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Fabien Jourdan

126
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Researcher identifiers

Presentation

**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

Publications

Genome scale metabolic network modelling for metabolic profile predictions

Juliette Cooke , Maxime Delmas , Cecilia Wieder , Pablo Rodríguez Mier , Clément Frainay
PLoS Computational Biology, 2024, 20 (2), pp.e1011381. ⟨10.1371/journal.pcbi.1011381⟩
Journal articles hal-04596969v1
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A strategy to detect metabolic changes induced by exposure to chemicals from large sets of condition-specific metabolic models computed with enumeration techniques

Louison Fresnais , Olivier Perin , Anne Riu , Romain Grall, , Alban Ott
BMC Bioinformatics, 2024, 25 (1), pp.234. ⟨10.1186/s12859-024-05845-z⟩
Journal articles hal-04652792v1

PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration

Cecilia Wieder , Juliette Cooke , Clement Frainay , Nathalie Poupin , Russell Bowler
PLoS Computational Biology, 2024, 20 (3), pp.e1011814. ⟨10.1371/journal.pcbi.1011814⟩
Journal articles hal-04597222v1
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Suggesting disease associations for overlooked metabolites using literature from metabolic neighbors

Maxime Delmas , Olivier Filangi , Christophe Duperier , Nils Paulhe , Florence Vinson
GigaScience, 2023, 12, pp.giad065. ⟨10.1093/gigascience/giad065⟩
Journal articles hal-04223426v1

PhysioFit: a software to quantify cell growth parameters and extracellular fluxes

Loïc Le Grégam , Yann Guitton , Floriant Bellvert , Stéphanie Heux , Fabien Jourdan
bioRxiv : n'est pas une revue mais un serveur de preprint, 2023, ⟨10.1101/2023.10.12.561695⟩
Journal articles hal-04253692v1
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Scaling-up metabolomics: Current state and perspectives

Ghina Hajjar , Millena Cristina Barros Santos , Justine Bertrand-Michel , Cécile Canlet , Florence A Castelli
Trends in Analytical Chemistry, 2023, 167 (20), pp.117225. ⟨10.1016/j.trac.2023.117225⟩
Journal articles hal-04188505v1
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Avoiding the Misuse of Pathway Analysis Tools in Environmental Metabolomics

Cecilia Wieder , Jacob Bundy , Clément Frainay , Nathalie Poupin , Pablo Rodríguez-Mier
Environmental Science and Technology, inPress, ⟨10.1021/acs.est.2c05588⟩
Journal articles hal-03799270v1
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PeakForest: a multi-platform digital infrastructure for interoperable metabolite spectral data and metadata management

Nils Paulhe , Cécile Canlet , Annelaure Damont , Lindsay Peyriga , Stéphanie Durand
Metabolomics, 2022, 18 (6), pp.40. ⟨10.1007/s11306-022-01899-3⟩
Journal articles hal-03695453v1
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Networks and Graphs Discovery in Metabolomics Data Analysis and Interpretation

Adam Amara , Clément Frainay , Fabien Jourdan , Thomas Naake , Steffen Neumann
Frontiers in Molecular Biosciences, 2022, 9, ⟨10.3389/fmolb.2022.841373⟩
Journal articles hal-03636716v1
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Gestational exposure to bisphenol A induces region-specific changes in brain metabolomic fingerprints in sheep

Davy Guignard , Cécile Canlet , Marie Tremblay-Franco , Elodie Chaillou , Roselyne Gautier
Environment International, 2022, 165, pp.107336. ⟨10.1016/j.envint.2022.107336⟩
Journal articles hal-03701070v1
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Multiplatform metabolomics for an integrative exploration of metabolic syndrome in older men

Blandine Comte , Stéphanie Monnerie , Marion Brandolini-Bunlon , Cécile Canlet , Florence Castelli
EBioMedicine, 2021, 69, ⟨10.1016/j.ebiom.2021.103440⟩
Journal articles hal-03283772v1
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DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks

Pablo Rodríguez-Mier , Nathalie Poupin , Carlo de Blasio , Laurent Le Cam , Fabien Jourdan
PLoS Computational Biology, 2021, 17 (2), ⟨10.1371/journal.pcbi.1008730⟩
Journal articles hal-03154775v1
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Mitochondrial metabolism supports resistance to IDH mutant inhibitors in acute myeloid leukemia

Lucille Stuani , Marie Sabatier , Estelle Saland , Guillaume Cognet , Nathalie Poupin
Journal of Experimental Medicine, 2021, 218 (5), pp.e20200924. ⟨10.1084/jem.20200924⟩
Journal articles hal-03563454v1
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Gaining Insights Into Metabolic Networks Using Chemometrics and Bioinformatics: Chronic Kidney Disease as a Clinical Model

Julien Boccard , Domitille Schvartz , Santiago Codesido , Mohamed Hanafi , Yoric Gagnebin
Frontiers in Molecular Biosciences, 2021, 8, pp.682559. ⟨10.3389/fmolb.2021.682559⟩
Journal articles hal-03318230v1

Osteogenic Response of Human Mesenchymal Stem Cells Analysed Using Combined Intracellular and Extracellular Metabolomic Monitoring

