research

Funded research projects, past and current

Ongoing Projects

  • 2023–2027
    DISCERN

    Discovering the causes of three poorly understood cancers in Europe

    Horizon Europe · 20 partners · Team leader, €250,000 for MIA Paris-Saclay

    DISCERN investigates the causes of three poorly understood cancers (renal, pancreatic, colorectal) and the geographical disparities in their incidence across Europe, notably the higher rates observed in Central and Eastern Europe. The 20-institution consortium, coordinated by IARC, combines epidemiological, exposomic and multi-omics approaches within the Horizon Europe Mission on Cancer. I co-lead the methodological work package with Imperial College.

  • 2024–2027
    CoBreeding

    PEPR Agroécologie Numérique · GQE Le Moulon, HeuDiaSyC (UTC)

    CoBreeding develops statistical and deep learning methods to predict the performance of maize hybrids from pools of parental lines, combining mixed models from quantitative genetics with neural network architectures, and transferring information between US and European maize line populations. Funds the PhD of François Victor.

  • 2024–2027
    HEPATOTWIN

    INRAE Metaprogramme DIGIT-BIO · INRAE (Toxalim, MIA-PS, NumeCan, UNH, TBI)

    HEPATOTWIN gathers INRAE units in toxicology, applied mathematics and nutrition to develop modelling approaches for liver toxicology.

Past Projects

  • 2020–2025
    EXPANSE

    EXposome Powered tools for healthy living in urbAN SEttings

    Horizon H2020 · Imperial College, Utrecht, Columbia, Inserm, IARC + 15 others

    EXPANSE studies how the urban exposome -- environmental exposures specific to city living -- affects cardiometabolic and pulmonary disease, Europe's leading disease burden. It combines exposome and health data from over 55 million Europeans, multi-omics data from 2 million individuals, and personalized exposure assessment for 5,000 participants across five urban regions.

  • 2020–2024
    G2WAS

    Grape Genes for WAter Scarcity

    ANR · MIA Paris-Saclay, AGAP, LEPSE (INRAE) · Team leader, €60,000 for MIA-Paris

    G2WAS aims to identify the genetic regulators of grapevine adaptation to water deficit through genome-wide association studies (GWAS), to support the breeding of drought-tolerant varieties in the context of climate change.

  • 2019–2024
    SingleStatOmics

    ANR · University of Lyon 1, Mines ParisTech, ENS Lyon, AgroParisTech/INRA · 12 months, co-PI and team leader, €210,000 for MIA-Paris

    SingleStatOmics develops statistical and machine learning methods for single-cell genomics, to study cell identity, cell differentiation dynamics, gene regulation and single-cell epigenomics, combining expertise in statistics, machine learning and optimal transport.

  • 2023–2024
    Behind the Count'her

    Estimating genetic parameters for high-dimensional count data with the Poisson-lognormal model

    INRAE Metaprogramme DIGIT-BIO · INRAE (GenPhyse, MIA-PS, MaIAGE), Sorbonne U

  • 2019–2023
    EcoNet

    Advanced statistical modelling of ecological networks

    ANR · Sorbonne, Lyon 1 and Lille Universities, AgroParisTech/INRAE, ISEM, IEES

    EcoNet develops statistical methods for the analysis of ecological networks (trophic, mutualistic, competitive, host-parasite), integrating space and time, multiple interaction types, covariate information and sampling effects, to predict how ecosystems respond to environmental change.

