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
ERC Plus Grants
• No career limit, current ERCs are not eligible
• Major challenge, transformative research
• Up to 7 million euros, up to 7 years
• 30 grants per year, 2 years, only once per lifetime
• Same application format, plus vision statement
• Deadline in September 2026, 2 stage evaluation
• No career limit, current ERCs are not eligible
• Major challenge, transformative research
• Up to 7 million euros, up to 7 years
• 30 grants per year, 2 years, only once per lifetime
• Same application format, plus vision statement
• Deadline in September 2026, 2 stage evaluation
Webinar on the new ERC Plus Grants live starting now www.youtube.com/live/Dzkas7f...
Webinar on the new ERC Plus Grants
YouTube video by European Research Council
www.youtube.com
November 28, 2025 at 2:19 PM
ERC Plus Grants
• No career limit, current ERCs are not eligible
• Major challenge, transformative research
• Up to 7 million euros, up to 7 years
• 30 grants per year, 2 years, only once per lifetime
• Same application format, plus vision statement
• Deadline in September 2026, 2 stage evaluation
• No career limit, current ERCs are not eligible
• Major challenge, transformative research
• Up to 7 million euros, up to 7 years
• 30 grants per year, 2 years, only once per lifetime
• Same application format, plus vision statement
• Deadline in September 2026, 2 stage evaluation
Reposted by Michael Kuhn
📣 Applications for the #EIPOD-Linc Postdoctoral Fellowships Programme are open!
Join us to work on self-designed interdisciplinary research on projects related to exploring life in context.
✍ Apply now: www.embl.org/about/info/p...
Join us to work on self-designed interdisciplinary research on projects related to exploring life in context.
✍ Apply now: www.embl.org/about/info/p...
November 28, 2025 at 10:02 AM
📣 Applications for the #EIPOD-Linc Postdoctoral Fellowships Programme are open!
Join us to work on self-designed interdisciplinary research on projects related to exploring life in context.
✍ Apply now: www.embl.org/about/info/p...
Join us to work on self-designed interdisciplinary research on projects related to exploring life in context.
✍ Apply now: www.embl.org/about/info/p...
Reposted by Michael Kuhn
📢 New preprint is out on bioRxiv 📢:
How much does virome prep influence our view of the human gut virome?
Short answer: a lot.
Long answer:
doi.org/10.1101/2025...
Different methods lead to distinct community structures, richness, and major virus-host abundance patterns.
🧵 1/5
How much does virome prep influence our view of the human gut virome?
Short answer: a lot.
Long answer:
doi.org/10.1101/2025...
Different methods lead to distinct community structures, richness, and major virus-host abundance patterns.
🧵 1/5
November 27, 2025 at 8:44 PM
📢 New preprint is out on bioRxiv 📢:
How much does virome prep influence our view of the human gut virome?
Short answer: a lot.
Long answer:
doi.org/10.1101/2025...
Different methods lead to distinct community structures, richness, and major virus-host abundance patterns.
🧵 1/5
How much does virome prep influence our view of the human gut virome?
Short answer: a lot.
Long answer:
doi.org/10.1101/2025...
Different methods lead to distinct community structures, richness, and major virus-host abundance patterns.
🧵 1/5
Reposted by Michael Kuhn
Even the the damn twitter card for this Nature Scientific Reports is clearly AI Slop.
November 27, 2025 at 6:56 PM
Even the the damn twitter card for this Nature Scientific Reports is clearly AI Slop.
Reposted by Michael Kuhn
One of our founding directors Anthony Hyman @hymanlab.bsky.social will become @embl.org Director General: www.mpi-cbg.de/news-outreac...
November 27, 2025 at 1:20 PM
One of our founding directors Anthony Hyman @hymanlab.bsky.social will become @embl.org Director General: www.mpi-cbg.de/news-outreac...
Reposted by Michael Kuhn
Anthony A. Hyman will become EMBL’s next Director General.
He joins EMBL from @mpi-cbg.de in Dresden. He is also Professor of Molecular Biology @tudresden.bsky.social, and was a group leader at EMBL Heidelberg from 1993 to 1999.
www.embl.org/news/people-...
He joins EMBL from @mpi-cbg.de in Dresden. He is also Professor of Molecular Biology @tudresden.bsky.social, and was a group leader at EMBL Heidelberg from 1993 to 1999.
www.embl.org/news/people-...