Amal Surrati , Evseev Sergey , Fabien Jourdan , Dong-Hyun Kim , Virginie Sottile
Cellular Physiology and Biochemistry, 2021, 55 (3), pp.311-326. ⟨10.33594/000000377⟩
Journal articles hal-03312596v1
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Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis

Cecilia Wieder , Clément Frainay , Nathalie Poupin , Pablo Rodríguez-Mier , Florence Vinson
PLoS Computational Biology, 2021, 17 (9), ⟨10.1371/journal.pcbi.1009105⟩
Journal articles hal-03344682v1
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Milk metabolome reveals variations on enteric methane emissions from dairy cows fed a specific inhibitor of the methanogenesis pathway

Bénédict Yanibada , Ulli Hohenester , Mélanie Pétéra , Cécile Canlet , Stéphanie Durand
Journal of Dairy Science, 2021, 104 (12), pp.12553-12566. ⟨10.3168/jds.2021-20477⟩
Journal articles hal-03351167v1
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FORUM: building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases

Maxime Delmas , Olivier Filangi , Nils Paulhe , Florence Vinson , Christophe Duperier
Bioinformatics, 2021, 37 (21), pp.3896-3904. ⟨10.1093/bioinformatics/btab627⟩
Journal articles hal-03361495v1
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ELIXIR and Toxicology: a community in development

Marvin Martens , Rob Stierum , Emma Schymanski , Chris Evelo , Reza Aalizadeh
F1000Research, 2021, 10, pp.1129. ⟨10.12688/f1000research.74502.1⟩
Journal articles pasteur-03680151v1
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Inhibition of enteric methanogenesis in dairy cows induces changes in plasma metabolome highlighting metabolic shifts and potential markers of emission

Bénédict Yanibada , Ulli Hohenester , Mélanie Pétéra , Cécile Canlet , Stéphanie Durand
Scientific Reports, 2020, 10 (1), ⟨10.1038/s41598-020-72145-w⟩
Journal articles hal-02949602v1
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Improving lipid mapping in Genome Scale Metabolic Networks using ontologies

Nathalie Poupin , Florence Vinson , Arthur Moreau , Aurélie Batut , Maxime Chazalviel
Metabolomics, 2020, 16 (4), ⟨10.1007/s11306-020-01663-5⟩
Journal articles hal-02935172v1
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Postprandial NMR-Based Metabolic Exchanges Reflect Impaired Phenotypic Flexibility across Splanchnic Organs in the Obese Yucatan Mini-Pig

Marie Tremblay-Franco , Nathalie Poupin , Aurélien Amiel , Cécile Canlet , Didier Remond
Nutrients, 2020, 12 (8), pp.2442. ⟨10.3390/nu12082442⟩
Journal articles hal-02927174v1
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1H-NMR metabolomics response to a realistic diet contamination with the mycotoxin deoxynivalenol

Imourana Alassane-Kpembi , Cecile Canlet , Marie Tremblay-Franco , Fabien Jourdan , Maxime Chalzaviel
Food and Chemical Toxicology, 2020, 138, pp.111222. ⟨10.1016/j.fct.2020.111222⟩
Journal articles hal-03331253v1
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Arterio-venous metabolomics exploration reveals major changes across liver and intestine in the obese Yucatan minipig

Nathalie Poupin , Marie Tremblay-Franco , Aurélien Amiel , Cécile Canlet , Didier Remond
Scientific Reports, 2019, 9 (1), ⟨10.1038/s41598-019-48997-2⟩
Journal articles hal-02282295v1
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Caractérisation des dangers des contaminants alimentaires : ce qui change; conséquences pour la recherche et l’évaluation

Jean Pierre J. P. Cravedi , Fabien Jourdan
Innovations Agronomiques, 2019, 73, pp.1-10. ⟨10.15454/ij9z4r⟩
Journal articles hal-02275513v1
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PhenoMeNal: processing and analysis of metabolomics data in the cloud

Kristian Peters , James Bradbury , Sven Bergmann , Marco Capuccini , Marta Cascante
GigaScience, 2019, 8 (2), pp.giy149. ⟨10.1093/gigascience/giy149⟩
Journal articles hal-02627233v1
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MetaboRank: network-based recommendation system to interpret and enrich metabolomics results

Clément Frainay , Sandrine Aros , Maxime Chazalviel , Thomas Garcia , Florence Vinson
Bioinformatics, 2019, 35 (2), pp.274-283. ⟨10.1093/bioinformatics/bty577⟩
Journal articles hal-02627792v1
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Large-Scale Modeling Approach Reveals Functional Metabolic Shifts during Hepatic Differentiation

Nathalie Poupin , Anne Corlu , Nicolas J. Cabaton , Hélène Dubois-Pot-Schneider , Cécile Canlet
Journal of Proteome Research, 2019, 18 (1), pp.204-216. ⟨10.1021/acs.jproteome.8b00524⟩
Journal articles hal-01937261v1
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Integrated transcriptomics and metabolomics reveal signatures of lipid metabolism dysregulation in HepaRG liver cells exposed to PCB 126

Robin Mesnage , Martina Biserni , Sucharitha Balu , Clément Frainay , Nathalie Poupin
Archives of Toxicology, 2018, 92 (8), pp.2533-2547. ⟨10.1007/s00204-018-2235-7⟩
Journal articles hal-02621552v1
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MetExploreViz: web component for interactive metabolic network visualization

