Pleased to share our latest paper, a summary of many years of work with the GOSH-ACE team. An absolute pleasure to work alongside @fionapk.bsky.social and combine our PhD efforts into lasting patient benefit. academic.oup.com/rheumatology...

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...

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

Very happy to share our preprint on a mathematical model for Streptococcus pneumoniae population dynamics after vaccine introductions. It's a reusable model that describes vaccine replacement dynamics and can help to determine strategies for genomic surveillance: doi.org/10.64898/2025.12.18.695090

Preprint Alert! With @tmthrz.bsky.social and @rayanchikhi.bsky.social we aim to tackle practical unitigs compression! A thread:

We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen. 1/n

ICYMI: catch up with our pangenomics webinar series. The recordings are now available on-demand: www.ebi.ac.uk/training/eve... Webinars were given by: Raymond Cheng, Leanne Haggerty, @samuelhorsfield.bsky.social, Alexander Leonard, Neil MacAlasdair, and @camillemrcht.bsky.social. 🧬🖥️📊🦠

Really grateful for the chance to discuss GNASTY on #ScienceInContext; massive thanks to @eonore.bsky.social for the invite!

New preprint: we looked into production of the bacterial toxin colibactin and found that MDR E. coli from the global north have co-evolved with endemic colibactin producers, acquiring colibactin resistance genes before undergoing clonal expansions. www.biorxiv.org/content/10.1...

Congratulations to @zaminiqbal.bsky.social from @milnerevolution.bsky.social on being awarded the 2026 Mary Lyon Medal!

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...

If you're interested in using pangenome graphs for comparative genomics, check out my webinar, part of EMBL-EBI's "Concepts, methods, and resources in pangenomics" series, available on-demand: www.ebi.ac.uk/training/eve...

UPDATE: The 2025-2026 list of faculty and postdoc positions in ecology and evolutionary biology is out! Be sure to check out this active and helpful community run resources! docs.google.com/spreadsheets...

There are millions of openly available microbial genomes, but searching them can be slow. Until now 🥁 Introducing LexicMap, a new alignment tool that lets scientists search these data in minutes, helping track antibiotic resistance, trace outbreaks, and more. www.ebi.ac.uk/about/news/r... 🦠

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

If you can't face reading War and Peace or my massive thread, I was interviewed on BBC Science in Action, you can hear me 12 mins into this episode (we are not the headline paper, which was on autism): www.bbc.co.uk/sounds/play/...

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...

Are you an AI expert who wants to stay in academia and change the world by understanding the most complex things we know - living organisms? Want to lead your own group, based in Heidelberg DE, working language English? @embl.org is hiring in AI embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

A little tool I've developed: ExpEvoAnalyzer (github.com/samhorsfield...) - a snakemake pipeline that compares isolate paired-read data from an experimental evolution study to a reference isolate, producing functionally-annotated SNPs in a presence/absence matrix.

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...

Academic authors, here's a peek into the black box of journal publishing from an journal editor if you can bear it:

In just a weeks time @chownbioinf.bsky.social is cycling over 200km to the @bsmm-meeting.bsky.social in Norwich, to raise money for @aspertrust.bsky.social This is a huge feat, and for such a great cause. Please consider sponsoring Harry! www.justgiving.com/page/harry-c...

Looking forward to seeing everyone, new and old, at the Microbial Population Biology GRS + GRC in just a couple days! go.bsky.app/GGxRjzC

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...

Amira: gene-space de Bruijn graphs to improve the detection of AMR genes from bacterial long reads https://www.biorxiv.org/content/10.1101/2025.05.16.654303v1

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

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... 🧬🖥️

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!