November 27, 2025 at 1:02 PM
Anthony A. Hyman will become EMBL’s next Director General.
He joins EMBL from @mpi-cbg.de in Dresden. He is also Professor of Molecular Biology @tudresden.bsky.social, and was a group leader at EMBL Heidelberg from 1993 to 1999.
www.embl.org/news/people-...
He joins EMBL from @mpi-cbg.de in Dresden. He is also Professor of Molecular Biology @tudresden.bsky.social, and was a group leader at EMBL Heidelberg from 1993 to 1999.
www.embl.org/news/people-...
Reposted by Michael Kuhn
So proud to watch Jana turn a side quest into an entire research programme. Couldn’t imagine a more well-deserved outcome. 😍
The mighty yeast reveals what we believe are general principles of centromere evolution!
Behind the curtain: communities.springernature.com/posts/counti...
#MEvoSky 🧪🌎
The mighty yeast reveals what we believe are general principles of centromere evolution!
Behind the curtain: communities.springernature.com/posts/counti...
#MEvoSky 🧪🌎
November 27, 2025 at 9:21 AM
So proud to watch Jana turn a side quest into an entire research programme. Couldn’t imagine a more well-deserved outcome. 😍
The mighty yeast reveals what we believe are general principles of centromere evolution!
Behind the curtain: communities.springernature.com/posts/counti...
#MEvoSky 🧪🌎
The mighty yeast reveals what we believe are general principles of centromere evolution!
Behind the curtain: communities.springernature.com/posts/counti...
#MEvoSky 🧪🌎
Reposted by Michael Kuhn
Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years
#phagesky
www.nature.com/articles/s41...
#phagesky
www.nature.com/articles/s41...
Long-read metagenomics reveals phage dynamics in the human gut microbiome - Nature
Complex prophage integration dynamics, including low-level induction, cross-family host range and transposase-mediated mobilization, challenge existing paradigms and deepen our understanding of phage–...
www.nature.com
November 26, 2025 at 9:55 PM
Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years
#phagesky
www.nature.com/articles/s41...
#phagesky
www.nature.com/articles/s41...
Reposted by Michael Kuhn
Every biologist knows the story of Fleming's chance discovery of penicillin. But is it true?
Here, with @asimovpress.bsky.social, I write about inconsistencies in the canonical story, and explore a few alternative theories about what really happened in that St. Mary's lab in the summer of 1928.
Here, with @asimovpress.bsky.social, I write about inconsistencies in the canonical story, and explore a few alternative theories about what really happened in that St. Mary's lab in the summer of 1928.
The Penicillin Myth
Competing theories seek to explain inconsistencies surrounding Alexander Fleming’s famed discovery.
press.asimov.com
November 24, 2025 at 5:00 PM
Every biologist knows the story of Fleming's chance discovery of penicillin. But is it true?
Here, with @asimovpress.bsky.social, I write about inconsistencies in the canonical story, and explore a few alternative theories about what really happened in that St. Mary's lab in the summer of 1928.
Here, with @asimovpress.bsky.social, I write about inconsistencies in the canonical story, and explore a few alternative theories about what really happened in that St. Mary's lab in the summer of 1928.
Reposted by Michael Kuhn
I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵
The missing heritability question is now (mostly) answered
Not with a bang but with a whimper
theinfinitesimal.substack.com
November 21, 2025 at 10:34 PM
I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵
Reposted by Michael Kuhn
"essays produced by ChatGPT are soulless, boring abominations. Words, phrases and punctuation rarely used by the average college student are pervasive." www.huffpost.com/entry/histor...
I Set A Trap To Catch My Students Cheating With AI. The Results Were Shocking.
"Students are not just undermining their ability to learn, but to someday lead."
www.huffpost.com
November 21, 2025 at 12:39 PM
"essays produced by ChatGPT are soulless, boring abominations. Words, phrases and punctuation rarely used by the average college student are pervasive." www.huffpost.com/entry/histor...
