Nick Dimonaco

Release Next time I'll try to be FASTA · tseemann/any2fasta New features Option -k is keep processing even when some inputs fail option -g to include GBK version suffix option s to strip desc from>id desc in ID lines Support for PDB protein structure forma...

💾 any2fasta 0.8.1 is released!

The FASTA format is now 40 years old (Pearson & Lipman) and any2fasta makes it easy for your scripts and pipelines that accept FASTA to also accept other formats, even if compressed! eg. .gbk.gz

#bioinformatiocs #microbiology #genomcs
github.com/tseemann/any...

💾 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...

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...

An old image of a salivary gland chromosome from Drosophila melanogaster, with lines across different segments indicating contact points.

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

This study begins by outlining the transparency paradox: that trust in science requires transparency, but being transparent about science, medicine and government reduces trust in science. A solution to the paradox is then advanced here: it is argued that, rather than just thinking in terms of transparency and opacity, it is important to think about what institutions are being transparent about. By attending to the particulars of transparency – especially with respect to whether good or bad news is disclosed – it is revealed that transparency about good news increases trust whereas transparency about bad news decreases it, thus explaining the apparent paradox. The apparent solution: to ensure that there is always only good news to report, which might require lying. This study concludes by emphasizing how problematic it is that, currently, the best way to increase public trust is to lie, suggesting that a better way forward (and the real solution to the transparency paradox) would be to resolve the problem of the public overidealizing science through science education and communication to eliminate the naïve view of science as infallible.

“[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...

Plasmid prevalence is independent of antibiotic resistance in environmental Enterobacteriaceae The rapid rise of antibiotic-resistant pathogens poses a critical threat to the treatment of infectious diseases. While the spread of antibiotic resistance genes (ARGs) via plasmid conjugation has bee...

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...

ExcludonFinder: mapping transcriptional overlaps between neighboring genes Abstract. Bacteria regulate neighboring genes via overlapping transcription in untranslated regions (UTRs), forming excludons. This overlap leads to transc

🚨🚨 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."

PyamilySeq (built for another purpose 😇) reveals how tiny tweaks (output flags, CPU/mem, decimal precision) warp core/accessory calls and how pangenome tools spit out misleading 'representative' sequences. If you care about transparent, reproducible gene clustering & pangenomes, check it out!

PyamilySeq: Exposing the fragility of conventional gene (re)clustering and pangenomic inference methods Pangenomics, the identification of shared genes across a taxonomic range, is essential for understanding microbial genetic diversity. Yet, gene clustering and pangenome tools often operate as one-size...

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

Chromosomal capture of beneficial genes drives plasmids toward ecological redundancy Abstract. Plasmids are a ubiquitous feature of bacterial genomes, but the forces driving genes and phenotypes to become associated with plasmids are poorly

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

From an AI-generated summary distributed on social media: Cognitive Science · Artículos Ciencia · 20 November 2024 · The article “Reclaiming AI as a Theoretical Tool for Cognitive Science” by van Rooij and Blokpoel, published in Cognitive Computation in October 2024, critically examines the evolving relationship between artificial intelligence (AI) and cognitive science. The authors argue that, … The real paper below (note that the AI-generated text got the journal name, the publication date, and the authors wrong): Computational Brain & Behavior (2024) 7:616-636 https://doi.org/10.1007/s42113-024-00217-5 ORIGINAL PAPER Check for updates Reclaiming Al as a Theoretical Tool for Cognitive Science Iris van Rooij1,2,3 • Olivia Guest,2 • Federico Adolf4,5 • Ronald de Haan® • Antonina Kolokolova' • Patricia Richs Accepted: 12 August 2024 / Published online: 27 September 2024

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

Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut - Nature Communications Microbes within the gut vary in how they encode genes, both in terms of the genetic codes and gene structures, which are often unexplored in metagenomic analysis. Here, the authors develop a lineage-s...

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!

It isn't technically wrong... Just not technically correct either.. No? (I do not call myself a microbiologist!)

Please mark this with a trigger warning.

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?

GitHub - NickJD/rORForise: Read-based gene coverage evaluation Read-based gene coverage evaluation. Contribute to NickJD/rORForise development by creating an account on GitHub.

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?