Maxime Chazalviel , Clément Frainay , Nathalie Poupin , Florence Vinson , Benjamin Merlet
Bioinformatics, 2018, 34 (2), pp.312-313. ⟨10.1093/bioinformatics/btx588⟩
Journal articles hal-02621786v1
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Mind the gap: mapping mass spectral databases in genome-scale metabolic networks reveals poorly covered Areas

Clément Frainay , Emma L. Schymanski , Steffen Neumann , Benjamin Merlet , Reza Mohammadi Salek
Metabolites, 2018, 8 (3), ⟨10.3390/metabo8030051⟩
Journal articles hal-02627086v1
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MetExplore: collaborative edition and exploration of metabolic networks

Ludovic Cottret , Clément Frainay , Maxime Chazalviel , Floréal Cabanettes , Yoann Gloaguen
Nucleic Acids Research, 2018, 46 (W1), 8 p. ⟨10.1093/nar/gky301⟩
Journal articles hal-01886470v1
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An untargeted metabolomics approach to explore the metabolic modulation of HepG2 cells exposed to low doses of bisphenol A and 17β-estradiol 2

Nicolas J. Cabaton , Nathalie Poupin , Cécile Canlet , Marie Tremblay-Franco , Marc Audebert
Frontiers in Endocrinology, 2018, 9, ⟨10.3389/fendo.2018.00571⟩
Journal articles hal-02618654v1
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Targeted versus untargeted omics — the CAFSA story

Maria del Mar Amador , Benoit Colsch , Foudil Lamari , Claude Jardel , Farid Ichou
Journal of Inherited Metabolic Disease, 2018, 41 (3), pp.1-10. ⟨10.1007/s10545-017-0134-3⟩
Journal articles hal-01777969v1
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MetaNetter 2: A Cytoscape plugin for ab initio network analysis and metabolite feature classification

Karl E.V. Burgess , Y. Borutzki , N. Rankin , R. Daly , Fabien Jourdan
Journal of Chromatography B - Analytical Technologies in the Biomedical and Life Sciences, 2017, 1071, pp.68-74. ⟨10.1016/j.jchromb.2017.08.015⟩
Journal articles hal-02620690v1
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The future of metabolomics in ELIXIR

M. van Rijswijk , C. Beirnaert , C. Caron , M. Cascante , V. Dominguez
F1000Research, 2017, 6 (Version 2), ⟨10.12688/f1000research.12342.2⟩
Journal articles hal-01630635v1

Computational methods to identify metabolic sub-networks based on metabolomic profiles

Clément Frainay , Fabien Jourdan
Briefings in Bioinformatics, 2017, 18 (1), pp.43-56. ⟨10.1093/bib/bbv115⟩
Journal articles hal-01608721v1

PathQuant: A bioinformatic tool to quantitatively annotate the relationship between genes and metabolites through metabolic pathway mapping

Sandra Therrien-Laperriere , S. Cherkaoui , G. Boucher , . Igenomed Consortium , Fabien Jourdan
FASEB Journal, 2017, 31 (1)
Journal articles hal-02622661v1
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A computational solution to automatically map metabolite libraries in the context of genome scale metabolic networks

Benjamin Merlet , Nils Paulhe , Florence Vinson , Clément Frainay , Maxime Chazalviel
Frontiers in Molecular Biosciences, 2016, 3, ⟨10.3389/fmolb.2016.00002⟩
Journal articles hal-02631089v1
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Bisphenol A exposure disrupts neurotransmitters through modulation of transaminase activity in the brain of rodents

Daniel Zalko , Ana Soto , Cécile Canlet , Marie Tremblay-Franco , Fabien Jourdan
Endocrinology, 2016, 157 (5), pp.1736-1739. ⟨10.1210/en.2016-1207⟩
Journal articles hal-02640118v1
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Dynamic metabolic disruption in rats perinatally exposed to low doses of bisphenol-A

Marie Tremblay-Franco , Nicolas J. Cabaton , Cécile Canlet , Roselyne Gautier , Cheryl M Schaeberle
PLoS ONE, 2015, 10 (10), ⟨10.1371/journal.pone.0141698⟩
Journal articles hal-02632321v1
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TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei

Sanu Shameer , Flora J. Logan-Klumpler , Florence Vinson , Ludovic Cottret , Benjamin Merlet
Nucleic Acids Research, 2015, 43 (D1), pp.D637 - D644. ⟨10.1093/nar/gku944⟩
Journal articles hal-02631222v1
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Can we Trust Untargeted Metabolomics: Results of the Metabo-ring Initiative, a Large-scale Multi-instruments Inter-laboratoire Study

Jean-Charles Martin , Mathieu Maillot , Gerard Mazerolles , Alexandre Verdu , Bernard Lyan
Metabolomics, 2015, 11 (4), pp.807-821. ⟨10.1007/s11306-014-0740-0⟩
Journal articles hal-01123343v1
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ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics

Ricardo R. Silva , Fabien Jourdan , Diego M. Salvanha , Fabien Letisse , Emilien L. Jamin
Bioinformatics, 2014, 30 (9), pp.1336 - 1337. ⟨10.1093/bioinformatics/btu019⟩
Journal articles hal-01268715v1
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Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure

