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.

  • 2026

    1. Ten common misconceptions about Galaxy (and why they are wrong!)
      Wendi Anne Bacon, Bérénice Batut, Sanjay Kumar Srikakulam, and 8 more authors
      PLoS Computational Biology, Feb 2026

    2025

    1. Establishing the ELIXIR Microbiome Community
      Robert D Finn, Bachir Balech, Josephine Burgin, and 24 more authors
      F1000Research, Sep 2025
    2. Guidance framework to apply best practices in ecological data analysis: lessons learned from building Galaxy-Ecology
      Coline Royaux, Jean-Baptiste Mihoub, Marie Jossé, and 26 more authors
      GigaScience, 2025
    3. PathoGFAIR: a collection of FAIR and adaptable (meta)genomics workflows for (foodborne) pathogens detection and tracking
      Engy Nasr, Anna Henger, Björn Grüning, and 2 more authors
      GigaScience, Sep 2025
    4. Strengthening bioinformatics education: e-learning initiatives across ELIXIR Nodes and Communities
      Monique Zahn-Zabala, Minna Ahokas, Bérénice Batut, and 18 more authors
      F1000Research, 2025
    5. Clouds influence the functioning of airborne microorganisms
      Raphaëlle Péguilhan, Florent Rossi, Muriel Joly, and 5 more authors
      Biogeosciences, Mar 2025
    6. Fostering and sustaining collaborative innovation: Insights from ELIXIR Europe’s life science Communities
      Clare Garrard, Katharina Heil, Maria Cristina Aspromonte, and 18 more authors
      F1000Research, Sep 2025

    2024

    1. The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update
      Linelle Ann L Abueg, Enis Afgan, Olivier Allart, and 126 more authors
      Nucleic Acids Research, Jul 2024

    2023

    1. Integrative meta-omics in Galaxy and beyond
      Valerie C Schiml, Francesco Delogu, Praveen Kumar, and 9 more authors
      Environmental Microbiome, Jul 2023
    2. The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond
      Simon Bray, John Chilton, Matthias Bernt, and 8 more authors
      Genome Research, Feb 2023
    3. Galaxy Training: A powerful framework for teaching!
      Saskia Hiltemann, Helena Rasche, Simon Gladman, and 30 more authors
      PLoS Computational Biology, Jan 2023
    4. An international consensus on effective, inclusive, and career-spanning short-format training in the life sciences and beyond
      Jason Williams, Rochelle Tractenberg, Bérénice Batut, and 26 more authors
      PLoS ONE, Nov 2023

    2022

    1. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update
      Enis Afgan, Anton Nekrutenko, Bjórn Grüning, and 103 more authors
      Nucleic Acids Research, Jul 2022
    2. Gut microbiota drives age-related oxidative stress and mitochondrial damage in microglia via the metabolite N6-carboxymethyllysine
      Omar Mossad, Bérénice Batut, Bahtiyar Yilmaz, and 16 more authors
      Nature Neuroscience, Mar 2022

    2021

    1. ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework
      Subina Mehta, Marie Crane, Emma Leith, and 11 more authors
      F1000Research, Apr 2021
    2. Fostering accessible online education using Galaxy as an e-learning platform
      Beatriz Serrano-Solano, Melanie Föll, Cristóbal Gallardo-Alba, and 11 more authors
      PLoS Computational Biology, May 2021

    2020

    1. The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR
      Daniel Wibberg, Bérénice Batut, Peter Belmann, and 13 more authors
      F1000Research, Sep 2020
    2. A single-cell RNA-sequencing training and analysis suite using the Galaxy framework
      Mehmet Tekman, Bérénice Batut, Alexander Ostrovsky, and 20 more authors
      GigaScience, Oct 2020
    3. Ten simple rules for making training materials FAIR
      Leyla Garcia, Bérénice Batut, Melissa Burke, and 20 more authors
      PLoS Computational Biology, May 2020
    4. Using the Galaxy Training Network tutorial library for bioinformatics training programs
      Dave Clements, Saskia Hiltemann, Bérénice Batut, and 3 more authors
      Journal of Biomolecular Techniques, Aug 2020
    5. Genome Evolution: Mutation Is the Main Driver of Genome Size in Prokaryotes
      Gabriel A.B. Marais, Bérénice Batut, and Vincent Daubin
      Current Biology, Oct 2020

