I am hiring in this round – please do apply if you are interested in: machine learning (protein/genome/gene language models), methods for pathogen data analysis, pangenomes (or share with any students who might want to work with us)

EMBL@embl.org · 4w ago

Recruitment for the EMBL International PhD Programme is officially open! 📣 At EMBL, we train young scientists to become skilled and creative future leaders in academia, industry and other sectors. Start your career in the life sciences with us! 🔎 Read more and apply here: bit.ly/4x9Edss

I’m at ECCB 2026 this week! I’ll be presenting my new eukaryote pangenome simulator, PansimNuc (github.com/samhorsfield...), at Poster C-G.38 on Wednesday 2nd September - drop by if you’re interested in modelling pangenome evolution! @eccb-europe.bsky.social

GitHub - samhorsfield96/PansimNuc: A nucleotide-level pangenome simulator.

A nucleotide-level pangenome simulator. Contribute to samhorsfield96/PansimNuc development by creating an account on GitHub.

github.com

Thrilled to share that I'll be starting my lab at the Swedish Museum of Natural History in Stockholm as a DDLS Fellow in November! 🧑‍🔬🧬🎉 Of course, we will be delving into all things mobile DNA & evolution, as well as developing AI approaches for biodiversity genomics #newPI #TEsky #TEworldwide

Biology has plenty of data—the challenge is making it usable. AllTheBacteria transforms 2.44 million public bacterial and archaeal genomes into an open, uniformly processed, searchable, AI-ready resource. www.biorxiv.org/content/10.1...

AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics

Public microbial genomes encode an immense record of biological diversity, evolution and molecular function, but much of this information remains difficult to reuse because raw sequencing data are not...

biorxiv.org

Unfortunately, due to data storage restrictions, we have had to remove the individual SPIRE and mOTUs gene predictions datasets from HuggingFace. However, this data is still available in BacCorpus, with deduplicated gene predictions huggingface.co/collections/...

BacCorpus - a AllTheBacteria Collection

A dataset of diverse bacterial genomes across habitats. Includes deduplicated genomes, proteins and intergenic sequences.

huggingface.co

I've been working on a new pangenome simulator for eukaryotes - PansimNuc! A Rust-based nucleotide-level simulator that models mutation, selection, recombination, gene and TE mobility and demography. It's still under development, with plans to tweak it for prokaryotes github.com/samhorsfield...

GitHub - samhorsfield96/PansimNuc: A nucleotide-level pangenome simulator.

A nucleotide-level pangenome simulator. Contribute to samhorsfield96/PansimNuc development by creating an account on GitHub.

github.com

🧬 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...

Fast Set Operations for Compact k-mer Sets https://www.biorxiv.org/content/10.64898/2026.05.24.727514v1

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...

I did some public outreach last year - it was super rewarding, and made me realise the importance of grassroots science engagement. Not only does it inspire the next generation of scientists, but fosters public trust in science, something that is very important right now.

EMBL@embl.org · 6mo ago

From DNA Days to ocean nanoplastics to science videos in Catalan – EMBL scientists are finding new and interesting ways to engage the public and make the wonders of scientific discoveries more accessible to everyone. Learn more: www.embl.org/news/people-...

ggCallaroo v0.1.0 is now out! This snakemake pipeline predicts, clusters and annotates bacterial genes using ggCaller, Panaroo and Bakta. It generates Panaroo files with functional annotations already integrated, which can then be used with the usual downstream tools. github.com/samhorsfield...

🎉 EarlGrey ParTEA v0.1.6 is here! Huge thanks to everyone who's tried the pipeline and shared feedback — your suggestions directly shaped these new features. 🍵 #TEworldwide #transposableelements #bioinformatics #genomics

Two new bioinformatics internships available in @johnlees.bacpop.org group at EMBL-EBI: 1) testing and developing ML methods for identification of bacterial promoter regions; 2) Applying innovations in protein structure prediction to search massive datasets. Apply here: www.bacpop.org/jobs/

ggCaller v1.5.0 is out! We've removed the integrated clustering to enable users to benefit from new Panaroo features. Now, ggCaller generates GFFs that can be used with any clustering method. But for fans of an integrated ggCaller pangenome workflow read on... github.com/bacpop/ggCal...

