Publications

51 Wieder C, Cooke J, Frainay C, Poupin N, Bowler R, Jourdan F, Kechris KJ, Lai RP, Ebbels T (2024). PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration. PLoS Comput Biol. 2024. In press.

50 Cooke J, Delmas M, Wieder C, Rodríguez Mier P, Frainay C, Vinson F, Ebbels T, Poupin N, Jourdan F (2024). Genome scale metabolic network modelling for metabolic profile predictions. PLoS Comput Biol. 2024 Feb 22;20(2):e1011381. doi: 10.1371/journal.pcbi.1011381. PMID: 38386685; PMCID: PMC10914266.

49 Michael Witting, Adnan Malik, Andrew Leach, Alan Bridge, Lucila Aimo, Matthew J Conroy, Valerie B O'Donnell, Nils Hoffmann, Dominik Kopczynsk, Franck Giacomoni, Nils Paulhe , Amaury Cazenave Gassiot, Nathalie Poupin, Fabien Jourdan  and Justine Bertrand-Michel (2024). Challenges and perspectives for naming lipids in the context of lipidomics. Metabolomics. 20(1):15. doi: 10.1007/s11306-023-02075-x. 

48 Liesa Salzer, Elva María Novoa-Del-Toro, Clément Frainay, Kohar Annie B Kissoyan, Fabien Jourdan, Katja Dierking and Michael Witting (2023). APEX: an Annotation Propagation Workflow through Multiple Experimental Networks to Improve the Annotation of New Metabolite Classes in Caenorhabditis elegans. Analytical Chemistry. 5;95(48):17550-17558. doi: 10.1021/acs.analchem.3c02797.

47 Ghina Hajjar, Millena C. Barros Santos, Justine Bertrand-Michel, Cécile Canlet, Florence Castelli, Nicolas Creusot, Sylvain Dechaumet, Binta Diémé, Franck Giacomoni, Patrick Giraudeau, Yann Guitton, Etienne Thévenot, Marie Tremblay-Franco, Christophe Junot, Fabien Jourdan, François Fenaille, Blandine Comte, Pierre Pétriacq and Estelle Pujos-Guillot  (2023). Scaling-up metabolomics: Current state and perspectives. TrAC Trends in Analytical Chemistry. Volume 167, 2023, 117225, https://doi.org/10.1016/j.trac.2023.117225.  [IF: 13,6, CHEMISTRY ANALYTICAL, Q1, 1/86]

46 Wieder, Cecilia; Bundy, Jacob; Frainay, Clement; Poupain, Nathalie; Rodriguez-Mier, Pablo; Vinson, Florence; Cooke, Juliette; Lai, Rachel; Jourdan, Fabien; Ebbels, Timothy (2022). Avoiding the misuse of pathway analysis tools in environmental metabolomics. Environmental Science & Technology. 2022 56, 20, 14219–14222. doi.org/10.1021/acs.est.2c05588, https://hal.science/hal-03799270 [IF: 11,357, ENVIRONMENTAL SCIENCES, Q2, 22/279]

45 Paulhe N, Canlet C, Damont A, Peyriga L, Durand S, Deborde C, Alves S, Bernillon S, Berton T, Bir R, Bouville A, Cahoreau E, Centeno D, Costantino R, Debrauwer L, Delabrière A, Duperier C, Emery S, Flandin A, Hohenester U, Jacob D, Joly C, Jousse C, Lagree M, Lamari N, Lefebvre M, Lopez-Piffet C, Lyan B, Maucourt M, Migne C, Olivier MF, Rathahao-Paris E, Petriacq P, Pinelli J, Roch L, Roger P, Roques S, Tabet JC, Tremblay-Franco M, Traïkia M, Warnet A, Zhendre V, Rolin D, Jourdan F, Thévenot E, Moing A, Jamin E, Fenaille F, Junot C, Pujos-Guillot E, Giacomoni F (2022). PeakForest: a multi-platform digital infrastructure for interoperable metabolite spectral data and metadata management. Metabolomics. 2022 Jun 14;18(6):40. doi: 10.1007/s11306-022-01899-3, https://hal.archives-ouvertes.fr/hal-03695453v1.  [IF: 4.747, ENDOCRINOLOGY & METABOLISM, Q2, 54/146]

