PhD | Computer Science — Computational biology
Research scientist
Inria Bordeaux - France
Research interests
Systems biology, Computational biology
Microbial communities, Metabolic modelling
Machine learning, Machine reasoning
Answer Set Programming, Symbolic AI
Gut microbiome, Agroecology, Marine biology
Latest news
June 2026 -- Publication -- New preprint - "Hydrogen metabolism shapes gut microbiome into health-associated configurations", from the PhD of Mathilde Sola. Read more on BioRxiv.
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May 2026 -- Publication -- New preprint - From Concept to Perspective, Digital Twins of Microbial Systems. Read more on HAL.
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April 2026 -- New team member -- Niels Roudeau joins the team as an intern, working on dimensionality reduction techniques using machine learning.
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February 2026 -- New team member -- Sarah Toubal joins the team as an intern, working on the Le French Gut project. She is hosted at INRAE MetaGenoPolis lab, in Jouy-en-Josas.
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Latest publications
- Juliette Audemard, Nicolas Creusot, Julie Leloup, Charlotte Duval, Sébastien Halary, Lou Mary, Mélissa Eon, Thomas Forjonel, Mohamed Mouffok, Rémy Puppo, Elodie Belmonte, Véronique Gautier, Jeanne Got, Marie Lefebvre, Gabriel V Markov, Coralie Muller, Benjamin Marie, Binta Diémé, and Clémence Frioux. Integrating metagenome-scale metabolic modelling and metabolomics to identify biochemical interactions in Microcystis phycospheres. BioRxiv, 2026. http://doi.org/10.64898/2026.03.18.712574Olivia Bulka, Chabname Ghassemi Nedjad, Loïc Paulevé, Sylvain Prigent, and Clémence Frioux. Prediction of source nutrients for microorganisms using metabolic networks. arXiv, 2026. http://doi.org/10.48550/arxiv.2602.21993Coralie Muller, Juliette Audemard, Sylvain Prigent, and Clémence Frioux. MetaNetMap: automatic mapping of metabolomic data onto metabolic networks. BioRxiv, 2026. http://doi.org/10.64898/2026.01.05.697697Mathilde Sola, Anne Hiol, Giacomo Vitali, Sébastien Fromentin, Marine Gilles, Emmanuelle Le Chatelier, Christian Morabito, Florian Plaza Oñate, Nicolas Pons, Benoît Quinquis, Florence Thirion, Jordan Denis, Renaud Léonard, Corinne Cruaud, Patrick Wincker, Pedro H Oliveira, Le French Gut Consortium, Catherine Robbe Masselot, Mathieu Almeida, Hervé Blottière, Joël Doré, Dusko S Ehrlich, Robert Benamouzig, Clémence Frioux, Magali Berland, and Patrick Veiga. Hydrogen metabolism shapes gut microbiome into health-associated configurations. BioRxiv, 2026. http://doi.org/10.64898/2026.05.05.722951Simon Labarthe, Nicolas Creusot, Clémence Frioux, Guillaume Gautreau, Elie Desmond-Le Quéméner, Lorenzo Sala, Agustín G. Yabo, Paul Dou, Gabriel Capson-Tojo, Eric Dugat-Bony, Andrea Fernandez Diaz, Mathieu Mezache, Coralie Muller, Sthyve Junior Tatho Djeanou, Sahak Yeghiazaryan, Jérôme Harmand, Jean-Roch Mouret, Thibault Nidelet, Sylvain Prigent, Ludovic Cottret, Anne Goelzer, Isabelle Lesur Kupin, Lionel Rigottier-Gois, Franck Salin, Valentina Baldazzi, Céline Casenave, Hélène Falentin, Mahendra Mariadassou, Rafael Muñoz-Tamayo, Milka Popova, Alain Rapaport, David James Sherman, Jean-Philippe Steyer, and Corinne Vacher. From Concept to Perspective: Digital Twins of Microbial Systems. 