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.
You can change the denomination to euro. It’s general for people with a finite amount of time and more than one option for what grant to write.
January 29, 2026 at 1:35 PM
You can change the denomination to euro. It’s general for people with a finite amount of time and more than one option for what grant to write.
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
its for "entertainment" purposes only :)
January 15, 2026 at 2:43 PM
its for "entertainment" purposes only :)
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.
Open source & freely available:
github.com/alanbeavan/PanForest
Congrats to Alan on leading this work! 🎉
github.com/alanbeavan/PanForest
Congrats to Alan on leading this work! 🎉
GitHub - alanbeavan/PanForest: Pangenome analysis using random forests
Pangenome analysis using random forests. Contribute to alanbeavan/PanForest development by creating an account on GitHub.
github.com
January 14, 2026 at 10:25 PM
Open source & freely available:
github.com/alanbeavan/PanForest
Congrats to Alan on leading this work! 🎉
github.com/alanbeavan/PanForest
Congrats to Alan on leading this work! 🎉
Outputs both prediction accuracy (how predictable is each gene?) and feature importance (which genes matter most for each prediction?). Useful for understanding genome organisation, synthetic biology, and molecular ecology.
January 14, 2026 at 10:25 PM
Outputs both prediction accuracy (how predictable is each gene?) and feature importance (which genes matter most for each prediction?). Useful for understanding genome organisation, synthetic biology, and molecular ecology.
Case study: antimicrobial resistance genes. Certain AMR genes reliably predict other AMR genes for the same drug. But we also found unexpected associations with genes NOT previously linked to resistance. New targets for investigation?
January 14, 2026 at 10:25 PM
Case study: antimicrobial resistance genes. Certain AMR genes reliably predict other AMR genes for the same drug. But we also found unexpected associations with genes NOT previously linked to resistance. New targets for investigation?
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.
January 14, 2026 at 10:25 PM
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.
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.
January 14, 2026 at 10:25 PM
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.
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
Open source & freely available:
github.com/alanbeavan/PanForest
Congrats to Alan on leading this work! 🎉
github.com/alanbeavan/PanForest
Congrats to Alan on leading this work! 🎉
GitHub - alanbeavan/PanForest: Pangenome analysis using random forests
Pangenome analysis using random forests. Contribute to alanbeavan/PanForest development by creating an account on GitHub.
github.com
January 14, 2026 at 10:22 PM
Open source & freely available:
github.com/alanbeavan/PanForest
Congrats to Alan on leading this work! 🎉
github.com/alanbeavan/PanForest
Congrats to Alan on leading this work! 🎉
Outputs both prediction accuracy (how predictable is each gene?) and feature importance (which genes matter most for each prediction?). Useful for understanding genome organisation, synthetic biology, and molecular ecology.
January 14, 2026 at 10:22 PM
Outputs both prediction accuracy (how predictable is each gene?) and feature importance (which genes matter most for each prediction?). Useful for understanding genome organisation, synthetic biology, and molecular ecology.
Case study: antimicrobial resistance genes. Certain AMR genes reliably predict other AMR genes for the same drug. But we also found unexpected associations with genes NOT previously linked to resistance. New targets for investigation?
January 14, 2026 at 10:22 PM
Case study: antimicrobial resistance genes. Certain AMR genes reliably predict other AMR genes for the same drug. But we also found unexpected associations with genes NOT previously linked to resistance. New targets for investigation?
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.
January 14, 2026 at 10:22 PM
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.
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.
January 14, 2026 at 10:22 PM
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.
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.
It’s always the ones you expect.
January 10, 2026 at 12:15 AM
It’s always the ones you expect.
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