I did some public outreach last year - it was super rewarding, and made me realise the importance of grassroots science engagement. Not only does it inspire the next generation of scientists, but fosters public trust in science, something that is very important right now.
Our new preprint is out! We train a transformer on gene order and gene content of bacterial pathogens, applying it to a range of epidemiological and evolutionary analyses (1/8) www.biorxiv.org/content/10.6...
Fast Set Operations for Compact k-mer Sets https://www.biorxiv.org/content/10.64898/2026.05.24.727514v1
Overall, we lay the groundwork for using transformer models in a whole host of epi analyses. PanBART is available on GitHub, and we provide scripts and workflows to help you to train it on your species of interest! (8/8) github.com/samhorsfield...
PanBART can also be used to predict whether a genome will "take-up" a gene of interest. We are able to accurately identify E. coli lineages which are likely to gain an extended-spectrum antibiotic resistance gene, meaning we can predict which strains might become drug resistant! (6/8)