Paulo Vieira Milreu , Cecilia Coimbra Klein , Ludovic Cottret , Vicente Acuña , Etienne E. Birmelé
Bioinformatics, 2014, 30 (1), pp.61-70. ⟨10.1093/bioinformatics/btt597⟩
Journal articles hal-00922567v1
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Telling stories: Enumerating maximal directed acyclic graphs with a constrained set of sources and targets

Vicente Acuña , Etienne Birmelé , Ludovic Cottret , Pierluigi Crescenzi , Fabien Jourdan
Theoretical Computer Science, 2012, 457, pp.1--9. ⟨10.1016/j.tcs.2012.07.023⟩
Journal articles hal-00764025v1
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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

Amine Ghozlane , Frédéric Bringaud , Hayssam Soueidan , Isabelle Dutour , Fabien Jourdan
Advances in Bioinformatics, 2012, 2012, 16 p., Article ID 159423. ⟨10.1155/2012/159423⟩
Journal articles hal-00723179v1
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Intuitive Visualization and Analysis of Multi-Omics Dataand Application to Escherichia coli Carbon Metabolism

Brice Enjalbert , Fabien Jourdan , Jean-Charles Portais
PLoS ONE, 2011, 6 (6), pp.e21318. ⟨10.1371/journal.pone.0021318⟩
Journal articles hal-01137055v1

Communities and hierarchical structures in dynamic social networks: analysis and visualization

Frédéric Gilbert , Paolo Simonetto , Faraz Zaidi , Fabien Jourdan , Romain Bourqui
Social Network Analysis and Mining, 2011, 1 (2), pp.85-95. ⟨10.1007/s13278-010-0002-8⟩
Journal articles hal-00520936v1
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MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks.

Ludovic Cottret , David Wildridge , Florence Vinson , Michael P Barrett , Hubert Charles
Nucleic Acids Research, 2010, 38 (Web Server issue), pp.W132-7. ⟨10.1093/nar/gkq312⟩
Journal articles hal-00690651v1

Graph methods for the investigation of metabolic networks in parasitology

Ludovic Cottret , Fabien Jourdan
Parasitology, 2010, 137, pp.1393-1407. ⟨10.1017/S0031182010000363⟩
Journal articles hal-02661590v1
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Use of reconstituted metabolic networks to assist in metabolomic data visualization and mining

Fabien Jourdan , Ludovic Cottret , Laurence Huc , David Wildridge , Richard Scheltema
Metabolomics, 2010, 6 (2), pp.312-321. ⟨10.1007/s11306-009-0196-9⟩
Journal articles hal-02662801v1
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Un algorithme stable de décomposition pour l'analyse des réseaux sociaux dynamiques

Romain Bourqui , Paolo Simonetto , Fabien Jourdan
Revue des Nouvelles Technologies de l'Information, 2009, pp.337-348
Journal articles hal-00406437v1

MetaNetter: inference and visualization of high-resolution metabolomic networks

Fabien Jourdan , Rainer Breitling , Michael Barrett , Gilbert David
Bioinformatics, 2008, 24 (1), pp.143-145. ⟨10.1093/bioinformatics/btm536⟩
Journal articles hal-03318375v1
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Exploration multi-omique et in silico des effets transgénérationels et sexe-spécifiques induits par le TBT, un composé obésogène, sur le métabolisme hépatique de la souris

Nathalie Poupin , Fabien Jourdan , Raquel Chamorro-García , Toshi Shioda , Richard C Chang
15èmes journées scientifiques du Réseau Français de Métabolomique et Fluxomique (RFMF), May 2023, Perpignan, France
Conference papers hal-04596856v1
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Automatising 13 C-fluxomics flux calculations through a workflow hosted on the Workflow4Metabolomics Galaxy platform

Loïc Le Grégam , Pierre Millard , Serguei Sokol , Yann Guitton , Gildas Le Corguillé
Analytics 2022, RFMF; AFSEP; AFSM, Sep 2022, Nantes (Cité des Congrès), France
Conference papers hal-04352460v1
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Modelling the muscle metabolic response in anabolic and catabolic states using arterio-venous blood metabolomics profiles

Nathalie Poupin , Florence A Castelli , Emeline Chu-Van , Didier Remond , Dominique Dardevet
8. Conference on Constraint-Based reconstruction and Analysis (COBRA 2022), Sep 2022, Galway, Ireland
Conference papers hal-03807737v1
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SAMBA, a recommendation system for biomarker discovery using metabolic networks

Juliette Cooke , Nathalie Poupin , Maxime Delmas , Clément Frainay , Florence Vinson
8th Conference on Constraint-Based reconstruction and Analysis (COBRA 2022), Sep 2022, Galway, Ireland
Conference papers hal-03807772v1
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Modelling intrahepatic metabolic rewiring during the onset of obesity using arterio- venous blood metabolomics profiles

Nathalie Poupin , Marie Tremblay-Franco , Cécile Canlet , Aurélien Amiel , Didier Rémond
European RFMF Metabomeeting 2020, Jan 2020, Toulouse, France
Conference papers hal-02948334v1
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Inhibition of enteric methanogenesis in cows induces changes in plasma metabolome highlighting potential emission markers

