Arnaud Belcour

Postdoctoral fellow at the Inria

INRIA Grenoble – Rhône-Alpes
655 avenue de l’Europe, Montbonnot
38334 Saint-Ismier cedex, France
Tel. +33 4 76 61 52 67
first.last@inria.fr
Secretary: Diane Courtiol
Tel. +33 4 76 61 52 59

Curriculum vitae

I have a Bachelor’s degree in Biology, Master’s degrees in Behavioural Biology and in Bioinformatics and a PhD Thesis in Informatics. More information are available in my website.

Research interests

  • Comparative genomics: use of genome comparison to help the reconstruction of metabolic models.

  • Knowledge representation and reasoning: developing logical formulation of biological hypothesis to explore metabolic possibilities.

  • Knowledge engineering: searching and querying knowledge databases (such as metabolic databases).

Research projects

I am a post-doctoral fellow at the Inria working with Delphine Ropers and Hidde de Jong. My work focuses on modelling the metabolism of organisms in two projects.

The first one focuses on the microbial communities in salt caverns. To understand their impact on hydrogen, I have developed a workflow, Tabigecy. This workflow predicts the impact of microbial communities on major biogeochemical cycles (carbon, sulfur, nitrogen and phosphorous) from metabarcoding data (by using the taxonomic affiliations identified by such sequencing approach). This workflow is presented and applied to salt caverns in a preprint.

A second project explores the metabolism of the family Mycobacteriaceae. The goal is to compare metabolic information from models to known phenotypes.

Selected Publications

All my publications are listed on: my website, ORCID and Google Scholar.

  • Predicting coarse-grained representations of biogeochemical cycles from metabarcoding data.
    Arnaud Belcour, Loris Megy, Sylvain Stephant, Caroline Michel, Sétareh Rad, Petra Bombach, Nicole Dopffel, Hidde de Jong and Delphine Ropers.
    BiorXiv (2025).
  • Estimating consensus proteomes and metabolic functions from taxonomic affiliations.
    Arnaud Belcour, Pauline Hamon-Giraud, Alice Mataigne, Baptiste Ruiz, Yann Le Cunff, Jeanne Got, Lorraine Awhangbo, Mégane Lebreton, Clémence Frioux, Simon Dittami, Patrick Dabert, Anne Siegel, Samuel Blanquart.
    BiorXiv (2025).

  • Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe.
    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​.
    Article at Genome Research (2023).

  • PhD Thesis: Combining knowledge-based and sequence comparison approaches to elucidate metabolic functions, from pathways to communities .
    Document at HAL (2022).

  • Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species.
    Arnaud Belcour, Clémence Frioux, Méziane Aite, Anthony Bretaudeau, Falk Hildebrand and Anne Siegel.
    Article at eLife (2020), code.

  • Inferring biochemical reactions and metabolite structures to cope with metabolic pathway drift.
    Arnaud Belcour, Jean Girard, Méziane Aïte, Ludovic Delage, Camille Trottier, Charlotte Marteau, Cédric Leroux, Simon M Dittami, Pierre Sauleau, Erwan Corre, Jacques Nicolas, Catherine Boyen, Catherine Leblanc, Jonas Collén, Anne Siegel and Gabriel Markov.
    Article at iScience (2020), bibtex, code.

Selected software

I developed several software and tools that are available on my GitHub account. Here a short list:

  • tabigecy. Prediction of the impact of microbial communities on biogeochemical cycles from metabarcoding data. It combines EsMeCaTa and bigecyhmm.
  • bigecyhmm. Prediction of the impact of microbial communities on biogeochemical cycles from protein sequences.

  • esmecata.
    EsMeCaTa: Estimating Metabolic Capabilties from Taxonomic annotations.

  • aucome.
    AUtomatic COmparison of MEtabolism.

  • metage2metabo.
    From annotated genomes to metabolic screening in large scale microbiotas.

  • mpwt: Pathway-Tools multiprocessing package.
    A little package to launch multiple runs of Pathway-Tools on different genomes, using genbank files.

  • pathmodel.
    Prototype applying the metabolic pathway drift hypothesis to infer ab initio reaction using known reactions.

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