Bérénice Batut

Bérénice Batut

@bebatut.bsky.social

She/her. Bioinformatics. Microbiome 🦠. Open Science. Training. Mentoring. Galaxy. OLS. ELIXIR Microbiome Community. Mother

899 followers1.5K following87 posts

Bérénice Batut reposted

IFB/ELIXIR-Fr
@ifb-elixir-fr.bsky.social

Check out this presentation by @bebatut.bsky.social , ELIXIR-France (IFB/ELIXIR-FR) co-lead for the FAIRyMAGs project! 🙏

ELIXIR Europe@elixir-europe.org

ELIXIR’s internal project, FAIRyMAGs, is developing #FAIR Galaxy workflows 💡, benchmarking approaches and training materials for metagenome-assembled genomes. 🙌 Support reproducible analysis for researchers to apply consistent workflows. 🔗 Watch project update: https://loom.ly/NnhPL3M

youtu.beFAIRyMAGs: Optimising Metagenomics Assembled Genomes buildingELIXIR Europe
Bérénice Batut
@bebatut.bsky.social

🎉 Thrilled to have co-led FAIRyMAGs with Paul Zierep! We used @galaxyproject.bsky.social to implement FAIR workflows and @galaxytraining.bsky.social training materials (also available on YouTube)

ELIXIR Europe@elixir-europe.org

The ELIXIR-funded FAIRyMAGs project has released a set of 🙌 openly available workflows, training materials and example #datasets to support researchers working with metagenome-assembled genomes 👉 loom.ly/yh_aNFE @ifb-elixir-fr.bsky.social @ebi.embl.org @denbi.bsky.social @elixir-it.bsky.social

Bérénice Batut reposted

bigdatabiology.bsky.social
@bigdatabiology.bsky.social

How well do ARG detection pipelines agree when applied to the same data? Spoiler: not very well. In our new preprint, we ran 10 pipelines on 270M microbial unigenes from GMGCv1. The same data can support conflicting biological conclusions! 🧵 www.biorxiv.org/content/10.6...

biorxiv.orgThe elusive resistome: a global comparison reveals large discrepancies among detection pipelinesIdentifying antibiotic resistance genes (ARGs) from metagenomic data is critical for studying antimicrobial resistance across microbial communities and pathogens. However, there is no standardized methodology for ARG annotation. Here, we compare ten commonly used ARG detection pipelines by analysing over 270 million prokaryotic genes from the Global Microbial Gene Catalogue across 13 distinct habitats. We observed up to a 45-fold difference in the number of reported ARGs, with a mean Jaccard index of only 16% between pipelines. Pipeline selection profoundly impacted downstream biological interpretations, with drastic changes to estimates of ARG relative abundance and richness, to the characterization of pan- and core-resistomes, and to the class-level composition of the inferred resistome. ARG detection pipelines make different, defensible trade-offs, and no single approach should be treated as authoritative. Therefore, users should justify and communicate choices carefully, as our analyses show that, taken uncritically, the same data can support conflicting biological and ecological interpretations. ### Competing Interest Statement The authors have declared no competing interest. National Health and Medical Research Council of Australia (NHMRC), 2031902 Australian Research Council (ARC), FT230100724 International Development Research Centre (IDRC), 109304-001 Deutsche Forschungsgemeinschaft (DFG), FO1279/6-1 Bundesministerium für Bildung und Forschung (BMBF), F01KI1909A, 01KI2404B Swedish Research Council (VR), 2024-06123, 2019-00299, 2023-01721 Knut and Alice Wallenberg Foundation, KAW 2020.0239 Swedish Foundation for Strategic Research, FFL21-0174
Bérénice Batut
@bebatut.bsky.social

I'm thrilled to co-organize and teach at the first-ever training event focused on advanced Galaxy features: workflows, API, and more! Registration is now open until June 5, so don’t miss your chance to dive deep into these powerful tools.

training.galaxyproject.orgGalaxy Beyond Basics: Mastering Workflows, Automation, and ScalabilityJoin us for an **intensive, week-long, in-person training** designed to elevate your Galaxy expertise to new heights. This workshop is tailored for **data scientists, advanced Galaxy users, and team l...
IFB/ELIXIR-Fr@ifb-elixir-fr.bsky.social

📢 Galaxy Advanced Training: Mastering Workflows, Automation, and Scalability: pre-registration open until June 5 2026!

