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Michael Kuhn

@biocs.bsky.social
326 followers 184 following 59 posts

Computational biologist. Research staff scientist and research coordinator in the @borklab.bsky.social at @embl.org Heidelberg.

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Reposted by Michael Kuhn
kottke.org @kottke.org · 07/10/2026
AI-generated images don’t have to look like AI-generated images…they can be any style you want. (It’s just going to get more and more difficult to tell…) [john.hartnup.uk]
john.hartnup.uk
AI-generated posters don’t have to be horrible
Why AI-generated event posters all look alike — and how naming a design style and era, from Bauhaus to punk fanzine, gets far better results.
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Matt Olm @mattolm.bsky.social · 07/10/2026
My final postdoc project is out today in Nature! We show microbes co-migrated with humans out of Africa; three independent methods agree, and timing matches archaeological / genetic evidence (Fig. 4c). Seeing Fig. 4c for 1st time was one of my most memorable "eureka" moments! doi.org/10.1038/s415...
doi.org
Prehistoric global migration of vanishing gut microbes with humans - Nature
Microbial species disappearing from industrialized populations have evolved with humans over millennia and migrated worldwide with them—this may have consequences for human health.
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Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 06/10/2026
🏁 That's a wrap! The @biohub.org Cell Tracking machine learning challenge on @kaggle.com is over: 4,478 participants, 3,947 teams, 120 countries, 95,438 submissions, tracking every cell of zebrafish embryos. 🧪🔬🧵 kaggle.com/competition... #microscopy
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Anna Mankowski @oceanna.bsky.social · 02/10/2026
I am still a bit speechless but my main PhD project is finally out in Science Advances. It was a long process, but I am so happy with the final results! Massive thanks to everyone involved, especially my co-authors and everyone involved in sampling! www.science.org/doi/10.1126/...
science.org
Stability in flexibility: Shifting alliances stabilize the symbioses of marine animals over 150 million years
Many animals benefit from microbial symbionts that aid digestion, supply essential nutrients, or provide defense. When this dependence becomes obligate, as in gutless marine oligochaetes that have los...
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EMBL Events @events.embl.org · 28/09/2026
Thanks to additional funding, the registration fees for #EMBLBorkMemorial have been set at a reduced rate. This symposium will reflect on Peer Bork's past achievements and explore future directions of fields such as protein biology and more. Submit your abstract by 10 Nov: s.embl.org/pbs27-01-bl
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Jesse Shapiro @bjesseshapiro.bsky.social · 29/09/2026
Our latest, spearheaded by the truly indefatigable @emderrick.bsky.social in which we search for selective sweeps in nature and genetic targets of selection within a species in the context of a diverse background community @isme-microbes.bsky.social doi.org/10.1093/isme... 🧵 1/n
doi.org
Validate User
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Carl T. Bergstrom @carlbergstrom.com · 19/09/2026
When we talk about the costs that LLMs impose on society we should not forget the fact that nothing works anymore because everyone is so scared of getting their shit scraped. I can't even use google scholar from my university or starlink because they send too much traffic.
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Ed Yong is offline @edyong209.bsky.social · 17/09/2026
Briefly popping my head back in to unveil the cover of my upcoming book, LIFE BEYOND MEASURE: Nature's Hidden Wonders at Every Scale. It’ll be out on April 6 in the U.S. and April 29 in the U.K. and you can pre-order it right now! www.penguinrandomhouse.com/books/757705... 1/
A book cover featuring a beautiful closely cropped portrait of an Anna's hummingbird. The cover says LIFE BEYOND MEASURE: Nature's Hidden Wonders at Every Scale, by Ed Yong. The image also says US: 4/06/27 and UK: 4/29/27
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Jim Shaw @jimshaw.bsky.social · 15/09/2026
The sylph metagenome profiler is v1.0.0! sylph-docs.github.io A new DB format + approach --> huge performance gains: GTDB-R232 (200k species) now takes < 5 GB of RAM and ~30s (2GB fq.gz). Huge thanks to @benjwoodcroft.bsky.social and his ongoing performance efforts (github.com/wwood/weebill)
sylph-docs.github.io
Documentation for sylph - ultrafast, precise metagenomic profiling
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Jacobo de la Cuesta-Zuluaga @jdlcz.bsky.social · 14/09/2026
Just out! @kiranrpatil.bsky.social @lisamaierlab.bsky.social and I wrote about how compounds not considered antibiotics (pharmaceutical, dietary, industrial, agricultural) can still impact the #microbiome 🦠 and human #health nature.com/articles/s41575-026-01258-w @natrevgastrohep.nature.com
Diagram of how non-antibiotic chemicals (from food, drugs, industry, and farming) interact with gut bacteria. Left side lists each source with an example compound and its structure: carboxymethyl cellulose from diet, metformin from pharmaceuticals, perfluorooctanoic acid from industry, chlorpyrifos from agriculture. In the center, arrows connect host and microbiome in both directions, labeled "Pharmacoecology" and "Pharmacomicrobiomics." The right side shows six effects on bacteria: bioaccumulation, direct killing, growth inhibition, horizontal gene transfer, cross-sensitization, and cross-protection. Boxes along the bottom flag the variables that shape these outcomes: exposure timing and dose, host diet and physiology, and the microbiome's existing structure.
