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
Pinned
Dissecting Phylogenetic Support: Unified Decay Indices, AU Tests, and Branch-Site Specific Visualizations. https://www.biorxiv.org/content/10.64898/2025.12.05.692543v1
Latest preprint with @hairyllama.bsky.social and @evol-molly.bsky.social This is a program that helps calculate several phylogenetic support measures.
Very interesting paper. www.science.org/doi/10.1126/...
Bacteriophages mobilize bacterial defense systems via lateral transduction
Bacteriophages and PICIs spread bacterial defenses via lateral transduction, shaping microbial immunity and pathogen evolution.
www.science.org
January 24, 2026 at 1:24 PM
Very interesting paper. www.science.org/doi/10.1126/...
Reposted by James McInerney
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...
Grant Portfolio Evaluator
Rank and prioritize research funding opportunities. Calculate EV/hour and decide which grants are worth your time.
mol-evol.github.io
January 15, 2026 at 2:22 PM
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 McInerney
PanForest: predicting genes in genomes using random forests academic.oup.com/bioinformati... #jcampubs
PanForest: predicting genes in genomes using random forests
AbstractMotivation. The presence or absence of some genes in a genome can influence whether other genes are likely to be present or absent. Understanding t
academic.oup.com
January 12, 2026 at 2:30 PM
PanForest: predicting genes in genomes using random forests academic.oup.com/bioinformati... #jcampubs
Reposted by James McInerney
Dissecting Phylogenetic Support: Unified Decay Indices, AU Tests, and Branch-Site Specific Visualizations. https://www.biorxiv.org/content/10.64898/2025.12.05.692543v1
December 5, 2025 at 11:33 PM
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...
Grant Portfolio Evaluator
Rank and prioritize research funding opportunities. Calculate EV/hour and decide which grants are worth your time.
mol-evol.github.io
January 15, 2026 at 2:22 PM
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 McInerney
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...
PanForest: predicting genes in genomes using random forests
AbstractMotivation. The presence or absence of some genes in a genome can influence whether other genes are likely to be present or absent. Understanding t
doi.org
January 15, 2026 at 12:27 PM
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...
Reposted by James McInerney
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. https://www.biorxiv.org/content/10.64898/2025.12.05.692543v1
December 5, 2025 at 11:56 PM
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
🔗 doi.org/10.1093/bioinformatics/btag005
PanForest: predicting genes in genomes using random forests
AbstractMotivation. The presence or absence of some genes in a genome can influence whether other genes are likely to be present or absent. Understanding t
doi.org
January 14, 2026 at 10:25 PM
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
🔗 doi.org/10.1093/bioinformatics/btag005
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
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
Un viaggio all’origine dei sistemi nervosi
Il nuovo progetto GRNevo, finanziato con un grant FIS-3 Advanced da 1,9 milioni di euro, studierà come si formano i neuroni durante lo sviluppo in specie animali molto distanti tra loro: dal moscerino...
magazine.unibo.it
January 13, 2026 at 2:16 PM
Well done Roberto.
Anybody involved in leadership at any level in universities should read this article. Twice. www.rte.ie/brainstorm/2...
How Manchester Utd became a textbook example of a toxic workplace
The ongoing turmoil at Old Trafford shows how a toxic work environment can quietly destroy performance from the inside out
www.rte.ie
January 9, 2026 at 12:10 PM
Anybody involved in leadership at any level in universities should read this article. Twice. www.rte.ie/brainstorm/2...
Reposted by James McInerney
the program will output multiple support measures for internal branches
December 6, 2025 at 12:07 AM
the program will output multiple support measures for internal branches
Reposted by James McInerney
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.
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.
January 8, 2026 at 9:34 AM
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.
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 McInerney
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.
In fact, watching people like Graham Linehan slide further and further into Right Wing and Far Right ideology confirmed that they are the ideologues.
January 8, 2026 at 9:29 AM
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.
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/...
Independent origins of spicules reconcile paleontological and molecular evidence of sponge evolutionary history
Sponges have a cryptic Ediacaran history because ancestral sponges were soft-bodied and had low fossilization potential.
www.science.org
January 8, 2026 at 10:02 AM
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 McInerney
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...
github.com
June 1, 2025 at 7:28 PM
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...
Human-plant hybrid cells reveal truth about dark DNA in our genome
It has been claimed that because most of our DNA is active, it must be important, but now human-plant hybrid cells have been used to show this activity is mostly random noise
www.newscientist.com
December 31, 2025 at 6:48 PM
It’s junk. It has always been junk. www.newscientist.com/article/2508...
Reposted by James McInerney
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 👀
December 19, 2025 at 10:12 PM
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...
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.
www.statnews.com
December 10, 2025 at 7:37 AM
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
December 6, 2025 at 12:07 AM
the program will output multiple support measures for internal branches
The software is here: github.com/mol-evol/pan...
December 6, 2025 at 12:01 AM
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.
Dissecting Phylogenetic Support: Unified Decay Indices, AU Tests, and Branch-Site Specific Visualizations. https://www.biorxiv.org/content/10.64898/2025.12.05.692543v1
December 5, 2025 at 11:56 PM
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.
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