John Lees

Person standing outside next to a building wearing a red jacket

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...

Research Group Leader Do 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...

We are hiring for group leaders again — EBI is a great place to start your research group!

embl.wd103.myworkdayjobs.com/EMBL/job/Hin...

Fine, Le Guin from now on

Wow

🎉 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." 🧵:

STUdying Balancing Evolution (Nfds) To Investigate GEnome Replacement (also a German word for cat)

Thank you for asking, yes Stubentiger does indeed stand for STUdying Balancing Evolution (Nfds) To Investigate GEnome Replacement

There's also an R package: github.com/bacpop/Stube...
So others can more easily apply/reuse/adapt this important model

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

good god haha

At least nothing else is getting worse

It’s behind cloudflare captcha now (although I’m now wondering if that’s just the genome campus IPs) — so paperpile at least can’t auto download the pdf

Looks very promising!!

One thing I didn't quite follow, when you mention 'a novel parameter for trait simulation that accounts for uncertainty in deep ancestral branches of a phylogeny' -- is that referring to the time to first event parameter?

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)

The data was collected by the CABBAGE project, which has just been preprinted too: www.biorxiv.org/content/10.1...

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

Historical genomics of the declining red squirrel in Britain | Aries Dr Anders Bergström, School of Biological Sciences, University of East Anglia Professor Cock van Oosterhout, School of Environmental Sciences, University of East Anglia Dr Selina Brace…

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!

GitHub - samhorsfield96/ExpEvoAnalyzer: A workflow to analyse experimental evolution data. A workflow to analyse experimental evolution data. - samhorsfield96/ExpEvoAnalyzer

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...

Specificity, length and luck drive gene rankings in association studies - Nature Genetic association tests prioritize candidate genes based on different criteria.

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 :)

BIOMICS hackathon at EMBL-EBI Hackathon held in Hinxton 2026

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...