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

EMBL-EBI@ebi.embl.org · last wk.

📣 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

Very proud of this preprint out of my lab, our first (of hopefully many) host-microbe spatial transcriptomics paper. www.biorxiv.org/content/10.6... Amazing insights into P. aeruginosa biology and chronic airway disease @cysticfibrosis.org.uk @sangerinstitute.bsky.social @asthmaandlung.org.uk

Are you a computational immunologist or bioinformatician interested in impactful vaccine research? We're hiring a postdoc to join @psioxford.bsky.social work in vaccine immunology and evaluation, working on the ChAdOx1 Nipah vaccine. Please get in touch! my.corehr.com/pls/uoxrecru...

We'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@johannavw.bsky.social · 2mo ago

🧬 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...

As many people guessed... MenB vaccine catch up campaign incoming for students in England, Wales and Scotland www.bbc.co.uk/news/article...

Meningitis B vaccine to be offered to thousands of young people in July

The decision for the one-off vaccine programme follows the unprecedented outbreak in Kent this year.

bbc.co.uk

The video recordings of the legend 2025 conference held last December on machine learning for evolutionary genomics are now online ! Feel free to have a look if you missed the conference. www.canal-u.tv/chaines/lisn...

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) - Wikipedia

en.wikipedia.org

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...

New 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 Horsfield@samuelhorsfield.bsky.social · 3mo ago

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...

Applications now open for the UNIL Summer School on Modelling for Evolutionary Biology (31 Aug–5 Sep 2026, Lausanne)! For PhD & postdocs interested in formal approaches to evolutionary ecology (incl. social evo, life-history, species interactions). Scholarships available, Pls RP! shorturl.at/fo1GA

How diverse is bacterial immunity ? We report in @science.org how language models allowed us to predict 2.4M antiphage proteins spanning >23K novel potential systems. 👏 @emordret.bsky.social, @alexhv.bsky.social & al doi.org/10.1126/scie... Explore them here defensefinder.mdmlab.fr/wiki/refseq_...

Alex Kramer, Alan Zhang and friends posted our preprint today. In it, we introduce Panmap, a tool for phylogenetic placement, assembly, lineage abundance estimation, and eDNA assignment using phylogenetic pangenomes. 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...

A quick rant on people vibe-translating our Rust libraries to other languages That's the second time in a week that I see new bioinformatics tools with a vibe-coded translation of our Rust libraries to C/C++. I have two major issues with that:

...because I'm also releasing ggCallaroo! This is an-easy-to-use snakemake pipeline that runs ggCaller, Panaroo and then functionally-annotates representative proteins using Bakta, all in one tool. github.com/samhorsfield...

We 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/

Welcome, @stephlo.bsky.social, our new Team Leader for Protein Function. Find out how Stephanie’s experience in genomics shaped her approach to protein curation and AI integration. #ProteinScience #AI www.embl.org/news/people-...

Here 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

Some provisional analysis on one of the genomes from the menB outbreak detailed below: johnlees.me/posts/menb-o...

John Lees@johnlees.bacpop.org · 5mo ago

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

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

John Lees@johnlees.bacpop.org · 5mo ago

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

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

You 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)

New preprint where @lbobay.bsky.social and I were motivated by the fact that non-synonymous substitutions are commonly analyzed in molecular evolution studies, but the similarity of the amino acids being substituted is an understudied area. doi.org/10.64898/202...

New paper showing that bacteria with more genes for cooperation can live in a broader range of habitats and that genes for cooperation are more more likely to be in the accessory genome www.pnas.org/doi/10.1073/... @lauriebelch.bsky.social

Delighted to see over 17 million new protein structure predictions from novel proteins in AllTheBacteria are now integrated into the AlphaFold Database at @ebi.embl.org ! Huge work from @gbouras13.bsky.social @oschwengers.bsky.social and friends to generate these. www.ebi.ac.uk/about/news/u...

AlphaFold Database welcomes community datasets

Latest AlphaFold Database update adds high-value datasets for microbial and viral proteins, generated by specialist communities

ebi.ac.uk

How 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 Horsfield@samuelhorsfield.bsky.social · 6mo ago

At 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...

Super excited to announce the release of gene and intergenic region annotation from the largest bacterial genome and MAG datasets available, including AllTheBacteria, GTDB, SPIRE, HRGM, mOTUs and MGnify - dereplicated and available from HuggingFace huggingface.co/AllTheBacteria

Hugging Face – The AI community building the future.

We’re on a journey to advance and democratize artificial intelligence through open source and open science.

huggingface.co