Sam Horsfield
@samuelhorsfield.bsky.social
Postdoc @ EMBL-EBI, Pathogen Informatics and Modelling Group 🦠 Working on methods to study bacterial evolution and epidemiology using pangenomics 🧬
Reposted by Sam Horsfield
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...
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...
www.biorxiv.org
November 18, 2025 at 6:41 AM
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...
www.biorxiv.org/content/10.1...
Reposted by Sam Horsfield
Congratulations to @zaminiqbal.bsky.social from @milnerevolution.bsky.social on being awarded the 2026 Mary Lyon Medal!
November 14, 2025 at 12:36 PM
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
November 7, 2025 at 3:07 PM
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...
Pangenome graphs as a new paradigm in comparative genomics -
Pangenome graphs as a new paradigm in comparative genomics -
www.ebi.ac.uk
November 6, 2025 at 11:40 AM
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...
Reposted by Sam Horsfield
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...
ecoevojobs.net 2025-26
docs.google.com
September 19, 2025 at 9:47 PM
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...
Reposted by Sam Horsfield
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...
🦠
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...
🦠
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.
www.ebi.ac.uk
September 30, 2025 at 9:47 AM
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...
🦠
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...
🦠
Reposted by Sam Horsfield
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
Thread 1/n
September 25, 2025 at 9:29 PM
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
Thread 1/n
Reposted by Sam Horsfield
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/...
www.bbc.co.uk/sounds/play/...
September 25, 2025 at 9:50 PM
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/...
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...
GitHub - bacpop/ggCaller: Bifrost graph gene caller.
Bifrost graph gene caller. Contribute to bacpop/ggCaller development by creating an account on GitHub.
github.com
September 24, 2025 at 1:27 PM
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...
Reposted by Sam Horsfield
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...
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...
embl.wd103.myworkdayjobs.com
September 8, 2025 at 11:43 AM
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.
GitHub - samhorsfield96/ExpEvoAnalyzer: A workflow to analyse experimental evolution data.
A workflow to analyse experimental evolution data. - samhorsfield96/ExpEvoAnalyzer
github.com
September 11, 2025 at 2:16 PM
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.
Reposted by Sam Horsfield
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...
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...
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.
www.nature.com
September 10, 2025 at 9:12 AM
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...
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...
Reposted by Sam Horsfield
Academic authors, here's a peek into the black box of journal publishing from an journal editor if you can bear it:
September 6, 2025 at 11:09 PM
Academic authors, here's a peek into the black box of journal publishing from an journal editor if you can bear it:
Reposted by Sam Horsfield
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...
This is a huge feat, and for such a great cause. Please consider sponsoring Harry! www.justgiving.com/page/harry-c...
August 30, 2025 at 9:01 AM
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...
This is a huge feat, and for such a great cause. Please consider sponsoring Harry! www.justgiving.com/page/harry-c...
Reposted by Sam Horsfield
Looking forward to seeing everyone, new and old, at the Microbial Population Biology GRS + GRC in just a couple days!
go.bsky.app/GGxRjzC
go.bsky.app/GGxRjzC
July 3, 2025 at 8:25 PM
Looking forward to seeing everyone, new and old, at the Microbial Population Biology GRS + GRC in just a couple days!
go.bsky.app/GGxRjzC
go.bsky.app/GGxRjzC
Reposted by Sam Horsfield
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...
www.biorxiv.org/content/10.1...
May 19, 2025 at 9:28 AM
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...
www.biorxiv.org/content/10.1...
Reposted by Sam Horsfield
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
May 19, 2025 at 4:47 AM
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
Reposted by Sam Horsfield
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
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
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...
arxiv.org
May 7, 2025 at 9:27 AM
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
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
Reposted by Sam Horsfield
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...
🧬🖥️
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...
🧬🖥️
April 24, 2025 at 10:03 AM
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...
🧬🖥️
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!
SPECIAL ISSUE Part 2! This month @genomeresearch.bsky.social publishes a diverse collection of articles offering novel biological and clinical insights gained using long-read DNA and RNA sequencing technologies and other long molecule approaches.
tinyurl.com/Genome-Res-3...
tinyurl.com/Genome-Res-3...
April 16, 2025 at 11:05 AM
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!
Reposted by Sam Horsfield
Australia’s reefs are on fire 🔥
March 20, 2025 at 8:02 AM
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...
Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy
algorithm
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
genome.cshlp.org
March 5, 2025 at 2:18 PM
Our pangenome graph-based Nanopore Adaptive Sampling (NAS) tool, GNASTy, is available now in Genome Research! genome.cshlp.org/content/earl...
Reposted by Sam Horsfield
🚨🚨🚨 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
March 2, 2025 at 2:25 PM
🚨🚨🚨 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
Reposted by Sam Horsfield
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. 🧪
CELEBRIMBOR: core and accessory genes from metagenomes
AbstractMotivation. Metagenome-Assembled Genomes (MAGs) or Single-cell Amplified Genomes (SAGs) are often incomplete, with sequences missing due to errors
academic.oup.com
February 10, 2025 at 4:11 PM
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. 🧪
Reposted by Sam Horsfield
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.
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.
January 10, 2025 at 8:04 AM
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.
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.