Bérénice Batut reposted

A. Murat Eren (Meren)
@merenbey.bsky.social

How every layer of science's "self-correcting machinery" failed when Iva Veseli and I simply wanted to reproduce the findings of a high-profile study on gut microbiome and autism: merenlab.org/2026/04/15/u...

merenlab.orgUnfalsifiable by Design: A Year of Trying and Failing to Reproduce a Human Microbiome and Autism StudyThe myth of open data, reproducibility, responsibility, and accountability in science, and your role in it

Bérénice Batut reposted

FEMS
@femsmicro.org

✨ Know a woman making an impact in microbiology? Nominate her for recognition on the FEMS website and socials this International Women’s Day. 🗓️ Submit by 4 March: buff.ly/AKyMbQD Let’s elevate the female voices driving microbiology forward. #IWD2026

Bérénice Batut
@bebatut.bsky.social

We are thrilled to announce that "Ten Common Misconceptions About Galaxy (And Why They Are Wrong!)" has just been published! This is the result of passionate discussions, collaborative debates, and a shared commitment to clarifying what Galaxy @galaxyproject.bsky.social truly is and what it can do.

BF Francis Ouellette@bffo.bsky.social

From @bebatut.bsky.social @abretaud.bsky.social @hrhotz.bsky.social et al. in @plos.org #Computational #Biology | Ten common misconceptions about Galaxy (and why they are wrong!) | #Bioinformatics #Education #UseGalaxy 🧬 🖥️ 🧪 🔓 CC/ @galaxyproject.bsky.social ⬇️ journals.plos.org/ploscompbiol...

journals.plos.orgTen common misconceptions about Galaxy (and why they are wrong!)Author summary Galaxy is a free, community-built web interface that helps scientists analyse data in a way that’s easy to use, transparent and reproducible. While it is widely used in biology and othe...
Bérénice Batut
@bebatut.bsky.social

Whether you are a longtime Galaxy user or new to the platform, this paper challenges assumptions and highlights Galaxy's versatility, scalability, and impact across disciplines. Read more about the paper, the story behind, and why it matters in our blog post: galaxyproject.org/news/2026-02...

galaxyproject.orgTen Common Misconceptions About Galaxy (And Why They're Wrong!)We are thrilled to announce that 'Ten Common Misconceptions About Galaxy (And Why They Are Wrong!)' has just been published in PLOS Computational Biology! This paper is the result of passionate discus

Bérénice Batut reposted

BF Francis Ouellette
@bffo.bsky.social

From @bebatut.bsky.social @abretaud.bsky.social @hrhotz.bsky.social et al. in @plos.org #Computational #Biology | Ten common misconceptions about Galaxy (and why they are wrong!) | #Bioinformatics #Education #UseGalaxy 🧬 🖥️ 🧪 🔓 CC/ @galaxyproject.bsky.social ⬇️ journals.plos.org/ploscompbiol...

journals.plos.orgTen common misconceptions about Galaxy (and why they are wrong!)Author summary Galaxy is a free, community-built web interface that helps scientists analyse data in a way that’s easy to use, transparent and reproducible. While it is widely used in biology and othe...
Bérénice Batut
@bebatut.bsky.social

The Galaxy Community Conference is coming to my hometown this year! 🎉 Mark your calendars & register by the end of February for early bird rates. It’s a fantastic opportunity to connect with the global Galaxy Community. Looking forward to seeing you there! @ifb-elixir-fr.bsky.social

Galaxy Project@galaxyproject.bsky.social

⏳ Reminder: Early bird registration for GCC2026 closes February 28, 2026! Join us in Clermont-Ferrand, France, June 22–24, followed by CoFest June 25–26. Learn more and register now: galaxyproject.org/events/gcc20...

Bérénice Batut reposted

Rob Waterhouse
@rmwaterhouse.bsky.social

#Communities of experts collaborating on #scientific or technical projects are drivers of innovation across the life #sciences f1000research.com/articles/14-... @elixir-europe.org @sib.swiss @ergabiodiv.bsky.social #biodiversity #genomics

f1000research.comF1000Research Article: Fostering and sustaining collaborative innovation: Insights from ELIXIR Europe's life science Communities.Read the latest article version by Clare Garrard, Katharina F Heil, Maria Cristina Aspromonte, Bérénice Batut, Magda Chegkazi, John M Hancock, Elaine Harrison, Naveed Ishaque, Giselle Ke...