Reposted by Michael Kuhn
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 Michael Kuhn
HTTP has a new method: QUERY. Tl;dr: GET with a body.
https://www.ietf.org/archive/id/draft-ietf-httpbis-safe-method-w-body-14.html
#ietf
https://www.ietf.org/archive/id/draft-ietf-httpbis-safe-method-w-body-14.html
#ietf
The HTTP QUERY Method
This specification defines the QUERY method for HTTP. A QUERY requests that the request target process the enclosed content in a safe and idempotent manner and then respond with the result of that processing. This is similar to POST requests but can be automatically repeated or restarted without concern for partial state changes.
www.ietf.org
November 20, 2025 at 9:39 PM
HTTP has a new method: QUERY. Tl;dr: GET with a body.
https://www.ietf.org/archive/id/draft-ietf-httpbis-safe-method-w-body-14.html
#ietf
https://www.ietf.org/archive/id/draft-ietf-httpbis-safe-method-w-body-14.html
#ietf
Reposted by Michael Kuhn
I am by no means a prominent public intellectual, but my inbox is increasingly filled with messages from people who have been convinced by sycophantic chatbots that they have discovered revolutionary theories that entirely upend our scientific understanding of the universe.
November 21, 2025 at 2:49 AM
I am by no means a prominent public intellectual, but my inbox is increasingly filled with messages from people who have been convinced by sycophantic chatbots that they have discovered revolutionary theories that entirely upend our scientific understanding of the universe.
Reposted by Michael Kuhn
Our latest paper is out with @adiop.bsky.social and @gmdouglas.bsky.social. We analyzed the extent of homologous recombination between bacterial species (introgression) and how it affects species borders (it can vary a lot depending on the approach used to classify species!). rdcu.be/eQAMf
Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy
Nature Communications - It is commonly thought that bacterial species borders tend to be fuzzy, due to frequent exchange of DNA. Here, Diop et al. quantify the patterns of gene flow between core...
rdcu.be
November 18, 2025 at 9:01 PM
Our latest paper is out with @adiop.bsky.social and @gmdouglas.bsky.social. We analyzed the extent of homologous recombination between bacterial species (introgression) and how it affects species borders (it can vary a lot depending on the approach used to classify species!). rdcu.be/eQAMf
Reposted by Michael Kuhn
Now online! Nutrient competition predicts gut microbiome restructuring under drug perturbations
Nutrient competition predicts gut microbiome restructuring under drug perturbations
Systematic profiling of 707 drugs on their impact on stool-derived microbial communities shows that nutrient competition explains and predicts species shifts under drug treatment and that post-drug recovery is driven by ecological interactions like extinction and strain swapping.
dlvr.it
November 17, 2025 at 7:51 PM
Now online! Nutrient competition predicts gut microbiome restructuring under drug perturbations
Reposted by Michael Kuhn
Excellent read. My general experience is that AI isn't going to create good, complicated code from scratch...but if you have specific things to do or translation like this, it does indeed save time.
I just wish it weren't being marketed as the be-all/end-all...coders no longer needed solution.
I just wish it weren't being marketed as the be-all/end-all...coders no longer needed solution.
November 15, 2025 at 3:55 PM
Excellent read. My general experience is that AI isn't going to create good, complicated code from scratch...but if you have specific things to do or translation like this, it does indeed save time.
I just wish it weren't being marketed as the be-all/end-all...coders no longer needed solution.
I just wish it weren't being marketed as the be-all/end-all...coders no longer needed solution.
Reposted by Michael Kuhn
Good post.
I just published my weekly newsletter to >10K subscribers: The truth about AI coding for bioinformatics divingintogeneticsandgenomics.kit.com/posts/ai-po...
AI ported 6,000+ lines of Python in 8 hours. Here’s the catch
divingintogeneticsandgenomics.kit.com
November 15, 2025 at 3:50 PM
Good post.
Reposted by Michael Kuhn
Bug in Springer Nature metadata may be causing ‘significant, systemic’ citation inflation
Bug in Springer Nature metadata may be causing ‘significant, systemic’ citation inflation
Millions of researchers could be affected by a “dramatic distortion of citation counts” likely caused by flaws in how the academic publishing giant Springer Nature handles article metadata, accordi…
retractionwatch.com
November 11, 2025 at 5:54 PM
Bug in Springer Nature metadata may be causing ‘significant, systemic’ citation inflation
Reposted by Michael Kuhn
@sacrozhangt.bsky.social and I wrote a commentary on Jordi van Gestel and Carol Gross's latest paper, check it out!
www.pnas.org/doi/10.1073/...
