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Reposted by Sam Horsfield

Corrie Moreau @corriemoreau.bsky.social · 19d

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

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Reposted by Sam Horsfield

EMBL-EBI @ebi.embl.org · 8d

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...
🦠

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

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Reposted by Sam Horsfield

Zamin Iqbal @zaminiqbal.bsky.social · 13d

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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Reposted by Sam Horsfield

Zamin Iqbal @zaminiqbal.bsky.social · 13d

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/...

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Sam Horsfield @samuelhorsfield.bsky.social · 12d

v1.4.1 now available on conda!

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Sam Horsfield @samuelhorsfield.bsky.social · 14d

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

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Reposted by Sam Horsfield

Ewan Birney @ewanbirney.bsky.social · Sep 8

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

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Sam Horsfield @samuelhorsfield.bsky.social · 26d

Now works with assemblies too!

Sam Horsfield @samuelhorsfield.bsky.social · 27d

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

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Reposted by Sam Horsfield

Zamin Iqbal @zaminiqbal.bsky.social · 28d

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...

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

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Reposted by Sam Horsfield

Ben Williamson @benpatrickwill.bsky.social · Sep 6

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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Reposted by Sam Horsfield

Jo Rhodes @drjorhodes.com · Aug 30

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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Reposted by Sam Horsfield

Mike Blazanin @mikeblazanin.bsky.social · Jul 3

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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Sam Horsfield @samuelhorsfield.bsky.social · May 19

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

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Reposted by Sam Horsfield

Zamin Iqbal @zaminiqbal.bsky.social · May 19

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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Reposted by Sam Horsfield

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · May 19

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

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Reposted by Sam Horsfield

Leonie Lorenz @leonielorenz.bsky.social · May 7

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

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

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Reposted by Sam Horsfield

EMBL-EBI @ebi.embl.org · Apr 24

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 · Apr 16

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!

Genome Research @genomeresearch.bsky.social · Apr 14

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...

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Reposted by Sam Horsfield

Hamish 💧🐚 @hamishoz.bsky.social · Mar 20

Australia’s reefs are on fire 🔥

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Sam Horsfield @samuelhorsfield.bsky.social · Mar 5

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

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Sam Horsfield @samuelhorsfield.bsky.social · Mar 5

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.

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Sam Horsfield @samuelhorsfield.bsky.social · Mar 5

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.

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Sam Horsfield @samuelhorsfield.bsky.social · Mar 5

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.

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Sam Horsfield @samuelhorsfield.bsky.social · Mar 5

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.

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