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Bérénice Batut

@bebatut.bsky.social

898 followers 1.5K following 87 posts

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

Posts Replies Media

Bérénice Batut @bebatut.bsky.social · 08/12/2025

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...

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Bérénice Batut @bebatut.bsky.social · 17/09/2025

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.

This image presents the Microbiology Galaxy Lab, a platform dedicated to One Health and ecological integrity, illustrating how it connects humans, animals, and the environment through the analysis of DNA, RNA, proteins, and metabolites using 315+ tool suites and 115+ workflows. On the left, it highlights ecosystem dynamics and biodiversity, covering areas such as microbial diversity, interactions, ecosystem modeling, strain discovery, pathway analysis, population omics, and temporal dynamics. On the right, it focuses on health and disease, addressing topics like clinical microbiota, antimicrobial resistance, pathogen profiling (viruses, bacteria, fungi, protozoa), virulence assessment, dysbiosis analysis, abundance quantification, outbreak modeling, biomarker correlation, and host interaction. The lab also emphasizes citizen science, education, and 35+ tutorials, promoting accessibility and knowledge sharing in microbiology research.

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Bérénice Batut @bebatut.bsky.social · 15/04/2025

🌟 Join Us for Optimising Metagenomics Assembled Genomes (MAGs) Building Workflows! 🌟 galaxyproject.org/events/2025-... MAGs building wfs are crucial for building new genomes & reducing microbial dark matter! Join our hackathon to collaboratively improve these workflows! #Metagenomics #Workflows

The image features a vibrant and engaging graphic promoting the FAIRyMAGs Hybrid Hackathon 2025. At the top, the title 'FAIRyMAGs Hybrid Hackathon 2025: Optimising Metagenomics Assembled Genomes building' is prominently displayed, accompanied by a rocket icon. Below the title, the event dates 'October 06-10th, 2025' are highlighted with a flag icon.

In the center, there are illustrations of three individuals collaborating on a project. One person is standing and pointing at a large screen displaying a graph, another person is sitting on a desk with a coffee mug, and the third person is sitting on the desk with a laptop. The background is minimalistic, focusing attention on the collaborative scene.
At the bottom, logos of the supporting organizations are displayed: de.NBI (German Network for Bioinformatics Infrastructure), IFB (Institut Français de Bioinformatique), and ELIXIR.

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Bérénice Batut @bebatut.bsky.social · 09/04/2025

Happy to be in Barcelona for the @elixir-europe.org Microbiome meeting, as co-lead and a representative of @ifb-elixir-fr.bsky.social french Microbiome community

2 women smiling in front of tables with men and slide

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Bérénice Batut @bebatut.bsky.social · 03/04/2025

#standupforscience #clermont-ferrand

A smiling woman holding a sign for Stand up for Science

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Bérénice Batut @bebatut.bsky.social · 08/01/2025

📚 Training is a core focus of microGalaxy! 45+ materials support researchers of all levels bridging the gap between learning and doing! 🧑‍🏫✨ Tools integrated into training contexts, grouped by EDAM operations:

Heatmap illustrating the presence of microGalaxy tool suites within the available microGalaxy training materials, grouped by EDAM topics. The tool suites are organized based on their corresponding EDAM operations, highlighting the breadth of tools utilized for different training contexts.

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Bérénice Batut @bebatut.bsky.social · 08/01/2025

🔧 microGalaxy workflows in action! 65+ ready-to-use workflows streamline complex analyses, from genome reconstruction to multi-omics integration. Here's how tools are grouped across workflows by EDAM operations: #Reproducibility

Heatmap illustrating the presence of microGalaxy tool suites within the available microGalaxy workflows, grouped by three levels of development. The tool suites are organized based on their corresponding EDAM operations, highlighting the breadth of tools utilized for different workflows.

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Bérénice Batut @bebatut.bsky.social · 08/01/2025

⚙️ Always evolving: (A) Tool availability spans 220+ tool suites across various Galaxy servers. (B) Usage trends show increasing adoption of microGalaxy tools over time. (C) The platform has gradually added hundreds of tools since its inception!

Heatmap illustrating the availability of microGalaxy tool suites (x-axis) across various Galaxy servers (y-axis), grouped by EDAM topics. Tool suites may appear in multiple clusters, as they can be annotated with several topics. A logarithmic scale is applied for improved visualization.

Scatter plots showing the usability of microGalaxy tool suites over the past five years across all Galaxy main servers, categorized by their EDAM operations. The x-axis represents the total number of tool users, while the y-axis also denotes the total number of tool users (potentially correct this redundancy).

Cumulative number of tools added to Galaxy over time, based on the date of the first commit for each tool suite.

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Bérénice Batut @bebatut.bsky.social · 08/01/2025

🌍 Community-driven innovation! In 2023, we surveyed researchers to uncover key needs in microbial data analysis. 🔹 Targeted tools 🔹 Challenges of Galaxy and non-Galaxy users 🔹 Deployment preferences Your input shaped microGalaxy! 🙌

Barplots with anonymous responses highlighting the main research targets, techniques, and analyses used or desired by microbial researchers. The figure also reports challenges faced by users who rarely or never use Galaxy, survey responses by continent, and preferences regarding tool deployment in Galaxy.

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Bérénice Batut @bebatut.bsky.social · 08/01/2025

🔧 Galaxy has been a key player in microbial research. See how microbial-specific studies contribute to its growing impact in this citation trend analysis.

Barplot showing the annual publication trends with the total number of citations (blue) alongside those specific to microbial research (brown)

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Bérénice Batut @bebatut.bsky.social · 08/01/2025

Here's a sneak peek of what microGalaxy offers: 🔍 Overview of supported microbial data analysis tasks (e.g., genomics, proteomics, multi-omics) and their outputs. #Reproducibility

Overview of microbial isolate data analysis tasks with corresponding tool suites and potential workflows available on microGalaxy.
This figure illustrates the diverse range of microbial isolate analysis tasks, grouped by data types (e.g., genomics, transcriptomics, proteomics, and multi-omics approaches). Each task is linked to intermediate and final outputs, with annotations indicating the tool suites that could be used for these analyses.

Overview of microbiome data analysis tasks with corresponding tool suites and potential workflows available on microGalaxy.
This figure illustrates the diverse range of microbiome analysis tasks, grouped by data types (e.g., metagenomics, metatranscriptomics, metaproteomics, and multi-omics approaches). Each task is linked to intermediate and final outputs, with annotations indicating the tool suites that could be used for these analyses.

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Bérénice Batut @bebatut.bsky.social · 08/01/2025

🌟 What is microGalaxy? It's a community-driven platform for microbial data analysis! 🔹 220+ tools 🔹 65+ workflows 🔹 45+ tutorials Built with FAIR principles to empower microbiology research from genomes to multi-omics. Learn more below!

Overview of microGalaxy's applications across Environment, Health, and Agri-Food domains, supporting DNA, RNA, protein, and metabolite analysis. Key topics include biogeochemical cycles, antimicrobial resistance, and pathogen monitoring. Centered on One Health, the platform integrates 220+ tool suites, 65+ workflows, and 45+ tutorials, promoting FAIR principles, citizen science, and education.

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