiricota, Fabien Jourdan, Guy Melançon. Multiscale Visualization of Small World Networks. InfoVis: Information Visualization, Oct 2003, Seattle, WA, United States. pp.75-81. ⟨lirmm-00269770⟩

Poster communications13 documents

  • Maxime Chazalviel, Adrien Rohan, Nathalie Poupin, Florence Vinson, Clément Frainay, et al.. MetExplore: Omics data analysis in the context of metabolic networks. European RFMF Metabomeeting 2020, Jan 2020, Toulouse, France. ⟨hal-02948391⟩
  • Stéphanie Monnerie, Mélanie Pétéra, Cécile Canlet, Florence Castelli, Benoit Colsch, et al.. INPUT OF DEEP PHENOTYPING IN THE METABOLIC SYNDROME STRATIFICATION. European RFMF Metabomeeting 2020, Jan 2020, Toulouse, France. 262 p., 2020, Oral and Poster Abstracts European RMF Metabomeeting 2020. ⟨hal-02505908⟩
  • Pablo Rodríguez-Mier, Nathalie Poupin, Carlo de Blasio, Laurent Le Cam, Fabien Jourdan. Improving prediction of essential genes using context-specific metabolic network ensembles. European RFMF Metabomeeting 2020, Jan 2020, Toulouse, France. ⟨hal-02948371⟩
  • Joran Villaret-Cazadamont, Noemie Butin, Cécile Canlet, Marie A Tremblay-Franco, Roselyne Gautier, et al.. Study of the hepatic metabolic effects induced by PFOA exposure using a multiplatform metabolomics approach. 55. Congress of the European-Societies-of-Toxicology (EUROTOX) - Toxicology - Science Providing Solutions, Sep 2019, Helsinki, Finland. ELSEVIER IRELAND LTD, 2019, TOXICOLOGY LETTERS. ⟨hal-02306108⟩
  • Sergio Polakof, Marie A Tremblay-Franco, Cécile Canlet, Jérémie David, Fabien Jourdan, et al.. Hepatic metabolomics and transcriptomics provide valuable insights on inflammatory and metabolic features in rats fed on a high fat diet but showing similar clinical phenotyping alterations. 12. Journées Scientifiques du Réseau Francophone de Métabolomique et Fluxomique RFMF, May 2019, Clermont-Ferrand, France. 168 p., 2019, Livre des résumés. ⟨hal-02162582⟩
  • Nathalie Poupin, Marie A Tremblay-Franco, Aurélien Amiel, Cécile Canlet, Didier Remond, et al.. Modelling hepatic metabolic changes during the onset of obesity using NMR metabolomics arterio-venous blood exploration in minipigs. 12. Journées Scientifiques du Réseau Francophone de Métabolomique et Fluxomique RFMF, May 2019, Clermont-Ferrand, France. 168 p., 2019, Livre des résumés. ⟨hal-02162584⟩
  • Nathalie Poupin, Marie A Tremblay-Franco, Aurélien Amiel, Cécile Canlet, Didier Remond, et al.. Modeling hepatic metabolic changes during the onset of obesity from metabolomics arterio-venous blood exploration in minipigs. Copenhagen Bioscience Conference 2017: Where big-data gets translated into knowledge, May 2017, Copenhague, Netherlands. 2017, Bioscience Conference 2017. ⟨hal-01606420⟩
  • Florence Maurier, Fabien Jourdan, Sophie S. Colombie. Reconstruction du réseau métabolique de la tomate. 8. Journées Scientifiques du Réseau Français de Métabolomique et Fluxomique RFMF, May 2014, Lyon, France. 1 p., 2014. ⟨hal-02799581⟩
  • Jean-Charles Martin, Mathieu Maillot, Gerard Mazerolles, Alexandre Verdu, Bernard Lyan, et al.. Can we Trust Untargeted Metabolomics: Results of the Metabo-ring Initiative, a Large-scale Multi-instruments Inter-laboratoire Study. 9. Annual Conference of the Metabolomics Society, Jul 2013, Glasgow, United Kingdom. 2013, 9th Annual Conference of the Metabolomics Society. ⟨hal-01123136⟩
  • Alexandre Verdu, Bernard Lyan, Carole Migné, Catherine Defoort, Cécile Canlet, et al.. Can we trust untargeted metabolomics: first results of the metabo-ring study. 8. Annual International Meeting of the Metabolomics Society, Jun 2012, Washington, United States. 2012. ⟨hal-01595487⟩
  • Ludovic Cottret, Florence Vinson, Nicolas J. Cabaton, Maria-Helena Meireles, Daniel Zalko, et al.. MetExplore, a framework for the analysis of metabolic networks: applications in the field of metabolomics data and the study of endocrine disruptors. 6th Copenhagen Workshop on Endocrine Disrupters, Apr 2011, Copenhagen, Denmark. 2011. ⟨hal-02802904⟩
  • Flora Logan-Klumpler, Ludovic Cottret, Florence Vinson, Fabien Jourdan, Michael Barrett. TrypanoCyc: a community effort towards the development of a metabolic pathway database for Trypanosoma brucei.. Kinetoplastid Molecular Cell Biology Meeting (KMCB 2011), 2011, Inconnue, France. 2011. ⟨hal-02803549⟩
  • Ludovic Cottret, David Wildridge, Florence Vinson, Michael P. Barrett, Marie-France Sagot, et al.. MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks. JOBIM 2010, Sep 2010, Montpellier, France. 1 p., 2010, JOBIM 2010 Montpellier, Journée Ouvertes Biologie Informatique Mathématique, Montpellier, France, 7 - 9 septembre 2010. ⟨hal-02821730⟩

