Michael Kuhn
@biocs.bsky.social
Computational biologist. Research staff scientist and research coordinator in the @borklab.bsky.social at @embl.org Heidelberg.
Reposted by Michael Kuhn
Bweeps, what's the best short term for "GTDB species cluster that belongs to a known genus but has only a number for a species"? "Unnamed species"? "Novel species cluster"? "Candidate species"? "Thinger that no true biologist believes"? #bioinformatics
February 1, 2026 at 4:08 PM
Bweeps, what's the best short term for "GTDB species cluster that belongs to a known genus but has only a number for a species"? "Unnamed species"? "Novel species cluster"? "Candidate species"? "Thinger that no true biologist believes"? #bioinformatics
Reposted by Michael Kuhn
It's easy to see these academics as individual bad actors. But I'd argue--they were enabled by "elite" schools' look-the-other-way approach to dealing with big-name abusers, and by the fact that, societially, we treat people associated with "elite" schools as automatically deserving of deference.
Academics vying for a spot in Epstein‘s world. There are so many. I feel the need to make a thread, so I don’t keep confusing them. 1/
January 31, 2026 at 10:49 PM
It's easy to see these academics as individual bad actors. But I'd argue--they were enabled by "elite" schools' look-the-other-way approach to dealing with big-name abusers, and by the fact that, societially, we treat people associated with "elite" schools as automatically deserving of deference.
Reposted by Michael Kuhn
“We found that using AI assistance led to a statistically significant decrease in mastery.”
Props to Anthropic for studying the effects of their creation and reporting results that are not probably what they wished for
www.anthropic.com/research/AI-...
Props to Anthropic for studying the effects of their creation and reporting results that are not probably what they wished for
www.anthropic.com/research/AI-...
How AI assistance impacts the formation of coding skills
Anthropic is an AI safety and research company that's working to build reliable, interpretable, and steerable AI systems.
www.anthropic.com
January 31, 2026 at 3:50 AM
“We found that using AI assistance led to a statistically significant decrease in mastery.”
Props to Anthropic for studying the effects of their creation and reporting results that are not probably what they wished for
www.anthropic.com/research/AI-...
Props to Anthropic for studying the effects of their creation and reporting results that are not probably what they wished for
www.anthropic.com/research/AI-...
Reposted by Michael Kuhn
Thank you to everyone who reached out or shared what he meant to them and how he inspired them! We will keep working together, striving to fulfill Peer's scientific legacy. We hope you'll follow along! (3/3)
January 30, 2026 at 3:05 PM
Thank you to everyone who reached out or shared what he meant to them and how he inspired them! We will keep working together, striving to fulfill Peer's scientific legacy. We hope you'll follow along! (3/3)
Reposted by Michael Kuhn
Peer did pioneering work in so many research fields, and we aim that our research on the microbiome within the human gut and across environments will continue in his spirit. We have many ongoing projects, papers under review, and some coming out soon. (2/3)
January 30, 2026 at 3:05 PM
Peer did pioneering work in so many research fields, and we aim that our research on the microbiome within the human gut and across environments will continue in his spirit. We have many ongoing projects, papers under review, and some coming out soon. (2/3)
Reposted by Michael Kuhn
It has been two weeks since the unexpected death of Peer Bork, and all of us in his research group are deeply missing him. His scientific vision brought us together as a team, and we are immensely grateful for the time we spent together. 🧵
EMBL is deeply saddened by the passing of our Interim Director General Peer Bork, a pioneering scientist who left an indelible imprint on life science research in Europe and beyond.
We extend our deepest condolences to his family, friends, and colleagues.
www.embl.org/news/people-...
We extend our deepest condolences to his family, friends, and colleagues.
www.embl.org/news/people-...
January 30, 2026 at 3:05 PM
It has been two weeks since the unexpected death of Peer Bork, and all of us in his research group are deeply missing him. His scientific vision brought us together as a team, and we are immensely grateful for the time we spent together. 🧵
Reposted by Michael Kuhn
Archaea may not be well known, nor well studied, but these microorganisms can live in the most extreme environments, but also right on our skin. They’re everywhere.
EMBL researchers are now exploring their unique ecosystem adaptability and link to evolution.
www.embl.org/news/science...
EMBL researchers are now exploring their unique ecosystem adaptability and link to evolution.
www.embl.org/news/science...
January 29, 2026 at 9:36 AM
Archaea may not be well known, nor well studied, but these microorganisms can live in the most extreme environments, but also right on our skin. They’re everywhere.