Bénédict Yanibada , Ulli Hohenester , Mélanie Pétéra , Cécile Canlet , Stéphanie Durand
7. Greenhouse Gas and Animal Agriculture Conference, Aug 2019, Foz do Iguassu, Brazil
Conference papers hal-02788492v1
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Modélisation du réseau métabolique des cellules de Leucémies Aiguës Myéloïdes pour comprendre les différences métaboliques liées à la mutation sur IDH1

Laurent Fernando , Lucille Stuani , Tony Lionel Palama , Tony Kaoma , Jean-Emmanuel Sarry
Congrès de Spectrométrie de Masse, Métabolomique et Fluxomique (SMMAP), Oct 2017, Marne-la-Vallée, France
Conference papers hal-02946080v1

Reconstruction du réseau métabolique de la tomate

Florence Maurier , Clément Frainay , Fabien Jourdan , Sophie S. Colombie
9. Journées scientifiques du RFMF, Réseau Francophone de Métabolomique et Fluxomique (RFMF). FRA., Jun 2015, Lille, France
Conference papers hal-02742882v1
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MetaboHUB and RFMF : two tools at the service of metabolomics and fluxomics in France

Dominique Rolin , Floriant Bellvert , Justine Bertrand-Michel , Cécile Canlet , Richard Cole
MERLION Metabolomics Workshop Singapore 2014, Nov 2014, Singapour, Singapore
Conference papers hal-02798242v1

MetaboHUB: une infrastructure nationale au service de la métabolomique

Dominique D. Rolin , Alice A. Agasse , Justine Bertrand-Michel , R. R. Cole , B. B. Colsch
Séance thématique "La métabolomique : son application en recherche pharmaceutique et diagnostique", Académie Nationale de Pharmacie. FRA., Feb 2013, Paris, France
Conference papers hal-01002248v1

MetaboHUB: a national infrastructure dedicated to metabolomics and fluxomics

Dominique D. Rolin , Alice A. Agasse , Justine Bertrand-Michel , R. R. Cole , B. B. Colsch
7. Journées scientifiques du Réseau Français de Métabolomique et de Fluxomique (RFMF), Jun 2013, Amiens, France
Conference papers hal-01002241v1

MetaboHUB: a french infrastructure dedicated to metabolomics and fluxomics

Dominique D. Rolin , Alice A. Agasse , Justine Bertrand-Michel , R. R. Cole , Sophie S. Colombie
Metabolomics 2013 - 9. Annual conference of the Metabolomics Society, Jul 2013, Glasgow, United Kingdom
Conference papers hal-01002247v1
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Visualization of time-series data in the context of metabolic networks with Systrip Software

Jonathan Dubois , Ludovic Cottret , Amine Ghozlane , David Auber , Frédéric Bringaud
Journées Ouvertes Biologie Informatique Mathématiques (JOBIM 2013), Jul 2013, France
Conference papers hal-00838725v1

Peut-on faire confiance à la métabolomique: résultats de l'initiative MetaboRing

Alexandre Verdu , Bernard Lyan , Carole Migné , Catherine Defoort , Cécile Canlet
6. Journées Scientifiques du Réseau Français de Métabolomique et Fluxomique (RFMF), May 2012, Nantes, France
Conference papers hal-01594993v1
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Systrip: a visual environment for the investigation of time-series data in the context of metabolic networks

Jonathan Dubois , Ludovic Cottret , Amine Ghozlane , David Auber , Frédéric Bringaud
16th International Conference on Information Visualization (IV'12), Jul 2012, Montpellier, France. pp.4771a204
Conference papers hal-00742176v1

Can we trust untargeted metabolomics: results of the metabo-ring study

Alexandre Verdu , Bernard Lyan , Carole Migné , Catherine Defoort , Cécile Canlet
2. African-European Conference on Chemometrics - Afrodata 2012, Nov 2012, Stellenbosch, South Africa
Conference papers hal-01595486v1
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Metabolomics for food and environmental toxicology : from targeted to global integrative approaches

Laurent Debrauwer , Emilien L. Jamin , Isabelle Jouanin , Sylvie S. Chevolleau , Marlène Z. Lacroix
LC-MS Montreux Symposium 2012, Nov 2012, Montreux, Switzerland
Conference papers hal-02745532v1

Approche métabonomique pour l'étude in vivo, in vitro et in silico de la toxicologie des faibles doses

Daniel Zalko , Nicolas J. Cabaton , Cécile Canlet , Marie Tremblay-Franco , Fabien Jourdan
. 5emes Journées scientifiques TOXALIM, Ville service., Dec 2011, Toulouse, France
Conference papers hal-02811476v1

Extraction d'"histoires métaboliques" dans les réseaux métaboliques à partir de données métabolomiques

Fabien Jourdan
5eme journées du RFMF, Saisissez le nom du laboratoire, du service ou du département., Ville service., May 2011, Paris, France
Conference papers hal-02803297v1

Use of reconstituted metabolic networks to assist in metabolomic data visualization and mining

Fabien Jourdan
Metabolomics 2011, Saisissez le nom du laboratoire, du service ou du département., Ville service., Jun 2011, Cairns, Australia
Conference papers hal-02802559v1

