James McInerney
Evolutionary Biologist & Computational Scientist
Professor & Head of Evolution, Ecology and Behaviour · University of Liverpool
Former President · Society for Molecular Biology and Evolution (2022)
About
I study how bacterial genomes evolve, using bioinformatics, statistics, and machine learning. My research focuses on pangenomics—understanding the complete set of genes across bacterial species—and how horizontal gene transfer shapes microbial diversity.
I'm particularly interested in applying transformer models and AI to decode the "grammar" of bacterial genomes, with applications in antimicrobial resistance prediction and synthetic biology. This work sits at the intersection of evolutionary biology and modern machine learning.
Pangenome AI
Revolutionising bioscience with Large Pangenome Models that extract evolutionary wisdom from millions of genomes.
Software
panGPT
A Generative Pre-Trained Transformer package for pangenomes. Train language models on bacterial gene content.
GCUA
General Codon Usage Analysis. Analyse codon usage patterns and biases across genomes.
panDecay
Calculate support measures for phylogenies using pangenomic data and phylogenetic decay analysis.
ML Phylogenetics
A teaching tool to explain Maximum Likelihood calculations in phylogenetic inference.
Grant Evaluator
Web tool for evaluating and scoring research grant applications.
View all on GitHub
Browse the complete collection of tools and software packages.