    2019

    1. The RNA workbench 2.0: next generation RNA data analysis
      Jörg Fallmann, Pavankumar Videm, Andrea Bagnacani, and 7 more authors
      Nucleic Acids Research, Jul 2019

    2018

    1. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update
      Enis Afgan, Dannon Baker, Bérénice Batut, and 17 more authors
      Nucleic Acids Research, Jul 2018
    2. Community-Driven Data Analysis Training for Biology
      Bérénice Batut, Saskia Hiltemann, Andrea Bagnacani, and 33 more authors
      Cell Systems, Jun 2018
    3. ASaiM: a Galaxy-based framework to analyze microbiota data
      Bérénice Batut, Kevin Gravouil, Clemence Defois, and 4 more authors
      GigaScience, May 2018

    2017

    1. The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy
      Björn Grüning, Jörg Fallmann, Dilmurat Yusuf, and 17 more authors
      Nucleic Acids Research, Jul 2017
    2. Four simple recommendations to encourage best practices in research software
      Rafael Jiménez, Mateusz Kuzak, Monther Alhamdoosh, and 46 more authors
      F1000Research, Jun 2017
    3. Environmental Pollutant Benzo[a]Pyrene Impacts the Volatile Metabolome and Transcriptome of the Human Gut Microbiota
      Clémence Defois, Jérémy Ratel, Sylvain Denis, and 5 more authors
      Frontiers in Microbiology, Aug 2017
    4. ENASearch: A Python library for interacting with ENA’s API
      Bérénice Batut and Björn Grüning
      Journal of Open Source Software, Oct 2017

    2014

    1. Reductive genome evolution at both ends of bacterial population size spectrum
      Bérénice Batut, Carole Knibbe, Gabriel Marais, and 1 more author
      Nature Reviews Microbiology, Dec 2014

    2013

    1. In silico experimental evolution: a tool to test evolutionary scenarios
      Bérénice Batut, David P. Parsons, Stephan Fischer, and 2 more authors
      BMC Bioinformatics, 2013
  • 2026

    1. MiCoReCa (Microbiome Community Resource Catalogue) - Towards Centralized Curation And Integration Of Microbiome Bioinformatics Resources
      Vivek Ashokan, Clara Emery, Agnès Barnabé, and 5 more authors
      Jan 2026
      working paper or preprint

    2025

    1. Ten Common Misconceptions About Galaxy (and Why They Are Wrong!)
      Wendi Anne Bacon, Sanjay Kumar Srikakulam, Bérénice Batut, and 8 more authors
      2025
      working paper or preprint
    2. Community-Curated Galaxy Interfaces with the Galaxy Labs Engine
      Cameron Hyde, Anna Syme, Bérénice Batut, and 4 more authors
      Sep 2025
      working paper or preprint
    3. Microbiology Galaxy Lab: The first community-driven gateway for reproducible and FAIR analysis of microbial data
      Engy Nasr, Nikos Pechlivanis, Nikolaos Strepis, and 32 more authors
      Sep 2025
      working paper or preprint