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Ian Sudbery @iansudbery.bsky.social · 12/09/2026
Holy moly, @ensembl.org killed biomart! Hope many R scripts are there out there that depend on biomaRt? How many people have informatics practicals, or undergraduate project instructions that depend on a web interface for bulk selection of data?
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Terence Tao @teorth.bsky.social · 11/09/2026
A group of 25 Fields Medalists, including myself, have made a joint declaration on Math and AI: mathandai.org . We welcome additional signatories. See also this article in the Economist announcing the declaration: www.economist.com/science-and-...
mathandai.org
Declaration — Math and AI
Read the declaration and add your name.
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Michael Kuhn @biocs.bsky.social · 09/09/2026
Yes, Jaime is still the driving force behind eggNOG, and has been pushing the new eggNOG-mapper version forward. We had some trouble with the cloud computing for the mapper, but I'm not sure about the latest status.
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EMBL Events @events.embl.org · 07/09/2026
At the start of 2026, EMBL lost long-serving colleague and Interim Director General Peer Bork. Join us in commemorating Peer and his legacy at the #EMBLBorkMemorial. Submit your abstract by 10 November: s.embl.org/pbs27-01-bl
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Lars Juhl Jensen @larsjuhljensen.bsky.social · 03/09/2026
I've personally set 10% funding rate as my absolute minimum for being willing to review for a funding agency. If you fund less that you are just wasting everyone's time, because you're not even funding the excellent proposals.
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Bork Group at EMBL Heidelberg @borklab.bsky.social · 01/09/2026
We've been very moved by the tributes paid to Peer at conferences around the world: e.g. at ISME by Jeroen Raes, at ECCB by Christian von Mering, and at the Tara conference by Chris Bowler. Thank you! @isme-microbes.bsky.social @eccb-europe.bsky.social @taraoceans-science.bsky.social @raeslab.org
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Pedro Beltrao @pedrobeltrao.bsky.social · 26/08/2026
So many cool results from @katjaluck.bsky.social and @martinsteinegger.bsky.social s lab defining a dictionary of protein interface types. 22 years ago @robrussell.bsky.social and @ptck72.bsky.social guessed there would be 10k types but they were off by a bit :) www.nature.com/articles/nbt...
nature.com
Ten thousand interactions for the molecular biologist - Nature Biotechnology
Nature Biotechnology - Ten thousand interactions for the molecular biologist
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Egon Willighagen @egonw.social.edu.nl.ap.brid.gy · 21/08/2026
"In memory of Professor Reinhard Schneider" www.uni.lu/lcsb-en/news/in-memory-o… I am trying to make Schneider's @wdscholia profile more complete, but Schneider has left a very long and rich track record in systems biology and protein structure […]
social.edu.nl
Original post on social.edu.nl
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Richard Sever @richardsever.bsky.social · 18/08/2026
In the past I [could] detect fraudulent stuff...formulaic, tortured phrases, too good to be true...This [was] different... I wonder if I'd have identified [it] if it hadn't concerned my own datasets. I have strong doubts academic publishing is ready for this" deevybee.blogspot.com/2026/08/acce...
deevybee.blogspot.com
Acceleration of the arms race between fraudsters and honest researchers
I was recently asked to review a paper that piqued my curiosity. From the abstract it sounded as if it was a secondary analysis of a datas...