Sadly, the Editors at PNAS rejected our initial introduction, which was a David Attenborough style voice over of the microbial Serengeti (included below)
www.pnas.org/doi/10.1073/...
Sadly, the Editors at PNAS rejected our initial introduction, which was a David Attenborough style voice over of the microbial Serengeti (included below)
November 13, 2025 at 2:54 PM
@sacrozhangt.bsky.social and I wrote a commentary on Jordi van Gestel and Carol Gross's latest paper, check it out!
www.pnas.org/doi/10.1073/...
Sadly, the Editors at PNAS rejected our initial introduction, which was a David Attenborough style voice over of the microbial Serengeti (included below)
www.pnas.org/doi/10.1073/...
Sadly, the Editors at PNAS rejected our initial introduction, which was a David Attenborough style voice over of the microbial Serengeti (included below)
Reposted by Michael Kuhn
“Bin Chicken” is now published in Nature Methods! It substantially improves genome recovery through rational coassembly 🧬🖥️. Applied to public 🌍 metagenomes, we recovered 24,000 novel species 🦠, including 6 new phyla.
doi.org/10.1038/s415...
@benjwoodcroft.bsky.social @rhysnewell.bsky.social
🧵1/6
doi.org/10.1038/s415...
@benjwoodcroft.bsky.social @rhysnewell.bsky.social
🧵1/6
November 13, 2025 at 10:09 AM
“Bin Chicken” is now published in Nature Methods! It substantially improves genome recovery through rational coassembly 🧬🖥️. Applied to public 🌍 metagenomes, we recovered 24,000 novel species 🦠, including 6 new phyla.
doi.org/10.1038/s415...
@benjwoodcroft.bsky.social @rhysnewell.bsky.social
🧵1/6
doi.org/10.1038/s415...
@benjwoodcroft.bsky.social @rhysnewell.bsky.social
🧵1/6
Reposted by Michael Kuhn
Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
November 11, 2025 at 5:15 PM
Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Michael Kuhn
Sarah Kendzior was suspended this month for referencing famous Johnny Cash song lyrics in October when commenting on a WSJ article shitting on Johnny Cash. Mmmkay. Bluesky is super serious.
Wait, was she referring the fucking WSJ article that was arguing that Johnny Cash was considered uncool by music fans? The one where the fucking author just announced that he's a fucking musical illiterate?
The article referred to here:
savingcountrymusic.com/wall-street-...
The article referred to here:
savingcountrymusic.com/wall-street-...
‘Wall Street Journal’ Causes Stir By Initially Calling Johnny Cash...
'The Wall Street Journal' stepped in it pretty good late last week while strangely deciding to step into the realm of country music by initially characterizing Johnny Cash as "uncool."
savingcountrymusic.com
November 13, 2025 at 5:59 AM
Sarah Kendzior was suspended this month for referencing famous Johnny Cash song lyrics in October when commenting on a WSJ article shitting on Johnny Cash. Mmmkay. Bluesky is super serious.
Reposted by Michael Kuhn
In a rare case of Substack notes usefulness, I just learned that Sarah Kendzior (author of They Knew and a brilliant writer) got bounced from Bluesky. What the hell? new @sarahkendzior.bsky.social
November 11, 2025 at 4:09 AM
In a rare case of Substack notes usefulness, I just learned that Sarah Kendzior (author of They Knew and a brilliant writer) got bounced from Bluesky. What the hell? new @sarahkendzior.bsky.social
Reposted by Michael Kuhn
Half of microbial eukaryote literature focuses on only twelve human parasites
#microbiology #protists #eukaryotes
@isme-microbes.bsky.social
academic.oup.com/ismej/articl...
#microbiology #protists #eukaryotes
@isme-microbes.bsky.social
academic.oup.com/ismej/articl...
Half of microbial eukaryote literature focuses on only 12 human parasites
Abstract. Although microbial eukaryotes comprise the majority of eukaryotic phylogenetic diversity and inhabit nearly all ecosystems globally, most researc
academic.oup.com
November 9, 2025 at 10:10 AM
Half of microbial eukaryote literature focuses on only twelve human parasites
#microbiology #protists #eukaryotes
@isme-microbes.bsky.social
academic.oup.com/ismej/articl...
#microbiology #protists #eukaryotes
@isme-microbes.bsky.social
academic.oup.com/ismej/articl...