EMBL researchers are now exploring their unique ecosystem adaptability and link to evolution.
www.embl.org/news/science...
EMBL researchers are now exploring their unique ecosystem adaptability and link to evolution.
www.embl.org/news/science...
Reposted by Michael Kuhn
We are looking for new editors for Microbiology, the flagship journal of @microbiologysociety.org
Deadline for applications is 16 Feb 2026
microbiologysociety.org/who-we-are/j...
Deadline for applications is 16 Feb 2026
microbiologysociety.org/who-we-are/j...
Jobs
View the current job vacancies at the Microbiology Society.
microbiologysociety.org
January 28, 2026 at 8:44 AM
We are looking for new editors for Microbiology, the flagship journal of @microbiologysociety.org
Deadline for applications is 16 Feb 2026
microbiologysociety.org/who-we-are/j...
Deadline for applications is 16 Feb 2026
microbiologysociety.org/who-we-are/j...
Reposted by Michael Kuhn
I think that is the core of the peer-review crisis. If we were to only do peer review of the scientific work that is both important enough and non-trivial, we would all save a lot of time. It will obviously be a challenge to decide what needs to be reviewed, I acknowledge that.
January 28, 2026 at 1:33 PM
I think that is the core of the peer-review crisis. If we were to only do peer review of the scientific work that is both important enough and non-trivial, we would all save a lot of time. It will obviously be a challenge to decide what needs to be reviewed, I acknowledge that.
Reposted by Michael Kuhn
What a fucking disaster.
Not only are OpenAI and the likes unleashing this shit on the world, they are deliberately leaning into the harms that their business model causes with products like Prism.
Not only are OpenAI and the likes unleashing this shit on the world, they are deliberately leaning into the harms that their business model causes with products like Prism.
Research Notes of the AAS in particular, which was set up to handle short, moderated contributions especially from students, is getting swamped. Often the authors clearly haven’t read what they’ve submitting, (Descriptions of figures that don’t exist or don’t show what they purport to)
January 28, 2026 at 6:38 AM
What a fucking disaster.
Not only are OpenAI and the likes unleashing this shit on the world, they are deliberately leaning into the harms that their business model causes with products like Prism.
Not only are OpenAI and the likes unleashing this shit on the world, they are deliberately leaning into the harms that their business model causes with products like Prism.
Reposted by Michael Kuhn
On the importance of preprints, regardless of whether you are Team Sponge or Team Jelly:
'King says that she wishes she had posted the study as a preprint so that the errors could have been caught sooner.'
www.nature.com/articles/d41...
'King says that she wishes she had posted the study as a preprint so that the errors could have been caught sooner.'
www.nature.com/articles/d41...
What were the first animals? The fierce sponge–jelly battle that just won’t end
For almost two decades, scientists have debated whether sponges or comb jellies are the first animal lineage. Now some are calling for a more harmonious approach.
www.nature.com
January 27, 2026 at 2:38 PM
On the importance of preprints, regardless of whether you are Team Sponge or Team Jelly:
'King says that she wishes she had posted the study as a preprint so that the errors could have been caught sooner.'
www.nature.com/articles/d41...
'King says that she wishes she had posted the study as a preprint so that the errors could have been caught sooner.'
www.nature.com/articles/d41...
Reposted by Michael Kuhn
📢Job opportunity📢 Two year Alliance Interinstitutional #Postdoc position in "mapping antibiotic resistance spread among human gut microbes" available in my group in collaboration with Heidelberg University Hospital www.bioquant.uni-heidelberg.de/groups/khedk... #AMR #microbiome
January 27, 2026 at 9:59 AM
📢Job opportunity📢 Two year Alliance Interinstitutional #Postdoc position in "mapping antibiotic resistance spread among human gut microbes" available in my group in collaboration with Heidelberg University Hospital www.bioquant.uni-heidelberg.de/groups/khedk... #AMR #microbiome
Reposted by Michael Kuhn
This is a key point: "When we hand a task to an LLM, we often don’t even notice how much agency we are giving up. This is because it is often only in the course of making decisions that we realize how many individual choices go into what seemed, at first glance, rather straightforward." 🌟
January 27, 2026 at 4:43 AM
This is a key point: "When we hand a task to an LLM, we often don’t even notice how much agency we are giving up. This is because it is often only in the course of making decisions that we realize how many individual choices go into what seemed, at first glance, rather straightforward." 🌟
Reposted by Michael Kuhn
"The reason these aspects of our jobs have been so challenging to automate is that they rely on something even more precious than our time: namely, our capacity for scientific decision-making. It is worth considering what we lose when we cede that—and our agency—to machines."
