Very pleased to announce that my Crick postdoc work has just been published in Nature Communications: www.nature.com/articles/s41... Big thank you to @bpradel.bsky.social, @jaksonluk.bsky.social, @maxgg.bsky.social and the rest of the host-pathogen interactions in TB lab that made it all possible!

Really pleased to announce my promotion to Professor of Respiratory Infection and Epithelial Biology @ucl.ac.uk. I couldn't have got here without some amazing people and mentors along the way, and the hard work of current and past group members. #FirstGenPhD #FirstGenProf #promotions

Delighted with the publication in @cp-trendsmicrobiol.bsky.social of a concept note where we propose a new framework to capture the complexity of infections in vivo: metapopulation infection biology. Supported by Klebsiella and Cryptococcus research among other pathogens www.cell.com/trends/micro...

Beyond intracellular–extracellular divide toward metapopulation infection biology

The binary classification of pathogens as intracellular or extracellular fails to capture the complexity of infections in vivo. We propose the metapopulation infection biology framework, in which infe...

cell.com

Delighted to share our new paper, out now in @natureportfolio.nature.com where we show that neutrophil myeloperoxidase (MPO) tracks RSV severity in infants, and can be used as a functional readout of therapeutic efficacy in the lab. 📄 Read it (open access) 👉 rdcu.be/ftx53

Neutrophil myeloperoxidase as a functional biomarker for RSV severity: implications for in vitro therapeutic screening

Nature Communications - Preclinical human models are needed to investigate mechanisms and evaluate therapies for severe respiratory syncytial virus (RSV) infection in children. The authors here...

rdcu.be

Read: 'Phylo-Plex: A phylogenetically informed, low-cost amplicon sequencing platform for deployable high-resolution genomic epidemiology' in @natcomms.nature.com here 👇 https://www.nature.com/articles/s41467-026-75002-y

Phylo-Plex: a phylogenetically informed, low-cost amplicon sequencing platform for deployable high-resolution genomic epidemiology

Nature Communications - Whole genome sequencing of pathogens is costly to implement, and partial sequencing sacrifices information. Here, the authors present Phylo-Plex, a method for identifying...

nature.com

👀👇 New work on sexually transmitting Shigella (press-friendly: bit.ly/4bBarEL) From continued collaboration with @clairejenkins2.bsky.social @ukhsa.bsky.social, @pducambridge.bsky.social co-lead @hsalje.bsky.social, a talented student Julia Marshall www.linkedin.com/in/julia--ma..., and others! 🧫🧬💊

The Lancet Infectious Diseases@thelancetinfdis.bsky.social · last mo.

New Research The spread of sexually transmissible drug-resistant shigellosis in England: a genomic epidemiology study www.thelancet.com/journals/lan...

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

Have you registered for Genome Science yet? www.genomescience.org.uk Its going to be in mad for it Manchester September 14th-16th 2026. Lots of great microbial genomics and bioinformatics speakers so make sure you secure a place. Early bird registration ends on 31/7/26.

Liam Gallagher: Oasis Rooftop Walk

ALT: Liam Gallagher: Oasis Rooftop Walk

static.klipy.com

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...

It took years after my masters to publish BaGPipe, now it's out! It's a Nextflow pipeline to run end-to-end bacterial GWAS, heavily tested and benchmarked on different datasets, and now in good hands of the Sanger's Pathogen Informatics Team. link.springer.com/article/10.1...

BaGPipe: an automated, reproducible, and flexible pipeline for bacterial genome-wide association studies - BMC Microbiology

BMC Microbiology - Microbial genome-wide association studies (GWAS) are crucial for linking genetic variation to phenotypic traits in bacteria. However, current tools often involve complex manual...

link.springer.com

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...

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-...

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

Am stoked and thrilled that our latest paper is now out. A longitudinal study of invasive E. coli from children in the Netherlands over 50 years www.sciencedirect.com/science/arti...

Lineage dynamics of invasive Escherichia coli isolates in the Netherlands from 1975 to 2021: a retrospective longitudinal genomic analysis

Escherichia coli is a common cause of invasive infections such as bloodstream and cerebrospinal fluid infections in neonates. Strains positive for the…

sciencedirect.com

@oldenoughtosay.com I see that your house has recently been visited by the Bad Enterovirus Fairy, aka Hand, foot and mouth disease. I got so het up about baby germs that I wrote a 9.5k word review article on them (800 word version here theconversation.com/if-you-think...). Normal response, right?!

If you think your toddler’s often ill, you’re right – what going to nursery means for catching colds and building immunity

Having an under five in your household increases your risk as an adult of having diarrhoea and vomiting.

theconversation.com

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)

I always speak politely to AI as there is a non-zero chance that this will be a situation in the future:

So I pleased to announce the conceptual spawn of FigTree: PearTree (acronym still to be finalised). If you want to dive right in it is hosted as a web app here: artic-network.github.io/peartree (click the “Example...” button for immediate candy and then click every button you can find).

The genomic diversity and spatial patterns of Mycobacterium bovis in Ireland revealed by whole genome sequencing rdcu.be/e50zT

Terrible headline (this is NOT what the new research - link below - shows!), terrible AI image! Argh! Here’s the actual research: www.science.org/doi/10.1126/... Where do I start?! 1/4

In case you missed it: our review titled "Spatial structure: shaping the ecology and evolution of microbial communities" is out! 🚨 Let me hit you with some highlights on why spatial structure matters. (and why you should care!) Sharing is appreciated 🙏 🧵👇 doi.org/10.1093/fems...

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

Incredible time at #AIR2026 covering breadth of respiratory infection, microbiomes and immunology with some really beautiful biology. Thanks to fellow committee members @resp-micro.bsky.social @drclairesmith.bsky.social @ewanharrison.bsky.social , Alex Kayongo and organisers @eventswcs.bsky.social

Fantastic final day at #AIR2026. A masterclass in in vitro modelling by Scott Randall followed by a great panel discussion with funders @asthmaandlung.org.uk @wellcometrust.bsky.social @cysticfibrosis.org.uk @karlstaples.bsky.social

Another insightful day of science, discussion and making new friends at #AIR2026 Day 2 Highlights: making sense of big data, spatial transcriptomics and in vitro modelling of respiratory infections @eventswcs.bsky.social @sangerinstitute.bsky.social

Always good to be back at Wellcome Genome Campus, this time for the #AIR2026 conference on Genomic and systems approaches to respiratory infection, microbiomes and immunity

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...

Startling that this is being broadcast in the absence of any public communications by @ukri.org The academic community has a right to expect to be told first hand what is happening with response mode funding and what the immediate future looks like www.researchprofessionalnews.com/rr-news-uk-r...

MRC instructs grant review boards to slash funding rates - Research Professional News

Boards asked to recommend just three applications for funding, as BBSRC also suspends calls

researchprofessionalnews.com

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

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...

embl.wd103.myworkdayjobs.com

EMBL is deeply saddened by the passing of our Interim Director General Peer Bork, a pioneering scientist who left an indelible imprint on life science research in Europe and beyond. We extend our deepest condolences to his family, friends, and colleagues. www.embl.org/news/people-...