💾 Prokka 1.15.6 is released! This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to. #bioinformatics #microbiology #genomics github.com/tseemann/pro...

Our new preprint, spelling out what a genomic-data-aware version control system could do to make #bioinformatics better for everyone.

It was really fun and hopeful, describing the potential for a better future with @nickdimonaco.bsky.social (QUB) and Martin Vickers (JIC). Although bioRxiv doesn't accept review paper preprints, here it is on Figshare figshare.com/articles/pre... 6/6

New blog post – A quick look at Roche's SBX lh3.github.io/2025/09/11/a...

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...

The original circos plot? From the 1947-1948 Carnegie Yearbook, the page prior to McClintock's Mutable Loci in Maize paper.

“[The public] should understand that science ‘proves’ nothing, that conflicts of interest don’t automatically entail bias or fraud, that anomalous studies don’t falsify a whole body of literature and, above all, the public needs to understand that the scientist is human.” doi.org/10.1007/s111...

If you ever find yourself needing evidence for ‘Plasmids are just as common in microbes without resistance genes,’ we’ve got you covered! Check our new paper, out today: www.microbiologyresearch.org/content/jour...

🚨🚨 New paper in @narjournal.bsky.social! 🍾 Excludons are pairs of overlapping genes that block each other’s expression (basically, reverse operons). We built a tool to identify them in bacterial genomes using transcriptomic data, in an awesome collab led by Iñigo Lasa and Álvaro San Martín. 👇

"Our analysis identified 16 divergent and 165 convergent excludons in E. coli, as well as 10 divergent and 28 convergent excludons in S. aureus."

www.biorxiv.org/content/10.1... After spotting weird gene‐clustering and 'pangenome' quirks, I dug deep and found it’s not just one tool. It’s how we misuse and misassume how 'black-box' clustering and pangenome tools work. #pangenomics #bioinformatics #geneclustering

New paper with @rwheatley8.bsky.social and Cedric Lood Actual title: Chromosomal capture of beneficial genes drives plasmids towards ecological redundancy. Sensationalist title: Plasmids carry useless genes academic.oup.com/ismej/articl...

Absolutely amazing calibre of presentations in the first student competition at #CSM2025 today! I’m always so impressed by how much I learn from these, the next generation!

And ditto again in part 2 today! Everything from insect-microbe interactions to GM to remove AMR to dynamics in micro colonies. The future of Canadian microbiology is bright #CSM2025

Oh, the irony of people using generative AI to "summarise" my papers 🫠 (here the real paper: link.springer.com/article/10.1...)

PyamilySeq: Exposing the fragility of conventional gene (re)clustering and pangenomic inference methods https://www.biorxiv.org/content/10.1101/2025.05.30.657108v1

Using these proteins as a base, the magnificent Matt Schmitz developed a tool to study the prevalence of proteins within the human gut. This is InvestiGUT: github.com/Matt-Schmitz.... To allow its instant use we have made InvestiGUT accessible on our Galaxy instance: protologger.bi.denbi.de

Ever wondered if we are correctly predicting proteins from metagenomes? If so, we are happy to present our new work improving the prediction of proteins from the human gut microbiome: www.nature.com/articles/s41...! We corrected how each taxon's proteins are predicted and found WAY more proteins!

2 days until this PDRA opportunity closes! Come join us as part of @mermanchester.bsky.social in (sometimes) sunny Manchester. #microsky #microbiome

Here's our #GenomeInformatics24 poster on evaluating predictors of coding regions on raw reads (rather than on assembled genomes) doi.org/10.6084/m9.f... Why might you want to choose a predictor of coding regions for reads?

With rORForise (similar to ORForise) we aim to enumerate/tabulate all the possibilities, and to use these to let users know which predictors are more suitable for their task. It's still work in progress but here's early release code to keep an eye on github.com/NickJD/rORFo... (preprint coming soon)

Here's a link to our #GenomeInformatics24 poster on "Finding the most diverse subset of proteins" that was presented yesterday. doi.org/10.6084/m9.f... Why do we want to find the most diverse set of proteins?