January 27, 2026 at 4:22 AM
"The reason these aspects of our jobs have been so challenging to automate is that they rely on something even more precious than our time: namely, our capacity for scientific decision-making. It is worth considering what we lose when we cede that—and our agency—to machines."
Reposted by Michael Kuhn
🚨We are hiring a Bioinformatician who will be embedded in our lab and work with members of the NCCR Microbiomes at ETH Zurich, as well as the Institute of Microbiology.🚨
nccr-microbiomes.ch
jobs.ethz.ch/job/view/JOP...
nccr-microbiomes.ch
jobs.ethz.ch/job/view/JOP...
Bioinformatician in Microbiome Research
jobs.ethz.ch
January 23, 2026 at 2:31 PM
🚨We are hiring a Bioinformatician who will be embedded in our lab and work with members of the NCCR Microbiomes at ETH Zurich, as well as the Institute of Microbiology.🚨
nccr-microbiomes.ch
jobs.ethz.ch/job/view/JOP...
nccr-microbiomes.ch
jobs.ethz.ch/job/view/JOP...
Reposted by Michael Kuhn
MaAsLin 3: a comprehensive, flexible framework for microbiome association studies. @hutlab.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
MaAsLin 3: refining and extending generalized multivariable linear models for meta-omic association discovery - Nature Methods
MaAsLin 3 is a comprehensive and flexible framework for microbiome association studies with expanded toolsets of statistical models, tests and types of inference.
www.nature.com
January 22, 2026 at 2:05 PM
MaAsLin 3: a comprehensive, flexible framework for microbiome association studies. @hutlab.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Michael Kuhn
Zotero 8 is out in stable: www.zotero.org/blog/zotero-8/
A bunch of new stuff -- the new citation dialog especially is a huge (and long overdue) improvement; massively speeds up anything I do in Word/GDocs with Zotero
A bunch of new stuff -- the new citation dialog especially is a huge (and long overdue) improvement; massively speeds up anything I do in Word/GDocs with Zotero
Zotero Blog » Blog Archive » Zotero 8
Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
www.zotero.org
January 22, 2026 at 7:15 PM
Zotero 8 is out in stable: www.zotero.org/blog/zotero-8/
A bunch of new stuff -- the new citation dialog especially is a huge (and long overdue) improvement; massively speeds up anything I do in Word/GDocs with Zotero
A bunch of new stuff -- the new citation dialog especially is a huge (and long overdue) improvement; massively speeds up anything I do in Word/GDocs with Zotero
Reposted by Michael Kuhn
Our latest. Led by the very talented @ahoiching.bsky.social
Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation www.nature.com/articles/s41... #jcampubs 🌊
Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation www.nature.com/articles/s41... #jcampubs 🌊
Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation - Nature Microbiology
Without key cell cycle control genes, SAR11 cells experience aneuploidy and growth inhibition when exposed to changes in nutrients, carbon sources or temperature stress, a vulnerability that may repre...
www.nature.com
January 22, 2026 at 2:24 PM
Our latest. Led by the very talented @ahoiching.bsky.social
Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation www.nature.com/articles/s41... #jcampubs 🌊
Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation www.nature.com/articles/s41... #jcampubs 🌊
Reposted by Michael Kuhn
EMBL is deeply saddened by the passing of our Interim Director General Peer Bork, a pioneering scientist who left an indelible imprint on life science research in Europe and beyond.
We extend our deepest condolences to his family, friends, and colleagues.
www.embl.org/news/people-...
We extend our deepest condolences to his family, friends, and colleagues.
www.embl.org/news/people-...
January 22, 2026 at 7:40 AM
EMBL is deeply saddened by the passing of our Interim Director General Peer Bork, a pioneering scientist who left an indelible imprint on life science research in Europe and beyond.
We extend our deepest condolences to his family, friends, and colleagues.
www.embl.org/news/people-...
We extend our deepest condolences to his family, friends, and colleagues.
www.embl.org/news/people-...
Reposted by Michael Kuhn
🗜️⚡ If you use gzip/gunzip a lot in your pipelines, switch to the faster"libdeflate" versions instead! They use modern CPU capabilities to achieve a 2-3x speedup.
libdeflate is in conda, and "libdeflate-gzip" and "libdeflate-gunzip" are drop-in replacements. #unix
github.com/ebiggers/lib...
libdeflate is in conda, and "libdeflate-gzip" and "libdeflate-gunzip" are drop-in replacements. #unix
github.com/ebiggers/lib...
