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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
	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
	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
	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
	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
	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
	Atopic dermatitis or eczema? Consequences of ambiguity in disease name for biomedical literature mining Clément Frainay , Yoann Pitarch , Sarah Filippi , Marina Evangelou , Adnan Custovic Clinical and Experimental Allergy, 2021, 51 (9), pp.1185-1194. ⟨10.1111/cea.13981⟩ Journal articles hal-03311466v1
	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
	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
	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
	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
	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
	Machine learning to identify pairwise interactions between specific IgE antibodies and their association with asthma: A cross-sectional analysis within a population-based birth cohort Sara Fontanella , Clément Frainay , Clare S. Murray , Angela Simpson , Adnan Custovic PLoS Medicine, 2018, 15 (11), 22 p. ⟨10.1371/journal.pmed.1002691⟩ Journal articles hal-02626228v1
	Classification of pediatric asthma: from phenotype discovery to clinical practice Ceyda Oksel , Sadia Haider , Sara Fontanella , Clément Frainay , Adnan Custovic Frontiers in Pediatrics, 2018, 6, ⟨10.3389/fped.2018.00258⟩ Journal articles hal-02626193v1
	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
	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
	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
	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
	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
	Hypoxia induces VEGF-C expression in metastatic tumor cells via a HIF-1α-independent translation-mediated mechanism Florent Morfoisse , Anna Kuchnio , Clément Frainay , Anne Gomez-Brouchet , Marie-Bernadette Delisle Cell Reports, 2014, 6 (1), pp.155-167. ⟨10.1016/j.celrep.2013.12.011⟩ Journal articles hal-02631811v1

	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

	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
	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
	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

	Système de recommandation basé sur les réseaux pour l'interprétation de résultats de métabolomique Clément Frainay Médecine humaine et pathologie. Université Paul Sabatier - Toulouse III, 2017. Français. ⟨NNT : 2017TOU30297⟩ Theses tel-01988413v1

Clément Frainay

Presentation

Publications

A strategy to detect metabolic changes induced by exposure to chemicals from large sets of condition-specific metabolic models computed with enumeration techniques

Genome scale metabolic network modelling for metabolic profile predictions

Suggesting disease associations for overlooked metabolites using literature from metabolic neighbors

Networks and Graphs Discovery in Metabolomics Data Analysis and Interpretation

Avoiding the Misuse of Pathway Analysis Tools in Environmental Metabolomics

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

Atopic dermatitis or eczema? Consequences of ambiguity in disease name for biomedical literature mining

Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis

Large-Scale Modeling Approach Reveals Functional Metabolic Shifts during Hepatic Differentiation

MetaboRank: network-based recommendation system to interpret and enrich metabolomics results

Targeted versus untargeted omics — the CAFSA story

Integrated transcriptomics and metabolomics reveal signatures of lipid metabolism dysregulation in HepaRG liver cells exposed to PCB 126

Machine learning to identify pairwise interactions between specific IgE antibodies and their association with asthma: A cross-sectional analysis within a population-based birth cohort

Classification of pediatric asthma: from phenotype discovery to clinical practice

Mind the gap: mapping mass spectral databases in genome-scale metabolic networks reveals poorly covered Areas

MetExplore: collaborative edition and exploration of metabolic networks

MetExploreViz: web component for interactive metabolic network visualization

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

A computational solution to automatically map metabolite libraries in the context of genome scale metabolic networks

Hypoxia induces VEGF-C expression in metastatic tumor cells via a HIF-1α-independent translation-mediated mechanism

Plant genome-scale metabolic networks

Genome-scale metabolic networks

A strategy to detect metabolic changes induced by exposure to chemicals from large sets of condition-specific metabolic models computed with enumeration techniques

Suggesting disease associations for overlooked metabolites using literature from metabolic neighbours

Pathway analysis in metabolomics: pitfalls and best practice for the use of over-representation analysis

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

Système de recommandation basé sur les réseaux pour l'interprétation de résultats de métabolomique