Interesting. www.rte.ie/brainstorm/2...

What's even wilder is that models like scGPT and Geneformer are now doing this at the single-cell level — learning gene regulatory patterns from raw expression data with zero biological annotation. They're rediscovering cell types and disease states purely from the structure of the data.

A transformer model trained on raw DNA, with no biological instruction whatsoever, learned to distinguish between genetic codes. Nobody taught it what a codon is. That is just “wow”.

We have a new Masters programme in Liverpool. Please pass on to anybody you think might be interested: news.liverpool.ac.uk/2026/02/13/n...

This looks really great. I’ve been following this for a while.

On this last point: the implication is (and I wrote this in the paper) that evolution is not optimising biochemical (or other) activity as a primary focus, but the context-dependent function. And this is liable to change often.

I'm thankful to MBE for publishing this paper. I wan't sure anybody would. The handling editor (I now know was Jeff Townsend) was great, as were the 2 reviewers. It is not an outcome/product/discovery, it is my way of thinking about HGT & pangenomes 1/3 academic.oup.com/mbe/article/...

True story.

@jomcinerney.bsky.social proposes that genomes do not encode fixed functions but rather “probability distributions” over functional and phenotypic outcomes, and introduces “genomic perplexity” as a measure of gene-context incompatibility. 🔗 doi.org/10.1093/molbev/msag041 #evobio #molbio

@guigau.bsky.social Saw PanGBank earlier. Very nice 👍

This looks absolutely great. For those of us interested in pangenomes, I am sure this will be a super place to get data and the interface is very clean (plotly). Congrats to the authors (I don't know if they are on bsky): pangbank.genoscope.cns.fr

I'm in a coffee shop wrestling with Endnote, while 1980s power ballads blast out from a giant speaker. The sun is shining for the first time this year, but I got paper submission deadlines. I hope nobody sees me cry.

New paper out in MBE! 🧵 "Genomic Perplexity and the Evolution of Context-Dependent Function" The big idea: genes don't have fixed functions. Function emerges from context - genomic, cellular, environmental. And we can quantify this. academic.oup.com/mbe/article/...

MENI is back! Join us in Dublin this August 2026 for our 3rd Meeting for Microbial Evolution in Ireland. We are delighted to have @rachelmwheatley.bsky.social @drrebeccajhall.bsky.social @jpjhall.bsky.social and @tweethinking.bsky.social join us as keynote speakers this year. miniurl.com/MENI

Very interesting paper. www.science.org/doi/10.1126/...

Ever wondered if writing a grant proposal was actually worth your time? Presenting....The Grant Portfolio Evaluator - (for entertainment only) mol-evol.github.io/grant-evalua...

PanForest: predicting genes in genomes using random forests academic.oup.com/bioinformati... #jcampubs

Dissecting Phylogenetic Support: Unified Decay Indices, AU Tests, and Branch-Site Specific Visualizations. https://www.biorxiv.org/content/10.64898/2025.12.05.692543v1

Ever wondered if writing a grant proposal was actually worth your time? Presenting....The Grant Portfolio Evaluator - (for entertainment only) mol-evol.github.io/grant-evalua...

Interested in pangenomics ? This paper just out from Alan Beavan (not on socials), @blackpassiflora.bsky.social and @jomcinerney.bsky.social is a must: doi.org/10.1093/bioi...

Latest preprint with @hairyllama.bsky.social and @evol-molly.bsky.social This is a program that helps calculate several phylogenetic support measures.

New paper out in Bioinformatics! PanForest uses random forests to predict gene presence/absence in bacterial genomes based on other genes present. Joint work with Alan Beavan & Maria Rosa Domingo-Sananes. 🔗 doi.org/10.1093/bioinformatics/btag005

Well done Roberto.

