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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

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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September 2024 -- New team member -- Coralie Muller starts her PhD in the team, supervised by Sylvain Prigent (INRAE BFP) and myself.
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July 2024 -- New project -- H2Rumen, a project led by Rafael Muñoz-Tamayo (INRAE MoSAR) has been funded by ANR. More info.
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Latest publications

  1. 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/10.1101/2024.09.26.615309
  2. Maxime 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.2024.02.014
  3. Klara 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
  4. Clémence 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.2023.05.024
  5. Arnaud 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.277056.122
  6. Clémence 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