    2024

    1. microGalaxy: A gateway to tools, workflows, and training for reproducible and FAIR analysis of microbial data
      Engy Nasr, Pierre Amato, Anshu Bhardwaj, and 27 more authors
      Dec 2024
      working paper or preprint
    2. How to improve the annotation of Galaxy resources? Outcomes of an online hackathon for improving the annotation of Galaxy resources for microbial data resources
      Bérénice Batut, Matthias Bernt, Mina Hojat Ansari, and 8 more authors
      2024
      working paper or preprint
    3. Clouds influence the functioning of airborne microorganisms
      Raphaëlle Péguilhan, Florent Rossi, Muriel Joly, and 5 more authors
      Sep 2024
      working paper or preprint
    4. How to increase the findability, visibility, and impact of Galaxy tools for your scientific community
      Paul Zierep, Bérénice Batut, Matúš Kalaš, and 6 more authors
      Jun 2024
      working paper or preprint
    5. Optimizing Short-format Training: an International Consensus on Effective, Inclusive, and Career-spanning Professional Development in the Life Sciences and Beyond
      Jason Williams, Rochelle Tractenberg, Bérénice Batut, and 26 more authors
      Jul 2024
      working paper or preprint
    6. Clouds, oases for airborne microbes – Differential metagenomics/ metatranscriptomics analyses of cloudy and clear atmospheric situations
      Raphaëlle Péguilhan, Florent Rossi, Muriel Joly, and 5 more authors
      Jun 2024
      working paper or preprint
    7. Exploring the landscape of the genomic wastewater surveillance ecosystem: a roadmap towards standardization
      Fotis Psomopoulos, Konstantinos Kyritsis, Ivan Topolsky, and 3 more authors
      Jun 2024
      working paper or preprint
    8. Empowering the community with notebooks for bespoke microbiome analyses
      Alexander Rogers, Bérénice Batut, Virginie Grosboillot, and 1 more author
      Jul 2024
      working paper or preprint

    2022

    1. Planemo: a command-line toolkit for developing, deploying, and executing scientific data analyses
      Simon Bray, Matthias Bernt, Nicola Soranzo, and 8 more authors
      Mar 2022
      working paper or preprint

    2020

    1. A single-cell RNA-seq Training and Analysis Suite using the Galaxy Framework
      Mehmet Tekman, Bérénice Batut, Alexander Ostrovsky, and 22 more authors
      Jun 2020
      working paper or preprint

    2018

    1. Community-Driven Data Analysis Training for Biology
      Bérénice Batut, Saskia Hiltemann, Andrea Bagnacani, and 32 more authors
      Apr 2018
      La version finale de l’article a été déposée sur PMC. The final version of this article has been deposed on PMC

    2017

    1. Bioconda: A sustainable and comprehensive software distribution for the life sciences
      Björn Grüning, Ryan Dale, Andreas Sjödin, and 153 more authors
      Oct 2017
      working paper or preprint
    2. ASaiM: a Galaxy-based framework to analyze raw shotgun data from microbiota
      Bérénice Batut, Kévin Gravouil, Clémence Defois, and 4 more authors
      Sep 2017
      working paper or preprint
  • 2021

    1. RNA-Seq Data Analysis in Galaxy
      Bérénice Batut, Marius Beek, Maria Doyle, and 1 more author
      In RNA Bioinformatics, Apr 2021
  • 2025

    1. ELIXIR Microbiome Community – 2025 face to face/hybrid meeting report
      Bérénice Batut and Eric Pelletier
      Apr 2025

    2023

    1. EOSC-Life Report on the work of the Open Call Projects
      Arina Rybina, Pauline Audergon, Claudia Pfander, and 103 more authors
      Aug 2023
  • 2014

    1. Étude de l’évolution réductive des génomes bactériens par expériences d’évolution in silico et analyses bioinformatiques
      Bérénice Batut
      Nov 2014
  • 2025

