Michael Stadler
@mbstadler.bsky.social
Reposted by Michael Stadler
🧬 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
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
October 29, 2025 at 9:02 AM
🧬 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
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!
Paper alert! doi.org/10.1038/s443... - "A scheduler for rhythmic gene expression". We show how 9 txn factors suffice for rhythmic gene expression of thousands of genes with any phase or amplitude in #Celegans larvae (and also look at the tissues where oscillations happen) 1/n
October 13, 2025 at 2:31 PM
I think this is a beautiful example of evolution having come up with a simple and elegant solution to a complex gene regulation task!
Reposted by Michael Stadler
📣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...
September 12, 2025 at 7:02 AM
📣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...
Reposted by Michael Stadler
🚨 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...
Innovative scientists in genome regulation, RNA metabolism, or protein homeostasis—especially using cutting-edge approaches—apply now at www.fmi.ch/education-ca...
September 8, 2025 at 8:15 AM
🚨 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...
Innovative scientists in genome regulation, RNA metabolism, or protein homeostasis—especially using cutting-edge approaches—apply now at www.fmi.ch/education-ca...
Reposted by Michael Stadler
🙏 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)
August 15, 2025 at 1:08 PM
🙏 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)
Reposted by Michael Stadler
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
fmicompbio.github.io
August 15, 2025 at 1:08 PM
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/
Reposted by Michael Stadler
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)
📄 joss.theoj.org/papers/10.2110… (1/3)
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
joss.theoj.org
August 15, 2025 at 1:07 PM
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)
📄 joss.theoj.org/papers/10.2110… (1/3)
Reposted by Michael Stadler
📝 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
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
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
blog.bioconductor.org
July 7, 2025 at 12:36 PM
📝 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
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
Reposted by Michael Stadler
🎓 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
📍 Barcelona | Bulk & Single-cell RNA-seq
📅 Sept 15–16 | Hands-on training
🎟️ Limited spots. Register now: eurobioc2025.bioconductor.org
#Bioinformatics #EuroBioC2025
June 12, 2025 at 8:58 AM
🎓 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
📍 Barcelona | Bulk & Single-cell RNA-seq
📅 Sept 15–16 | Hands-on training
🎟️ Limited spots. Register now: eurobioc2025.bioconductor.org
#Bioinformatics #EuroBioC2025
Reposted by Michael Stadler
📣 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
📍 Barcelona, 17–19 Sept 2025
Join us for keynotes, talks, workshops & more on open-source bioinformatics & Bioconductor.
🔗 eurobioc2025.bioconductor.org/pages/regist...
#EuroBioC2025 #Bioinformatics
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.bioconductor.org
May 19, 2025 at 7:41 AM
📣 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
📍 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:
Just published in JOSS: 'ez-zarr: A Python package for easy access and visualisation of OME-Zarr filesets' https://doi.org/10.21105/joss.07882
May 18, 2025 at 7:30 AM
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:
Reposted by Michael Stadler
Eleven (!) quick tips for writing a Bioconductor package from @csoneson.bsky.social et al. from @fmiscience.bsky.social
journals.plos.org/ploscompbiol...
journals.plos.org/ploscompbiol...
Eleven quick tips for writing a Bioconductor package
journals.plos.org
March 20, 2025 at 9:49 AM
Eleven (!) quick tips for writing a Bioconductor package from @csoneson.bsky.social et al. from @fmiscience.bsky.social
journals.plos.org/ploscompbiol...
journals.plos.org/ploscompbiol...
Reposted by Michael Stadler
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/...
@pombase.bsky.social www.fmi.ch/news-events/...
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...
www.fmi.ch
February 27, 2025 at 7:14 AM
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/...
@pombase.bsky.social www.fmi.ch/news-events/...
Reposted by Michael Stadler
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! 🙌
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! 🙌
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
February 26, 2025 at 4:41 PM
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! 🙌
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! 🙌
Reposted by Michael Stadler
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
Legitmately thrilled to share our latest work, in which @fernpizza.bsky.social solved an experimental challenge in plasmid biology as old as the field: measuring how plasmids compete and evolve within individual cells!
February 22, 2025 at 3:04 PM
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
Reposted by Michael Stadler
📣 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
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
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…
buff.ly
February 20, 2025 at 9:09 AM
📣 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
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
Reposted by Michael Stadler
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/...
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...
biorxiv.org
January 15, 2025 at 5:32 PM
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...
Friedrich Miescher Institute, open position
Friedrich Miescher Institute, open position
www.fmi.ch
January 15, 2025 at 1:44 PM
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...
Reposted by Michael Stadler
📣 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...
December 16, 2024 at 11:50 AM
📣 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...
Reposted by Michael Stadler
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
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
Bioconductor - Bioconductor 3.20 Released
The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and dat...
bioconductor.org
October 30, 2024 at 10:04 PM
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
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