44 Davy Guignard, Cécile Canlet, Marie Tremblay-Franco, Elodie Chaillou, Roselyne Gautier, Véronique Gayrard, Nicole Picard-Hagen, Henri Schroeder, Fabien Jourdan, Daniel Zalko, Catherine Viguié and Nicolas J. Cabaton (2022). BPA gestational exposure induces region-specific changes in brain metabolomic fingerprints in the sheep. Environment International. doi: 10.1016/j.envint.2022.107336, https://hal.archives-ouvertes.fr/hal-03701070. [IF: 13.352, ENVIRONMENTAL SCIENCES, Q1, 16/279]

43 Adam Amara, Clément Frainay, Fabien Jourdan, Thomas Naake, Steffen Neumann, Elva María Novoa-del-Toro, Reza M Salek, Liesa Salzer, Sarah Scharfenberg and Michael Witting (2022). Networks and Graphs Discovery in Metabolomics Data Analysis and Interpretation. Frontiers in Molecular Biosciences. 9:841373. doi: 10.3389/fmolb.2022.841373, https://hal.archives-ouvertes.fr/hal-03636716v1 [IF: 6.113, BIOCHEMISTRY & MOLECULAR BIOLOGY, Q1, 73/296]

42 Marvin Martens,  Rob Stierum, Emma L. Schymanski, Chris T. Evelo, Reza Aalizadeh, Hristo Aladjov, Kasia Arturi, Karine Audouze8, Pavel Babica, Karel Berka, Jos Bessems, Ludek Blaha, Evan E. Bolton, Montserrat Cases, Dimitrios Ε. Damalas, Kirtan Dave, Marco Dilger, Thomas Exner, Daan P. Geerke, Roland Grafström, Alasdair Gray, John M. Hancock, Henner Hollert, Nina Jeliazkova, Danyel Jennen, Fabien Jourdan, Pascal Kahlem, Jana Klanova, Jos Kleinjans, Todor Kondic, Boï Kone, Iseult Lynch, Uko Maran, Sergio Martinez Cuesta, Hervé Ménager, Steffen Neumann, Penny Nymark, Herbert Oberacher, Noelia Ramirez, Sylvie Remy, Philippe Rocca-Serra, Reza M. Salek, Brett Sallach, Susanna-Assunta Sansone, Ferran Sanz, Haralambos Sarimveis, Sirarat Sarntivijai, Tobias Schulze, Jaroslav Slobodnik, Ola Spjuth, Jonathan Tedds, Nikolaos Thomaidis, Ralf J.M. Weber, Gerard J.P. van Westen, Craig E. Wheelock, Antony J. Williams, Hilda Witters, Barbara Zdrazil, Anže Županič and Egon L. Willighagen (2021). ELIXIR and Toxicology: a community in development. F1000Research. [version 1; peer review: awaiting peer review].

41 Cecilia Wieder, Clément Frainay, Nathalie Poupin, Pablo Rodríguez-Mier, Florence Vinson, Juliette Cooke, Rachel PJ Lai, Jacob G Bundy, Fabien Jourdan and Timothy Ebbels (2021). Plos Computational Biology. 17(9):e1009105. doi: 10.1371/journal.pcbi.1009105 https://hal.archives-ouvertes.fr/hal-03344682v1 [IF: 4.779, MATHEMATICAL & COMPUTATIONAL BIOLOGY, Q1, 9/67] 

40 Maxime Delmas, Olivier Filangi, Nils Paulhe, Florence Vinson, Christophe Duperier, William Garrier, P.-E. Saunier, Yoann Pitarch, Fabien Jourdan, Franck Giacomoni and Clément Frainay (2021). FORUM: Building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases. Bionformatics. 37(21):3896-3904. doi: 10.1093/bioinformatics/btab627, https://hal.archives-ouvertes.fr/hal-03361495v1. [IF: 6.931, MATHEMATICAL & COMPUTATIONAL BIOLOGY, Q1, 4/67]

39 Bénédict Yanibada, Ulli Hohenester, Mélanie Pétéra, Cécile Canlet, Stéphanie Duran, Fabien Jourdan, Anne Ferlay, Diego P. Morgavi, and Hamid Boudra (2021). Milk metabolome reveals variations on enteric methane emissions from dairy cows. Journal of Dairy Science. 104(12):12553-12566. doi: 10.3168/jds.2021-20477, https://hal.archives-ouvertes.fr/hal-03351167v1. [IF: 4.225, FOOD SCIENCE & TECHNOLOGY, Q1, 17/164]

