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

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

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...

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

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

Meet Leonie Johanna Lorenz 🇩🇪, a Predoctoral Fellow at EMBL-EBI who is bringing mathematical modelling to microbes. Find out more about how Leonie’s passion for modelling patterns extends from bacterial evolution to sewing 🧵 www.ebi.ac.uk/about/news/p...

We are hiring for group leaders again — EBI is a great place to start your research group! embl.wd103.myworkdayjobs.com/EMBL/job/Hin...

🎉 New year, NEW PREPRINT! Bacteria exhibit astonishing genetic diversity, but where do new genes come from? My best friend Arya Kaul (/labmate in the @baym lab) investigates how advantageous deletions can spawn new genes - "deletion-born fusions." 🧵:

Our new preprint which reimplements "the NFDS model" (of Corander et al) to forecast populations after vaccination as a compartmental model, and uses new bioinformatic tools to create and process the pangenome data We look at which surveillance strategies are best to correctly forecast changes

RIP automated downloads of PDFs from biorxiv it seems, I suppose we have AI to thank for that

Some blogging from over the holiday, something for everyone I'm sure: Cooking johnlees.me/posts/xmas-d... Video games johnlees.me/posts/review... DIY johnlees.me/posts/towel-... (back to preprints tomorrow)

We're organising a microbes & deep learning session at SMBE next year -- looking forward to seeing your abstracts!

Nice to see some of our tools getting used in public health (in this case PopPIPE, which is downstream subclustering/transmission tool to be run on PopPUNK data)

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

A PhD project on historical genomics in the declining red squirrel in Britain is available in my group, through the @aries-dtp.bsky.social. Use historical genomes to track the effects of decline and genetic rescue in this charismatic species. aries-dtp.ac.uk/studentships...

Congratulations to Zam!

Just a quick plug: I've made a few updates to ExpEvoAnalyzer (variant functional annotation in experimental evolution studies) to use bwa as well as ska2, and to use existing or de novo annotations. It just might help streamline your pesky bioinformatics analysis! github.com/samhorsfield...

How do GWAS and rare variant burden tests rank gene signals? In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck! 🧬🧪🧵 www.nature.com/articles/s41...

Going through @samuelhorsfield.bsky.social presentation on pangenome graphs in comparative genomics, courtesy of @training.ebi.embl.org. Fascinating tidbit on history of alignment based sequence graph - it goes all the way back to 1989 (Hein), era of Apple IIs and IBM PS/2s. Great talk! 💻🧬🦠🧫

Bonjour! Masters students in France 🇫🇷, we’ve got an internship for you, in collaboration with the French Embassy in London. Aimed at students of computer science, statistics or bioinformatics. Deadline: 7 December 2025 Find out more and apply: www.ebi.ac.uk/about/jobs/i...

🧬Join us for the next TARGetAMR webinar! 💊Dangerous Miracle: A Brief History of Antibiotics 🗓️Wednesday 19 November🕐 1–2pm 💻 Online 🎙️With Liam Shaw, Computational Biologist at University of Bristol 🔗Register now! www.targetamr.org.uk/hdrevents/ta...

Are the faithful doing worse than random? www.johnlees.me/posts/traito... Not really

Very happy about this work on phylogenetic neural inference, led by @lblassel.bsky.social :)

We are running a hackathon at EBI in Feb: biomics.bacpop.org If you are at EMBL, ETH Zurich, GRC or GIMM working on a biological problem in data science or programming, consider putting a project forwards!

Proud to see my lab's work on M. tuberculosis and P. aeruginosa highlighted in this blog post

Now published, our tool to run (almost) all biological models interactively in your web browser Paper: academic.oup.com/bioinformati... Website: biomodels.bacpop.org Code: github.com/bacpop/SBMLt...

A new ggCaller version is out! v1.4 includes tweaks to improve efficiency, outputs Panaroo-friendly GFFs, and enables iterative gene calling; if you have already called a gene set, you can now add more genomes either one by one or in batches github.com/bacpop/ggCal...