    1. FAIRyMAGS – Optimising Metagenomics Assembled Genomes building: workflow finalisation, training material development, real data evaluation, and resource allocation tool creation
      Paul Zierep, Bérénice Batut, Giuseppe Defazio, and 3 more authors
      In ELIXIR All Hands Meeting, 2025, Jun 2025
    2. 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 analysis
      Engy Nasr, Nikos Pechlivanis, Nikolaos Strepis, and 2 more authors
      In European Galaxy Days, Oct 2025
    3. ATELIER - Dépôt et curation de données - Communauté Biologie et Santé (plateforme de bioanalyses Galaxy)
      Cléa Siguret, Bérénice Batut, and Nadia Goué
      In Printemps de la donnée 2025, May 2025

    2024

    1. Galaxy France: an example of a national UseGalaxy server
      Clea Siguret, Thomas Chaussepied, Romane Libouban, and 5 more authors
      In GCC 2024 - Galaxy Community Conference, Jun 2024
    2. Misconceptions about Galaxy debunked by the (French) Galaxy Community
      Romane Libouban, Eva Mercier, Thomas Chaussepied, and 3 more authors
      In JOBIM 2024 - Journées Ouvertes Biologie Informatique Mathématiques, Jun 2024
    3. Galaxy CoDex for finding tools, workflows, and training
      Bérénice Batut, Wendi Bacon, Paul Zierep, and 3 more authors
      In GCC 2024 - Galaxy Community Conference, Jun 2024
    4. PathoGFAIR: collection of Galaxy FAIR workflows for pathogen detection and samples comparison
      Engy Nasr, Anna Henger, Bjoern Gruening, and 2 more authors
      In GCC 2024 - Galaxy Community Conference, Jun 2024
    5. ABRomics : Une plateforme basée sur Galaxy pour la recherche sur la résistance aux antibiotiques et la santé publique
      Cléa Siguret, Bérénice Batut, Raphaël Tackx, and 10 more authors
      In Journée d’animation annuelle de la plateforme AuBi 2024, Dec 2024
    6. Open seeds by OLS: A virtual mentoring & training program for open science ambassadors
      Pradeep Eranti, Yochannah Yehudi, Sara El-Gebali, and 1 more author
      In Bioinformatics Open Source Conference, Jul 2024

    2023

    1. Developing Galaxy as part of an international network
      Bérénice Batut
      In ELIXIR All Hands Meeting 2023, Jun 2023

    2021

    1. ASaiM - From a local project to a global effort to support microbiome data analysis.
      Bérénice Batut
      In Holistic Bioinformatic Approaches used in Microbiome Research - BVCN, Jun 2021

    2020

    1. Empowering usable, and comprehensive bioinformatics training
      Bérénice Batut
      In ISMB 2020 - 28th Intelligent Systems for Molecular Biology Conference, Jul 2020

    2019

    1. Street Science Community: make science tangible & accessible by bringing it to the “street” with open science workshops
      Teresa Müller and Bérénice Batut
      In 2019 Galaxy Community Conference (GCC2019), Jul 2019
    2. Galaxy and training 2019 updates from the Galaxy Training Network
      Bérénice Batut, Saskia Hiltemann, Helena Rasche, and 5 more authors
      In GCC2019 - 2019 Galaxy Community Conference, Jul 2019
    3. Metaproteomics Powered By Metatranscriptomics: Towards a Multi-omic Functional Microbiome Analysis Within Galaxy
      Pratik D Jagtap, Subina Mehta, Praveen Kumar, and 12 more authors
      In 2019 Galaxy Community Conference (GCC2019), Jul 2019
    4. Single-cell RNA Analysis in Galaxy on 10X Datasets
      Mehmet Tekman, Bérénice Batut, and Björn Grüning
      In 2019 Galaxy Community Conference (GCC2019), Jul 2019

    2018

    1. Community-driven training for biological data analysis with the Galaxy Training Network
      Bérénice Batut
      In Galaxy Africa conference, Apr 2018
    2. A fruitful year for the Galaxy Training materials
      Bérénice Batut, Saskia Hiltemann, and Björn Grüning
      In Galaxy Community Conference (GCC2018) and Bioinformatics Open Source Conference (BOSC2018), Jun 2018