Australia’s reefs are on fire 🔥

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

🚨🚨🚨 For everyone who's using BLAST+ through EBI be aware, the default settings for some tools differ and will give different results and will take a lot longer than you're used unless you change these parameters. 🚨🚨🚨 1/n

This morning's reading in both the "everyone loves Lord of the Rings" and "everyone loves contrived acronyms" files: CELEBRIMBOR (Core ELEment Bias Removal In Metagenome Binned ORthologs), a snakemake-based workflow to better identify core genes for pangenomes from metagenomic assemblies. 🧪

NEW: 2024 has just been confirmed as the warmest year on record, and the first to breach the 1.5C threshold. We used a ridgeline (Joy Division inspired) chart to visualise daily temperature anomalies since 1940. 2024 clearly stands out with 100% of its days above 1.3C and 75% above 1.5C.

I'm putting together a Microbial Bioinformatics starter pack to help get everyone connected in our community. Let me know if there are any bluesky users to be added and share so that twitter refugees can tune back in to the fantastic world microbes go.bsky.app/3ezLo7e

Just a little tool release before the holidays: WTBcluster ("Woooowww That's Big"-cluster), a snakemake pipeline to predict and iteratively cluster billions (and billions...) of bacterial genes using pyrodigal and MMseqs2. It's a work in progress so any issues let me know! github.com/samhorsfield...

New paper: We show that population exposure to colibactin producing E. coli lineages ST95 and ST73 largely explains global variation in colorectal cancer incidence. Same STs are also major causes of UTIs and may be similarly involved in urinary tract cancers. www.sciencedirect.com/science/arti...

New tool from me: I wrote a local aligner that can do approximate reference-based alignment and find genes in a query microbial genome, without a separate indexing step or any temporary disk space usage. Written fully in Rust and there will be a browser version out later: github.com/tmaklin/kbo 1/3

A thread with some new starter packs in genomics and bioinformatics 🧵 1/13...

We have a paid internship opportunity in our group at EMBL-EBI (Cambridge) starting in February 2025, working on pneumococcal serotyping using deep learning. (1/3)

Bifrost 1.3.0 is out. Compared to 1.2.0, this new version brings up to 30% memory/running time improvements (depending on the input dataset), adds a couple of useful features to the graph search CLI and fixes a few minor bugs. github.com/pmelsted/bif...

There is still time to register for our SMBE satellite meeting on pangenomes and transmission in Tokyo (until 31st October) See our website for more details, and now a provisional schedule too! smbepangenomes.bacpop.org

CELEBRIMBOR is now out in Bioinformatics! If you want to identify core genes that are systematically underestimated in bacterial MAG data, or you're just interested to see how we made that acronym work, go take a look: academic.oup.com/bioinformati...

Great to see publication of PANGWES in Genome Research - a tool which uses pangenome graphs to detect epistasis in both the core and accessory genome of bacteria. Check it out here genome.cshlp.org/content/34/7...

Quite a while after its first release, ggCaller is now up and working on conda (linux only, apologies Mac users, there's still a few hoops to jump through). Give it a go on your bacterial genomes: anaconda.org/bioconda/ggc...

The Continuous Language of Protein Structure https://www.biorxiv.org/content/10.1101/2024.05.11.593685v1

I've added another module to these notes on recursion and closures: iprogramming.bacpop.org/recursion.html

New short paper from Joel Hellewell and @samuelhorsfield.bsky.social and on making pangenome (specifically frequency estimates) from metagenome data: www.biorxiv.org/content/10.1...

We have now written up the paper for SKA2 (ska.rust): biorxiv.org/cgi/content/... This is the successor to SKA, which uses split k-mers XXXX[-]XXXX to rapidly variant call microbial genomes, either reference-free or reference-based

Excited to be at my first annual conference of the microbiology society #microbio24! Come by my poster (B082) on Wednesday if you want to talk about mathematical modelling and/or the population genetics of Streptococcus pneumoniae.

Heading up to Edinburgh for #MicroBio24! I’ll be presenting on Wednesday afternoon about our group’s work on GNASTy, a nanopore adaptive sampling method for typing S. pneumoniae. Drop me a message if you fancy a chat!