Pathogen informatics and modelling http://bacpop.org (Research group leader at EMBL-EBI - http://ebi.ac.uk/research/lees/)
Nick Croucher, Ewan Harrison and I have a project available here 'Pathogen antigen discovery and immune profiling': www.embl.org/editorhub/wp... Applications open until 27th September
www.embl.orgEMBL-EBI📣 We're recruiting for the EMBL-EBI-Sanger Postdoctoral (ESPOD) programme! ESPOD builds on the collaborative relationship between EMBL-EBI and the @sangerinstitute.bsky.social, offering projects that combine wet and dry-lab experience. Learn more & apply: www.ebi.ac.uk/research/pos...
What is an 'everyday task' and what is a 'complex problem' in bioinformatics software engineering? Feels more important use the right model now they're not so heavily subsidised! I did a small comparison on an optimisation task: johnlees.me/posts/ska2-c... Small/cheap model wasn't good enough
Credit use of AI models for bioinformatics: a tiny benchmarkAgentic coding models such as codex and claude code are really useful for software engineering tasks. We sadly (and unsurprisingly) seem to be exiting the era of highly subsidised costs to get us hook...johnlees.meWe've been looking at how to compare and cluster large numbers of genomes, such as those in large isolate databases such as AllTheBacteria, and metagenome assemblies (e.g. SPIRE, MGnify). On a combined dataset of 5.6 million assemblies, we can now cluster/dereplicate everything in under a day!
Johanna von Wachsmann🧬 New preprint! We clustered 5.6 million bacterial genomes into genomically cohesive units (GCUs) 500× faster than existing tools. (In just 14 hours, 16.5 GB RAM using 48 CPUs). 🦠🐙Meet gemsparcl 💎✨! www.biorxiv.org/content/10.6...
If anyone likes Boards of Canada they have a new album which is good, only a mere 13 years since Tomorrow's Harvest en.wikipedia.org/wiki/Inferno...
Inferno (Boards of Canada album) - Wikipediaen.wikipedia.orgNew work on using transformers (using gene order) for tasks in genomic epidemiology: www.biorxiv.org/content/10.6... We trained BART models (w/ extended context windows) on E.coli and S.pneumo from AllTheBacteria and tested if the model could find new strains, insertions (blaCTX-M) and co-selection
Sam HorsfieldOur 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...
Minor update on genomics of the menB outbreak. UKHSA have updated with four more outbreak isolates, and a high quality assembly of the earlier genome. tl;dr ran ska+gubbins again, same results, all of these genomes look basically identical www.bacpop.org/blog/menb_up...
Updated genomic analysis of the 2026 menB outbreak in Kent, UKThis is a brief update to the previous menB analysis we’d posted here. UKHSA have released a technical briefing and further data which includes four further isolates from the outbreak, and a high qual...www.bacpop.orgWe have two paid internships available in our group starting this summer, suitable for master's / pre-PhD students: - Protein structure search - Promoter variation For full details and how to apply see: www.bacpop.org/jobs/
JobsWorking with uswww.bacpop.orgHere is some initial population analysis on the menB outbreak genome we have done: www.bacpop.org/blog/menb/ Some recombination in e.g. pilus and porB, but nothing I can see that is hugely unexpected
Initial genomic analysis of the 2026 menB outbreak in Kent, UKWe’ve done a quick analysis on the meningitis outbreak genome to try and answer whether there is anything obviously genetically unusual about the publicly available outbreak strain. We aimed for three...www.bacpop.orgSome provisional analysis on one of the genomes from the menB outbreak detailed below: johnlees.me/posts/menb-o...
menB outbreak in Kent -- first genomePrevious posts on menB: First thoughts and summary Working hypothesis for outbreak UKHSA have sequenced one of the isolates from the outbreak, which is on PubMLST (190637). This is excellent and UKHSA...johnlees.meJohn LeesSome more thoughts on why this outbreak (large, happening quickly, in one place) might be happening: johnlees.me/posts/menb-o... Perhaps strain + immunity + high transmission
Some more thoughts on why this outbreak (large, happening quickly, in one place) might be happening: johnlees.me/posts/menb-o... Perhaps strain + immunity + high transmission
menB outbreak in Kent -- more thoughtsPosted some thoughts on the menB outbreak yesterday. Now nine more cases, total at 27. A few more thoughts today, also after discussing with some others. A local factor seems necessary. I think pathog...johnlees.meJohn LeesI did my PhD on bacterial meningitis, finding whether there are genetic factors which make meningitis more likely. Wrote down some initial thoughts on the current outbreak in Kent: johnlees.me/posts/menb-o... I tried to think of factors and their likelihood to explain why this is happening now
I did my PhD on bacterial meningitis, finding whether there are genetic factors which make meningitis more likely. Wrote down some initial thoughts on the current outbreak in Kent: johnlees.me/posts/menb-o... I tried to think of factors and their likelihood to explain why this is happening now
menB outbreak in Kent -- initial thoughtsA cluster of meningitis cases is currently dominating the UK news. At least five of the cases have been confirmed as serotype B (menB), from what I can tell the others have not yet been analysed. My P...johnlees.meYou can now view a tree of 2,399,238 bacterial genomes we made from AllTheBacteria (on the great Taxonium): taxonium.org/atb That's a big tree! (unless you're used to SC2 trees)
TaxoniumInteractive exploration of large phylogenetic treestaxonium.orgHow do bacterial pangenomes evolve, what controls their dynamics, why do they exist? Fitting a mechanistic model to 450 species from allthebacteria.org suggesting fast vs slow gene exchange (i.e. amount of MGEs) is a major differentiating factor, correlated with phylogeny rather than lifestyle
Sam HorsfieldAt long last, my final PhD chapter is out: we developed a novel evolutionary simulator of bacterial pangenomes, Pansim, fitting it to data from >600K genomes using a likelihood-free framework, PopPUNK-mod, to explore neutral and adaptive pangenome dynamics www.biorxiv.org/content/10.6...
We are hiring for group leaders again — EBI is a great place to start your research group! embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
Research Group LeaderDo you want to lead groundbreaking research in computational biology? Join us at EMBL-EBI! EMBL's European Bioinformatics Institute (EMBL-EBI) is seeking talented and highly-motivated scientists to jo...embl.wd103.myworkdayjobs.com