Bérénice Batut
@bebatut.bsky.social
She/her. Bioinformatics. Microbiome 🦠. Open Science. Training. Mentoring. Galaxy. OLS. ELIXIR Microbiome Community. Mother
Reposted by Bérénice Batut
Data visualization is a critical step in data analysis. 8 links to bookmark for better data visualization:🧵
December 28, 2025 at 2:45 PM
Data visualization is a critical step in data analysis. 8 links to bookmark for better data visualization:🧵
Reposted by Bérénice Batut
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
#NewMicrobes
December 10, 2025 at 11:01 AM
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
#NewMicrobes
How effective are AI assistants like Claude and ChatGPT for literature reviews? Anton Nekrutenko ran a systematic experiment using multiple AI-assisted approaches to survey RNA-seq studies on Candida auris, a multidrug-resistant fungal pathogen. Summary here:
galaxyproject.org/news/2025-12...
galaxyproject.org/news/2025-12...
December 8, 2025 at 2:52 PM
How effective are AI assistants like Claude and ChatGPT for literature reviews? Anton Nekrutenko ran a systematic experiment using multiple AI-assisted approaches to survey RNA-seq studies on Candida auris, a multidrug-resistant fungal pathogen. Summary here:
galaxyproject.org/news/2025-12...
galaxyproject.org/news/2025-12...
Reposted by Bérénice Batut
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 👇
Life Identification Numbers: A bacterial strain nomenclature approach
Unified strain taxonomies are needed for the epidemiological surveillance of bacterial pathogens and international communication in microbiological research. Core genome multilocus sequence typing (cg...
doi.org
November 30, 2025 at 7:51 PM
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 👇
Reposted by Bérénice Batut
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
STREAMS guidelines: standards for technical reporting in environmental and host-associated #microbiome studies. www.nature.com/articles/s41... @natmicrobiol.nature.com
STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies - Nature Microbiology
This Consensus Statement presents the standards for technical reporting in environmental and host-associated microbiome studies (STREAMS) guidelines.
www.nature.com
December 1, 2025 at 7:44 PM
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
STREAMS guidelines: standards for technical reporting in environmental and host-associated #microbiome studies. www.nature.com/articles/s41... @natmicrobiol.nature.com
Reposted by Bérénice Batut
LorMe: a streamlined and interoperable R framework for end-to-end microbiome analysis www.biorxiv.org/content/10.1... #Rstats 🧬🖥️🧪 github.com/wangnq111/Lo...
December 1, 2025 at 3:00 PM
LorMe: a streamlined and interoperable R framework for end-to-end microbiome analysis www.biorxiv.org/content/10.1... #Rstats 🧬🖥️🧪 github.com/wangnq111/Lo...
Reposted by Bérénice Batut
📢🚀💻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
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
November 28, 2025 at 1:01 PM
📢🚀💻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
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
Reposted by Bérénice Batut
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.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
🖥️🧬🦠
GlobDB: a comprehensive species-dereplicated microbial genome resource
AbstractMotivation. Over the past years, substantial numbers of microbial species’ genomes have been deposited outside of conventional INSDC databases.Resu
doi.org
November 21, 2025 at 4:21 PM
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.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
🖥️🧬🦠
Reposted by Bérénice Batut
🧬 🔎 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 !
November 20, 2025 at 1:44 PM
🧬 🔎 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 !
Reposted by Bérénice Batut
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 !
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 !
Le beurre, l’argent du beurre et le c*l des chercheurs- La chronique de Tania Louis dans La dernière
YouTube video by Radio Nova
www.youtube.com
November 12, 2025 at 6:37 PM
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 !
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 !
Reposted by Bérénice Batut
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
...
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
...
L'intégrale : "La dernière" du 9 novembre 2025 avec Audrey Dussutour
Sur 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 ...
podcasts.nova.fr
November 12, 2025 at 6:37 PM
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
...
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
...
Reposted by Bérénice Batut
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...
Metagenomic classification survey
Background: 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...
docs.google.com
November 10, 2025 at 6:24 PM
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...
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!
🚀👩💻🧑💻 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 👏
November 7, 2025 at 3:16 PM
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!
Reposted by Bérénice Batut
🚀👩💻🧑💻 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 👏
November 7, 2025 at 12:29 PM
🚀👩💻🧑💻 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 👏
Reposted by Bérénice Batut
On Day 1 of European Galaxy Days, Mina Hojat Ansari presented FAIRYMAGS: A Galaxy Workflow for MAG Recovery Applied to Termite Microbiomes.
Read more: https://elixir-europe.org/how-we-work/scientific-programme/commissioned-services/science/bfsp/fairymags
##termite ##EGD2025 ##microbiomes (1/2)
Read more: https://elixir-europe.org/how-we-work/scientific-programme/commissioned-services/science/bfsp/fairymags
##termite ##EGD2025 ##microbiomes (1/2)
October 1, 2025 at 10:32 AM
On Day 1 of European Galaxy Days, Mina Hojat Ansari presented FAIRYMAGS: A Galaxy Workflow for MAG Recovery Applied to Termite Microbiomes.