    2017

    1. Building an open, collaborative, online infrastructure for bioinformatics training
      Bérénice Batut, Dave Clements, and Björn Grüning
      In Galaxy Community Conference 2017, Jun 2017

    2016

    1. Tool deployment and sustainability in bioinformatics: Fixed!
      Bérénice Batut, Jonas Weber, Rolf Backofen, and 1 more author
      In Bioinformatics for Human Health and Disease, Nov 2016

    2015

    1. ASaiM: An intuitive and adjustable pipeline to process metatranscriptomic data from intestinal microbiota
      Bérénice Batut, Clémence Defois, Céline Ribière, and 4 more authors
      In JOBIM 2015 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015

    2013

    1. An alife game to teach evolution of antibiotic resistance
      Guillaume Beslon, Bérénice Batut, David P. Parsons, and 2 more authors
      In Artificial Life Conference Proceedings, Sep 2013
    2. In silico experimental evolution: a tool to test evolutionary scenarios
      Bérénice Batut, David P. Parsons, Stephan Fischer, and 2 more authors
      In 11th RECOMB - Comparative Genomics 2013, Oct 2013
  • 2025

    1. IFB/ELIXIR-FR contributions to the ELIXIR Training Platform Programme
      Olivier Sand, Bérénice Batut, Frédéric Lamotte, and 3 more authors
      Jul 2025
      Poster
    2. Contributing to the ELIXIR training life-cycle from the GTN perspective
      Helena Rasche, Saskia Hiltemann, Lisanna Paladin, and 3 more authors
      Jun 2025
      Poster
    3. ABRomics-analysis : developing Metagenomic Workflows for National Antibiotic Resistance Surveillance Platform
      Hugo Lefeuvre, Audrey Bihouée, Bérénice Batut, and 3 more authors
      Jul 2025
      Poster
    4. Exploring the Richness of the French Galaxy Ecosystem
      Bérénice Batut, Gildas Le Corguillé, and Anthony Bretaudeau
      Jul 2025
      Poster
    5. Building a standardized database for honey bee microbiome: Addressing metadata and data comparability gaps
      Bérénice Batut, Cléa Siguret, Hugo Serville, and 5 more authors
      Jul 2025
      Poster
    6. Galaxy training: A powerful framework for teaching!
      Helena Rasche, Saskia Hiltemann, Björn Grüning, and 1 more author
      Jul 2025
      Poster
    7. Breaking myths: The reality of Galaxy’s capabilities and impact
      Gildas Le Corguillé, Anthony Bretaudeau, Björn Grüning, and 2 more authors
      Jul 2025
      Poster

    2024

    1. Exploring the richness of the French Galaxy Ecosystem
      Bérénice Batut, Gildas Le Corguillé, Yvan Le Bras, and 3 more authors
      Jun 2024
      Poster
    2. FAIRing Research Data to Live @AuBi Platform
      Francis Ogereau, Mateo Hiriart, Pierre Marin, and 14 more authors
      Jun 2024
      Poster
    3. The ABRomics platform - a One Health Antimicrobial resistance analysis service
      Julie Lao, Raphael Tackx, Pierre Marin, and 12 more authors
      Jun 2024
      Poster
    4. microGalaxy SIG: microbial data analysis resources in Galaxy
      Paul Zierep, Engy Nasr, Saim Momin, and 6 more authors
      Jun 2024
      Poster
    5. ABRomics: A Galaxy-based one health antimicrobial resistance platform
      Pierre Marin, Bérénice Batut, Kenzo-Hugo Hillion, and 8 more authors
      Jun 2024
      Poster