38 Pablo Rodríguez-Mier, Nathalie Poupin, Carlo de Blasio, Laurent Le Cam, Fabien Jourdan (2021). DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks. PLoS Computational Biology 17(2):e1008730. doi: 10.1371/journal.pcbi.1008730, https://hal.archives-ouvertes.fr/hal-03154775v1. [IF: 4.779, MATHEMATICAL & COMPUTATIONAL BIOLOGY, Q1, 9/67] 

37 Blandine Comte, Stéphanie Monnerie, Marion Brandolini-Bunlon, Cécile Canlet, Florence Castelli, Emeline Chu-Van, Benoit Colsch, François Fenaille, Charlotte Joly, Fabien Jourdan, Natacha Lenuzza, Bernard Lyan, Jean-François Martin, Carole Migné, José Morais, Mélanie Pétéra, Nathalie Poupin, Florence Vinson, Etienne Thevenot, Christophe Junot, Pierrette Gaudreau, Estelle Pujos-Guillot (2021). Multiplatform metabolomics for an integrative exploration of metabolic syndrome in older men. EBioMedicine. 69:103440 https://hal.archives-ouvertes.fr/hal-03283772, doi: 10.1016/j.ebiom.2021.103440. [IF: 11.205, MEDICINE, RESEARCH & EXPERIMENTAL, Q1, 11/195]

36 Lucille Stuani, Marie Sabatier, Estelle Saland, Guillaume Cognet, Nathalie Poupin, Claudie Bosc, Florence A Castelli, Lara Gales, Evgenia Turtoi, Camille Montersino , Thomas Farge, Emeline Boet, Nicolas Broin, Clément Larrue, Natalia Baran, Madi Y Cissé, Marc Conti, Sylvain Loric, Tony Kaoma, Alexis Hucteau, Aliki Zavoriti, Ambrine Sahal, Pierre-Luc Mouchel, Mathilde Gotanègre, Cédric Cassan, Laurent Fernando, Feng Wang, Mohsen Hosseini, Emeline Chu-Van, Laurent Le Cam, Martin Carroll, Mary A Selak, Norbert Vey, Rémy Castellano, François Fenaille, Andrei Turtoi, Guillaume Cazals, Pierre Bories, Yves Gibon, Brandon Nicolay, Sébastien Ronseaux, Joseph R Marszalek, Koichi Takahashi, Courtney D DiNardo, Marina Konopleva, Véra Pancaldi, Yves Collette, Floriant Bellvert, Fabien Jourdan, Laetitia K Linares, Christian Récher, Jean-Charles, Jean-Emmanuel Sarry (2021). Mitochondrial metabolism supports resistance to IDH mutant inhibitors in acute myeloid leukemia.  Journal of Experimental Medicine. 218(5):e20200924. doi: 10.1084/jem.20200924, https://hal.archives-ouvertes.fr/hal-03563454v1. [IF: 17.579, MEDICINE, RESEARCH & EXPERIMENTAL, Q1, 5/195]

35 Amal Surrati A, Sergey Evseev, Fabien Jourdan, Dong-Hyun Kim, Virginie Sottile (2021). Osteogenic Response of Human Mesenchymal Stem Cells Analysed Using Combined Intracellular and Extracellular Metabolomic Monitoring. Cellular Physiology & Biochemistry. 55(3):311-326. doi: 10.33594/000000377, https://hal.inrae.fr/hal-03312596 [IF: 5.500, CELL BIOLOGY, Q1, 45/190]

34 Julien Boccard, Domitille Schvartz D, Santiago Codesido, Mohamed Hanafi, Yoric Gagnebin Y, Celén Ponte, Fabien Jourdan, Serge Rudaz (2021). Gaining Insights Into Metabolic Networks Using Chemometrics and Bioinformatics: Chronic Kidney Disease as a Clinical Model. Frontiers in Molecular Biosciences. 14;8:682559. doi: 10.3389/fmolb.2021.682559, https://hal.archives-ouvertes.fr/hal-03318230  [IF: 6.113, BIOCHEMISTRY & MOLECULAR BIOLOGY, Q1, 73/296]. 

