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! ☀️

💥 Excited to introduce Bacformer 🦠 - the first foundation model for bacterial genomics. Bacformer represents genomes as sequences of ordered proteins, learning the “grammar” of how genes are arranged, interact and evolve. Preprint 📝: biorxiv.org/content/10.1... 🧵 1/n

Paper alert! We present Oreo a tools that reorder long reads datasets in a way to compress them efficiently with ANY universal compressor like gz, zstd, xz ... TLDR: You can get state of the art compression WITHOUT a dedicated compressor/decompressor! academic.oup.com/bioinformati... A thread!

The important point about the CLT is that *sums* of lots of little effects tend to be normal. In statistics, this justifies a normal model for "noise", but the small numbers of big effects can do anything, that's what we seek to measure in observation and / or experiment.

I was lucky to go dog sledding earlier this year which, naturally, made me think about the Central Limit Theorem Quick posts about the CLT: www.johnlees.me/posts/dogs-c... (and some pictures of dogs)

New preprint! Deacon is a versatile tool for filtering FASTA/FASTQ files and streams at hundreds of megabases per second using minimizers, built with rapid metagenomic host depletion in mind, but equally useful for search. github.com/bede/deacon

Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social). myloasm-docs.github.io

Delighted to see this paper from danderson123.bsky.social 's PhD out. We have been building tools for AMR gene detection for over a decade now, but multicopy genes remain challenging. Dan shows that with a gene-space de Bruijn graph and long reads, you can do well www.biorxiv.org/content/10.1...

Eva is looking for people looking to start their own group at the intersection of infection and strucutral biology/imaging -- and has an event coming up to connect between these fields. Please pass on to anyone who might be interested!

Very happy and proud to announce that the first preprint of my PhD is out: arxiv.org/abs/2504.20710 We developed an R package to translate mathematical models in SBML format into executable odin models and visualise models from @biomodels.bsky.social on our website Menelmacar biomodels.bacpop.org

Some silly pedantry, mostly to do with typesetting www.johnlees.me/posts/pedant...

Happy to share the first preprint from my lab. Great work by Lewis Fisher and collaboration with Jukka Corander www.biorxiv.org/content/10.1...

A bit of a different one from us (@leonielorenz.bsky.social did all the work!): we used modelling tools developed as part of the COVID-19 response to automatically run, visualise and make interactive (nearly) all life science models: biomodels.bacpop.org

Small update from AllTheBacteria (allthebacteria.org). Assemblies can be bulk downloaded from OSF as before, or you can now get individual assemblies from AWS. We now also have a LexicMap index on AWS, so you can align your favourite gene against 2.4million bacteria (next post for price estimates)

Code for PopPIPE here: github.com/bacpop/PopPIPE Thanks to some thorough editing in review we ironed out some errors that can arise, made the installation simpler, and added more automated output from the transmission pipline steps

Our subclustering and transmission pipeline, PopPIPE has now been published: www.microbiologyresearch.org/content/jour...

Tracking different serotypes of Streptococcus pneumoniae can be tricky. GNASTy is a scalable analysis method for use with portable Nanopore Adaptive Sampling for real-time detection of S. pneumoniae, helping track vaccine performance. Find out more 👇 genome.cshlp.org/content/earl... 🧬🖥️

1/ We made a tool called Vizitig to explore sequencing datasets visually, interactively, and with metadata. It uses a colored de Bruijn graph under the hood.

Great to see our work on GNASTy made it into the long-read special issue at Genome Research alongside some super innovative applications and methods!

1 week until deadline for this postdoc position. Really key position in my lab working on amazing datasets

New Postdoc position alert: a very exciting opportunity to join a new group led by @sumanasharma.bsky.social who is a visionary scientist and a fantastic person. Looking for a computational person to work on a project related to studying immune checkpoint signalling: my.corehr.com/pls/uoxrecru...

Trying to find an image of vaccine conjugation and google mostly coming up with the one from this paper www.mdpi.com/2076-393X/9/... Terrible resolution. I thought the font seemed really familiar too

Our extension to ska, 'ska lo' (for 'left-out') which can additionally, and still very quickly, find indels and SNPs closers than the k-mer distance is now out: academic.oup.com/mbe/advance-... This addresses a long standing challenge for reference-free variant callers

We were able to host an SMBE-funded satellite conference on pathogen pangenomes last year thanks to these fees going back into the community. Thanks to all MBE and GBE authors for supporting SMBE rather than for-profit companies!

Playing with #vizitig again to prepare for the 1.0 release. This is the SNAP25 human gene expressed in 3 SRA datasets linked to cancers. Exons have one color each, and exon junctions are in yellow. The rest is new/noise.

Our pangenome graph-based Nanopore Adaptive Sampling (NAS) tool, GNASTy, is available now in Genome Research! genome.cshlp.org/content/earl...

New preprint is out! We investigate how well you can call variants directly from genome assemblies compared to traditional read-based variant calling. Read it here: www.biorxiv.org/content/10.1... Data & code: github.com/rrwick/Are-r... (1/8)

We are happy to announce that registration for our new EMBO practical course on methods for infectious disease modelling using genomics is open for applications (closing 25th May) www.ebi.ac.uk/training/eve... The course will run 14-19th September at EBI, Hinxton

Oluwaremilekun Grace Ajakaye established the Laboratory of Molecular Parasitology & Genomics of Neglected Tropical Diseases at Adekunle Ajasin University Nigeria. Her work focuses on the genetic variations that drive parasite transmission & evolution. At EMBL, Grace joined the @bacpop.org group