Sam Horsfield

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

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

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...

Thanks Laura! Hope it’s useful

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...

Thank you! Hope it was useful and informative.

ecoevojobs.net 2025-26

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...

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.

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/...

v1.4.1 now available on conda!

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...

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...

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...

Now works with assemblies too!

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.

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.

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

Really nice work guys, glad to see this is out!

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

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...

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 🔥

A massive thanks to Basil Fok, Yuhan Fu, @paulturnermicro.bsky.social, @bacpop.org and Nick Croucher for all their hard work getting this out.

We show that when a novel variant, in this case a serotype, is present in a sample but not captured in the target database, GNASTy enables greater target enrichment compared to linear alignment. GNASTy also works well on complex samples potentially containing multiple serotypes.

Finally, we wanted to improve the ability of NAS to enrich novel variants not present in a target database. We developed GNASTy (Graph-based Nanopore Adaptive Sampling Typing), using graph pseudoalignment to enable flexible, and thus more sensitive, alignment of reads compared to linear references.

We then targeted the Capsular Biosynthetic Locus (CBL) of S. pneumoniae, the operon which defines its serotype. We show targeting the CBL is much better at distinguishing S. pneumoniae from closely related species than using NAS for the whole genome, and can detect multiple serotypes at once.

Before developing GNASTy, we first applied NAS to mock communities containing Streptococcus pneumoniae mixed with increasingly closely-related bacterial strains, showing that whole genome enrichment performs worse the more closely related a target genome is to non-target genomes in a mixed sample.