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Jon Owen @anotherjon.bsky.social · 17/08/2026
An investigation by @propublica.org and @drilledmedia.bsky.social has found that the same modelers who overestimated the potential of CCS repeatedly underestimated solar power - one of the energy technologies that would allow more oil to remain in the ground. projects.propublica.org/why-carbon-c...
Two line charts are depicted. At the top, the line chart is labeled "Carbon Capture Capacity." The y-axis is "megatons" and the x-axis is years (2010-2040). More than a dozen blue lines show a steady increase from the left edge of the chart to the right edge of the chart. Some of the blue lines exceed 4,000 megatons between years 2030 and 2040. The blue lines are labeled "Projections". A maroon line is at around 0 megatons from 2010 to 2025. The maroon line is labeled "Actual carbon storage". 

The second chart is labeled "Solar Power". The y-axis is "terawatt-hour" and the x-axis is years (2010-2040). Dozens of blue lines increase from around 0 on the left side of the chart, showing moderate growth from 2010 to 2040. The blue lines are labeled "Projections". A maroon line starts at 0 in 2010 and rises sharply to over 2,000 in 2024. The maroon line is obviously increasing much faster than the blue lines. The maroon line is labeled "Actual solar electricity production."
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Carl T. Bergstrom @carlbergstrom.com · 17/08/2026
So many of the norms underlying academic culture relied on frictions associated with writing. It was entirely predictable that academia would be profoundly harmed when a machine came along to remove those frictions by making (insincere, inaccurate) communication effortless.
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Marco Arment @marcoarment.bsky.social · 14/08/2026
My new app is now released! Unforgetful: marco.org/2026/08/14/unforgetful Imagine if Reminders was optimized for ADHD, procrastination, and forgetfulness. Never lose a task. You'll always be reminded, with zero shame or judgment. That's Unforgetful.
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Luis Pedro Coelho @luispedrocoelho.bsky.social · 13/08/2026
I made an ice breaker game: Uncommon Ground. luispedro.substack.com/p/uncommon-g...
luispedro.substack.com
Uncommon Ground.
an ice breaker game
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Falk Hildebrand @bioinf.bsky.social · 07/08/2026
After a very long time, I'm very proud that we have now Joachim "magnus opum" on www.biorxiv.org/content/10.6... Protal is a ultra fast metagenomic species profiler. More precise than other profiled software, faster than most (not sylph though), but generates strain resolution instead.
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Bork Group at EMBL Heidelberg @borklab.bsky.social · 29/07/2026
New preprint from the lab! "Planetary structure and drivers of diazotroph communities reveal key reservoirs of nitrogen-fixation potential" Nitrogen fixation is scattered right across the prokaryotic tree — but it's heterotrophs, not cyanobacteria, that dominate the potential. 🧵
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Nadine Ziemert @nadineziemert.bsky.social · 27/07/2026
Looking for BGCs in large metagenomic datasets? Our new biorxiv preprint introduces metaSMASH, a scalable fork of antiSMASH designed specifically for metagenome-scale BGC detection and analysis : www.biorxiv.org/cgi/content/... Thanks @canerbagci.bsky.social and @kblin.bsky.social ❤️
biorxiv.org
metaSMASH: Scalable Biosynthetic Gene Cluster Detection for Large Metagenomic Assemblies
antiSMASH is widely used for biosynthetic gene cluster (BGC) detection and annotation, but its standard workflow is poorly suited to large metagenomic assemblies, where massive contig counts create severe runtime bottlenecks and complicate downstream result exploration. We present metaSMASH, a re-engineered fork of antiSMASH for metagenome-scale BGC analysis. metaSMASH preserves the original antiSMASH detection and annotation logic while introducing streaming, memory-bounded execution, record-level parallelisation, optional output filtering, and an interactive dashboard for large result sets. Across 25 benchmark metagenome datasets, metaSMASH reproduced identical BGC detection results while dramatically reducing computational cost. Relative to the default antiSMASH configuration, metaSMASH was a geometric-mean 38x faster. It also outperformed an ad hoc chunked antiSMASH workflow: in the default configuration it achieved a geometric-mean 2.9x speed-up and 1.7x lower peak memory, and with extended-analysis modules enabled it was 2.7x faster and used 3.1x less memory while completing all datasets, whereas the ad hoc workflow ran out of memory on the two largest assemblies. By substantially reducing the computational burden of large-scale metagenome analysis without sacrificing result equivalence, metaSMASH makes routine mining of assembled metagenomes more practical and provides a scalable foundation for natural product discovery from complex microbial communities. ### Competing Interest Statement The authors have declared no competing interest. German Center for Infection Research, TTU Novel Antibiotics 09.716 Volkswagen Foundation, 0072511-00
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Pedro Beltrao @pedrobeltrao.bsky.social · 20/07/2026
New lab preprint - Deep learning models are most often difficult to interpret black box models. What if we engineer them with interpretation in mind? Dennis Gankin carefully studied so-called biologically inspired neural networks and found an interesting phenomenon www.biorxiv.org/content/10.6...
