Publications
I practice open science to ensure my research is accessible, transparent, and reusable. My work is published in open-access journals to maximize reach and impact. Preprints are systematically shared on bioRxiv and BioHackrXiv to enable early access and recognize all contributors.
All publications are archived on HAL and linked to my ORCID profile. Research data are annotated and deposited in public databases, while code, workflows, and training materials are released under open licenses on GitHub or GitLab. Software versions are archived on Zenodo (with DOIs) and registered on bio.tools. Protocols are published on Protocols.io and workflows on WorkflowHub.
To ensure quality and credit, software is submitted to peer-reviewed journals like the Journal of Open Source Software (JOSS). Conference presentations and posters are openly shared, often on F1000Research with DOIs.
For a complete list of my publications, visit my HAL profile.
- Peer-Reviewed Journals
- Non Peer-reviewed Journals and Preprints
- Book Chapters
- Reports
- Thesis
- Talks
- Posters
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2026
- Ten common misconceptions about Galaxy (and why they are wrong!)PLoS Computational Biology, Feb 2026
2025
- PathoGFAIR: a collection of FAIR and adaptable (meta)genomics workflows for (foodborne) pathogens detection and trackingGigaScience, Sep 2025
- Fostering and sustaining collaborative innovation: Insights from ELIXIR Europe’s life science CommunitiesF1000Research, Sep 2025
2024
2023
- An international consensus on effective, inclusive, and career-spanning short-format training in the life sciences and beyondPLoS ONE, Nov 2023
2022
- Gut microbiota drives age-related oxidative stress and mitochondrial damage in microglia via the metabolite N6-carboxymethyllysineNature Neuroscience, Mar 2022
2021
- ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy frameworkF1000Research, Apr 2021
- Fostering accessible online education using Galaxy as an e-learning platformPLoS Computational Biology, May 2021
2020
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- Using the Galaxy Training Network tutorial library for bioinformatics training programsJournal of Biomolecular Techniques, Aug 2020
2019
2018
2017
- The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in GalaxyNucleic Acids Research, Jul 2017
- Four simple recommendations to encourage best practices in research softwareF1000Research, Jun 2017
- ENASearch: A Python library for interacting with ENA’s APIJournal of Open Source Software, Oct 2017
2014
- Reductive genome evolution at both ends of bacterial population size spectrumNature Reviews Microbiology, Dec 2014
2013
- In silico experimental evolution: a tool to test evolutionary scenariosBMC Bioinformatics, 2013
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2026
- MiCoReCa (Microbiome Community Resource Catalogue) - Towards Centralized Curation And Integration Of Microbiome Bioinformatics ResourcesJan 2026working paper or preprint
2025
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- Community-Curated Galaxy Interfaces with the Galaxy Labs EngineSep 2025working paper or preprint
- Microbiology Galaxy Lab: The first community-driven gateway for reproducible and FAIR analysis of microbial dataSep 2025working paper or preprint
2024
- Optimizing Short-format Training: an International Consensus on Effective, Inclusive, and Career-spanning Professional Development in the Life Sciences and BeyondJul 2024working paper or preprint
- Clouds, oases for airborne microbes – Differential metagenomics/ metatranscriptomics analyses of cloudy and clear atmospheric situationsJun 2024working paper or preprint
- Empowering the community with notebooks for bespoke microbiome analysesJul 2024working paper or preprint
2022
- Planemo: a command-line toolkit for developing, deploying, and executing scientific data analysesMar 2022working paper or preprint
2020
- A single-cell RNA-seq Training and Analysis Suite using the Galaxy FrameworkJun 2020working paper or preprint
2018
2017
- ASaiM: a Galaxy-based framework to analyze raw shotgun data from microbiotaSep 2017working paper or preprint
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2021
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2025
2023
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2014
- Étude de l’évolution réductive des génomes bactériens par expériences d’évolution in silico et analyses bioinformatiquesNov 2014
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2025
