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
September 2025 -- Publication -- New preprint - Accurate MAG reconstruction from complex soil microbiome through combined short- and HiFi long-reads metagenomics. Read more on BioRxiv.
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September 2025 -- Conference -- Chabname Ghassemi Nedjad will present her work entitled "Seed inference in interacting microbial communities using combinatorial optimization" at the CMSB 2025 international conference in Lyon, France.
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June 2025 -- New team member -- Killian Duguépéroux joins the team as an intern for 7 weeks. He is a Bachelor student in computer science at ENS Lyon and will be supervised by Guilhem Sommeria-Klein and I.
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June 2025 -- Publication -- A part of Nicolas Maurice's PhD work is now published in Bioinformatics - Mapler, A pipeline for assessing assembly quality in taxonomically rich metagenomes sequenced with HiFi reads. More info here.
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Latest publications
- Arnaud 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/10.1101/2025.09.12.675765Nicolas 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_20Constanza 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