biorxiv.org
Leveraging multiplicity in biologically informed neural networks to uncover disease heterogeneity
Biologically inspired neural networks (BINNs) embed pathway, ontology, or protein-interaction structure directly into neural networks, promising interpretable disease prediction where hidden nodes map...
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Michael Baym @baym.lol · 09/07/2026
I wish I could teach people just how grating it is to get the fourth clearly AI job application of the week that reads like "While I'm interested in X, to be honest what truly drew me to your lab was Y. You not only do A; you also do B."
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Will Shoemaker @shoestrapped.bsky.social · 09/07/2026
Great to see this important study published. For some time I've pointed to the preprint version when students ask about co-evolution between humans and their microbiota. "Limited codiversification of the gut microbiota within humans"
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Luis Pedro Coelho @luispedrocoelho.bsky.social · 10/07/2026
I've been thinking of how to make tools "AI-ready" so it's not just an empty buzzword I'd like to hear other opinions, but this is what I'm trying with SemiBin: 1) bundle skills with the tool SemiBin2 install-skills will (in the next release) install a skill for claude/codex/...
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Michael Kuhn @biocs.bsky.social · 09/07/2026
Ah, good point by Martin. If you start a new project Claude does not share the memory with the rest of the conversations. Like I could ask Fable "what do you know about me" in my private life project, but not in my general profile where I chat about bioinformatics
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Michael Kuhn @biocs.bsky.social · 06/07/2026
I remember reading the snarky "Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision" during my PhD 20 years ago. nsmn1.uh.edu/dgraur/Artic... pubmed.ncbi.nlm.nih.gov/14746989/ certainly a classic takedown, but it's great that the methods advanced!
pubmed.ncbi.nlm.nih.gov
Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision - PubMed
For almost a decade now, a team of molecular evolutionists has produced a plethora of seemingly precise molecular clock estimates for divergence events ranging from the speciation of cats and dogs to ...
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Michael Kuhn @biocs.bsky.social · 05/07/2026
There's a biorxiv MCP server and a few days ago I asked Claude to use the same approach to get full text articles given a DOI. Not sure if you need full text for some or all articles? New articles could be retrieved via RSS including abstracts
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Michael Kuhn @biocs.bsky.social · 02/07/2026
AI feedback for structure and general flow, or for language and rhetoric? I rather want to see an early draft where the parts haven't been joined and polished and give structural feedback on what we want to say and in which order, rather than having something that already looks sleek
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Michael Kuhn @biocs.bsky.social · 01/07/2026
Also, the message cannot be that incoming phd students need to do everything manually at first. But rather to identify points that can be handed off to AI tools and verified (like identifier mapping scripts or installing tools) and where it makes sense to build expertise
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Michael Kuhn @biocs.bsky.social · 01/07/2026
We disagreed eg with documenting every AI interaction. I strongly agreed with writing paper drafts yourself and not letting the AI turn bullet points into prose. Main takeaway: more people need to try the desktop coding tools instead of pasting stuff into the website
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Michael Kuhn @biocs.bsky.social · 01/07/2026
We've discussed this guide in the lab: zenodo.org/records/1845... and found it a good starting point to responsibile AI usage. Researchers still need to understand all of their pipelines and be answerable for their output, which is impossible if all of it is AI and agent generated
zenodo.org
Expertise before augmentation: a practical guide to using generative AI during research training
This comprehensive implementation guide accompanies the framework described in "Build expertise first: why PhD training must sequence AI use after foundational skill development" (Krishnan, 2026, DOI:...
