Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible. www.nature.com/articles/s41...

New work from my team, identifying drug targets in M. abscessus. Pre-print posted here: www.biorxiv.org/content/10.6...

💾 Prokka 1.15.6 is released! This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to. #bioinformatics #microbiology #genomics github.com/tseemann/pro...

Our new paper from my PhD work is online. It shows how bacterial population structure can trick machine learning—sampling matters! Many thanks to @lbarquist.bsky.social for the support and guidance! dx.plos.org/10.1371/jour...

Which LLM writes the best R code? posit.co/blog/r-llm-e... Interestingly, GPT-5.2 underperformed OpenAI’s own older/legacy GPT-5, as well as Gemini 3 and all the Claude models. #Rstats

I'm proud to share the latest methods work from my group. Led by @revathykri.bsky.social we wrote a book chapter on how we process and analyse viromes. Thanks to co-authors @rikhaagmans.bsky.social @ryancook94.bsky.social & Alise Ponsero link.springer.com/protocol/10....

proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes. #ProkaryoticGenomes #AnnotatedGenomes #Bioinformatics #Genomics #NAR @narjournal.bsky.social 🧪🧬 🖥️ academic.oup.com/nar/advance-...

Surveillance of genomic diversity and antimicrobial resistance in enterotoxigenic Escherichia coli in England, 2015–2023. Published Open Access and fee-free in JMM using a Publish and read agreement: doi.org/10.1099/jmm.... #JMM #PublishAndRead

Really pleased to share the first paper to come out of the lab. We found that hospital patients were frequently colonised with P. aeruginosa and that the same clone was shared between the gut and the lung. The phylogenies indicate that the clones moved from lung->gut www.nature.com/articles/s41...

Our manuscript on bovine deep-time paleogenomics at Denisova Cave and in the broader mid-latitude Asia is online! doi.org/10.1093/gbe/... 🦬🦴🧬 Main findings in the 🧵 below ⬇️ @cpgsthlm.bsky.social @genomebiolevol.bsky.social #aDNA

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

Tuberculosis (TB) that doesn’t respond to standard drugs is called drug-resistant TB and emerges when TB medicines are used inappropriately. Although the number of people developing drug-resistant TB has declined since 2015, it remains a global public health crisis affecting 390 000 people in 2024.

I'm very pleased to be back at Noguchi Memorial Institute for Medical Research helping run our "Working with Bacterial Genomes" course for the first time outside of Cambridge. A big thank you to the funding provided by GIZ, CRIT, my collaborator Dr Prince Asare and the ongoing support from NMIMR.

Thread is worth reading as well...

Our method for genome size estimation from long-read overlaps is now published 🥳 academic.oup.com/bioinformati...

Leveraging the subgenus category to address monophyletic genus over-splitting: illustration with recently proposed Mycobacteriales genera. Published Open Access and fee-free in IJSEM using a Publish and Read agreement: doi.org/10.1099/ijse... #IJSEM #PublishAndRead

The @crick.ac.uk is recruiting Early Career Group Leaders - Lab set-up, research costs, salaries for up to 5 researchers - Support for up to 12 years - Access to our core facilities - Competitive salary - Fantastic colleagues - All areas of biology Deadline 27 Nov www.crick.ac.uk/careers-stud...

New respiratory 🫁 infection and microbiomes conference in Hinxton with stellar line up of speakers. 🚨 Submit your abstracts now! 🚨 Please RT coursesandconferences.wellcomeconnectingscience.org/event/air-20...

Phylodynamics and genome-wide association studies reveal the expansion of modern Streptococcus canis in Germany https://www.biorxiv.org/content/10.1101/2025.09.29.679251v1

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols. Thread 1/n

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

Great to see this out there! We infer the evolutionary pathways behind patterns of AMR in Klebsiella across 102 states, finding globally consistent principles, state-specific deviations (and covariates), and validating evol predictions with new genomes. biorxiv.org/content/10.1... 1/

Really excited to announce the v1.9 release of the `rich-click` library 🎉 It's a Python library that uses builds on top of command-line help output from click, giving you beautiful output with only a couple of lines of code 🪄 ✨ 🌈 v1.9 TLDR: We have themes!

Come and join us at @shigellameeting.bsky.social in Paris 2026. Registrations are now open! www.shigella2026.conferences-pasteur.org/home and follow the Shigella starter pack go.bsky.app/6Vbwhjc (message to be added)! 215 days to go!