Read more: https://elixir-europe.org/how-we-work/scientific-programme/commissioned-services/science/bfsp/fairymags
##termite ##EGD2025 ##microbiomes (1/2)
Read more: https://elixir-europe.org/how-we-work/scientific-programme/commissioned-services/science/bfsp/fairymags
##termite ##EGD2025 ##microbiomes (1/2)
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
Slides: f1000research.com/slides/14-1021
#EGD
October 1, 2025 at 10:14 AM
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
Slides: f1000research.com/slides/14-1021
#EGD
Reposted by Bérénice Batut
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)
Read more: https://doi.org/10.1101/2024.12.23.629682 (1/2)
October 1, 2025 at 10:05 AM
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)
Read more: https://doi.org/10.1101/2024.12.23.629682 (1/2)
Today is #InternationalMicroorganismDay, a chance to celebrate the invisible powerhouses shaping our health and ecosystems. With @galaxyproject.bsky.social, we're proud to support global research that decodes the secrets of microbes, from deadly pathogens to life-sustaining bacteria.
September 17, 2025 at 2:17 PM
Today is #InternationalMicroorganismDay, a chance to celebrate the invisible powerhouses shaping our health and ecosystems. With @galaxyproject.bsky.social, we're proud to support global research that decodes the secrets of microbes, from deadly pathogens to life-sustaining bacteria.
📄 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...
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...
September 10, 2025 at 1:46 PM
📄 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...
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...
Reposted by Bérénice Batut
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 !
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 !
September 10, 2025 at 10:22 AM
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 !
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 !
Reposted by Bérénice Batut
TDM & NLP 💻 applied to #taxonomy & #biodiversity literature 📚 will facilitate #data synthesis studies & #literature reviews, identification of knowledge gaps & biases, & data-informed investigation of #ecological & #evolutionary trends & patterns bdj.pensoft.net/article/1530...
From literature to biodiversity data: mining arthropod organismal traits with machine learning
The fields of taxonomy and biodiversity research have witnessed an exponential growth in published literature. This vast corpus of articles holds information on the diverse biological traits of organi...
bdj.pensoft.net
September 7, 2025 at 9:40 AM
TDM & NLP 💻 applied to #taxonomy & #biodiversity literature 📚 will facilitate #data synthesis studies & #literature reviews, identification of knowledge gaps & biases, & data-informed investigation of #ecological & #evolutionary trends & patterns bdj.pensoft.net/article/1530...
Reposted by Bérénice Batut
taxburst v0.3.0 is now released - this is an update of the Krona visualization system for microbiome/metagenome taxonomy analyses. Enjoy!
Announcing taxburst, an update of the Krona software for taxonomy exploration
Announcing taxburst for metagenome taxonomy!
ivory.idyll.org
August 8, 2025 at 2:19 PM
taxburst v0.3.0 is now released - this is an update of the Krona visualization system for microbiome/metagenome taxonomy analyses. Enjoy!
Reposted by Bérénice Batut
✨ 📹 Pour se replonger encore un peu dans cette belle édition de JOBIM Bordeaux qui s'est déroulée début juillet, découvrez notre vidéo ! www.youtube.com/shorts/U2sPu...
L'IFB/ELIXIR-FR à JOBIM Bordeaux - Juillet 2025
YouTube video by French Institute of Bioinformatics
www.youtube.com
July 25, 2025 at 12:16 PM
✨ 📹 Pour se replonger encore un peu dans cette belle édition de JOBIM Bordeaux qui s'est déroulée début juillet, découvrez notre vidéo ! www.youtube.com/shorts/U2sPu...
Reposted by Bérénice Batut
@abretaud.bsky.social and @bebatut.bsky.social presenting @galaxyproject.bsky.social France during the @ifb-elixir-fr.bsky.social network presentation at @jobim2025.bsky.social !
July 10, 2025 at 8:00 AM
@abretaud.bsky.social and @bebatut.bsky.social presenting @galaxyproject.bsky.social France during the @ifb-elixir-fr.bsky.social network presentation at @jobim2025.bsky.social !
As a follow-up to our poster at the @elixir-europe.org All Hands Meeting in June, Lisanna Paladin and I wrote the following blog post on how the Galaxy Training Network aligns with the Training Life-Cycle and @elixir-europe.org SPLASH recommendations.
#Training @galaxyproject.bsky.social
#Training @galaxyproject.bsky.social
Enhancing Scientific Training: The Galaxy Training Network’s Role in the ELIXIR Training Life-Cycle
Read more at https://training.galaxyproject.org/training-material/news/2025/07/01/gtn-elixir-life-cycle.html
@galaxyproject.bsky.social
Read more at https://training.galaxyproject.org/training-material/news/2025/07/01/gtn-elixir-life-cycle.html
@galaxyproject.bsky.social
July 7, 2025 at 2:13 PM
As a follow-up to our poster at the @elixir-europe.org All Hands Meeting in June, Lisanna Paladin and I wrote the following blog post on how the Galaxy Training Network aligns with the Training Life-Cycle and @elixir-europe.org SPLASH recommendations.
#Training @galaxyproject.bsky.social
#Training @galaxyproject.bsky.social