Bérénice Batut reposted

Valentin Loux
@vloux.bsky.social

Connexion directe de Galaxy à Recherche Data Gouv

Galaxy Project@galaxyproject.bsky.social

Galaxy + Dataverse = better data sharing Galaxy now integrates with Dataverse, making it easier to publish, access, and reuse research data directly within your workflows, supporting FAIR and reproducible science. Learn more: galaxyproject.org/news/2026-01...

galaxyproject.orgIntegration of the Dataverse with GalaxyGalaxy users can now connect to a Dataverse as a repository source, browse and search datasets directly from the Upload dialog, import files into histories and utilize them for scientific analyses.

Bérénice Batut reposted

Galaxy Project
@galaxyproject.bsky.social

Get ready for GCC2026! Join the Galaxy community June 22–24, 2026, in Clermont-Ferrand, France, to learn new tools, share your work, and connect with researchers and developers from around the world. Followed by CoFest on June 25–26. galaxyproject.org/events/gcc20...

galaxyproject.org2026 Galaxy Community Conference (GCC2026)The annual gathering of the Galaxy Community with opportunities to hear latest developments, get training, and meet everyone involved.

Bérénice Batut reposted

FEMS
@femsmicro.org

As 2025 wraps up, we’re looking back at some of the most intriguing microbes that made their scientific debut this year. This blog highlights standout bacterial species that caught our eye. Read the full #FEMSmicroBlog: buff.ly/2wz7k16 #NewMicrobes

Bérénice Batut reposted

sylvain Brisse
@sylvainbrisse.bsky.social

Huge preprint if you are interested in bacterial strain taxonomy! The why and how of cgMLST LIN codes: An extensively revised and expanded version doi.org/10.1101/2024... I will summarize it for you in this thread 👇

doi.orgLife Identification Numbers: A bacterial strain nomenclature approachUnified strain taxonomies are needed for the epidemiological surveillance of bacterial pathogens and international communication in microbiological research. Core genome multilocus sequence typing (cg...

Bérénice Batut reposted

Dan Sprockett
@danielsprockett.bsky.social

Proud to have contributed to this important work! STREAMS guidelines: standards for technical reporting in environmental and host-associated #microbiome studies. www.nature.com/articles/s41... @natmicrobiol.nature.com

nature.comSTREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies - Nature MicrobiologyThis Consensus Statement presents the standards for technical reporting in environmental and host-associated microbiome studies (STREAMS) guidelines.

Bérénice Batut reposted

IFB/ELIXIR-Fr
@ifb-elixir-fr.bsky.social

📢🚀💻Le nouveau site internet de l’IFB/ELIXIR-FR est en ligne !!! Lancé début 2025, le projet de refonte/création du nouveau site internet de l’IFB/ELIXIR-FR atteint aujourd’hui l’une de ses étapes cruciales : sa publication ! www.ifb-elixir.fr

Bérénice Batut reposted

Daan Speth
@daanspeth.bsky.social

Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social doi.org/10.1093/bioa... The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives. More information on globdb.org 1/5 🖥️🧬🦠

doi.orgGlobDB: a comprehensive species-dereplicated microbial genome resourceAbstractMotivation. Over the past years, substantial numbers of microbial species’ genomes have been deposited outside of conventional INSDC databases.Resu

Bérénice Batut reposted

IFB/ELIXIR-Fr
@ifb-elixir-fr.bsky.social

🧬 🔎 Ce 17 novembre a eu lieu la journée du consortium ABRomics à l’Institut Pasteur. L’occasion de présenter aux différents représentants de nos parties prenantes l’avancement du projet et les développements en cours !

Bérénice Batut reposted

Tania Louis
@tanialouis.fr

Replying to @tanialouis.fr

De mon côté on m'a confié le micro pour la chronique sciences. Cette fois j'ai décidé de parler du fonctionnement scandaleux de l'édition scientifique, peu connu en dehors des labos : www.youtube.com/watch?v=Yg2C... Mais 4 minutes c'est court, alors j'ajoute quelques ressources ci-dessous !

youtube.comLe beurre, l’argent du beurre et le c*l des chercheurs- La chronique de Tania Louis dans La dernièreYouTube video by Radio Nova

Bérénice Batut reposted

Tania Louis
@tanialouis.fr

Dimanche dernier @ladernierenova.bsky.social était de retour à Toulouse. L'invitée de l'émission était @docteur-drey.bsky.social donc je recommande chaudement d'écouter le podcast entier : podcasts.nova.fr/radio-nova-l... @laradionova.bsky.social ...

podcasts.nova.frL'intégrale : "La dernière" du 9 novembre 2025 avec Audrey DussutourSur Radio Nova ce dimanche : Audrey Dussutour (biologiste), Doully, Florence Mendez et Tania Louis. La dernière, le dimanche à 18h en direct sur Radio Nova et ...

