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The GOLIATH Project: Towards an Internationally Harmonised Approach for Testing Metabolism Disrupting Compounds.
Published in:
International Journal of Molecular Sciences, 2020, v. 21, n. 10, p. 3480, doi. 10.3390/ijms21103480
By:
- Legler, Juliette;
- Zalko, Daniel;
- Jourdan, Fabien;
- Jacobs, Miriam;
- Fromenty, Bernard;
- Balaguer, Patrick;
- Bourguet, William;
- Munic Kos, Vesna;
- Nadal, Angel;
- Beausoleil, Claire;
- Cristobal, Susana;
- Remy, Sylvie;
- Ermler, Sibylle;
- Margiotta-Casaluci, Luigi;
- Griffin, Julian L.;
- Blumberg, Bruce;
- Chesné, Christophe;
- Hoffmann, Sebastian;
- Andersson, Patrik L.;
- Kamstra, Jorke H.
Publication type:
Article
Mind the Gap: Mapping Mass Spectral Databases in Genome-Scale Metabolic Networks Reveals Poorly Covered Areas.
Published in:
Metabolites (2218-1989), 2018, v. 8, n. 3, p. 51, doi. 10.3390/metabo8030051
By:
- Frainay, Clément;
- Schymanski, Emma L.;
- Neumann, Steffen;
- Merlet, Benjamin;
- Salek, Reza M.;
- Jourdan, Fabien;
- Yanes, Oscar
Publication type:
Article
MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks.
Published in:
Nucleic Acids Research, 2010, v. 38, n. suppl_2, p. W132, doi. 10.1093/nar/gkq312
By:
- Cottret, Ludovic;
- Wildridge, David;
- Vinson, Florence;
- Barrett, Michael P.;
- Charles, Hubert;
- Sagot, Marie-France;
- Jourdan, Fabien
Publication type:
Article
PhysioFit: a software to quantify cell growth parameters and extracellular fluxes.
Published in:
Bioinformatics, 2024, v. 40, n. 8, p. 1, doi. 10.1093/bioinformatics/btae488
By:
- Grégam, Loïc Le;
- Guitton, Yann;
- Bellvert, Floriant;
- Heux, Stéphanie;
- Jourdan, Fabien;
- Portais, Jean-Charles;
- Millard, Pierre
Publication type:
Article
FORUM: building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases.
Published in:
Bioinformatics, 2021, v. 37, n. 21, p. 3896, doi. 10.1093/bioinformatics/btab627
By:
- Delmas, Maxime;
- Filangi, Olivier;
- Paulhe, Nils;
- Vinson, Florence;
- Duperier, Christophe;
- Garrier, William;
- Saunier, Paul-Emeric;
- Pitarch, Yoann;
- Jourdan, Fabien;
- Giacomoni, Franck;
- Frainay, Clément
Publication type:
Article
Suggesting disease associations for overlooked metabolites using literature from metabolic neighbors.
Published in:
GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad065
By:
- Delmas, Maxime;
- Filangi, Olivier;
- Duperier, Christophe;
- Paulhe, Nils;
- Vinson, Florence;
- Rodriguez-Mier, Pablo;
- Giacomoni, Franck;
- Jourdan, Fabien;
- Frainay, Clément
Publication type:
Article
PhenoMeNal: processing and analysis of metabolomics data in the cloud.
Published in:
GigaScience, 2019, v. 8, n. 2, p. N.PAG, doi. 10.1093/gigascience/giy149
By:
- Peters, Kristian;
- Bradbury, James;
- Bergmann, Sven;
- Capuccini, Marco;
- Cascante, Marta;
- de Atauri, Pedro;
- Ebbels, Timothy M D;
- Foguet, Carles;
- Glen, Robert;
- Gonzalez-Beltran, Alejandra;
- Günther, Ulrich L;
- Handakas, Evangelos;
- Hankemeier, Thomas;
- Haug, Kenneth;
- Herman, Stephanie;
- Holub, Petr;
- Izzo, Massimiliano;
- Jacob, Daniel;
- Johnson, David;
- Jourdan, Fabien
Publication type:
Article
Dynamic Metabolic Disruption in Rats Perinatally Exposed to Low Doses of Bisphenol-A.