33 Bénédict Yanibada, Ulli Hohenester, Mélanie Pétéra, Cécile Canlet, Stéphanie Durand, Fabien Jourdan, Julien Boccard, Cécile Martin, Maguy Eugène, Diego P Morgavi and Hamid Boudra (2020). Inhibition of enteric methanogenesis in dairy cows induces changes in plasma metabolome highlighting metabolic shifts and potential markers of emission. Scientific Reports, 2020, 10 (1), https://dx.doi.org/10.1038/s41598-020-72145-w,  https://hal.inrae.fr/hal-02949602 [IF: 4.996, MULTIDISCIPLINARY SCIENCES, Q1, 19/134]

32 Marie Tremblay-Franco, Nathalie Poupin, Aurélien Amiel, Cécile Canlet, Didier Remond, Laurent Debrauwer, Dominique Dardevet, Fabien Jourdan, Isabelle Savary-Auzeloux, Sergio Polakof (2020). Postprandial NMR-Based Metabolic Exchanges Reflect Impaired Phenotypic Flexibility across Splanchnic Organs in the Obese Yucatan Mini-Pig. Nutrients, 12 (8), 2442, https://dx.doi.org/10.3390/nu12082442, https://hal.inrae.fr/hal-02927174 [IF: 6.706, NUTRITION & DIETETICS, Q1, 21/109]

31 Juliette Legler, Daniel Zalko, Fabien Jourdan, Miriam Jacobs, Bernard Fromenty, Patrick Balaguer, William Bourguet, Vesna Kos, Angel Nadal, Claire Beausoleil, Susana Cristobal, Sylvie Rémy, Sibylle Ermler, Luigi Margiotta-Casaluci, Julian Griffin, Bruce Blumberg, Christophe Chesné, Sebastian Hoffmann, Patrik Andersson, Jorke Kamstra (2020). The GOLIATH Project: Towards an Internationally Harmonised Approach for Testing Metabolism Disrupting Compounds. International Journal of Molecular Sciences, 21 (10), 3480, https://dx.doi.org/10.3390/ijms21103480, https://hal.inrae.fr/hal-02638423 [IF: 6.076, BIOCHEMISTRY & MOLECULAR BIOLOGY, Q1, 69/296]

30 Imourana Alassane-Kpembi, Cecile Canlet, Marie Tremblay Franco, Fabien Jourdan, Maxime Chalzaviel, Philippe Pinton, Anne Marie Cossalter, Caroline Achard, Mathieu Castex, Sylvie Combes, Ana Paula L. Bracarense, Isabelle P Oswald (2020). 1H-NMR metabolomics response to a realistic diet contamination with the mycotoxin deoxynivalenol: Effect of probiotics supplementation. Food and Chemical Toxicology, in press 111222, https://dx.doi.org/10.1016/j.fct.2020.111222, https://hal.inrae.fr/hal-02627840 [IF: 5.572, TOXICOLOGY, Q1, 7/100].

29 Nathalie Poupin, Florence Vinson, Arthur Moreau, Aurélie Batut, Maxime Chazalviel, Benoit Colsch, Laetitia Fouillen, Sarah Guez, Spiro Khoury, Jessica Dalloux-Chioccioli, Anthony Tournadre, Pauline Le Faouder, Corinne Pouyet, Pierre Van Delft, Fanny Viars, Justine Bertrand Miche and Fabien Jourdan. (2020). Improving lipid mapping in Genome Scale Metabolic Networks using ontologies. Metabolomics. 16(4):44, https://dx.doi.org/10.1007/s11306-020-01663-5, https://hal.archives-ouvertes.fr/hal-02935172 [IF: 4.747, ENDOCRINOLOGY & METABOLISM, Q2, 54/146]

28 Kristian Peters, James Bradbury, Sven Bergmann, Marco Capuccini, Marta Cascante, Pedro de Atauri, Timothy M. D. Ebbels, Carles Foguet, Robert Glen, Alejandra Gonzalez-Beltran, Ulrich L. Günther, Evangelos Handakas, Thomas Hankemeier, Kenneth Haug, Stephanie Herman, Petr Holub, Massimiliano Izzo, Daniel Jacob, David Johnson, Fabien Jourdan, Namrata Kale, Ibrahim Karaman, Bita Khalili, Payam Emami Khonsari, Kim Kultima, Samuel Lampa, Anders Larsson, Christian Ludwig, Pablo Moreno, Steffen Neumann, Jon Ander Novella, Claire O'Donovan, Jake T. M. Pearce, Alina Peluso, Marco Enrico Piras, Luca Pireddu, Michelle A. C. Reed, Philippe Rocca-Serra, Pierrick Roger, Antonio Rosato, Rico Rueedi, Christoph Ruttkies, Noureddin Sadawi, Reza M. Salek, Susanna-Assunta Sansone, Vitaly Selivanov, Ola Spjuth, Daniel Schober, Etienne A. Thevenot, Mattia Tomasoni, Merlijn van Rijswijk, Michael van Vliet, Mark R. Viant, Ralf J. M. Weber, Gianluigi Zanetti and Christoph Steinbeck (2019). PhenoMeNal: processing and analysis of metabolomics data in the cloud. GigaScience, 8 (2), 12 p., giy149, https://dx.doi.org/10.1093/gigascience/giy149, https://hal.inrae.fr/hal-02627233 [IF: 7.658, MULTIDISCIPLINARY SCIENCES, Q1, 15/134]