    2023

    1. Open seeds by OLS: A mentoring & training program for open science ambassadors
      Mallory Freeberg, Fotis Evangelos Psomopoulos, Diana Pilvar, and 1 more author
      Jun 2023
      Poster
    2. Establishing the ELIXIR microbiome community
      Bérénice Batut, Eric Pelletier, Robert D. Finn, and 1 more author
      Jun 2023
      Poster
    3. Galaxy Training: A powerful framework for teaching!
      Helena Rasche, Saskia Hiltemann, and Bérénice Batut
      Jun 2023
      Poster
    4. Accessible and scalable pipelines for fast and easy (foodborne) pathogens detection and tracking
      Engy Nasr, Anna Henger, Tobias Schindler, and 3 more authors
      Sep 2023
      Poster
    5. Accessible and scalable pipelines for fast and easy (foodborne) pathogens detection and tracking
      Engy Nasr, Anna Henger, Tobias Schindler, and 3 more authors
      Jun 2023
      Poster
    6. Accessible and scalable pipelines for fast and easy (foodborne) pathogens detection and tracking
      Engy Nasr, Anna Henger, Tobias Schindler, and 3 more authors
      May 2023
      Poster
    7. Accessible and scalable pipelines for fast and easy (foodborne) pathogens detection and tracking
      Engy Nasr, Anna Henger, Tobias Schindler, and 3 more authors
      Jul 2023
      Poster

    2019

    1. Galaxy for long read ONT data analysis and public education
      Bérénice Batut, Milad Miladi, Saskia Hiltemann, and 2 more authors
      Sep 2019
      Poster
    2. Metaproteomics Powered By Metatranscriptomics:Towards a multi-omic functional microbiome analysis
      Pratik D Jagtap, Praveen Kumar, Francesco Delogu, and 13 more authors
      Jun 2019
      Poster
    3. Galaxy and Training: 2019 updates from the Galaxy Training Network
      Bérénice Batut, Saskia Hiltemann, Helena Rasche, and 6 more authors
      Jul 2019
      Poster

    2018

    1. Community-driven training for biological data analysis with the Galaxy training network
      Bérénice Batut, Saskia Hiltemann, and Björn Grüning
      May 2018
      Poster
    2. A fruitful year for the Galaxy Training materials
      Bérénice Batut, Saskia Hiltemann, and Björn Grüning
      Jun 2018
      Poster

    2017

    1. Building an open, collaborative, online infrastructure for bioinformatics training
      Bérénice Batut, Dave Clements, and Björn Grüning
      Jul 2017
      Poster
    2. Scaling bioinformatics training: an ELIXIR, GOBLET & Galaxy Training Network collaboration
      Bérénice Batut, Björn Grüning, Frederik Coppens, and 4 more authors
      Jul 2017
      Poster
    3. A Galaxy-based framework to analyze raw sequencing data from microbiota
      Bérénice Batut, Clémence Defois, Kevin Gravouil, and 3 more authors
      Jun 2017
      Poster
    4. How to analyze raw sequencing data from microbiota? Using ASaiM!
      Bérénice Batut, Clémence Defois, Kevin Gravouil, and 3 more authors
      Sep 2017
      Poster

    2016

    1. Analyze your microbiota sequencing data using a Galaxy-based framework References
      Bérénice Batut, Clémence Defois, Kevin Gravouil, and 5 more authors
      Jun 2016
      Poster
    2. Stratégies de reconstruction de génomes microbiens à partir de métagenomes
      Kevin Gravouil, Corentin Hochart, Bérénice Batut, and 6 more authors
      Jun 2016
      Poster
    3. Unexpected genome inflation and streamlining in variable environments
      Bérénice Batut, Guillaume Beslon, and Carole Knibbe
      Jun 2016
      Poster
    4. Benzo[a]pyrene impacts human gut microbiota volatile metabolome and metatranscriptome
      Clémence Defois, Bérénice Batut, Jérémy Ratel, and 7 more authors
      2016
      Poster

    2012

    1. Simulating evolutionary scenarios to test whether they can induce reductive evolution
      Bérénice Batut, Mathilde Dumond, Gabriel Marais, and 2 more authors
      Jun 2012
      Poster