Published in:
PLoS ONE, 2015, v. 10, n. 10, p. 1, doi. 10.1371/journal.pone.0141698
By:
- Tremblay-Franco, Marie;
- Cabaton, Nicolas J.;
- Canlet, Cécile;
- Gautier, Roselyne;
- Schaeberle, Cheryl M.;
- Jourdan, Fabien;
- Sonnenschein, Carlos;
- Vinson, Florence;
- Soto, Ana M.;
- Zalko, Daniel
Publication type:
Article
Intuitive Visualization and Analysis of Multi-Omics Data and Application to Escherichia coli Carbon Metabolism.
Published in:
PLoS ONE, 2011, v. 6, n. 6, p. 1, doi. 10.1371/journal.pone.0021318
By:
- Enjalbert, Brice;
- Jourdan, Fabien;
- Portais, Jean-Charles
Publication type:
Article
A strategy to detect metabolic changes induced by exposure to chemicals from large sets of condition-specific metabolic models computed with enumeration techniques.
Published in:
BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05845-z
By:
- Fresnais, Louison;
- Perin, Olivier;
- Riu, Anne;
- Grall, Romain;
- Ott, Alban;
- Fromenty, Bernard;
- Gallardo, Jean-Clément;
- Stingl, Maximilian;
- Frainay, Clément;
- Jourdan, Fabien;
- Poupin, Nathalie
Publication type:
Article
Challenges and perspectives for naming lipids in the context of lipidomics.
Published in:
Metabolomics, 2024, v. 20, n. 1, p. 1, doi. 10.1007/s11306-023-02075-x
By:
- Witting, Michael;
- Malik, Adnan;
- Leach, Andrew;
- Bridge, Alan;
- Aimo, Lucila;
- Conroy, Matthew J.;
- O’Donnell, Valerie B.;
- Hoffmann, Nils;
- Kopczynski, Dominik;
- Giacomoni, Franck;
- Paulhe, Nils;
- Gassiot, Amaury Cazenave;
- Poupin, Nathalie;
- Jourdan, Fabien;
- Bertrand-Michel, Justine
Publication type:
Article
Improving lipid mapping in Genome Scale Metabolic Networks using ontologies.
Published in:
Metabolomics, 2020, v. 16, n. 4, p. 1, doi. 10.1007/s11306-020-01663-5
By:
- Poupin, Nathalie;
- Vinson, Florence;
- Moreau, Arthur;
- Batut, Aurélie;
- Chazalviel, Maxime;
- Colsch, Benoit;
- Fouillen, Laetitia;
- Guez, Sarah;
- Khoury, Spiro;
- Dalloux-Chioccioli, Jessica;
- Tournadre, Anthony;
- Le Faouder, Pauline;
- Pouyet, Corinne;
- Van Delft, Pierre;
- Viars, Fanny;
- Bertrand-Michel, Justine;
- Jourdan, Fabien
Publication type:
Article
Can we trust untargeted metabolomics? Results of the metabo-ring initiative, a large-scale, multi-instrument inter-laboratory study.
Published in:
Metabolomics, 2015, v. 11, n. 4, p. 807, doi. 10.1007/s11306-014-0740-0
By:
- Martin, Jean-Charles;
- Maillot, Matthieu;
- Mazerolles, Gérard;
- Verdu, Alexandre;
- Lyan, Bernard;
- Migné, Carole;
- Defoort, Catherine;
- Canlet, Cecile;
- Junot, Christophe;
- Guillou, Claude;
- Manach, Claudine;
- Jabob, Daniel;
- Bouveresse, Delphine;
- Paris, Estelle;
- Pujos-Guillot, Estelle;
- Jourdan, Fabien;
- Giacomoni, Franck;
- Courant, Frédérique;
- Favé, Gaëlle;
- Gall, Gwenaëlle
Publication type:
Article
Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis.
Published in:
PLoS Computational Biology, 2021, v. 17, n. 9, p. 1, doi. 10.1371/journal.pcbi.1009105
By:
- Wieder, Cecilia;
- Frainay, Clément;
- Poupin, Nathalie;
- Rodríguez-Mier, Pablo;
- Vinson, Florence;
- Cooke, Juliette;
- Lai, Rachel PJ;
- Bundy, Jacob G.;
- Jourdan, Fabien;
- Ebbels, Timothy
Publication type:
Article
Arterio-venous metabolomics exploration reveals major changes across liver and intestine in the obese Yucatan minipig.