- FAIRyMAGS – Optimising Metagenomics Assembled Genomes building: workflow finalisation, training material development, real data evaluation, and resource allocation tool creationIn ELIXIR All Hands Meeting, 2025, Jun 2025
- The microbiology galaxy lab: The effort of the microGalaxy community to build the first community-driven gateway for reproducible and FAIR analysis of microbial data analysisIn European Galaxy Days, Oct 2025
- ATELIER - Dépôt et curation de données - Communauté Biologie et Santé (plateforme de bioanalyses Galaxy)In Printemps de la donnée 2025, May 2025
2024
- Misconceptions about Galaxy debunked by the (French) Galaxy CommunityIn JOBIM 2024 - Journées Ouvertes Biologie Informatique Mathématiques, Jun 2024
- ABRomics : Une plateforme basée sur Galaxy pour la recherche sur la résistance aux antibiotiques et la santé publiqueIn Journée d’animation annuelle de la plateforme AuBi 2024, Dec 2024
2023
2021
- ASaiM - From a local project to a global effort to support microbiome data analysis.In Holistic Bioinformatic Approaches used in Microbiome Research - BVCN, Jun 2021
2020
- Empowering usable, and comprehensive bioinformatics trainingIn ISMB 2020 - 28th Intelligent Systems for Molecular Biology Conference, Jul 2020
2019
- Street Science Community: make science tangible & accessible by bringing it to the “street” with open science workshopsIn 2019 Galaxy Community Conference (GCC2019), Jul 2019
- Galaxy and training 2019 updates from the Galaxy Training NetworkIn GCC2019 - 2019 Galaxy Community Conference, Jul 2019
- Metaproteomics Powered By Metatranscriptomics: Towards a Multi-omic Functional Microbiome Analysis Within GalaxyIn 2019 Galaxy Community Conference (GCC2019), Jul 2019
- Single-cell RNA Analysis in Galaxy on 10X DatasetsIn 2019 Galaxy Community Conference (GCC2019), Jul 2019
2018
- Community-driven training for biological data analysis with the Galaxy Training NetworkIn Galaxy Africa conference, Apr 2018
- A fruitful year for the Galaxy Training materialsIn Galaxy Community Conference (GCC2018) and Bioinformatics Open Source Conference (BOSC2018), Jun 2018
2017
- Building an open, collaborative, online infrastructure for bioinformatics trainingIn Galaxy Community Conference 2017, Jun 2017
2016
- Tool deployment and sustainability in bioinformatics: Fixed!In Bioinformatics for Human Health and Disease, Nov 2016
2015
- ASaiM: An intuitive and adjustable pipeline to process metatranscriptomic data from intestinal microbiotaIn JOBIM 2015 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015
2013
- An alife game to teach evolution of antibiotic resistanceIn Artificial Life Conference Proceedings, Sep 2013
- In silico experimental evolution: a tool to test evolutionary scenariosIn 11th RECOMB - Comparative Genomics 2013, Oct 2013
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2025
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- ABRomics-analysis : developing Metagenomic Workflows for National Antibiotic Resistance Surveillance PlatformJul 2025Poster
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- Building a standardized database for honey bee microbiome: Addressing metadata and data comparability gapsJul 2025Poster
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2024
2023
- Accessible and scalable pipelines for fast and easy (foodborne) pathogens detection and trackingSep 2023Poster
- Accessible and scalable pipelines for fast and easy (foodborne) pathogens detection and trackingMay 2023Poster
- Accessible and scalable pipelines for fast and easy (foodborne) pathogens detection and trackingJul 2023Poster
2019
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- Metaproteomics Powered By Metatranscriptomics:Towards a multi-omic functional microbiome analysisJun 2019Poster
2018
- Community-driven training for biological data analysis with the Galaxy training networkMay 2018Poster
- A fruitful year for the Galaxy Training materialsJun 2018Poster
2017
2016
- Analyze your microbiota sequencing data using a Galaxy-based framework ReferencesJun 2016Poster
- Stratégies de reconstruction de génomes microbiens à partir de métagenomesJun 2016Poster
- Unexpected genome inflation and streamlining in variable environmentsJun 2016Poster
- Benzo[a]pyrene impacts human gut microbiota volatile metabolome and metatranscriptome2016Poster
2012
- Simulating evolutionary scenarios to test whether they can induce reductive evolutionJun 2012Poster
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