Computing "metabolic stories" in genome scale metabolic networks based on metabolomics data.(2011)

Fabien Jourdan
Metabolomics 2011, Ville service., Jun 2011, Cairns, Australia
Conference papers hal-02803877v1

Telling Stories

Vicente Acuña , Etienne Birmele , Ludovic Cottret , Pierluigi Crescenzi , Fabien Jourdan
ICALP 2011 satellite workshop: Graph Algorithms and Applications (GA), 2011, Zurich, Switzerland. ⟨10.1016/j.tcs.2012.07.023⟩
Conference papers hal-00748788v1
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Domain specific vs Generic Network Visualization: an evaluation with metabolic networks

Romain Bourqui , Helen Purchase , Fabien Jourdan
Australasian Conference on User Interface, Jan 2011, Australia. pp.9-18
Conference papers hal-00579230v1

Development of metabolomics method associating NMR and UPLC-HRMS

Emilien L. Jamin , Cécile Canlet , Maria-Helena Meireles , Marc Dubois , Marie Tremblay-Franco
SMAP 2011, Saisissez le nom du laboratoire, du service ou du département., Ville service., Sep 2011, Avignon, France
Conference papers hal-02804072v1

Metaboflux : a method to analyze flux distribution in metabolic networks

Amine Ghozlane , Frédéric Bringaud , Fabien Jourdan , Patricia Thebault
Workshop Metabolomics2010, AmsterdamRAI, the Netherlands, 2010, Amsterdam, Netherlands
Conference papers hal-00648759v1
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Detecting structural changes and command hierarchies in dynamic social networks

Romain Bourqui , Frédéric Gilbert , Paolo Simonetto , Faraz Zaidi , Umang Sharan
Advances in Social Network Analysis and Data Mining, 2009, Greece. pp.83-88
Conference papers hal-00406240v1
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Revealing subnetwork roles using contextual visualization: comparison of metabolic networks

Romain Bourqui , Fabien Jourdan
12th International Conference on Information Visualisation, Jul 2008, London, United Kingdom. pp.638-643
Conference papers hal-00343889v1

Comparaison Visuelle de Réseaux Métaboliques

Romain Bourqui , Fabien Jourdan
8èmes Journées Ouvertes Biologie Informatique Mathématiques, 2007, France. pp.285-286
Conference papers hal-00306674v1

Multiscale scatterplot matrix for visual and interactive exploration of metabonomic data

Fabien Jourdan , Alain Paris , Pierre-Yves Koenig , Guy Melançon
1st Visual Information Expert Workshop (VIEW), Apr 2006, Paris, France
Conference papers hal-02751211v1
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Multiscale scatterplot matrix for visual and interactive exploration of metabonomics data

Fabien Jourdan , Alain Paris , Pierre-Yves Koenig , Guy Melançon
Visual Information Expert Workshop, Apr 2006, Paris, France. pp.202-215, ⟨10.1007/978-3-540-71027-1_18⟩
Conference papers lirmm-00091360v1

Metabolic network visualization using constraint planar graph drawing Algorithm

Romain Bourqui , David Auber , Vincent Lacroix , Fabien Jourdan
IV 06: Proceedings of the 10 International Conference on Information Visualisation (IV06), 2006, United States. pp.489 - 496
Conference papers hal-00306676v1

Un Algorithme Contraint de Dessin de Graphe Planaire pour la Visualisation de Réseaux Métaboliques

Romain Bourqui , David Auber , Vincent Lacroix , Fabien Jourdan
Quatrième édition du congrés francophone de doctorants en STIC, MajecSTIC, 2006, France. pp.électronique
Conference papers hal-00306673v1
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Une Approche MDS Hybride pour l'Exploration Visuelle Interactive

Fabien Jourdan , Guy Melançon , Christophe Douy , Alexandre Gasne
Conférence Francophone sur l'Interaction Homme-Machine, Sep 2005, Toulouse, France
Conference papers lirmm-00106468v1
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Metric-Based Network Exploration and Multiscale Scatterplot

Yves Chiricota , Fabien Jourdan , Guy Melançon
InfoVis: Information Visualization, Oct 2004, Austin, United States. pp.135-142, ⟨10.1109/INFVIS.2004.47⟩
Conference papers lirmm-00108871v1
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Multiscale hybrid MDS

Fabien Jourdan , Guy Melançon
IV: Information Visualization, Jul 2004, London, United Kingdom. pp.388-393, ⟨10.1109/IV.2004.1320173⟩
Conference papers lirmm-00108864v1

Drawing, Clustering and Visualization of Biological Pathways

Fabien Jourdan
International Symposium on Networks in Bio-Informatics, Mar 2004, Paris, France
Conference papers lirmm-00109131v1
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Software Components Capture using Graph Clustering

Yves Chiricota , Fabien Jourdan , Guy Melançon
IEEE International Workshop on Program Comprehension, 2003, Portland, Oregon, United States. pp.217-226
Conference papers lirmm-00191947v1

A Tool for Metabolic and Regolatory Pathways Visual Analysis

Fabien Jourdan , Guy Melançon
Conference on Visualization and Data Analysis, Jan 2003, Santa Clara, United States. pp.46-55
Conference papers lirmm-00269772v1
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Multiscale Visualization of Small World Networks

