James McInerney
@jomcinerney.bsky.social
Writing a book about horizontal gene transfer and non treelike evolution. Bioinformatics, Evolutionary Biology. Pangenomes. Chair in Evolutionary Biology. 🇮🇪 http://github.com/mol-evol/panGPT
Sundown this evening.
November 25, 2025 at 5:35 PM
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."
November 20, 2025 at 3:48 PM
"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 McInerney
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
Xenotypes: organisms that share genetic material that has been acquired through horizontal transfer, regardless of quantity, mechanism of transfer, or phenotypic effect
November 20, 2025 at 3:48 PM
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
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 McInerney
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
🔗 doi.org/10.1093/molbev/msaf279
#evobio #molbio
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
doi.org
November 20, 2025 at 3:48 PM
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
🔗 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.
November 13, 2025 at 10:10 PM
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?
November 12, 2025 at 10:12 AM
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
November 7, 2025 at 8:48 PM
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.
November 7, 2025 at 5:35 PM
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 McInerney
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.
November 6, 2025 at 6:52 PM
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.
Reposted by James McInerney
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
🎥 All sessions available here: www.youtube.com/playlist?lis...
(Day 3 to be added soon!)
#conference #genomics #science @biogeneurope.bsky.social
Genomics for Biodiversity Conference 2025 - YouTube
https://www.erga-biodiversity.eu/post/genomics-for-biodiversity-conference-from-genomes-to-impact
www.youtube.com
November 3, 2025 at 10:39 AM
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
🎥 All sessions available here: www.youtube.com/playlist?lis...
(Day 3 to be added soon!)
#conference #genomics #science @biogeneurope.bsky.social
Reposted by James McInerney
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...
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...
cee.mit.edu
November 5, 2025 at 7:27 PM
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
GitHub - mol-evol/gcua: GCUA - General Codon Usage Analysis (v2)
GCUA - General Codon Usage Analysis (v2). Contribute to mol-evol/gcua development by creating an account on GitHub.
github.com
November 5, 2025 at 3:36 PM
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 McInerney
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...
www.findaphd.com/phds/project...
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
www.findaphd.com
November 4, 2025 at 11:13 AM
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...
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)?
November 1, 2025 at 10:07 PM
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...
The value of public R&D
www.gov.uk
October 30, 2025 at 10:53 PM
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/...
Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes academic.oup.com/mbe/article/...
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
academic.oup.com
October 30, 2025 at 11:36 AM
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/...
Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes academic.oup.com/mbe/article/...
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
academic.oup.com
October 30, 2025 at 11:33 AM
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/...
Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes academic.oup.com/mbe/article/...
Currently locked in battle with a data pipeline that's decided to move slower than continental drift. We have reached a mutual understanding: I'll wait, it'll go slowly. Career choices have been questioned.
October 24, 2025 at 9:14 AM
Currently locked in battle with a data pipeline that's decided to move slower than continental drift. We have reached a mutual understanding: I'll wait, it'll go slowly. Career choices have been questioned.
I'm developing an irrational affection for the mmseqs2 program. It's almost like magic. You can see its inner workings being described here: github.com/soedinglab/M...
GitHub - soedinglab/MMseqs2: MMseqs2: ultra fast and sensitive search and clustering suite
MMseqs2: ultra fast and sensitive search and clustering suite - soedinglab/MMseqs2
github.com
October 24, 2025 at 9:01 AM
I'm developing an irrational affection for the mmseqs2 program. It's almost like magic. You can see its inner workings being described here: github.com/soedinglab/M...
Two months writing a pipeline in python, and testing the daylights out of it, only to figure out that a bunch of small shell scripts do the job just as good. 🤯
October 24, 2025 at 8:54 AM
Two months writing a pipeline in python, and testing the daylights out of it, only to figure out that a bunch of small shell scripts do the job just as good. 🤯
using a new HPC and the installs are murdering me. A long a time ago, we used to have all kinds of distributions that had every bioinformatics tool you'd ever heard of in it. Does that exist anymore?
October 16, 2025 at 11:59 AM
using a new HPC and the installs are murdering me. A long a time ago, we used to have all kinds of distributions that had every bioinformatics tool you'd ever heard of in it. Does that exist anymore?
Last day to apply to come work with me on developing AI approaches to understanding pangenome evolution www.jobs.ac.uk/job/DOU184/p...
Postdoctoral Research Associate - Grade 7 at University of Liverpool
An opportunity for an academic position as a Postdoctoral Research Associate - Grade 7 is available, as advertised on jobs.ac.uk. Apply now and explore other academic job openings.
www.jobs.ac.uk
October 14, 2025 at 11:09 AM
Last day to apply to come work with me on developing AI approaches to understanding pangenome evolution www.jobs.ac.uk/job/DOU184/p...
Just one week to go until the deadline. www.jobs.ac.uk/job/DOU184/p... #ai #pangenome #genomics #evolution #microbiology
Postdoctoral Research Associate - Grade 7 at University of Liverpool
Apply for the Postdoctoral Research Associate - Grade 7 role on jobs.ac.uk, the top job board for academic positions in higher education. View details and apply now.
www.jobs.ac.uk
October 7, 2025 at 3:42 PM
Just one week to go until the deadline. www.jobs.ac.uk/job/DOU184/p... #ai #pangenome #genomics #evolution #microbiology
Reposted by James McInerney
The job is still open. Get your application in ASAP. Or just pass it on to somebody that might be interested.
OK, here it is. Come work with me at the University of Liverpool making ALL THE AI models from ALL THE prokaryote pangenome data. Heck, we will make models from ALL the pangenomes, even eukaryotes!!! (link below👇) 1/4
October 1, 2025 at 1:14 PM
The job is still open. Get your application in ASAP. Or just pass it on to somebody that might be interested.
The job is still open. Get your application in ASAP. Or just pass it on to somebody that might be interested.
OK, here it is. Come work with me at the University of Liverpool making ALL THE AI models from ALL THE prokaryote pangenome data. Heck, we will make models from ALL the pangenomes, even eukaryotes!!! (link below👇) 1/4
October 1, 2025 at 1:14 PM
The job is still open. Get your application in ASAP. Or just pass it on to somebody that might be interested.