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

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

Happy to share our new AMR resource which has phenotypic AMR (usually MIC data) collected from publications and databases. This is paired with assemblies and annotations

We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use

Congrats Tabea!! 🤩🥳

Is there only one "path" that evolution tends to take when a new trait arises? Or can the trait arise in more than one way? In other words, walking back from a particular evolutionary "destination", do we always take the same path? The answer might be "no", at least some of the time. In fact... 1/n

Genomic constraints shape the evolution of alternative routes to drug resistance in prokaryotes. Background: Variation within the prokaryotic pangenome is not random, and natural selection that favours particular combinations of genes appears to dominate over random drift. What is less clear is w...

New preprint from the group: @lucydillon.bsky.social analysis of 16,000+ genomes finds Bacteria cannot combine certain resistance genes as they are mutually exclusive, forcing them down incompatible evolutionary paths.
biorxiv.org/content/10.1101/2025.08.20.671315v1
@jomcinerney.bsky.social

Thank you very much! ☺️

A few days left to apply for this Postdoc working with microbes and flies! 🧫 🪰 🦠

PhD grad 🥳 Special thanks to my family, friends, and all of the Creevey lab - especially my supervisor @hairyllama.bsky.social! I couldn’t have done it without you!

Excited to be attending VIBE conference this year! I will be presenting a poster on Friday using pangenomics and ML to investigate multidrug-resistance 🧬🧫👩🏼‍💻