Introducing AMR cartography - work by Andrew Balmer

🚨 An excellent opportunity for scientists in Africa, at all career stages, working on maternal & child microbiome research 🚨 📚 Blended learning (3 months) incl. prep modules, hands-on training (12-17 Apr 2026) & mentoring. coursesandconferences.wellcomeconnectingscience.org/event/human-...

X-Mapper 🦠🧬🧪 - a sequence aligner developed for microbes, now on Bioconda! 🚀 • 11–24× fewer suboptimal alignments (same for human genome) • 3–579× lower inconsistency • improves on ~30% of reads aligned to non-target species github.com/mathjeff/map... bioconda.github.io/recipes/x-ma... #microsky

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...

The next online version of our "Working with Bacterial Genomes" course is now open for registration. We aim to provide you with comprehensive training in analysing bacterial genomes covering everything from QC to clustering plasmids. Sign up here: www.training.cam.ac.uk/bioinformati...

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 🧬💻

This study describes the oldest microbial DNA ever sequenced go.nature.com/4nfIzcU

New preprint reveals bacteria can't just collect all resistance genes like Pokemon cards. We found mutually exclusive evolutionary pathways to multidrug resistance in E. coli & P. aeruginosa - some resistance mechanisms actively prevent others from coexisting www.biorxiv.org/content/10.1...

New blog post: Using OpenAI Codex in @posit.co Positron with a demo on developing an #Rstats package using the OpenAI Codex agent doi.org/10.59350/ste...

A coffee variety called liberica, which is gaining popularity for the distinctive flavour of its beans, is actually three species go.nature.com/4fFfx3F

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

A cross-environment comparison of nontuberculous mycobacterial diversity https://www.biorxiv.org/content/10.1101/2025.08.04.668438v1

If ever a species needed a large scale long-read genomics project it is Y. pestis. Great paper! www.nature.com/articles/s41...

The new version of MetaPhlAn v4.2.2 released! 📌taxonomic profiling of long-read metagenomes for the first time 📌new version of the MetaPhlAn db (vJan25_202503) containing >21k new SGBs Try it out & @hutlab.bsky.social and we are looking forward to your feedback! forum.biobakery.org/t/metaphlan-...

New from The Strain Team: 🎊 Springer Nature Discovers MDPI 🎊 Springer Nature has spawned a copycat journal series called "Discover" mimicking #MDPI journal titles and citation behaviours. We even made a browser game to prove it (see 🔗). Gross! 😀 1/n #ResearchIntegrity #SciPub #AcademicSky

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

Myself and @yekwah.bsky.social are running our bacterial AMR databases and genotype prediction course again with @eventswcs.bsky.social. Completely free and study at your own pace. Check out the course objectives below and sign up before June 9th to join us! www.futurelearn.com/courses/anti...

New blog post! In it, I benchmark the new version of Dorado from @nanoporetech.com, which comes with new DNA basecalling models. Short version: big accuracy gains for hac, small improvements for sup. Check it out for the full results: rrwick.github.io/2025/05/27/d...

Excited to share the first beta release of AMRrules at #ABPHM! (Poster 42 tonight) interpretamr.github.io/AMRrules

We will be running the next in person iteration of our bacterial genomics course in Cambridge at the beginning of July www.training.cam.ac.uk/bioinformati... Please let anyone who may be interested know.

New preprint! Autocycler is a tool for long-read consensus assembly of bacterial genomes. It's like Trycycler but can be run fully automated (without any human intervention). www.biorxiv.org/content/10.1... (1/6)

🥁 NEW: Commentary in @cellcellpress.bsky.social! by @msabrysarhan.bsky.social Giacomo Antonello @whansi.bsky.social @cengoni.bsky.social @dmascalzoni.bsky.social @leviwaldron1.bsky.social Nicola Segata, Christian Fuchsberger www.cell.com/cell/fulltex... 1/4

www.biorxiv.org/content/10.1... Autocycler, the automated successor to Trycycler from @rrwick.bsky.social has a pre-print out - overall, pretty awesome performance (and is very easy to use) github.com/rrwick/Autoc...

Wonder the "chemicals" between gut bug pairs? Check out this new preprint lead by @skamrad.bsky.social and am honored to contribute!

New opinion paper from the lab! www.cell.com/trends/micro...

Excited to launch "ggplot2 [un]charted" with @yan-holtz.bsky.social! 🎉 An online course to master #ggplot2 with exercises, quizzes, and modules—and hands-on code running in your browser! Still WIP—sign up now for a limited discount: 👉 www.ggplot2-uncharted.com #rstats #DataViz #DataVisualization