James McInerney

His lab was humming with discovery. After one year under Trump, it’s almost silent John Quackenbush built a lab that is at the forefront of human genetics research and bioinformatics. Trump administration cuts have put it in danger of collapse.

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.

A picture of sundown

A picture of sundown.

A picture of sundown

Sundown this evening.

MBE | Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes Fig. 2.A phylogenetic network illustrating the relationships between epaktovars, xenotypes, and the consequences of vertical inheritance. Taxa {A,B} share 50 genes with taxa {G,H}, making them xenotypes of one another (see text for details). Without phenotypic data, we would not be able to say whether these groups are epaktovars. Taxa A and E, labeled green, are epaktovars and xenotypes for some trait, thanks to the independent acquisition of a gene encoding a metabolic enzyme, which results in the same phenotype in both taxa. B and G, labeled red, have independently evolved resistance to a toxin, though HGT has not facilitated the evolution of this trait, making them epaktovars, but not xenotypes.

"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."

MBE | Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes Fig. 1. Clarification of the relationships between epaktovars and xenotypes.

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

Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes Abstract. The classification of living systems presents significant challenges due to the prevalence of gene transfer between genomes. Traditional taxonomi

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?

Indeed there are changes in the way. I am but a very small cog in the machine but have been supporting the process of change.

Obviously there is the other story where he was offensive when he visited. And the other story where he was offensive to my PhD student. But this particular story, simply by its slight surrealism is the one that appeals to me to tell.

Hs signed the sacred visitors book - leather bound, brand spanking new. Then he went for a tour of the building. 3 minutes later, a delivery guy appeared at the door with a package, scribbled his name across the page under Watson signature, dropped the package and left. I couldn’t stop laughing.

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.

Genomics for Biodiversity Conference 2025 - YouTube https://www.erga-biodiversity.eu/post/genomics-for-biodiversity-conference-from-genomes-to-impact

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

Faculty Position in the Department of Civil and Environmental Engineering and the Schwarzman College of Computing - cee.mit.edu The Department of Civil and Environmental Engineering (CEE), together with the Schwarzman College of Computing (SCC) at the Massachusetts Institute of Technology (MIT) in Cambridge MA, seeks candidate...

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

MRC DiMeN Doctoral Training Partnership: Global Pathogen, Local Impact: Genomic and Functional Dissection of S. Infantis in Peru at Newcastle University on FindAPhD.com PhD Project - MRC DiMeN Doctoral Training Partnership: Global Pathogen, Local Impact: Genomic and Functional Dissection of S. Infantis in Peru at Newcastle University, listed on FindAPhD.com

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...

Thanks Mat. Its a bit broader than microbial, though it is heavily microbial. So, I'll keep it in mind, but I might search about for a journal with a broader scope.

Oops. Its evolutionary genomics.

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

It was a pleasure.

The value of public R&D

Here in the uk, the government has found that £1 of spending on R&D results in £8 of benefit: www.gov.uk/government/p...

a man with blue paint on his face is screaming with the words freedoooom !!! below him ALT: a man with blue paint on his face is screaming with the words freedoooom !!! below him

I'm on the side of the rebels, whoever they are!

A conflict that goes back almost 4.5 billion years. Nobody knows why, nobody knows who started it, but you have to pick a side!!

I also talk about de-extinction in this paper & the need to have some name to call the organisms. Like many people, I know that the Colossal "Dire Wolves" are not the descendants of the extinct wolves they are named after. But they are *something*, so we need to have a name for them.