Book sections7 documents

  • Léo Gerlin, Clément Frainay, Fabien Jourdan, Caroline Baroukh, Sylvain Prigent. Plant genome-scale metabolic networks. Science Direct. Plant Metabolomics in full swing, 98, 2021, Advances in Botanical Research, ⟨10.1016/bs.abr.2020.09.021⟩. ⟨hal-03149497⟩
  • Clément Frainay, Fabien Jourdan. Genome-scale metabolic networks. Metabolomics: Practical Guide to Design and Analysis, Chapman and Hall, 290 p., 2019, 9781315370583. ⟨10.1201/9781315370583-8⟩. ⟨hal-02786295⟩
  • Francis Isidore Totanes, Sanu Shameer, David Westhead, Fabien Jourdan, Glenn Mcconkey. Understanding Protozoan Parasite Metabolism and Identifying Drug Targets through Constraint-Based Modeling. Comprehensive Analysis of Parasite Biology: From Metabolism to Drug Discovery, Wiley-VCH Verlag GmbH & Co. KGaA, pp.487-512, 2016, ⟨10.1002/9783527694082.ch21⟩. ⟨hal-03318814⟩
  • Nathalie Poupin, Fabien Jourdan. Analysing human metabolic networks using metabolomics. Metabolomics as a Tool in Nutrition Research, Elsevier, pp.85-114, 2015, ⟨10.1016/B978-1-78242-084-2.00005-8⟩. ⟨hal-03318813⟩
  • Fabien Jourdan, Nathalie Poupin. Human metabolic networks and metabolomics. Metabolomics as tool in nutrition research, Woodhead publishing Limited, 2014. ⟨hal-01187878⟩
  • Fabien Jourdan. Qualitative modelling of metabolic networks. Metabolomics coming of age with its technological diversity, 67, 2013, Advances in Botanical Research, ⟨10.1016/B978-0-12-397922-3.00012-5⟩. ⟨hal-02803214⟩
  • Romain Bourqui, Paolo Simonetto, Fabien Jourdan. A stable decomposition algorithm for dynamical social network analysis. Fabrice Guillet; Gilbert Ritschard; Djamel Abdelkader Zighed and Henri Briand. Advances in Knowledge Discovery and Management, Springer, pp.167-178, 2010, Studies in Computational Intelligence, ⟨10.1007/978-3-642-00580-0_10⟩. ⟨hal-00543175⟩

Preprints, Working Papers, ...4 documents

  • Maxime Delmas, Olivier Filangi, Nils Paulhe, Florence Vinson, Christophe Duperier, et al.. FORUM: Building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases. 2021. ⟨hal-03318295⟩
  • Cecilia Wieder, Clément Frainay, Nathalie Poupin, Pablo Rodríguez-Mier, Florence Vinson, et al.. Pathway analysis in metabolomics: pitfalls and best practice for the use of over-representation analysis. 2021. ⟨hal-03240376⟩
  • Lucille Stuani, Marie Sabatier, Feng Wang, Nathalie Poupin, Claudie Bosc, et al.. Combinatory therapy targeting mitochondrial oxidative phosphorylation improves efficacy of IDH mutant inhibitors in acute myeloid leukemia. 2020. ⟨hal-02935177⟩
  • Pablo Rodríguez-Mier, Nathalie Poupin, Carlo de Blasio, Laurent Le Cam, Fabien Jourdan. DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks. 2020. ⟨hal-02935163⟩

Reports1 document

  • Carole Caranta, Hervé Monod, Hugues Berry, Michaël Chelle, Michel Génard, et al.. Réflexion prospective interdisciplinaire. Approches prédictives pour la biologie et l’écologie. Rapport de synthèse.. [Autre] INRA. 2019, 40 pp. ⟨hal-02791153v2⟩