27 Clément Frainay, Sandrine Aros, Maxime Chazalviel, Thomas Garcia, Florence Vinson, Nicolas Weiss, Benoit Colsch, Frédéric Sedel, Dominique Thabut, Christophe Junot and Fabien Jourdan (2019). MetaboRank: network-based recommendation system to interpret and enrich metabolomics results. Bioinformatics, 35 (2), 274-283, https://dx.doi.org/10.1093/bioinformatics/bty577, https://hal.inrae.fr/hal-02627792 [IF: 6.931, MATHEMATICAL & COMPUTATIONAL BIOLOGY, Q1, 4/67]

26 Nathalie Poupin, Marie Tremblay Franco, Aurélien Amiel, Cecile Canlet, Didier Rémond, Laurent Debrauwer, Dominique Dardevet, Ines Thiele, Maike K. Aurich, Fabien Jourdan, Isabelle Savary-Auzeloux and Sergio Polakof (2019). Arterio-venous metabolomics exploration reveals major changes across liver and intestine in the obese Yucatan minipig. Scientific Reports, 9 (1), np, 12527, https://dx.doi.org/10.1038/s41598-019-48997-2, https://hal.inrae.fr/hal-02282295 [IF: 4.996, MULTIDISCIPLINARY SCIENCES, Q1, 19/134]

25 Nathalie Poupin, Anne Corlu, Nicolas J. Cabaton, Hélène Dubois-Pot-Schneider, Cecile Canlet, Elodie Person, Sandrine Bruel, Clément Frainay, Florence Vinson, Florence Maurier, Fabrice Morel, Marie-Anne Robin, Bernard Fromenty, Daniel Zalko and Fabien Jourdan (2018). Large-Scale Modeling Approach Reveals Functional Metabolic Shifts during Hepatic Differentiation. Journal of Proteome Research, 18 (1), 204-216, https://dx.doi.org/10.1021/acs.jproteome.8b00524, https://hal-univ-rennes1.inrae.fr/hal-01937261 [IF: 5.370, BIOCHEMICAL RESEARCH METHODS, Q1, 11/84]

24 Maria del Mar Amador, Benoit Colsch, Foudil Lamari, Claude Jardel, Farid Ichou, Agnès Rastetter, Frédéric Sedel, Fabien Jourdan, Clément Frainay, Ronald Wevers, Emmanuel Roze, Christel Depienne, Christophe Junot and Fanny Mochel (2018). Targeted versus untargeted omics — the CAFSA story. Journal of Inherited Metabolic Disease, 41 (3), 1-10, https://dx.doi.org/10.1007/s10545-017-0134-3, https://hal.sorbonne-universite.fr/hal-01777969 [IF: 4.750, GENETICS & HEREDITY, Q1, 38/191]

23 Maxime Chazalviel, Clément Frainay, Nathalie Poupin, Florence Vinson, Benjamin Merlet, Benjamin Gloaguen, Ludovic Cottret and Fabien Jourdan (2018). MetExploreViz: web component for interactive metabolic network visualization. Bioinformatics, 34 (2), 312-313, https://dx.doi.org/10.1093/bioinformatics/btx588, https://hal.inrae.fr/hal-02621786 [IF: 6.931, MATHEMATICAL & COMPUTATIONAL BIOLOGY, Q1, 4/67]

22 Robin Mesnage, Martina Biserni, Sucharitha Balu, Clément Frainay, Nathalie Poupin, Fabien Jourdan, Eva Wozniak, Theodoros Xenakis, Charles A. Mein and Michael N. Antoniou (2018). Integrated transcriptomics and metabolomics reveal signatures of lipid metabolism dysregulation in HepaRG liver cells exposed to PCB 126. Archives of Toxicology, 92 (8), 2533-2547, https://dx.doi.org/10.1007/s00204-018-2235-7, https://hal.inrae.fr/hal-02621552 [IF: 6.168, TOXICOLOGY, Q1, 9/100]

