iiinova — where your digital self keeps evolving

Reposted by Sam Horsfield

John Lees @johnlees.bacpop.org · 03/09/2026

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)

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Sam Horsfield @samuelhorsfield.bsky.social · 31/08/2026

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.com

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

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

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Reposted by Sam Horsfield

Toby Baril @tobybarilbio.bsky.social · 12/08/2026

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

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César de la Fuente @delafuentelab.bsky.social · 20/07/2026

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...

biorxiv.org

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...

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Sam Horsfield @samuelhorsfield.bsky.social · 09/07/2026

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/...

huggingface.co

BacCorpus - a AllTheBacteria Collection

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

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Sam Horsfield @samuelhorsfield.bsky.social · 26/06/2026

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.com

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

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

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Reposted by Sam Horsfield

Johanna von Wachsmann @johannavw.bsky.social · 16/06/2026

🧬 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...

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Reposted by Sam Horsfield

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 28/05/2026

Fast Set Operations for Compact k-mer Sets www.biorxiv.org/content/10.64898/20…

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Sam Horsfield @samuelhorsfield.bsky.social · 05/05/2026

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...

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Sam Horsfield @samuelhorsfield.bsky.social · 17/04/2026

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.

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Sam Horsfield @samuelhorsfield.bsky.social · 13/04/2026

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...

github.com

GitHub - samhorsfield96/ggCallaroo: A snakelike pipeline combining ggCaller and Panaroo.

A snakelike pipeline combining ggCaller and Panaroo. - samhorsfield96/ggCallaroo

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Reposted by Sam Horsfield

Toby Baril @tobybarilbio.bsky.social · 09/04/2026

🎉 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

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Sam Horsfield @samuelhorsfield.bsky.social · 31/03/2026

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/

Sam Horsfield @samuelhorsfield.bsky.social · 30/03/2026

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.com

GitHub - bacpop/ggCaller: Bifrost graph gene caller.

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

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Reposted by Sam Horsfield

Toby Baril @tobybarilbio.bsky.social · 17/03/2026

🎉🧬 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

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Sam Horsfield @samuelhorsfield.bsky.social · 17/03/2026

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.

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Reposted by Sam Horsfield

EMBL-EBI @ebi.embl.org · 16/03/2026

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...

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James Ferguson @psy-fer.bsky.social · 01/03/2026

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.com

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.

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Reposted by Sam Horsfield

EMBL-EBI @ebi.embl.org · 17/02/2026

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...

ebi.ac.uk

AlphaFold Database welcomes community datasets

Latest AlphaFold Database update adds high-value datasets for microbial and viral proteins, generated by specialist communities

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Sam Horsfield @samuelhorsfield.bsky.social · 07/02/2026

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...

biorxiv.org

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Sam Horsfield @samuelhorsfield.bsky.social · 05/02/2026

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

huggingface.co

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.

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Reposted by Sam Horsfield

Leonie Lorenz @leonielorenz.bsky.social · 22/12/2025

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

doi.org

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 ...

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Reposted by Sam Horsfield

Antoine Limasset @npmalfoy.bsky.social · 15/12/2025

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

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Reposted by Sam Horsfield

Aaron Quinlan (he/him) @aaronquinlan.bsky.social · 02/12/2025

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

quinlanlab.org

Intro to Bedder – The Quinlan Lab

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Reposted by Sam Horsfield

EMBL-EBI Training @training.ebi.embl.org · 20/11/2025

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. 🧬🖥️📊🦠

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Sam Horsfield @samuelhorsfield.bsky.social · 20/11/2025

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

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Reposted by Sam Horsfield

Tommi Mäklin @themaklin.bsky.social · 18/11/2025

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...

biorxiv.org

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...

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Reposted by Sam Horsfield

Genetics Society UK @gensocuk.bsky.social · 14/11/2025

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

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Sam Horsfield @samuelhorsfield.bsky.social · 07/11/2025

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.com

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

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

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Sam Horsfield @samuelhorsfield.bsky.social · 06/11/2025

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...

ebi.ac.uk

Pangenome graphs as a new paradigm in comparative genomics -

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Reposted by Sam Horsfield

Corrie Moreau @corriemoreau.bsky.social · 19/09/2025

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...

docs.google.com

ecoevojobs.net 2025-26

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EMBL-EBI @ebi.embl.org · 30/09/2025

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... 🦠

ebi.ac.uk

How to rapidly search the world’s microbial DNA

By making the world’s microbial DNA easier to explore, LexicMap helps researchers track outbreaks, study antibiotic resistance, and understand microbial diversity.

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Reposted by Sam Horsfield

Zamin Iqbal @zaminiqbal.bsky.social · 25/09/2025

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

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Zamin Iqbal @zaminiqbal.bsky.social · 25/09/2025

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/...

bbc.co.uk

Science In Action - Autism and the epigenetics of early brain development - BBC Sounds

Epigenetic changes during early brain development and the complexities of autism.

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Sam Horsfield @samuelhorsfield.bsky.social · 24/09/2025

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...

github.com

GitHub - bacpop/ggCaller: Bifrost graph gene caller.

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

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Reposted by Sam Horsfield

Ewan Birney @ewanbirney.bsky.social · 08/09/2025

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...

embl.wd103.myworkdayjobs.com

Group Leader – AI in Biology

Are you ready to lead groundbreaking research in AI for Biology? Join us at EMBL! We are seeking a visionary scientist to establish their own independent research group bridging innovations in machine...

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Sam Horsfield @samuelhorsfield.bsky.social · 11/09/2025

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.

github.com

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

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

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Zamin Iqbal @zaminiqbal.bsky.social · 10/09/2025

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...

nature.com

Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology

LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.

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Ben Williamson @benpatrickwill.bsky.social · 07/09/2025

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

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Jo Rhodes @drjorhodes.com · 30/08/2025

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...

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Mike Blazanin @mikeblazanin.bsky.social · 03/07/2025

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

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Zamin Iqbal @zaminiqbal.bsky.social · 19/05/2025

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...

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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 19/05/2025

Amira: gene-space de Bruijn graphs to improve the detection of AMR genes from bacterial long reads www.biorxiv.org/content/10.1101/202…

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Reposted by Sam Horsfield

Leonie Lorenz @leonielorenz.bsky.social · 07/05/2025

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

arxiv.org

SBMLtoOdin and Menelmacar: Interactive visualisation of systems biology models for expert and non-expert audiences

Motivation: Computational models in biology can increase our understanding of biological systems, be used to answer research questions, and make predictions. Accessibility and reusability of computati...

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Reposted by Sam Horsfield

EMBL-EBI @ebi.embl.org · 24/04/2025

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... 🧬🖥️

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Sam Horsfield @samuelhorsfield.bsky.social · 16/04/2025

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!

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Hamish @hamishoz.bsky.social · 20/03/2025

Australia’s reefs are on fire 🔥

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James Galbraith @gulbruth.bsky.social · 02/03/2025

🚨🚨🚨 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

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