David Auber , Yves Chiricota , Fabien Jourdan , Guy Melançon
InfoVis: Information Visualization, Oct 2003, Seattle, WA, United States. pp.75-81
Conference papers lirmm-00269770v1
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Software Components Capture using Graph Clustering

Yves Chiricota , Fabien Jourdan , Guy Melançon
IEEE International Workshop on Program Comprehension, 2003, Portland, Oregon, United States. pp.217-226
Conference papers lirmm-00269464v1
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PhysioFit: Quantifying cell growth parameters and uptake and production fluxes

Loïc Le Grégam , Yann Guitton , Floriant Bellvert , Fabien Jourdan , Jean-Charles Portais
15émes journées scientifiques du RFMF ( Réseau Francophone de Métabolomique et Fluxomique ), May 2023, Perpignan, France. 2023
Conference poster hal-04321321v1
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The CHaMP web-app:an interactive tool to infer biotransformation pathways from your MS peaks

Marine Valleix , Clément Frainay , Elodie Person , Jean-François Martin , Laurent Debrauwer
RFMF 2023, RFMF, 15émes journées scientifiques du Réseau Francophone de Métabolomique et Fluxomique,, May 2023, Perpignan, France
Conference poster hal-04405320v1
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Métabolomique multiplateforme (MS, RMN) : étude de l’impact de l'ajout de TSP sur les données MS

benedict Yanibada , Cécile Canlet , Carla Orlandi , Roselyne Gautier , Fabien Jourdan
Congrès Analytics 2022, Sep 2022, Nantes, France
Conference poster hal-04357965v1
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Improving prediction of essential genes using context-specific metabolic network ensembles

Pablo Rodríguez-Mier , Nathalie Poupin , Carlo de Blasio , Laurent Le Cam , Fabien Jourdan
European RFMF Metabomeeting 2020, Jan 2020, Toulouse, France
Conference poster hal-02948371v1
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MetExplore: Omics data analysis in the context of metabolic networks

Maxime Chazalviel , Adrien Rohan , Nathalie Poupin , Florence Vinson , Clément Frainay
European RFMF Metabomeeting 2020, Jan 2020, Toulouse, France.
Conference poster hal-02948391v1
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INPUT OF DEEP PHENOTYPING IN THE METABOLIC SYNDROME STRATIFICATION

Stéphanie Monnerie , Mélanie Pétéra , Cécile Canlet , Florence Castelli , Benoit Colsch
European RFMF Metabomeeting 2020, Jan 2020, Toulouse, France. , 262 p., 2020, Oral and Poster Abstracts European RMF Metabomeeting 2020
Conference poster hal-02505908v1

Study of the hepatic metabolic effects induced by PFOA exposure using a multiplatform metabolomics approach

Joran Villaret-Cazadamont , Noemie Butin , Cécile Canlet , Marie Tremblay-Franco , Roselyne Gautier
55. Congress of the European-Societies-of-Toxicology (EUROTOX) - Toxicology - Science Providing Solutions, Sep 2019, Helsinki, Finland. ELSEVIER IRELAND LTD, 2019, TOXICOLOGY LETTERS
Conference poster hal-02306108v1

Modelling hepatic metabolic changes during the onset of obesity using NMR metabolomics arterio-venous blood exploration in minipigs

Nathalie Poupin , Marie Tremblay-Franco , Aurélien Amiel , Cécile Canlet , Didier Remond
12. Journées Scientifiques du Réseau Francophone de Métabolomique et Fluxomique RFMF, May 2019, Clermont-Ferrand, France. 168 p., 2019, Livre des résumés
Conference poster hal-02162584v1
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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

Sergio Polakof , Marie Tremblay-Franco , Cécile Canlet , Jérémie David , Fabien Jourdan
12. Journées Scientifiques du Réseau Francophone de Métabolomique et Fluxomique RFMF, May 2019, Clermont-Ferrand, France. 168 p., 2019, Livre des résumés
Conference poster hal-02162582v1

Modeling hepatic metabolic changes during the onset of obesity from metabolomics arterio-venous blood exploration in minipigs

Nathalie Poupin , Marie Tremblay-Franco , Aurélien Amiel , Cécile Canlet , Didier Remond
Copenhagen Bioscience Conference 2017: Where big-data gets translated into knowledge, May 2017, Copenhague, Netherlands. 2017, Bioscience Conference 2017
Conference poster hal-01606420v1

Reconstruction du réseau métabolique de la tomate

Florence Maurier , Clément Frainay , Fabien Jourdan , Sophie S. Colombie
9. Journées scientifiques du RFMF, Jun 2015, Lille, France. 2015
Conference poster hal-02742705v1

Reconstruction du réseau métabolique de la tomate

Florence Maurier , Fabien Jourdan , Sophie S. Colombie
8. Journées Scientifiques du Réseau Français de Métabolomique et Fluxomique RFMF, May 2014, Lyon, France. 1 p., 2014
Conference poster hal-02799581v1

Can we Trust Untargeted Metabolomics: Results of the Metabo-ring Initiative, a Large-scale Multi-instruments Inter-laboratoire Study