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Michael Kuhn @biocs.bsky.social · 01/07/2026
From their examples, it unfortunately looks more like an abdication of domain expertise to AI rather than just handling friction points. Like the three sentence prompt to write a review article 🤢 and being proud of a host of AI agents having reviewed the papers rather than oneself
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Pedro Beltrao @pedrobeltrao.bsky.social · 30/06/2026
Claude Science - an AI workbench for science. This looks like an interesting attempt at making scientific workflows easier and more reproducible. I'm curious to give it a try. www.anthropic.com/news/claude-...
anthropic.com
Claude Science, an AI workbench for scientists
Claude Science is a customizable app that integrates the tools and packages researchers most often use, produces auditable artifacts, and provides flexible access to computing resources.
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Michael Kuhn @biocs.bsky.social · 01/07/2026
We've discussed this guide in the lab: zenodo.org/records/1845... and found it a good starting point to responsibile AI usage. Researchers still need to understand all of their pipelines and be answerable for their output, which is impossible if all of it is AI and agent generated
zenodo.org
Expertise before augmentation: a practical guide to using generative AI during research training
This comprehensive implementation guide accompanies the framework described in "Build expertise first: why PhD training must sequence AI use after foundational skill development" (Krishnan, 2026, DOI:...
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Michael Kuhn @biocs.bsky.social · 01/07/2026
From their examples, it unfortunately looks more like an abdication of domain expertise to AI rather than just handling friction points. Like the three sentence prompt to write a review article 🤢 and being proud of a host of AI agents having reviewed the papers rather than oneself
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Lisa Maier Lab | Tübingen @lisamaierlab.bsky.social · 29/06/2026
Don‘t forget to register for what promises to be an end-of-the-year highlight in functional microbiome research 👇🏻 !
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Cell Host & Microbe @cp-cellhostmicrobe.bsky.social · 25/06/2026
Universal microbiome signature for CRC Large gut microbiome meta-analysis of colorectal cancer uncovers CRC microbiome signatures universal across ages & sequencing methods & modifiable by dietary interventions, ie fiber. www.cell.com/cell-host-mi...
cell.com
Meta-analysis reveals microbiome signatures for colorectal cancer that are universal across age groups and sequencing methods
Pekel, Karcher, et al. present the largest gut microbiome meta-analysis of colorectal cancer to date, integrating 6,779 amplicon and shotgun sequencing profiles. They establish a robust microbiome sig...
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Claus Wilke @clauswilke.com · 25/06/2026
People always say "tell a story" but then don't explain how to do so! How is that helping? If we knew how to tell a story we wouldn't need the advice in the first place. 1/
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Ethan Mollick @emollick.bsky.social · 19/06/2026
More evidence, from a large-scale study in China, that using AI hurts learning if it undermines mental effort. When homework time drops due to AI use, so do test scores. Across studies, there is a clear theme: AI tutoring in support of classes is good, using AI to "help" with homework is bad.
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Mel Andrews @bayesianboy.bsky.social · 17/06/2026
When utilized in literature review, LLMs consistently 1. fail to mention female authors in female-led literatures, 2. insist that men are more influential or more heavily cited when this is contradicted by objective citation counts, and 3. attribute women’s work to hallucinated male scholars.
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Jase Gehring @skyjase.bsky.social · 17/06/2026
they even got the gradients right by pouring the H2O2 in from the side. it's a giga-plate fr @baym.lol is seeing his vision fully realized
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Crystal Fleming is on sabbatical @alwaystheself.bsky.social · 17/06/2026
I'm attending a digital humanities event in Montreal. There was a keynote on AI and something about the talk made me wonder if it had been written by Claude. I said as much in the Q&A. As I posed the question, the speaker shifted, looking slightly uncomfortable. What he said next shocked the room +
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Melanie I Stefan @melanieistefan.bsky.social · 17/06/2026
Interesting and thoughtful thread about thé poisoning of academic discourse (my interpretation) by AI
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Helena Klara Jambor @helenajambor.bsky.social · 16/06/2026
😎 to have this out! --> stay tuned, this is a series about 📊#dataviz for #science 🧪
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