  • 2022–2023
    PEERSIM

    Characterizing multiple stress in plants

    INRAE Metaprogramme DIGIT-BIO · INRAE (IPS2, MIA-PS, MIAT), IMT

  • 2022–2023
    GENIALEARN

    Merits and limits of statistical and deep learning for multi-trait genomic selection

    INRAE Metaprogramme DIGIT-BIO · INRAE (GABI, MIA-PS), UEVE

  • 2022–2023
    BovMovie2Pred

    Early bovine development and viability: exploration and prediction

    INRAE Metaprogramme DIGIT-BIO · INRAE (MaIAGE, MIA-PS, BREED)

  • 2018–2022
    Next-Gen. Biomonitoring

    Biomonitoring of change in ecosystem structure and function

    ANR · AgroParisTech, INRAE (Dijon, Bordeaux, Rennes, Réunion), Imperial College, Cirad

    Next Generation Biomonitoring combines high-throughput sequencing with statistical network reconstruction to detect ecosystem change across six ecosystems (microbial to macro-invertebrate), covering drivers such as invasion, disease, conservation and climate change.

  • 2018–2019
    KineTicks

    Network and modelling analyses to describe the dynamics of Ixodes ricinus microbiome and its influence on pathogen evolution

    INRA Metaprogramme MEM · INRAE (BIPAR, MaIAGE, MIAP)

  • 2017–2019
    SEARS

    Sampling strategies and network analysis of seed exchange networks

    Metaprogramme GloFoods · Led by Mathieu Thomas, CR Cirad, AGAP · 1 month

  • 2016–2018
    BrassicaDiv-Patho

    Microbial diversity and microbial networks associated to Brassica napus and its pathogens

    INRA Metaprogramme MEM · Led by Christophe Mougel (DR INRA, Rennes), Thierry Candresse (DR INRA, Bordeaux) · UMR IGEPP, UMR BFP, UMR BioGeCo, UMR EPGV, UMR BioGer

  • 2016–2018
    LIONS

    Large-scale Integrative approach to unravel the complex relationships between differentiatiON and tumorigenesiS

    Plan Cancer 2015 Inserm · IGMM/IBC, MAP5, iSSB Évry, Institut Curie, University of York

  • 2016–2018
    LearnBioControl

    Learning ecological networks from metabarcoding data: application to biological control

    INRA Metaprogramme MEM · INRA/UMR BioGeCo, Imperial College, AgroParisTech/INRA

  • 2015–2018
    Hydrogen

    Comparative Metagenomic for Measuring Biodiversity

    ANR · AgroParisTech/INRA, CEA-CNS-LABIS, INRIA Rennes/Genscale

  • 2012–2016
    ABS4NGS

    Algorithmic, Bioinformatic and Software solutions for the analysis of Next Generation Sequencing data

    Investissement d'avenir · Institut Curie, Mines ParisTech, University of Lyon 1, AgroParisTech/INRA

  • 2014–2016
    AREA

    Analysis of the evolutionary response of tropical forest trees to their environment: genomic and metabolomic approach

    CNRS Défi "Enviromics" · AgroParisTech/INRA, UMR EcoFoG, UMR 8638 (CNRS/P5)

  • 2015–2016
    BeFast

    Deriving Better learning procedures from FASTer algorithms to deal with a huge amount of Data

    PEPS CNRS Fascido · Led by Alain Célisse, MCF, University Lille 1

  • 2013–2015
    Reg4Sel

    Regularized methods for Genomic Selection

    SelGen / INRAE · Led by Tristan Mary-Huard, CR INRA/AgroParisTech · UMR MIAP, UMR Le Moulon, GABI

  • 2011–2015
    Ploid-Ploid wheat

    Unraveling bases of polyploidy and aneuploidy responses in flowering plants, using the wheat ploidy model

    ANR · INRA (Rennes, Versailles, Grignon), Génoscope, CNRS

  • 2013–2014
    ENORM

    Enumeration of Near-Optimal Regulation Misbehaviours

    PEPS CNRS · Led by Étienne Birmelé, PR University Paris 5

  • 2009–2011
    NeMo

    Network Motif in Biological Network

    ANR · AgroParisTech/INRA, University of Lyon 1, University of Évry

  • 2005–2008
    GD2GS

    From Genomic Data to Graph Structure

    ANR · Led by Florence d'Alché-Buc, PR Évry