Supervising

Current supervising

PhD students

2022 - 2025

Chabname Ghassemi Nedjad
Combinatorial problem solving for the detection of seeds in metabolic networks (Univ. Bordeaux).
co-director (50%) with Loïc Paulevé (CNRS, LaBRI)

2023 - 2026

Nicolas Maurice
Metagenomic assembly in complex microbial communities (PEPR Mistic, Inria, INRAE).
Co-supervisor (33%) with Riccardo Vicedomini (CNRS, IRISA-Inria Rennes) and Claire 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 Sylvain 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 Magali Berland (INRAE MGPS) and Patrick Veiga (INRAE MICALIS)

Engineers

2023 - 2025

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).

2025

Killian Duguépéroux
Bachelor (7 weeks) Computer science, ENS LYon
Dimensionality reduction of microbiome data. Co-supervised with Guilhem Sommeria-Klein.

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 Hélène Falentin (INRAE STLO) and David Sherman (Inria)

Engineers

2022 - 2024

Coralie Muller
Inria exploratory action Slimmest
Spatio-temporal modelling of microbial communities

2020 - 2022

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 Binta Diémé & Nicolas Creusot).

2024

Juliette Gronier
Bachelor (6 weeks) Computer science, ENS LYon
Numerical metabolic modelling of microbial communities

2023

Nicolas Maurice
Master 2 (6 months) Bio-informatique, Univ. de Bordeaux. Co-supervised with Claire Lemaitre (Inria)
Metagenomic assembly in complex ecosystems

2022

Léonard Brindel
Master 2 (6 months) Bio-informatique, Univ. de Bordeaux. Co-supervised with Franck 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 Simon 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 Camille Trottier (Univ. Nantes)
Exploration and characterization of the microbiome associated to Ectocarpus subulatus str. BFT

Scientific dissemination

Selection of talks in (relatively) recent selective conferences

This list also contains talks presented by students, in which case their names are indicated.

2025

Seed inference in interacting microbial communities using combinatorial optimization
23rd International conference on Computational Methods in Systems Biology (CMSB 2025) -- Lyon, France
Talk by Chabname Ghassemi Nedjad

2025

Metagenome-scale metabolic modelling for the characterization of cross-feeding interactions in freshwater cyanobacteria-associated microbial communities
JOBIM 2025 -- Bordeaux, France -- Best talk of the conference award
Talk by Juliette Audemard

2024

Assessing assembly quality in metagenomes of increasing complexity sequenced with HiFi long reads
Genome Informatics 2024 -- Hinxton, United Kingdom
Talk by Nicolas Maurice (HAL)

2023

Modelling the dynamics of Salmonella infection in the gut at the bacterial and host levels
7th International Symposium on Systems Biology of Microbial Infection -- Jena, Germany
Talk by Coralie Muller and Pablo Ugalde Salas (HAL)

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

2018

Scalable and exhaustive screening of metabolic functions carried out by microbial consortia
European Conference on Computational Biology, ECCB 2018 -- September 8th-12th 2018, Athens, Greece
Talk - Slides

Selection of (relatively) recent invited seminars and conferences

2025

Reasoning, statistical learning and numerical modelling for the characterization of microbial communities
IRISA DKM department -- Rennes, France
Seminar

2025

Exploration of microbial communities, from compositional patterns to metabolic models
Inria Chile -- Santiago, Chile
Seminar

2024

Exploration of microbial ecosystems - from compositional patterns to metabolic models
JOBIM 20024 -- Toulouse, France
Keynote

2023

Exploration of microbial ecosystems, from compositional patterns to metabolic models
Plant Health Institute, Montpellier, France
Seminar

2023

Exploration of microbial ecosystems, from compositional patterns to metabolic models
KU Leuven, Belgium
Seminar

2022

Logic modelling of metabolism - from individual networks to communities
Bordeaux Bioinformatics Center seminar, France
Seminar

2021

Logic modelling of metabolism - from individual networks to communities
French workshop on Metabolic Modelling, Bordeaux, France
Seminar

2021

Mathemetical and logic modelling in systems biology, applications to the metabolism of ecosystems
CEMRACS 2021, Marseille, France
Seminar

2020

Gap-filling metabolism in systems biology and microbial systems ecology
BioNum Seminar — LaBRI, February 2020, Bordeaux, France
Seminar

2019

Investigating host-microbiota cooperation with gap-filling optimization problems
Quadram Institute of Biosciences , May 2019, Norwich, UK
Seminar

2019

Investigating host-microbiota cooperation with gap-filling optimization problems
Institute of Quantitative and Theoretical Biology, HHU , January 2019, Düsseldorf, Germany
Seminar

2018

Investigating host-microbiota cooperation with gap-filling optimization problems
Bioinformatics research group, LRI , November 2018, Orsay, France
Seminar

2018

Scalable and exhaustive screening of metabolic functions in microbiotas
Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile , November 2018, Santiago, Chile
Seminar

2018

Scalable and exhaustive screening of metabolic functions in microbiotas
UMR Nutriomics, ICAN , October 2018, Paris, France
Seminar

Posters

This list is non-exhaustive and mostly refers to posters I presented myself. For a complete and recent list of posters that were presented by students or colleagues, please refer to HAL.

2018

Scalable and exhaustive screening of metabolic functions carried out by microbial consortia
XXIV Congreso Latinoamericano de Microbiologia, ALAM 2018, November 13th-16th 2018, Santiago, Chile
Poster

2018

Scalable and exhaustive screening of metabolic functions carried out by microbial consortia
European Conference on Computational Biology, ECCB 2018, September 8th-12th 2018, Athens, Greece
Poster - PDF

2018

Combinatorial approaches for interactions prediction and community selection in holobionts.
Gen2Bio 2018, March 2018, Rennes, France
Poster

2018

Combining size and exchange minimization enables scalable screening of microbial consortia
Applied Bioinformatics in Life Sciences ABLS 2018, March 8th-9th 2018, Leuven, Belgium
Poster

2017

Topology to elucidate the respective roles of species in a symbiotic community
International Conference on Holobionts, April 19th-21st 2017, Paris
Poster

2016

Combinatorial gap-filling for genome-scale metabolic networks using taxonomy and pathway information
École Jeunes Chercheurs et Jeunes Chercheuses CNRS – 3ème École thématique de modélisation formelle des réseaux de régulation biologique Bioregul, June 6th-10th, Porquerolles
Poster