Bérénice Batut reposted

Richard Leggett
@richardmleggett.bsky.social

Know metagenomics and could spare 2 mins? I'm applying for funding to build a visual repository for metagenomic classification data (not sequence data). To support the application, I have a short 2 minute survey and it would be a big help if you could fill it in: docs.google.com/forms/d/e/1F...

docs.google.comMetagenomic classification surveyBackground: We're seeking the views of researchers on the possibility of a repository for metagenomic classification data, which we're hoping to build. The rationale is that people are familiar with t...
Bérénice Batut
@bebatut.bsky.social

It was a really nice week working on building MiCoReCa, a catalogue of resources (tools, workflows, etc) for microbiome research, and more importantly networking with the large @elixir-europe.org community. Thank you all! See next year!

IFB/ELIXIR-Fr@ifb-elixir-fr.bsky.social

🚀👩‍💻🧑‍💻 End of this week of #BioHackEU25, organised by @elixir-europe.org , to advance all projects in synergy! Thank you to the IFB/ELIXIR-FR team (on-site and remotely), and to our colleagues at @genouest.bsky.social 👏

Bérénice Batut
@bebatut.bsky.social

Really happy to be back in Freiburg & at @uni-freiburg.de to present the Microbiology Galaxy Lab & the efforts of the microGalaxy community to build the first community-driven gateway for reproducible and FAIR analysis of microbial data. Slides: f1000research.com/slides/14-1021 #EGD

f1000research.comSlide: 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 has been published...Read this work by Batut B, at F1000Research.
Galaxy Project@galaxyproject.bsky.social

On Day 1 of European Galaxy Days, Bérénice Batut presented The Microbiology Galaxy Lab and the effort from the microGalaxy to build the first community-driven gateway for reproducible and FAIR analysis of microbial data. Read more: https://doi.org/10.1101/2024.12.23.629682 (1/2)

Bérénice Batut
@bebatut.bsky.social

📄 New preprint! After months/years of gathering insights and input from our incredible community, we're thrilled to share this important resource: "Ten Common Misconceptions About Galaxy (and Why They Are Wrong!)" www.preprints.org/manuscript/2...

preprints.orgpreprints.org
Galaxy Project@galaxyproject.bsky.social

after a long effort, gathering a lot of input from many people, we finaly put it all together: Ten Common Misconceptions About Galaxy (and Why They Are Wrong!) https://www.preprints.org/manuscript/202509.0823 Thank you very much to all people involved !

View full thread
Bérénice Batut
@bebatut.bsky.social

🔬 Why does this matter? Galaxy isn't just for genomics or teaching. It's a robust tool for cutting-edge research, education, and even clinical workflows. This paper shines a light on its real-world applications, technical strengths, and the vibrant community driving its evolution.

Bérénice Batut
@bebatut.bsky.social

📢 Let’s spread the word! Share your thoughts, tag colleagues who might benefit, and help us bust these myths once and for all. Together, we can empower more researchers, educators, and decision-makers to leverage Galaxy's full potential.

Bérénice Batut
@bebatut.bsky.social

📄 New preprint! After months/years of gathering insights and input from our incredible community, we're thrilled to share this important resource: "Ten Common Misconceptions About Galaxy (and Why They Are Wrong!)" www.preprints.org/manuscript/2...

preprints.orgpreprints.org
Galaxy Project@galaxyproject.bsky.social

after a long effort, gathering a lot of input from many people, we finaly put it all together: Ten Common Misconceptions About Galaxy (and Why They Are Wrong!) https://www.preprints.org/manuscript/202509.0823 Thank you very much to all people involved !

View full thread
Bérénice Batut
@bebatut.bsky.social

📄 New preprint! After months/years of gathering insights and input from our incredible community, we're thrilled to share this important resource: "Ten Common Misconceptions About Galaxy (and Why They Are Wrong!)" www.preprints.org/manuscript/2...

preprints.orgpreprints.org
Galaxy Project@galaxyproject.bsky.social

after a long effort, gathering a lot of input from many people, we finaly put it all together: Ten Common Misconceptions About Galaxy (and Why They Are Wrong!) https://www.preprints.org/manuscript/202509.0823 Thank you very much to all people involved !

Bérénice Batut
@bebatut.bsky.social

This preprint tackles persistent myths about Galaxy, from its perceived limitations in genomics to questions about scalability, usability, and its role in academia and industry. Spoiler alert: Galaxy is far more versatile, powerful, and impactful than many realize!