PhD | Computer Science — Computational biology
Junior researcher
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
November 2024 -- Conference organisation -- Simon Labarthe from Pleiade, other colleagues from Bordeaux and myself oganise the JOBIM 2025 Conference, the French national conference on Bioinformatics.
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November 2024 -- New team member -- Juliette Audemard is coming back to the team for her master's project.
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September 2024 -- Publication -- New preprint - Seed inference in metabolic networks with Seed2LP, on BioRxiv.
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September 2024 -- Publication -- Mathilde Sola starts her INRAE-Inria PhD, hosted in INRAE Metagenopolis lab, supervised by Magali Berland, Patrick Veiga and myself.
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Latest publications
- Chabname Ghassemi-Nedjad, Mathieu Bolteau, Lucas Bourneuf, Loic Pauleve, and Clemence Frioux. Seed2LP: seed inference in metabolic networks for reverse ecology applications. bioRxiv, 2024. http://doi.org/10.1101/2024.09.26.615309Maxime 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/10.1111/1751-7915.14396Clémence Frioux, Rebecca Ansorge, Ezgi Özkurt, Chabname Ghassemi Nedjad, Joachim Fritscher, Christopher Quince, Sebastian M. Waszak, and Falk Hildebrand. Enterosignatures define common bacterial guilds in the human gut microbiome. Cell Host & Microbe, 2023. http://doi.org/10.1016/j.chom.2023.05.024Arnaud Belcour, Jeanne Got, Méziane Aite, Ludovic Delage, Jonas Collén, Clémence Frioux, Catherine Leblanc, Simon M Dittami, Samuel Blanquart, Gabriel V Markov, and Anne Siegel. Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe. Genome Research, 2023. http://doi.org/10.1101/gr.277056.122Clémence Frioux, Sylvie Huet, Simon Labarthe, Julien Martinelli, Thibault Malou, David Sherman, Marie-Luce Taupin, and Pablo Ugalde-Salas. Accelerating metabolic models evaluation with statistical metamodels: application to Salmonella infection models. In: ESAIM: Proceedings and Surveys, pp. 187–217 2023. http://doi.org/10.1051/proc/202373187