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
December 2025 -- News -- Chabname Ghassemi Nedjad has defended her PhD entitled "Modelling and solving combinatorial optimisation problems for reverse ecology" on December 11th, 2025. Congratulations to her!
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December 2025 -- Publication -- The work of Mathilde Sola et al, "Modeling the emergent metabolic potential of soil microbiomes in Atacama landscapes" has been published as a preprint Read more.
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November 2025 -- Publication -- The work of Constanza Andreani et al, "Modeling the emergent metabolic potential of soil microbiomes in Atacama landscapes" has been published in Environmental Microbiome Read more.
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November 2025 -- New team member -- Pritam Kundu joined the team as a postdoctoral researcher. He is hired to work on the ANR funded project H2Rumen Read more.
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Latest publications
- Mathilde 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/10.1101/2025.09.12.675765Constanza 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.Constanza 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. bioRxiv, 2024. http://doi.org/10.1101/2024.12.23.630026Maxime Lecomte, Wenfan Cao, Julie Aubert, David James Sherman, Hélène Falentin, Clémence Frioux, and Simon Labarthe. Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling. Metabolic Engineering, 2024. http://doi.org/10.1016/j.ymben.2024.02.014Klara Cerk, Pablo Ugalde‐Salas, Chabname Ghassemi Nedjad, Maxime Lecomte, Coralie Muller, David J. Sherman, Falk Hildebrand, Simon Labarthe, and Clémence Frioux. Community‐scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing. Microbial Biotechnology, 17(1) :e14396, 2024. http://doi.org/10.1111/1751-7915.14396