Chabname Ghassemi Nedjad
Combinatorial problem solving for the detection of seeds in metabolic networks (Univ. Bordeaux). co-director (50%) with L. Paulevé (CNRS, LaBRI)
2023 - 2026
Nicolas Maurice
Metagenomic assembly in complex microbial communities (PEPR Mistic, Inria, INRAE). Co-supervisor (33%) with R. Vicedomini (CNRS, IRISA-Inria Rennes) and C. Lemaitre (Inria Rennes)
2024 - 2027
Coralie Muller
Generation of metabolomic informed models of metabolisms in mcirobial communities (PEPR Mistic, Inria, INRAE). co-director (50%) with S. Prigent (INRAE BFP)
2024 - 2027
Mathilde Sola
Characterization of "gut microbiome-diet-health" relationships in humans through combined approaches of computational microbial ecology, metabolic modeling, and AI (INRAE-Inria). Co-supervisor (35%) with M. Berland (INRAE MGPS) and P. Veiga (INRAE MGPS)
Engineers
2022 - 2024
Léonard Brindel
Visualisation of metabolic potential screening in microbial communities Inria ADT engineer
Interns
2024 - 2025
Juliette Audemard
Master 2 (apprenticeship) Bio-informatique, Univ. Paris Cité Metabolic modelling of cyanobacteria and their heterotrophic bacterial communities in the context of freshwater blooms (INRAE HOLOFLUX project led by Binta Diémé & Nicolas Creusot).
Past supervising
PhD students
2020 - 2024
Maxime Lecomte
Hybrid approach for explainable metabolic modelling of microbial ecosystems (HAL) (Inria-INRAE) co-supervisor (50%), co-supervised by H. Falentin (INRAE STLO) and D. Sherman (Inria)
Ariane Badoual
Inria ADT engineer Metagenomic data treatment
Interns
2024
Juliette Audemard
Master 1 (4 months) Bio-informatique, Univ. Paris Cité Metabolic modelling of the phycosphere (INRAE HOLOFLUX project led by B. Diémé & N. Creusot).
Nicolas Maurice
Master 2 (6 months) Bio-informatique, Univ. de Bordeaux. Co-supervised with C. Lemaitre (Inria) Metagenomic assembly in complex ecosystems
2022
Léonard Brindel
Master 2 (6 months) Bio-informatique, Univ. de Bordeaux. Co-supervised with F. Salin (INRAE) Metagenomic data analysis
2022
Chabname Ghassemi Nedjad
Master 2 (6 months) Bio-informatique, Univ. Paris Cité Metabolic modelling for large metagenomic studies
2021
Mathieu Bolteau
Master 2 (6 months) Bio-informatique, Univ. de Bordeaux Reverse ecology of microbial communities
2020
Maxime Lecomte
Master 2 (6 months) Bio-informatique, Univ. de Bordeaux. Co-supervised with S. Labarthe (INRAE) Metabolic modelling of a cheese bacterial community
2020
Ariane Badoual
Master 2 (6 months) Bio-Informatique et Génomique, Univ. de Rennes 1 Modelling competition in microbial communities
2019
Margot Wagner
Master 2 (6 months) Modélisation en écologie, Univ. de Rennes 1 Analysis of brown algae and microbiota's physiological response to varying growth conditions.
2018
Enora Fremy
Master 2 (6 months) Bio-Informatique et Génomique, Univ. de Rennes 1 In silico prediction of brown-algal bacterial interactions
2017
Claire Lippold
Master 1 (3 months) Bio-Informatique et Génomique, Univ. de Rennes 1. Co-supervised with C. Trottier (Univ. Nantes) Exploration and characterization of the microbiome associated to Ectocarpus subulatus str. BFT
Collective responsabilities
Scientific
2025
Co-head of the organisation committee of the French Conference of Bioinformatics JOBIM
2024
Proceedings Program Committee of International Conference on Intelligent Systems for Molecular Biology
2022
Co-organisation of a mini-symposium during the annual French bioinformatics conference (2022)
2021-2022
International Conference on Computational Methods in Systems Biology (CMSB) - steering committee (2021), programme committee (2021, 2022)
Institutional
2023-..
Member of the Commission des Emplois de Recherche of Inria Bordeaux, a committee that assesses the scientific quality of researchers’ applications prior their recruitment
2023-..
Member of the national committee for gender equality and inclusion at Inria
2022-..
Member and co-founder of a local committee for gender equality, diversity and in- clusion at Inria Bordeaux
2020-2022
Member of the Inria Bordeaux local committee for sustainable development
PhD jury
Jury member
2024
Mathieu Bolteau
Nantes Univ.
2023
Clémence Jospeh
KU Leuven (Belgium)
2023
Marie Burel
Univ. Paris-Saclay
2022
Déborah Boyenval
Univ. Côte d'Azur
2022
Antoine Régimbeau
Nantes Univ.
Scientific dissemination
Scientific communication
2024
Exploration of microbial ecosystems - from compositional patterns to metabolic models
Keynote speaker, JOBIM Toulouse, France Talk
2023
Exploration of microbial ecosystems, from compositional patterns to metabolic models
Invited seminar, Plant Health Institute, Montpellier, France Talk
2023
Exploration of microbial ecosystems, from compositional patterns to metabolic models
Invited seminar, KU Leuven, Belgium Talk
2022
Logic modelling of metabolism - from individual networks to communities
Bordeaux Bioinformatics Center seminar, France Talk
2021
Logic modelling of metabolism - from individual networks to communities
French workshop on Metabolic Modelling, Bordeaux, France Talk
2021
Metabolic complementarity applied to the screening of microbiota and the identification of key species
Computational Methods in Systems Biology 2021, Bordeaux, France Talk
2021
Metabolic complementarity applied to the screening of microbiota and the identification of key species
Metabolic Pathway Analysis 2021 (virtual) Talk
2020
Metabolic complementarity applied to the screening of microbiota and the identification of key species
JOBIM Conference (virtual), France Talk
2020
Gap-filling metabolism in systems biology and microbial systems ecology
BioNum Seminar — LaBRI, February 2020, Bordeaux, France Talk
2019
Investigating host-microbiota cooperation with gap-filling optimization problems
Invited seminar Quadram Institute of Biosciences , May 2019, Norwich, UK Talk
Investigating host-microbiota cooperation with gap-filling optimization problems
Invited research team seminar Bioinformatics research group, LRI , November 2018, Orsay, France Talk
Scalable and exhaustive screening of metabolic functions in microbiotas
Invited research team seminar UMR Nutriomics, ICAN , October 2018, Paris, France Talk
2018
Scalable and exhaustive screening of metabolic functions carried out by microbial consortia Journées scientifiques de Nantes 2018, June 2018, Nantes, France Talk
2018
Combinatorial approaches for interactions prediction and community selection in holobionts. Gen2Bio 2018, March 2018, Rennes, France Poster
Topology to elucidate the respective roles of species in a symbiotic community International Conference on Holobionts, April 19th-21st 2017, Paris Poster
Combinatorial gap-filling for genome-scale metabolic networks using taxonomy and pathway information
École Jeunes Chercheurs CNRS – 3ème École thématique de modélisation formelle des réseaux de régulation biologique Bioregul, June 6th-10th, Porquerolles Poster