Published in:
Scientific Reports, 2019, v. 9, n. 1, p. N.PAG, doi. 10.1038/s41598-019-48997-2
By:
- Poupin, Nathalie;
- Tremblay-Franco, Marie;
- Amiel, Aurélien;
- Canlet, Cécile;
- Rémond, Didier;
- Debrauwer, Laurent;
- Dardevet, Dominique;
- Thiele, Ines;
- Aurich, Maike K.;
- Jourdan, Fabien;
- Savary-Auzeloux, Isabelle;
- Polakof, Sergio
Publication type:
Article
Computational methods to identify metabolic sub-networks based on metabolomic profiles.
Published in:
Briefings in Bioinformatics, 2017, v. 18, n. 1, p. 43, doi. 10.1093/bib/bbv115
By:
- Frainay, Clément;
- Jourdan, Fabien
Publication type:
Article
DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks.
Published in:
PLoS Computational Biology, 2021, v. 17, n. 2, p. 1, doi. 10.1371/journal.pcbi.1008730
By:
- Rodríguez-Mier, Pablo;
- Poupin, Nathalie;
- de Blasio, Carlo;
- Le Cam, Laurent;
- Jourdan, Fabien
Publication type:
Article
Targeted versus untargeted omics — the CAFSA story.
Published in:
Journal of Inherited Metabolic Disease, 2018, v. 41, n. 3, p. 447, doi. 10.1007/s10545-017-0134-3
By:
- del Mar Amador, Maria;
- Colsch, Benoit;
- Lamari, Foudil;
- Jardel, Claude;
- Ichou, Farid;
- Rastetter, Agnès;
- Sedel, Frédéric;
- Jourdan, Fabien;
- Frainay, Clément;
- Wevers, Ronald A.;
- Roze, Emmanuel;
- Depienne, Christel;
- Junot, Christophe;
- Mochel, Fanny
Publication type:
Article
Inhibition of enteric methanogenesis in dairy cows induces changes in plasma metabolome highlighting metabolic shifts and potential markers of emission.
Published in:
Scientific Reports, 2020, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41598-020-72145-w
By:
- Yanibada, Bénédict;
- Hohenester, Ulli;
- Pétéra, Mélanie;
- Canlet, Cécile;
- Durand, Stéphanie;
- Jourdan, Fabien;
- Boccard, Julien;
- Martin, Cécile;
- Eugène, Maguy;
- Morgavi, Diego P.;
- Boudra, Hamid
Publication type:
Article
An Untargeted Metabolomics Approach to Investigate the Metabolic Modulations of HepG2 Cells Exposed to Low Doses of Bisphenol A and 17β-Estradiol.
Published in:
Frontiers in Endocrinology, 2018, p. N.PAG, doi. 10.3389/fendo.2018.00571
By:
- Cabaton, Nicolas J.;
- Poupin, Nathalie;
- Canlet, Cécile;
- Tremblay-Franco, Marie;
- Audebert, Marc;
- Cravedi, Jean-Pierre;
- Riu, Anne;
- Jourdan, Fabien;
- Zalko, Daniel
Publication type:
Article
PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration.
Published in:
PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011814
By:
- Wieder, Cecilia;
- Cooke, Juliette;
- Frainay, Clement;
- Poupin, Nathalie;
- Bowler, Russell;
- Jourdan, Fabien;
- Kechris, Katerina J.;
- Lai, Rachel PJ;
- Ebbels, Timothy
Publication type:
Article
Genome scale metabolic network modelling for metabolic profile predictions.
Published in:
PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011381
By:
- Cooke, Juliette;
- Delmas, Maxime;
- Wieder, Cecilia;
- Rodríguez Mier, Pablo;
- Frainay, Clément;
- Vinson, Florence;
- Ebbels, Timothy;
- Poupin, Nathalie;
- Jourdan, Fabien
Publication type:
Article
Integrated transcriptomics and metabolomics reveal signatures of lipid metabolism dysregulation in HepaRG liver cells exposed to PCB 126.
