Clément Frainay

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Publications

Image document

Genome scale metabolic network modelling for metabolic profile predictions

Juliette Cooke , Maxime Delmas , Cecilia Wieder , Pablo Rodríguez Mier , Clément Frainay et al.
PLoS Computational Biology, 2024, 20 (2), pp.e1011381. ⟨10.1371/journal.pcbi.1011381⟩
Article dans une revue hal-04596969 v1
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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 et al.
BMC Bioinformatics, 2024, 25 (1), pp.234. ⟨10.1186/s12859-024-05845-z⟩
Article dans une revue hal-04652792 v1
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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 et al.
GigaScience, 2023, 12, pp.giad065. ⟨10.1093/gigascience/giad065⟩
Article dans une revue hal-04223426 v1
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Networks and Graphs Discovery in Metabolomics Data Analysis and Interpretation

Adam Amara , Clément Frainay , Fabien Jourdan , Thomas Naake , Steffen Neumann et al.
Frontiers in Molecular Biosciences, 2022, 9, ⟨10.3389/fmolb.2022.841373⟩
Article dans une revue hal-03636716 v1
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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 et al.
Environmental Science and Technology, In press, ⟨10.1021/acs.est.2c05588⟩
Article dans une revue hal-03799270 v1
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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 et al.
Bioinformatics, 2021, 37 (21), pp.3896-3904. ⟨10.1093/bioinformatics/btab627⟩
Article dans une revue hal-03361495 v2
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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⟩
Article dans une revue hal-03311466 v1
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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 et al.
PLoS Computational Biology, 2021, 17 (9), ⟨10.1371/journal.pcbi.1009105⟩
Article dans une revue hal-03344682 v1
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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 et al.
Journal of Proteome Research, 2019, 18 (1), pp.204-216. ⟨10.1021/acs.jproteome.8b00524⟩
Article dans une revue hal-01937261 v1
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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 et al.
Bioinformatics, 2019, 35 (2), pp.274-283. ⟨10.1093/bioinformatics/bty577⟩
Article dans une revue hal-02627792 v1
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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⟩
Article dans une revue hal-02626228 v1
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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 et al.
Archives of Toxicology, 2018, 92 (8), pp.2533-2547. ⟨10.1007/s00204-018-2235-7⟩
Article dans une revue hal-02621552 v1
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MetExplore: collaborative edition and exploration of metabolic networks

Ludovic Cottret , Clément Frainay , Maxime Chazalviel , Floréal Cabanettes , Yoann Gloaguen et al.
Nucleic Acids Research, 2018, 46 (W1), 8 p. ⟨10.1093/nar/gky301⟩
Article dans une revue hal-01886470 v1
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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 et al.
Metabolites, 2018, 8 (3), ⟨10.3390/metabo8030051⟩
Article dans une revue hal-02627086 v1
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MetExploreViz: web component for interactive metabolic network visualization

Maxime Chazalviel , Clément Frainay , Nathalie Poupin , Florence Vinson , Benjamin Merlet et al.
Bioinformatics, 2018, 34 (2), pp.312-313. ⟨10.1093/bioinformatics/btx588⟩
Article dans une revue hal-02621786 v1
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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⟩
Article dans une revue hal-02626193 v1
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Targeted versus untargeted omics — the CAFSA story

Maria del Mar Amador , Benoit Colsch , Foudil Lamari , Claude Jardel , Farid Ichou et al.
Journal of Inherited Metabolic Disease, 2018, 41 (3), pp.1-10. ⟨10.1007/s10545-017-0134-3⟩
Article dans une revue hal-01777969 v1

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⟩
Article dans une revue hal-01608721 v1
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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 et al.
Frontiers in Molecular Biosciences, 2016, 3, ⟨10.3389/fmolb.2016.00002⟩
Article dans une revue hal-02631089 v1
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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 et al.
Cell Reports, 2014, 6 (1), pp.155-167. ⟨10.1016/j.celrep.2013.12.011⟩
Article dans une revue hal-02631811 v1

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⟩
Chapitre d'ouvrage hal-03149497 v1

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⟩
Chapitre d'ouvrage hal-02786295 v1