21 Ludovic Cottret, Clément Frainay, Maxime Chazalviel, Floréal Cabanettes, Yoann Gloaguen, Etienne Camenen, Benjamin Merlet, Stephanie Heux, Jean-Charles Portais, Nathalie Poupin, Florence Vinson and Fabien Jourdan (2018). MetExplore: collaborative edition and exploration of metabolic networks. Nucleic Acids Research, 46 (W1), 8 p., https://dx.doi.org/10.1093/nar/gky301, https://hal.inrae.fr/hal-01886470 [IF: 19.160, BIOCHEMISTRY & MOLECULAR BIOLOGY, Q1, 5/321]

20 Clément Frainay, Emma L. Schymanski, Steffen Neumann, Benjamin Merlet, Reza Mohammadi Salek, Fabien Jourdan, Oscar Yanes (2018). Mind the gap: mapping mass spectral databases in genome-scale metabolic networks reveals poorly covered Areas. Metabolites, 8 (3), e51, https://dx.doi.org/10.3390/metabo8030051, https://hal.inrae.fr/hal-02627086 [IF: 5.581, BIOCHEMISTRY & MOLECULAR BIOLOGY, Q2, 126/321] 10th anniversary best paper award.

19 Nicolas J. Cabaton, Nathalie Poupin, Cécile Canlet, Marie Tremblay Franco, Marc Audebert, Jean-Pierre Cravedi, Anne Riu, Fabien Jourdan and Daniel Zalko (2018). 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, 9 571, https://dx.doi.org/10.3389/fendo.2018.00571, https://hal.inrae.fr/hal-02618654 [IF: 6.055, ENDOCRINOLOGY & METABOLISM, Q1, 33/146]

18 Clément Frainay and Fabien Jourdan (2017). Computational methods to identify metabolic sub-networks based on metabolomic profiles. Briefings in Bioinformatics, 18 (1), 43-56, https://dx.doi.org/10.1093/bib/bbv115, https://hal.inrae.fr/hal-01608721 [IF: 13.994, MATHEMATICAL & COMPUTATIONAL BIOLOGY, Q1, 2/67]

17 Sandra Therrien-Laperriere, S. Cherkaoui, G. Boucher,  Igenomed Consortium, Fabien Jourdan, G. Lettre, J. D. Rioux, C. D. Rosiers (2017). PathQuant: A bioinformatic tool to quantitatively annotate the relationship between genes and metabolites through metabolic pathway mapping. FASEB Journal, 31 (1), Meeting Abstract: 769.3, https://hal.inrae.fr/hal-02622661 [IF: 5.834, BIOCHEMISTRY & MOLECULAR BIOLOGY, Q1, 75/321]

16 M. van Rijswijk, C. Beirnaert, C. Caron, M. Cascante, V. Dominguez, W. B. Dunn, T. M. D. Ebbels, Franck Giacomoni, A. Gonzalez-Beltran, T. Hankemeier, K. Haug, J. L. Izquierdo-Garcia, R. C. Jimenez, Fabien Jourdan, N. Kale, M. I. Klapa, O. Kohlbacher, K. Koort, K. Kultima, G. Le Corguille, N. K. Moschonas, S. Neumann, C. O'Donovan, M. Reczko, P. Rocca-Serra, A. Rosato, R. M. Salek, S. A. Sansone, V. Satagopam, D. Schober, R. Shimmo, R. A. Spicer, O. Spjuth, E. A. Thévenot, M. R. Viant, R. J. M. Weber, E. L. Willighagen, G. Zanetti, C. Steinbeck (2017). The future of metabolomics in ELIXIR. F1000Research, 6 (Version 2), np, eCollection 2017, https://dx.doi.org/10.12688/f1000research.12342.2, https://hal.inrae.fr/hal-01630635

15 Karl E.V. Burgess, Youri Borutzki, Naomi Rankin, Ronan Daly and Fabien Jourdan (2017). MetaNetter 2: A Cytoscape plugin for ab initio network analysis and metabolite feature classification. Journal of Chromatography B - Analytical Technologies in the Biomedical and Life Sciences, 1071 68-74, https://dx.doi.org/10.1016/j.jchromb.2017.08.015, https://hal.inrae.fr/hal-02620690 [IF: 3.318, CHEMISTRY, ANALYTICAL, Q2, 32/99]

14 Benjamin Merlet, Nils Paulhe, Florence Vinson, Clément Frainay, Maxime Chazalviel, Nathalie Poupin, Yoann Gloaguen, Franck Giacomoni and Fabien Jourdan (2016). A computational solution to automatically map metabolite libraries in the context of genome scale metabolic networks. Frontiers in Molecular Biosciences, 3 2, https://dx.doi.org/10.3389/fmolb.2016.00002, https://hal.inrae.fr/hal-02631089  [IF: 6.113, BIOCHEMISTRY & MOLECULAR BIOLOGY, Q1, 73/296].

