James McInerney
Writing a book about horizontal gene transfer and non treelike evolution. Bioinformatics, Evolutionary Biology. Pangenomes. Chair in Evolutionary Biology. 🇮🇪 github.com/mol-evol/panGPT
- Very interesting paper. www.science.org/doi/10.1126/...
- Reposted by James McInerneyPanForest: predicting genes in genomes using random forests academic.oup.com/bioinformati... #jcampubs
- Reposted by James McInerneyDissecting Phylogenetic Support: Unified Decay Indices, AU Tests, and Branch-Site Specific Visualizations. biorxiv.org/content/10.64898/20…
- 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...
- Reposted by James McInerneyInterested 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...
- 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
- The core insight: genes don't distribute randomly across genomes. Some genes "like" to co-occur, others avoid each other. PanForest learns these patterns and tells you which genes are predictable from their genomic context.
- We tested it on 1,000 E. coli genomes with ~12,700 accessory genes. Runs in ~5 hours on 8 processors. Scales to Network of Life pangenomes.
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View full threadOpen source & freely available: github.com/alanbeavan/PanForest Congrats to Alan on leading this work! 🎉
- Well done Roberto.
- Thrilled to share that I’ve been awarded a FIS-3 Advanced Grant (ERC-inspired) to study the evolution of neurogenic GRNs. Recruiting soon: 4 postdocs + 3 PhDs Press release in Italian — to decolonise scientific language 😄 magazine.unibo.it/it/articoli/... Email me if interested in joining the lab
- Anybody involved in leadership at any level in universities should read this article. Twice. www.rte.ie/brainstorm/2...
- Reposted by James McInerneyMy 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.
- Reposted by James McInerneyNot 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/...
- Reposted by James McInerneyThread: 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...
- Reposted by James McInerneyImagine 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...
- Dissecting Phylogenetic Support: Unified Decay Indices, AU Tests, and Branch-Site Specific Visualizations. biorxiv.org/content/10.64898/20…
- the program will output multiple support measures for internal branches
- The software is here: github.com/mol-evol/pan...
- 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.
- Latest preprint with @hairyllama.bsky.social and @evol-molly.bsky.social This is a program that helps calculate several phylogenetic support measures.
- Dissecting Phylogenetic Support: Unified Decay Indices, AU Tests, and Branch-Site Specific Visualizations. biorxiv.org/content/10.64898/20…
- Sundown this evening.
- Reposted by James McInerney"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."
- Reposted by James McInerneyEpaktovars: 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
- Reposted by James McInerneyIn 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
- 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 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.
- Reposted by James McInerneyNearly 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.
- Reposted by James McInerneyThe 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
- Reposted by James McInerneyIf 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
- Reposted by James McInerneyGlobal 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)?
- 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...
- 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.
- I've often wondered about what we should call organisms whose similarity might be due to acquired genetic material. It got a little complicated, but I made a stab at it here Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes academic.oup.com/mbe/article/...
- I've often wondered about what we should call organisms whose similarity might be due to acquired genetic material. It got a little complicated, but I made a stab at it here Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes academic.oup.com/mbe/article/...
- You can have acquired genetic material that produces no phenotype, or it does, or phenotypic similarity might not be due to genetic acquisition and so on.
- Also - just to say thank you to the two reviewers, whose comments and suggestions made the paper clearer and much better. Peer-review done right.
