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Dr Clément Frainay

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.

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Journal articles15 documents

  • Maxime Delmas, Olivier Filangi, Nils Paulhe, Florence Vinson, Christophe Duperier, et al.. FORUM: building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases. Bioinformatics, Oxford University Press (OUP), 2021, ⟨10.1093/bioinformatics/btab627⟩. ⟨hal-03361495⟩
  • Cecilia Wieder, Clément Frainay, Nathalie Poupin, Pablo Rodríguez-Mier, Florence Vinson, et al.. Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis. PLoS Computational Biology, Public Library of Science, 2021, 17 (9), ⟨10.1371/journal.pcbi.1009105⟩. ⟨hal-03344682⟩
  • Clément Frainay, Yoann Pitarch, Sarah Filippi, Marina Evangelou, Adnan Custovic. Atopic dermatitis or eczema? Consequences of ambiguity in disease name for biomedical literature mining. Clinical and Experimental Allergy, Wiley, 2021, 51 (9), pp.1185-1194. ⟨10.1111/cea.13981⟩. ⟨hal-03311466⟩
  • Nathalie Poupin, Anne Corlu, Nicolas J. Cabaton, Hélène Dubois-Pot-Schneider, Cécile Canlet, et al.. Large-Scale Modeling Approach Reveals Functional Metabolic Shifts during Hepatic Differentiation. Journal of Proteome Research, American Chemical Society, 2019, 18 (1), pp.204-216. ⟨10.1021/acs.jproteome.8b00524⟩. ⟨hal-01937261⟩
  • Clément Frainay, Sandrine Aros, Maxime Chazalviel, Thomas Garcia, Florence Vinson, et al.. MetaboRank: network-based recommendation system to interpret and enrich metabolomics results. Bioinformatics, Oxford University Press (OUP), 2019, 35 (2), pp.274-283. ⟨10.1093/bioinformatics/bty577⟩. ⟨hal-02627792⟩
  • Maria del Mar Amador, Benoit Colsch, Foudil Lamari, Claude Jardel, Farid Ichou, et al.. Targeted versus untargeted omics — the CAFSA story. Journal of Inherited Metabolic Disease, Springer Verlag, 2018, 41 (3), pp.1-10. ⟨10.1007/s10545-017-0134-3⟩. ⟨hal-01777969⟩
  • Robin Mesnage, Martina Biserni, Sucharitha Balu, Clément Frainay, Nathalie Poupin, et al.. Integrated transcriptomics and metabolomics reveal signatures of lipid metabolism dysregulation in HepaRG liver cells exposed to PCB 126. Archives of Toxicology, Springer Verlag, 2018, 92 (8), pp.2533-2547. ⟨10.1007/s00204-018-2235-7⟩. ⟨hal-02621552⟩
  • Maxime Chazalviel, Clément Frainay, Nathalie Poupin, Florence Vinson, Benjamin Merlet, et al.. MetExploreViz: web component for interactive metabolic network visualization. Bioinformatics, Oxford University Press (OUP), 2018, 34 (2), pp.312-313. ⟨10.1093/bioinformatics/btx588⟩. ⟨hal-02621786⟩
  • Ludovic Cottret, Clément Frainay, Maxime Chazalviel, Floréal Cabanettes, Yoann Gloaguen, et al.. MetExplore: collaborative edition and exploration of metabolic networks. Nucleic Acids Research, Oxford University Press, 2018, 46 (W1), 8 p. ⟨10.1093/nar/gky301⟩. ⟨hal-01886470⟩
  • Sara Fontanella, Clément Frainay, Clare S. Murray, Angela Simpson, Adnan Custovic. 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. PLoS Medicine, Public Library of Science, 2018, 15 (11), 22 p. ⟨10.1371/journal.pmed.1002691⟩. ⟨hal-02626228⟩
  • Ceyda Oksel, Sadia Haider, Sara Fontanella, Clément Frainay, Adnan Custovic. Classification of pediatric asthma: from phenotype discovery to clinical practice. Frontiers in Pediatrics, Frontiers, 2018, 6, ⟨10.3389/fped.2018.00258⟩. ⟨hal-02626193⟩
  • Clément Frainay, Emma L. Schymanski, Steffen Neumann, Benjamin Merlet, Reza Mohammadi Salek, et al.. Mind the gap: mapping mass spectral databases in genome-scale metabolic networks reveals poorly covered Areas. Metabolites, MDPI, 2018, 8 (3), ⟨10.3390/metabo8030051⟩. ⟨hal-02627086⟩
  • Clément Frainay, Fabien Jourdan. Computational methods to identify metabolic sub-networks based on metabolomic profiles. Briefings in Bioinformatics, Oxford University Press (OUP), 2017, 18 (1), pp.43-56. ⟨10.1093/bib/bbv115⟩. ⟨hal-01608721⟩
  • Benjamin Merlet, Nils Paulhe, Florence Vinson, Clément Frainay, Maxime Chazalviel, et al.. A computational solution to automatically map metabolite libraries in the context of genome scale metabolic networks. Frontiers in Molecular Biosciences, Frontiers Media, 2016, 3, ⟨10.3389/fmolb.2016.00002⟩. ⟨hal-02631089⟩
  • Florent Morfoisse, Anna Kuchnio, Clément Frainay, Anne Gomez-Brouchet, Marie-Bernadette Delisle, et al.. Hypoxia induces VEGF-C expression in metastatic tumor cells via a HIF-1α-independent translation-mediated mechanism. Cell Reports, Elsevier Inc, 2014, 6 (1), pp.155-167. ⟨10.1016/j.celrep.2013.12.011⟩. ⟨hal-02631811⟩

Book sections2 documents

  • Léo Gerlin, Clément Frainay, Fabien Jourdan, Caroline Baroukh, Sylvain Prigent. Chapter Eight - Plant genome-scale metabolic networks. Science Direct. Plant Metabolomics in full swing, 98, 2021, Advances in Botanical Research, ⟨10.1016/bs.abr.2020.09.021⟩. ⟨hal-03149497⟩
  • Clément Frainay, Fabien Jourdan. Genome-scale metabolic networks. Metabolomics: Practical Guide to Design and Analysis, Chapman and Hall, 290 p., 2019, 9781315370583. ⟨10.1201/9781315370583-8⟩. ⟨hal-02786295⟩

Preprints, Working Papers, ...1 document

  • Maxime Delmas, Olivier Filangi, Nils Paulhe, Florence Vinson, Christophe Duperier, et al.. FORUM: Building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases. 2021. ⟨hal-03318295⟩

Theses1 document

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