The EMBL PhD programme is open until 13th October (entry ~Sep 2026): www.embl.org/about/info/e... We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them

Thanks for all the trainers and attendees on this course, which was a lot of fun to run, and hopefully filled a gap in genomics/modelling training And especially co-organisers @leonielorenz.bsky.social @sonjalehtinen.bsky.social Joel Hellewell

Thank you to everyone who joined us this week for the @embo.org Practical Course 'Methods for infectious disease modelling using genomics'. Join us for 2026's EMBO Practical Course. Sign up for 'Causality in biomedicine' alerts and hear as this new course develops: www.ebi.ac.uk/training/eve... 🧬🧫

Just launched an interactive Bayesian epidemic modelling platform that runs entirely in your browser! No downloads, no installations, no expensive software licenses. Just open the link and start modelling disease dynamics with real-time parameter estimation. >> widget-bayesian-sir.davidhodgson.me

The EMBL PhD programme is open until 13th October (entry ~Sep 2026): www.embl.org/about/info/e... We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them

Sometimes you meet absolutely incredible bioinfo-magicians. It was a huge privilege when @shenwei356.bsky.social joined our group for a year on an @embl.org sabbatical. While here, he developed a new way of aligning to millions of bacteria, called LexicMap 1/n www.nature.com/articles/s41...

Mathematical models in biology are powerful, but often hard to run, visualise, or reuse without specialist skills. Menelmacar is a new platform that makes biological models interactive and easy to explore directly in the browser: biomodels.bacpop.org 🧬💻

Wow, more than 2.4M of assembled bacteria in the new release of ABT! We plan to index these using our efficient colored De Bruijn graph index, Fulgor. We recently conducted experiments with nearly 1M genomes…getting there :) www.biorxiv.org/content/10.1...

📢🚨📢🚨 Genome Informatics deadline extended to September 8! meetings.cshl.edu/meetings.asp.... Please spread the word. If you are like me and had at least one abstract that wasn't quite ready by last week's deadline, you get another swing. See you there!

Closing soon. Great opportunity to do spatial transcriptomics on pre-antibiotic TB

It's interesting to draw these parallels. (We definitely need to move beyond purely technological solutions to how we deal with infections in a future where antimicrobials are more scarce.) www.theguardian.com/books/2025/a...

Deacon 0.9.0 can filter FASTA at well over 2Gbp/s on an AMD CPU from 2021. Compression is very limiting, but I suspect ~1Gbp/s is possible for fastq.gz with a modern CPU. Thanks @curiouscoding.nl for a monumental perf PR! Release 0.9.0 github.com/bede/deacon/... www.biorxiv.org/content/10.1...

My PhD student @leonielorenz.bsky.social (with Eva Geissen) has made this nice (free) online course to introduce mathematical modelling for biology: www.ebi.ac.uk/training/onl... Including both molecular and epidemiological examples

Recruitment is now open for the EMBL-EBI–Sanger Postdoctoral Programme. ESPOD builds on the collaborative relationship between EMBL-EBI and the @sangerinstitute.bsky.social, offering projects that combine experimental and computational approaches. www.ebi.ac.uk/research/pos... 🧬🖥️🔬#postdocjob

📣 Deacon 0.8.0 available on Bioconda - Much faster search and depletion through improved work distribution on multicore systems. My fastq.gz benchmark now runs at 400Mbp/s on Apple M1. - Dual default match thresholds for greater accuracy Details: github.com/bede/deacon/... 1k downloads! 🐥

Two take-aways from a nice talk by John Jumper last week www.johnlees.me/posts/alphaf...

Blog from postdoc Victor in the group about some weird results we saw with ntHash at longer k-mer lengths, and how to reduce hash collisions: www.bacpop.org/blog/hunting...

Gave my first conference talk at #ISMBECCB2025. Presented *gemsparcl* 💎✨, my PhD tool for clustering millions of genomes into species-level clusters - fast. So grateful to have been selected for a talk and enjoyed connecting with so many great people! Preprint hopefully coming later this summer! ☀️