13 Daniel Zalko, Ana Soto, Cecile Canlet, Marie Tremblay Franco, Fabien Jourdan, Nicolas J. Cabaton (2016). Bisphenol A exposure disrupts neurotransmitters through modulation of transaminase activity in the brain of rodents. Endocrinology, 157 (5), 1736-1739, https://dx.doi.org/10.1210/en.2016-1207, https://hal.inrae.fr/hal-02640118 [IF: 5.051, ENDOCRINOLOGY & METABOLISM, Q2, 47/180]

12 Marie Tremblay-Franco, Nicolas J. Cabaton, Cécile Canlet, Roselyne Gautier,Cheryl M Schaeberle, Fabien Jourdan, Carlos Sonnenschein, Florence Vinson,Ana Soto and Daniel Zalko. (2015). Plos One. Dynamic Metabolic Disruption in Rats Perinatally Exposed to Low Doses of Bisphenol-A. 10(10):e0141698. doi: 10.1371/journal.pone.0141698, https://hal.inrae.fr/hal-02632321v1 [IF: 3.240, MULTIDISCIPLINARY SCIENCES, Q1, 29/126]

11 Shameer S, Logan-Klumpler FJ, Vinson F, Cottret L, Merlet B, Achcar F, Boshart M, Berriman M, Breitling R, Bringaud F, Bütikofer P, Cattanach AM , Bannerman-Chukualim B, Creek D, Crouch K, de Koning HP, Denise H, Ebikeme C, Fairlamb AH, Ferguson MAJ, Ginger ML, Hertz-Fowler C, Kerkhoven EJ, Mäser P, Michels PAM, Nayak A, Nes DW, Nolan DP, Olsen C, Silva-Franco F, Smith TK, Taylor MC, Tielens AGM, Urbaniak MD, van Hellemond JJ, Vincent IM, Wilkinson SR, Wyllie S, Opperdoes FR, Barrett MP, Jourdan F. TrypanoCyc: A community-led biochemical pathways database for Trypanosoma brucei. (2015) Nucleic Acids Research, 43 (Database issue):D637-44. https://doi.org/10.1093/nar/gku944, https://hal.archives-ouvertes.fr/hal-02631222v1 [IF: 19.160, BIOCHEMISTRY & MOLECULAR BIOLOGY, Q1, 5/321]

10 Martin JC, Maillot M, Mazerolles G, Verdu A, Lyan B, Migné C, Defoort C, Canlet C, Junot C, Guillou C, Manach C, Jacob D, Jouan-Rimbaud Bouveresse D,  Paris E, Pujos-Guillot E, Jourdan F, Giacomoni F, Courant F, Favé G, Le Gall G,  Chassaigne H, Tabet JC, Martin JF, Antignac JP, Shintu L, Defernez M, Philo M, Alexandre-Gouaubau MC, Amiot-Carlin MJ, Bossis M, Triba MN, Stojilkovic N, Banzet N, Molinié R, Bott R, Goulitquer S, Caldarelli S, Rutledge DN (2015). Can We Trust Untargeted Metabolomics: Results of the Metabo-Ring initiative, a large-scale multi-instruments inter-laboratory study. Metabolomics. 11(4):807-821. https://dx.doi.org/10.1007/s11306-014-0740-0, https://hal.archives-ouvertes.fr/hal-01123343v1 [IF: 4.747, ENDOCRINOLOGY & METABOLISM, Q2, 54/146]

9 Silva RR, Jourdan F, Salvanha DM, Letisse F, Jamin EL, Guidetti-Gonzalez S, Labate CA, Vêncio RZN (2014). ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS based metabolomics. Bioinformatics. 1;30(9):1336-7. https://dx.doi.org/10.1093/bioinformatics/btu019, https://hal.archives-ouvertes.fr/hal-01268715v1 [IF: 6.931, MATHEMATICAL & COMPUTATIONAL BIOLOGY, Q1, 4/67]

