Michael Stadler

We have an opening in our team! See the link below if you are interested:

🚀 EuroBioC2026 – Call for Abstracts is Now Open!

We invite submissions for short talks, posters, and workshops for EuroBioC2026 by Jan 30, 2026.

👉 Submit here: openreview.net/group?id=bio...

⚠️ Note: Register on OpenReview at least two weeks before the abstract deadline to be able to submit.

🧬 EuroBioC2026 is coming to Turku, Finland, from June 3–5, 2026!

Expect 3 exciting days with the Bioconductor community, showcasing the latest advances in Bioconductor software and emerging technologies shaping computational biology.

👉 More details soon at eurobioc2026.bioconductor.org

I think this is a beautiful example of evolution having come up with a simple and elegant solution to a complex gene regulation task!

📣The Turco group is seeking a computational biologist to analyze large omics datasets. Work on cutting-edge 3D organoid models of the human placenta and be embedded in our Computational Biology Platform (part of @sib.swiss). Apply here: www.fmi.ch/education-ca...

🚨 We're hiring, please share! The FMI seeks a tenure-track Group Leader (Assistant Prof) in Structural Biology 🔬
Innovative scientists in genome regulation, RNA metabolism, or protein homeostasis—especially using cutting-edge approaches—apply now at www.fmi.ch/education-ca...

🙏 A big thank you to the Liberali Lab, FMI community & the FAIM imaging platform for testing and giving valuable feedback - keeping ez_zarr sharp, fast & useful! (3/3)

From spatial sequencing data to 5D images & high-throughput plate screens, ez_zarr helps you navigate images & labels quickly. If you work with NGFF OME standards, give it a try — and let us know what features you’d like to see next 💡(2/3) 📚 Docs: fmicompbio.github.io/ez_zarr/

ez-zarr: A Python package for easy access and visualisation of OME-Zarr filesets Barbiero et al., (2025). ez-zarr: A Python package for easy access and visualisation of OME-Zarr filesets. Journal of Open Source Software, 10(109), 7882, https://doi.org/10.21105/joss.07882

We’re excited to share that ez_zarr now supports Zarr v3! 🚀 Huge thanks to @mbstadler.bsky.social & @csoneson.bsky.social who took on the challenge of creating this open-source tool for fast, programmatic access to OME-Zarr file sets + easy plotting 📊
📄 joss.theoj.org/papers/10.2110… (1/3)

Bioconductor and ggplot2 4.0.0: What’s Changing and How to Prepare – Bioconductor community blog Preparing for the upcoming update - key changes, potential breakages, and what developers and users can do

📝 New blog post: Bioconductor and ggplot2 4.0.0 - What’s Changing and How to Prepare

A major ggplot2 update is coming and may impact Bioconductor packages. What’s changing, how to test, and where to get help 👉 blog.bioconductor.org/posts/2025-0...

#Bioconductor #RStats

Flyer for EuroBioC2025 Carpentry Workshops in Barcelona, Sept 15–16, 2025. Includes two in-person workshops on bulk and single-cell RNA-seq analysis. Hosted at Universitat Pompeu Fabra. Features logos, QR code, and registration link: eurobioc2025.bioconductor.org.

🎓 Sharpen your RNA-seq skills at EuroBioC2025 Workshops!

📍 Barcelona | Bulk & Single-cell RNA-seq
📅 Sept 15–16 | Hands-on training
🎟️ Limited spots. Register now: eurobioc2025.bioconductor.org

#Bioinformatics #EuroBioC2025

registration – EuroBioC2025 The budget EuroBioC2025 is conceived to break even after the conference. As a result, the organization of the EuroBioC2025 is unable to offer individual refunds.

📣 EuroBioC2025 Registration is Open! 🎉

📍 Barcelona, 17–19 Sept 2025

Join us for keynotes, talks, workshops & more on open-source bioinformatics & Bioconductor.
🔗 eurobioc2025.bioconductor.org/pages/regist...

#EuroBioC2025 #Bioinformatics

If you look for an easy way to plot OME-zarr images in your scripts, I hope the ez-zarr python package will be useful:

Eleven quick tips for writing a Bioconductor package

Eleven (!) quick tips for writing a Bioconductor package from @csoneson.bsky.social et al. from @fmiscience.bsky.social

journals.plos.org/ploscompbiol...

Charting gene secrets: New insights into genetic switches Gene regulation underpins nearly every biological process—from cell development to responses to environmental changes, and understanding it can provide insights into cancer and other diseases. Now, FM...

Researchers led by @marcbuhler.bsky.social @merleskribbe.bsky.social @mbstadler.bsky.social @csoneson.bsky.social shed light on how transcription factors control genes in fission yeast—plus, they created FMI TFexplorer, a free tool for scientists!
@pombase.bsky.social www.fmi.ch/news-events/...

A comprehensive Schizosaccharomyces pombe atlas of physical transcription factor interactions with proteins and chromatin Transcription factors (TFs) are key regulators of gene expression, yet many of their targets and modes of action remain unknown. In Schizosaccharomyce…

www.sciencedirect.com/science/arti...

I am very excited to share our latest work on the protein and chromatin interactomes of transcription factors! 🧬

Huge thanks to everyone who contributed, especially @csoneson.bsky.social and @mbstadler.bsky.social for driving this story with me! 🙌

Btw this is an actual movie, shot with a Canon DSLR in a photo studio incubator, of fluorescence-expressing plasmids competing and segregating inside cells

European Bioconductor Conference 2025 EuroBioC2025 is the European edition of the Bioconductor conference that will take place on September 17th to 19th, 2025, in Barcelona, Spain. EuroBioC2025 will bring together the Bioconductor…

📣 EuroBioC2025: Abstract Submissions Open!

Join us in Barcelona, Spain 🇪🇸, Sep 17-19, 2025, for the European Bioconductor Conference! Submit your abstract for a short talk, workshop, or poster by Apr 24.

➡️ Submit https://buff.ly/3EN9w6P

#EuroBioC2025 #Bioinformatics #RStats #DataScience

Cell heterogeneity and fate bistability drive tissue patterning during intestinal regeneration Tissue regeneration relies on the ability of cells to undergo de novo patterning. While tissue patterning has been viewed as the transition from initially identical un-patterned cells to an arrangemen...

A perfect start in the new year! 🌱 Regenerating tissues are just an amazing spatio temporal controlled process! Our new manuscript explores how cell heterogeneity and bistability orchestrate intestinal regeneration. 🧵 biorxiv.org/cgi/content/...

Permanent position for a Linux Systems Engineer: Are you fond of scientific computing and/Linux/HPC and would enjoy working in a vibrant research environment? Have a look at our job opening: www.fmi.ch/education-ca...

📣 Please share: We’re hiring a tenure-track Group Leader in Multicellular Systems to explore the molecular and cellular mechanisms driving the formation, maintenance, or destabilization of tissues, organs and organisms. Apply at: www.fmi.ch/education-ca...

Bioconductor 3.20 is released! 🎉🌟
Thanks to all developers and community members for contributing to the project! 🙌
👉 See the full release announcement: bioconductor.org/news/bioc_3_...

#Bioconductor #DataScience #Bioinformatics #OpenSource