Jean-Charles Martin , Mathieu Maillot , Gerard Mazerolles , Alexandre Verdu , Bernard Lyan
9. Annual Conference of the Metabolomics Society, Jul 2013, Glasgow, United Kingdom. 2013, 9th Annual Conference of the Metabolomics Society
Conference poster hal-01123136v1

Can we trust untargeted metabolomics: first results of the metabo-ring study

Alexandre Verdu , Bernard Lyan , Carole Migné , Catherine Defoort , Cécile Canlet
8. Annual International Meeting of the Metabolomics Society, Jun 2012, Washington, United States. , 2012
Conference poster hal-01595487v1

MetExplore, a framework for the analysis of metabolic networks: applications in the field of metabolomics data and the study of endocrine disruptors

Ludovic Cottret , Florence Vinson , Nicolas J. Cabaton , Maria-Helena Meireles , Daniel Zalko
6th Copenhagen Workshop on Endocrine Disrupters, Apr 2011, Copenhagen, Denmark. 2011
Conference poster hal-02802904v1

TrypanoCyc: a community effort towards the development of a metabolic pathway database for Trypanosoma brucei.

Flora Logan-Klumpler , Ludovic Cottret , Florence Vinson , Fabien Jourdan , Michael Barrett
Kinetoplastid Molecular Cell Biology Meeting (KMCB 2011), 2011, Inconnue, France. 2011
Conference poster hal-02803549v1

MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks

Ludovic Cottret , David Wildridge , Florence Vinson , Michael P. Barrett , Marie-France Sagot
JOBIM 2010, Sep 2010, Montpellier, France. , 1 p., 2010, JOBIM 2010 Montpellier, Journée Ouvertes Biologie Informatique Mathématique, Montpellier, France, 7 - 9 septembre 2010
Conference poster hal-02821730v1

Plant genome-scale metabolic networks

Léo Gerlin , Clément Frainay , Fabien Jourdan , Caroline Baroukh , Sylvain Prigent
Science Direct. Plant Metabolomics in full swing, 98, 2021, Advances in Botanical Research, ⟨10.1016/bs.abr.2020.09.021⟩
Book sections hal-03149497v1

Genome-scale metabolic networks

Clément Frainay , Fabien Jourdan
Metabolomics: Practical Guide to Design and Analysis, 1ère édition, Chapman and Hall, 290 p., 2019, 9781315370583. ⟨10.1201/9781315370583-8⟩
Book sections hal-02786295v1

Understanding Protozoan Parasite Metabolism and Identifying Drug Targets through Constraint-Based Modeling

Francis Isidore Totanes , Sanu Shameer , David Westhead , Fabien Jourdan , Glenn Mcconkey
Comprehensive Analysis of Parasite Biology: From Metabolism to Drug Discovery, Wiley-VCH Verlag GmbH & Co. KGaA, pp.487-512, 2016, ⟨10.1002/9783527694082.ch21⟩
Book sections hal-03318814v1

Analysing human metabolic networks using metabolomics

Nathalie Poupin , Fabien Jourdan
Metabolomics as a Tool in Nutrition Research, Elsevier, pp.85-114, 2015, ⟨10.1016/B978-1-78242-084-2.00005-8⟩
Book sections hal-03318813v1

Human metabolic networks and metabolomics

Fabien Jourdan , Nathalie Poupin
Metabolomics as tool in nutrition research, Woodhead publishing Limited, 2014
Book sections hal-01187878v1

Qualitative modelling of metabolic networks

Fabien Jourdan
Metabolomics coming of age with its technological diversity, 67, 2013, Advances in Botanical Research, ⟨10.1016/B978-0-12-397922-3.00012-5⟩
Book sections hal-02803214v1
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A stable decomposition algorithm for dynamical social network analysis

Romain Bourqui , Paolo Simonetto , Fabien Jourdan
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⟩
Book sections hal-00543175v1
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A strategy to detect metabolic changes induced by exposure to chemicals from large sets of condition-specific metabolic models computed with enumeration techniques

Louison Fresnais , Olivier Perin , Anne Riu , Romain Grall , Alban Ott
2024
Preprints, Working Papers, ... hal-04188513v2

Suggesting disease associations for overlooked metabolites using literature from metabolic neighbours

M. Delmas , O. Filangi , Christophe Duperier , N. Paulhe , F. Vinson
2023
Preprints, Working Papers, ... hal-04188519v1

FORUM: Building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases

Maxime Delmas , Olivier Filangi , Nils Paulhe , Florence Vinson , Christophe Duperier
2021
Preprints, Working Papers, ... hal-03318295v1
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Pathway analysis in metabolomics: pitfalls and best practice for the use of over-representation analysis

Cecilia Wieder , Clément Frainay , Nathalie Poupin , Pablo Rodríguez-Mier , Florence Vinson
2021
Preprints, Working Papers, ... hal-03240376v1

DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks

Pablo Rodríguez-Mier , Nathalie Poupin , Carlo de Blasio , Laurent Le Cam , Fabien Jourdan
2020
Preprints, Working Papers, ... hal-02935163v1

Combinatory therapy targeting mitochondrial oxidative phosphorylation improves efficacy of IDH mutant inhibitors in acute myeloid leukemia

Lucille Stuani , Marie Sabatier , Feng Wang , Nathalie Poupin , Claudie Bosc
2020
Preprints, Working Papers, ... hal-02935177v1