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/...
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...
Thanks Camille!
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...
If you want to try it yourself: Pansim github.com/bacpop/Pansim and PopPUNK-mod github.com/samhorsfield...
We also did not find a relationship between speciesβ ecological niche diversity and the proportion of rapidly exchanged genes, instead finding ecological diversity is largely explained by the phylogeny also.
Fitting to >400 species across the bacterial domain, we found that rapidly exchanged genes explain the differences we observe between low and high diversity species, and detect a phylogenetic signal, meaning that closely related species have similar numbers of rapidly exchanged genes.
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...
Massive thanks to @macwiatrak.bsky.social , @johnlees.bacpop.org and Maria Ntemourtsidou for their efforts in putting these datasets together.
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
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
Preprint Alert!
With @tmthrz.bsky.social and @rayanchikhi.bsky.social we aim to tackle practical unitigs compression!
A thread:
We are thrilled to announce the first official release (v0.1.8) of #π―π²π±π±π²πΏ, the successor to one of our flagship tool, #π―π²π±ππΌπΌπΉπ! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen.
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Webinar series at EMBL-EBI. Concepts, methods, and resources in pangeomics. Going beyond the reference genome. Recordings now available. EMBL's European Bioinformatics Institute logo.
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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Link to the GNASTY paper if you're interested: genome.cshlp.org/content/35/4...
Really grateful for the chance to discuss GNASTY on #ScienceInContext; massive thanks to @eonore.bsky.social for the invite!
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...
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...
Thanks Laura! Hope itβs 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.
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...
There are millions of openly available microbial genomes, but searching them can be slow.
Until now π₯
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...
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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.
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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...
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!