Published in:
Archives of Toxicology, 2018, v. 92, n. 8, p. 2533, doi. 10.1007/s00204-018-2235-7
By:
- Mesnage, Robin;
- Biserni, Martina;
- Balu, Sucharitha;
- Frainay, Clément;
- Poupin, Nathalie;
- Jourdan, Fabien;
- Wozniak, Eva;
- Xenakis, Theodoros;
- Mein, Charles A.;
- Antoniou, Michael N.
Publication type:
Article
MetaNetter: inference and visualization of high-resolution metabolomic networks.
Published in:
Bioinformatics, 2008, v. 24, n. 1, p. 143, doi. 10.1093/bioinformatics/btm536
By:
- Fabien Jourdan;
- Rainer Breitling;
- Michael P. Barrett;
- David Gilbert
Publication type:
Article
Osteogenic Response of Human Mesenchymal Stem Cells Analysed Using Combined Intracellular and Extracellular Metabolomic Monitoring.
Published in:
Cellular Physiology & Biochemistry (Cell Physiol Biochem Press GmbH & Co. KG), 2021, v. 55, n. 3, p. 311, doi. 10.33594/000000377
By:
- Surrati, Amal;
- Evseev, Sergey;
- Jourdan, Fabien;
- Dong-Hyun Kim;
- Sottile, Virginie
Publication type:
Article
MetaboRank: network-based recommendation system to interpret and enrich metabolomics results.
Published in:
Bioinformatics, 2019, v. 35, n. 2, p. 274, doi. 10.1093/bioinformatics/bty577
By:
- Frainay, Clément;
- Aros, Sandrine;
- Chazalviel, Maxime;
- Garcia, Thomas;
- Vinson, Florence;
- Weiss, Nicolas;
- Colsch, Benoit;
- Sedel, Frédéric;
- Thabut, Dominique;
- Junot, Christophe;
- Jourdan, Fabien
Publication type:
Article
MetExploreViz: web component for interactive metabolic network visualization.
Published in:
Bioinformatics, 2018, v. 34, n. 2, p. 312, doi. 10.1093/bioinformatics/btx588
By:
- Chazalviel, Maxime;
- Frainay, Clément;
- Poupin, Nathalie;
- Vinson, Florence;
- Merlet, Benjamin;
- Gloaguen, Yoann;
- Cottret, Ludovic;
- Jourdan, Fabien
Publication type:
Article
ProbMetab: an R package for Bayesian probabilistic annotation of LC–MS-based metabolomics.
Published in:
Bioinformatics, 2014, v. 30, n. 9, p. 1336, doi. 10.1093/bioinformatics/btu019
By:
- Silva, Ricardo R.;
- Jourdan, Fabien;
- Salvanha, Diego M.;
- Letisse, Fabien;
- Jamin, Emilien L.;
- Guidetti-Gonzalez, Simone;
- Labate, Carlos A.;
- Vêncio, Ricardo Z. N.
Publication type:
Article
Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure.
Published in:
Bioinformatics, 2014, v. 30, n. 1, p. 61, doi. 10.1093/bioinformatics/btt597
By:
- Milreu, Paulo Vieira;
- Klein, Cecilia Coimbra;
- Cottret, Ludovic;
- Acuña, Vicente;
- Birmelé, Etienne;
- Borassi, Michele;
- Junot, Christophe;
- Marchetti-Spaccamela, Alberto;
- Marino, Andrea;
- Stougie, Leen;
- Jourdan, Fabien;
- Crescenzi, Pierluigi;
- Lacroix, Vincent;
- Sagot, Marie-France
Publication type:
Article
Postprandial NMR-Based Metabolic Exchanges Reflect Impaired Phenotypic Flexibility across Splanchnic Organs in the Obese Yucatan Mini-Pig.
Published in:
Nutrients, 2020, v. 12, n. 8, p. 2442, doi. 10.3390/nu12082442
By:
- Tremblay-Franco, Marie;
- Poupin, Nathalie;
- Amiel, Aurélien;
- Canlet, Cécile;
- Rémond, Didier;
- Debrauwer, Laurent;
- Dardevet, Dominique;
- Jourdan, Fabien;
- Savary-Auzeloux, Isabelle;
- Polakof, Sergio
Publication type:
Article

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