GitHub - bacpop/ggCaller: Bifrost graph gene caller.

Bifrost graph gene caller. Contribute to bacpop/ggCaller development by creating an account on GitHub.

github.com

🎉🧬 Multiple genomes/pangenome? Time for a parTEA! 🧬 ☕️ Tired of annotating TEs one genome at a time? Same. So we organised a parTEA! Introducing EarlGrey ParTEA v0.1.3 — consistent TE annotation across all your genomes, in parallel, with one command: github.com/TobyBaril/Ea... #TEworldwide #TEsky

Super excited to see this out! Massive effort from the group, generating thousands of ML trees and coming up with a means of merging them. Code for tree generation and merging will be made available soon with release of the ATB paper.

John Lees@johnlees.bacpop.org · 7mo ago

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)

You asked, we listened. Millions of AI-predicted protein complex structures are now available in the #AlphaFold Database. This spans homodimers from 20 of the most studied species, including humans, as well as the World Health Organization’s priority pathogens list. www.ebi.ac.uk/about/news/t...

Introducing kuva: A scientific plotting library in rust, along with cli binary with the option to plot directly into the terminal. Feel free to drop me some feedback as an issue on the repo github.com/Psy-Fer/kuva crates.io/crates/kuva/...

GitHub - Psy-Fer/kuva: A scientific plotting library in Rust

A scientific plotting library in Rust. Contribute to Psy-Fer/kuva development by creating an account on GitHub.

github.com

James Ferguson@psy-fer.bsky.social · 7mo ago

Okay now that i've figured out how to do a kinda scanline fill between the bresenham lines, Sankey plots on the terminal look pretty cool!!!

The AlphaFold Database, jointly developed with Google DeepMind, now contains datasets from specialist communities. This includes rich datasets for microbes, viruses & parasites associated with tropical diseases. Explore the new datasets in the AlphaFold Database. 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

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...

Clinical impact of whole exome sequencing: ten years of the Great Ormond Street Hospital Autoinflammation Centre of Excellence experience

AbstractObjective. To evaluate the diagnostic yield of whole exome sequencing (WES) vs targeted gene panel (TGP) testing in patients evaluated for autoinfl

academic.oup.com

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

Hugging Face – The AI community building the future.

We’re on a journey to advance and democratize artificial intelligence through open source and open science.

huggingface.co

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

A reusable model of pangenome selection informs optimal surveillance strategies over vaccine introductions

The human pathogen Streptococcus pneumoniae is a major cause of disease, including pneumonia and meningitis. The introduction of Pneumococcal Conjugate Vaccines (PCVs) initially reduced the burden of ...

doi.org

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

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 10mo ago

Inverted colored de Bruijn Graph for practical kmer sets storage https://www.biorxiv.org/content/10.64898/2025.12.08.692073v1

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!

MRC Centre for Global Infectious Disease Analysis@mrc-outbreak.bsky.social · 10mo ago

NEW EPISODE #ScienceInContext! @eonore.bsky.social joined by Dr Samuel Horsfield on diagnostic & surveillance methods & GNASTy improving our ability to detect variants that haven’t been seen before👇 @imperialcollegeldn.bsky.social @ox.ac.uk @rebecca-and.bsky.social @ebi.embl.org youtu.be/X7I-ZVyw9dw

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...

Co-evolution between colibactin production and resistance is linked to clonal expansions in Escherichia coli

Specific strains of Escherichia coli employ the polyketide synthase island to produce a metabolite called colibactin that is implicated in colorectal tumorigenesis via its genotoxic effect on human DN...

biorxiv.org

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...

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

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

github.com