Research projects

VITAE

I participate (WP1 co-lead with Corinne Vacher) to the VITAE project (PI: F.Delmotte) from the PPR CPA focusing on grapevine cultivation without pesticides. We specifically focus in WP1 on microbial biocontrol of powdery mildew with culturomics, synthetic community design and modelling approaches.

1. Fournier et al. (2022). The Functional Microbiome of Grapevine throughout Plant Evolutionary History and Lifetime . In Advances in Ecological Research. 10.1016/bs.aecr.2022.09.001

Pherosensor

I collaborate (WP3 lead) to the Pherosensor project (PI: P.Lucas) from the PPR CPA focusing on detecting insect pests with pheromones. In WP3, we work on data-assimilation and PDE inverse problem to build pest risk maps from pheromone sensor signals.

1. Malou et al. (2024). Biology-Informed inverse problems for insect pests detection using pheromone sensors https://hal.inrae.fr/hal-04572831
2. Malou et al. (2024). Pherosensor-toolbox: a Python package for Biology-Informed Data Assimilation . In Journal of Open Source Software. 10.21105/joss.06863 https://hal.inrae.fr/hal-04669546

Mistic

I belong (WP2 co-lead with V.Baldazzi) to the Mistic project (PI: D.Sherman and P.Abbad) from the PEPR Agroecology and ICT, dedicated to developping computational models of crop plant microbial biodiversity. In WP2, we develop digital twins of plant microbial communities and plant holobiont.

1. Cerk et al. (2024). Community-scale Models of Microbiomes: Articulating Metabolic Modelling and Metagenome Sequencing . In Microbial Biotechnology. 10.1111/1751-7915.14396
2. Lecomte et al. (2024). Revealing the Dynamics and Mechanisms of Bacterial Interactions in Cheese Production with Metabolic Modelling . In Metabolic Engineering. 10.1016/j.ymben.2024.02.014

Holovini

I participate (WP4 co-lead with A.L.Abraham) the the Holovini project (PI: I.Masneuf-Pomarede, J.L.Legras), a flagship project of the INRAE Holoflux metaprogram, dedicated to screening microbial fluxes in vineyards. We specifically focus in WP4 on scientific animation related to omics data analysis methods.

Arte-mis

Digital twins may have a strong potential in microbiology. In Arte-Mis, a project I lead, we work on overcoming methodological barriers to the creation of digital twins in microbial ecology. Arte-mis is funded by the INRAE Digit-bio metaprogram

Slimmest

Slimmest project, co-leaded with C.Frioux and funded by an Inria exploratory action, aims to solve computational issues raised when using metabolic models in system dynamics models of microbial community. Slimmest proposes to couple logical approximation and surrogate models to accelerate computations.

1. Frioux et al. (2023). Modéliser Les Communautés Bactériennes Pour Mieux Comprendre Leur Fonctionnement. https://hal.inrae.fr/hal-04120888
2. Frioux et al. (2023). Accelerating Metabolic Models Evaluation with Statistical Metamodels: Application to Salmonella Infection Models . In ESAIM: Proceedings and Surveys. 10.1051/proc/202373187