GitHub - ebiggers/libdeflate: Heavily optimized library for DEFLATE/zlib/gzip compression and decompression
Heavily optimized library for DEFLATE/zlib/gzip compression and decompression - ebiggers/libdeflate
github.com
January 20, 2026 at 1:37 AM
🗜️⚡ If you use gzip/gunzip a lot in your pipelines, switch to the faster"libdeflate" versions instead! They use modern CPU capabilities to achieve a 2-3x speedup.
libdeflate is in conda, and "libdeflate-gzip" and "libdeflate-gunzip" are drop-in replacements. #unix
github.com/ebiggers/lib...
libdeflate is in conda, and "libdeflate-gzip" and "libdeflate-gunzip" are drop-in replacements. #unix
github.com/ebiggers/lib...
Reposted by Michael Kuhn
One of my favourite pics of Peer.
Took this one on a summer day in 2021 during a lab get-to-together at his place.
Cheer to you too Peer.
#PeerBork
Took this one on a summer day in 2021 during a lab get-to-together at his place.
Cheer to you too Peer.
#PeerBork
January 19, 2026 at 9:09 AM
One of my favourite pics of Peer.
Took this one on a summer day in 2021 during a lab get-to-together at his place.
Cheer to you too Peer.
#PeerBork
Took this one on a summer day in 2021 during a lab get-to-together at his place.
Cheer to you too Peer.
#PeerBork
Reposted by Michael Kuhn
The new 2026 NAR Nucleic Acids Research Database Issue is now out! 🎉
Take a look at the Editorial here academic.oup.com/nar/article/...
and browse the whole Issue here
academic.oup.com/nar/issue/54...
Take a look at the Editorial here academic.oup.com/nar/article/...
and browse the whole Issue here
academic.oup.com/nar/issue/54...
The 2026 Nucleic Acids Research database issue and the online molecular biology database collection
Abstract. The 2026 Nucleic Acids Research database issue has 182 papers from across biology and neighbouring fields. Eighty-four of these papers describe n
academic.oup.com
January 18, 2026 at 11:37 AM
The new 2026 NAR Nucleic Acids Research Database Issue is now out! 🎉
Take a look at the Editorial here academic.oup.com/nar/article/...
and browse the whole Issue here
academic.oup.com/nar/issue/54...
Take a look at the Editorial here academic.oup.com/nar/article/...
and browse the whole Issue here
academic.oup.com/nar/issue/54...
Reposted by Michael Kuhn
This is such hard news to process. Such an amazing scientist and inspiration for so many of us.
www.embl.org/news/embl-an...
www.embl.org/news/embl-an...
In remembrance of Peer Bork | EMBL
EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.
www.embl.org
January 16, 2026 at 6:01 PM
This is such hard news to process. Such an amazing scientist and inspiration for so many of us.
www.embl.org/news/embl-an...
www.embl.org/news/embl-an...
Reposted by Michael Kuhn
Big news! The Data Management team/Data Science Centre at EMBL (i.e. my team) is hiring for a position based in Heidelberg (but working across all sites!). We are looking for a scientific workflows developer that will focus on multimodal pipelines. embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Scientific Workflows Developer
The European Molecular Biology Laboratory (EMBL) is Europe’s life sciences laboratory – an intergovernmental organisation with more than 110 independent research groups and service teams covering the ...
embl.wd103.myworkdayjobs.com
January 14, 2026 at 9:37 AM
Big news! The Data Management team/Data Science Centre at EMBL (i.e. my team) is hiring for a position based in Heidelberg (but working across all sites!). We are looking for a scientific workflows developer that will focus on multimodal pipelines. embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Reposted by Michael Kuhn
Closely related microbes tend to live in similar communities across Earth’s environments.
We call this pattern community conservatism - extending established ecological patterns to the microbial world.
🧬🌍 #MicrobialEcology #Evolution
Read the full article here: doi.org/10.1038/s415...
We call this pattern community conservatism - extending established ecological patterns to the microbial world.
🧬🌍 #MicrobialEcology #Evolution
Read the full article here: doi.org/10.1038/s415...
January 16, 2026 at 10:17 AM
Closely related microbes tend to live in similar communities across Earth’s environments.
We call this pattern community conservatism - extending established ecological patterns to the microbial world.
🧬🌍 #MicrobialEcology #Evolution
Read the full article here: doi.org/10.1038/s415...
We call this pattern community conservatism - extending established ecological patterns to the microbial world.
🧬🌍 #MicrobialEcology #Evolution
Read the full article here: doi.org/10.1038/s415...