8 Vieira Milreu P, Coimbra Klein C, Cottret L, Acuña V, Birmelé E, Borassi M, Junot C, Marchetti-Spaccamela A, Marino A, Stougie L, Jourdan F, Crescenzi P, Lacroix V. and Sagot MF (2014). Telling metabolic stories to explore metabolomics data: A case study on the Yeast response to cadmium exposure. Bioinformatics. 30(1): 61-70. [IF: 6.931, MATHEMATICAL & COMPUTATIONAL BIOLOGY, Q1, 4/67]

7 Ghozlane A, Bringaud F, Souedan H, Dutour I, Jourdan F and Thébault P (2012). Flux analysis of the Trypanosoma brucei glycolysis based on a multi-objective criteria bioinformatic approach. 2012:159423 Advances in Bioinformatics.  https://dx.doi.org/10.1155/2012/159423, https://hal.archives-ouvertes.fr/hal-00723179v1 [NO IF]

6 Acuña V, Birmelé E, Cottret L, Crescenzi P, Jourdan F, Lacroix V, Marchetti-Spaccamela A, Marino A, Vieira Milreu P, Sagot MF and Stougie L (2012). Telling Stories: Enumerating maximal directed acyclic graphs with a constrained set of sources and targets. Theoretical Computer Science. Elsevier. 457: 1-9. https://dx.doi.org/10.1016/j.tcs.2012.07.023, https://hal.archives-ouvertes.fr/hal-00764025v1 [IF: 1.002, COMPUTER SCIENCE, THEORY & METHODS, Q4, 109/142]

5 Brice Enjalbert, Fabien Jourdan and Jean-Charles Portais (2011) Intuitive visualization and analysis of multi-omics data and application to Escherichia coli carbon metabolism. Plos One. 6(6). https://dx.doi.org/10.1371/journal.pone.0021318, https://hal.archives-ouvertes.fr/hal-01137055v1 [IF: 3.752, MULTIDISCIPLINARY SCIENCES, Q1, 28/134]

4 Ludovic Cottret, David Wildridge, Florence Vinson, Michael P. Barrett, Hubert Charles, Marie-France Sagot and Fabien Jourdan (2010). MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks. Nucleic Acids Research. 1;38 Suppl:W132-7. https://dx.doi.org/10.1093/nar/gkq312, https://hal.archives-ouvertes.fr/hal-00690651 [IF: 19.160, BIOCHEMISTRY & MOLECULAR BIOLOGY, Q1, 5/321]

3 Fabien Jourdan, Ludovic Cottret, Laurence Huc, David Wildridge, Richard Scheltema, Anne Hillenweck, Michael P. Barrett, Daniel Zalko, David G. Watson and Laurent Debrauwer (2010). Use of reconstituted metabolic networks to assist in metabolomic data visualization and mining. Metabolomics. 6(2):312-321. https://dx.doi.org/10.1007/s11306-009-0196-9, https://hal.archives-ouvertes.fr/hal-02662801   [IF: 4.747, ENDOCRINOLOGY & METABOLISM, Q2, 54/146]

2 Fabien Jourdan, Rainer Breitling, Michael P. Barrett and David Gilbert (2008). MetaNetter: inference and visualization of high-resolution metabolomic networks. Bioinformatics, 24, 143-145. https://doi.org/10.1093/bioinformatics/btm536, https://hal.archives-ouvertes.fr/hal-03318375 [IF: 6.931, MATHEMATICAL & COMPUTATIONAL BIOLOGY, Q1, 4/67]

1 Romain Bourqui, Ludovic Cottret, Vincent Lacroix, David Aube, Patrick Mary, Marie-France Sagot and Fabien Jourdan (2007). Metabolic network visualization eliminating node redundance and preserving metabolic pathways. BMC Systems Biology, 1:29. [IF: 2.048, MATHEMATICAL & COMPUTATIONAL BIOLOGY, Q2, 22/59]

Romain Bourqui, Ludovic Cottret, Vincent Lacroix, David Aube, Patrick Mary, Marie-France Sagot and Fabien Jourdan (2007). Metabolic network visualization eliminating node redundance and preserving metabolic pathways. BMC Systems Biology, 1:29. [IF: 2.048, MATHEMATICAL & COMPUTATIONAL BIOLOGY, Q2, 22/59]