Clément Frainay

26
Documents

Presentation

I'm a French computational biologist working on system biology and biological networks. I'm primarily interested in the study of metabolism, and I'm currently working at the INRAE's Toxalim lab on the impact of food contaminant exposure on this system. My research interests focus on solutions to overcome the information overload faced when reasoning on such large scale, leveraging network science, information filtering, information visualisation and knowledge modelling.

See my page on Scholia: https://scholia.toolforge.org/author/Q57243195

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Publications

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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⟩
Journal articles hal-04652792 v1
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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⟩
Journal articles hal-04596969 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⟩
Journal articles 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⟩
Journal articles 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⟩
Journal articles hal-03799270 v1
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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⟩
Journal articles hal-03311466 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⟩
Journal articles hal-03361495 v2
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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⟩
Journal articles 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⟩
Journal articles 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⟩
Journal articles 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⟩
Journal articles 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⟩
Journal articles 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⟩
Journal articles hal-01886470 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⟩
Journal articles 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⟩
Journal articles hal-02626193 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⟩
Journal articles hal-02627086 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⟩
Journal articles 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⟩
Journal articles 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⟩
Journal articles 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⟩
Journal articles 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⟩
Book sections 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⟩
Book sections hal-02786295 v1