Anybody involved in leadership at any level in universities should read this article. Twice. www.rte.ie/brainstorm/2...

the program will output multiple support measures for internal branches

My word. The Taoiseach, in China, says "platforms can be misused and abused or they can be used for positive reasons as well..." and says that should be considered carefully "before jumping to conclusions" on whether it's appropriate for the Government to be on X.

Not once, in all my time on Twitter, did I come across a 'gender critical' activist who made me think, 'maybe I have this wrong?' In fact, watching people like Graham Linehan slide further and further into Right Wing and Far Right ideology confirmed that they are the ideologues.

Sponges are notoriously difficult to understand in evolutionary biology terms. I think this paper is a big step forward : www.science.org/doi/10.1126/...

Thread: Introducing GCUA v2.0 (General Codon Usage Analysis) - a Python tool for analysing codon usage patterns in DNA sequences! Originally developed in 1998, now completely rewritten with modern features. Let me walk you through what I like about this version (PLS RT) github.com/mol-evol/gcu...

It’s junk. It has always been junk. www.newscientist.com/article/2508...

Imagine my surprise to see that this guy, who write a piece in praise of RFK Jr, is one of the Danish researchers who will be doing this trial 👀

This is shocking stuff. John Quackenbush has been brilliant since forever. www.statnews.com/2025/12/05/r...

the program will output multiple support measures for internal branches

The software is here: github.com/mol-evol/pan...

Latest preprint with @hairyllama.bsky.social and @evol-molly.bsky.social This is a program that helps calculate several phylogenetic support measures.

Sundown this evening.

"The two concepts of epaktovars and xenotypes provide a framework for understanding how independently evolving lineages, whether prokaryotic, eukaryotic, plasmid, or viral, can acquire similar genomic patterns through gene transfer."

Epaktovars: organisms that have independently acquired similar phenotypes Xenotypes: organisms that share genetic material that has been acquired through horizontal transfer, regardless of quantity, mechanism of transfer, or phenotypic effect

In a new MBE Perspective, @jomcinerney.bsky.social introduces the concepts of epaktovars and xenotypes, providing a framework for describing phenotypic convergence and shared genetic material resulting from gene transfer across diverse lineages. 🔗 doi.org/10.1093/molbev/msaf279 #evobio #molbio

What’s your big annoyance with bioinformatics software? Mine is that most programs have only one output format.

Another really bad graphic on the BBC website at the moment. Anybody see anything wrong with this one?

I don’t have a particularly good James Watson story, but I found it amusing at the time. He visited the Irish National Diagnostics Centre, where I worked in 1995. The centre prepared a visitors book at the entrance and after giving a lecture in the university, Watson came to the research centre 1/2

I had a grant proposal rejected this week. With an 85% rejection rate for BBSRC responsive mode grants, there’s no shame in it. A lot of work gone to waste though. I could have written a paper or done a lot of analyses in the time it took to write the proposal. Onwards & upwards, dear friends.

Nearly two-thirds of European parents with children who are overweight or obese think their kids are underweight or normal weight, per a recent WHO report.

The Genomics for Biodiversity Conference had a hybrid format: hosted in Porto by BIOPOLIS/CIBIO 🇵🇹 and streamed live online for a global audience. 🎥 All sessions available here: www.youtube.com/playlist?lis... (Day 3 to be added soon!) #conference #genomics #science @biogeneurope.bsky.social

If you're looking for a faculty position at the intersection of ecology and computing (both broadly defined), please apply to this joint search between the CEE Department and the College of Computing at MIT: cee.mit.edu/people/share...

There is now a complete tutorial in the GCUA distribution. If you are running bioinformatics practicals or workshops and you want a complete out-of-the-box simple tutorial, with theory and nice outputs, then think about including this in your curriculum: github.com/mol-evol/gcua #bioinformatics

Global pathogen, local impact: Genomic and functional dissection of S. infantis in Peru. Supervised by Matt Bawn and @jomcinerney.bsky.social. www.findaphd.com/phds/project...

What's a good open access journal that will take an opinion article that is a bit long (4,500 words)?