2026.Ulysse Le Clanche, Melvin Selim Atay, Elise Bannier, Anaïs Baudot, Léa Bellenger, Alexandra Bodrug, Samuel Chaffron, Eric Charpentier, Erwan Corre, Clémence Frioux, Aurélie Lardenois, Frédéric Lemoine, Camille Maumet, Cyril Noël, Perrine Paul-Gilloteaux, Paul Simion, Morgane Térézol, Olivier Dameron, and Alban Gaignard. Ground-truth Construction and Evaluation of LLM Contribution to Life Sciences Tool Annotation. In: LLMs4KGOE, Workshop on LLM-driven Knowledge Graph and Ontology Engineering 2026. http://doi.org/TBDMathilde Sola, Adrien Paravel, Sandrine Auger, Jean-Marc Chatel, Florian Plaza Oñate, Emmanuelle Le Chatelier, Marion Leclerc, Patrick Veiga, Clémence Frioux, Mahendra Mariadassou, and Magali Berland. NeighborFinder: an R package inferring local microbial network around a species of interest. BioRxiv, 2025. http://doi.org/10.64898/2025.12.05.692507Arnaud Belcour, Pauline Hamon-Giraud, Alice Mataigne, Baptiste Ruiz, Yann Le Cunff, Jeanne Got, Lorraine Awhangbo, Mégane Lebreton, Clémence Frioux, Simon Dittami, Patrick Dabert, Anne Siegel, and Samuel Blanquart. Estimating consensus proteomes and metabolic functions from taxonomic affiliations. bioRxiv, :2022.03.16.484574, 2025. http://doi.org/10.1101/2022.03.16.484574Carole Belliardo, Nicolas Maurice, Arthur Pere, Samuel Mondy, Alain Franc, Marc Bailly-Bechet, Claire Lemaitre, Riccardo Vicedomini, Jean-Marc Frigerio, Pierre Abad, David Sherman, Elodie Belmonte, Franck Salin, Clémence Frioux*, and Etienne Danchin*. Accurate MAG reconstruction from complex soil microbiome through combined short- and HiFi long-reads metagenomics. BioRxiv, 2025. http://doi.org/10.1101/2025.09.12.675765Anthony Duncan, Wing Koon, Katarzyna Sidorczuk, Christopher Quince, Clémence Frioux, and Falk Hildebrand. Detecting signatures underlying the composition of biological data. Nucleic Acids Research, 53(22) :gkaf1388, 2025. http://doi.org/10.1093/nar/gkaf1388Constanza M. Andreani-Gerard, Natalia E. Jiménez, Ricardo Palma, Coralie Muller, Pauline Hamon-Giraud, Yann Le Cunff, Verónica Cambiazo, Mauricio González, Anne Siegel, Clémence Frioux*, and Alejandro Maass*. Modeling the emergent metabolic potential of soil microbiomes in Atacama landscapes. Environmental Microbiome, 20(1) :142, 2025. http://doi.org/10.1186/s40793-025-00749-8Nicolas Maurice, Claire Lemaitre, Riccardo Vicedomini, and Clémence Frioux. Mapler: A pipeline for assessing assembly quality in taxonomically rich metagenomes sequenced with HiFi reads. Bioinformatics, :btaf334, 2025. http://doi.org/10.1093/bioinformatics/btaf334Chabname Ghassemi Nedjad, Mathieu Bolteau, Lucas Bourneuf, Loïc Paulevé, and Clémence Frioux. Seed2LP: seed inference in metabolic networks for reverse ecology applications. Bioinformatics, :btaf140, 2025. http://doi.org/10.1093/bioinformatics/btaf140Chabname Ghassemi Nedjad, Sebastián Nelson Mendoza, Clémence Frioux, and Loïc Paulevé. Seed Inference in Interacting Microbial Communities Using Combinatorial Optimization. In: Computational Methods in Systems Biology, 23rd International Conference, CMSB 2025, Lyon, France, September 10–12, 2025, Proceedings, pp. 370–387, Springer, Cham, 2025. http://doi.org/10.1007/978-3-032-01436-8_20Clémence Frioux. HDR – Machine reasoning, dimensionality reduction and numerical modelling applied to the exploration of metabolism in microbial communities, Université de Bordeaux, September 2025.