How is dev going ? WELL....

Not going to lie; I'm kind of living it how close-minded and technically-mid devs are absolutely losing it over the Ubuntu uutils adoption and the announcement that Rust will replace Perl in Git 3 (and will be required). Welcome to the future, pal; you lost the argument & you were wrong.

don't release preprints without a Methods section don't release preprints with a Supplementary Materials section don't release preprints without data don't release preprints without code use preprint servers to share your science, not advertisements

With the new Grok 4 Fast, the price/performance curve for AI shifted again. I updated my chart to reflect this change. I have to update it every couple weeks now. I also think the GPQA Diamond benchmark is likely maxed out (the tests themselves have errors, making it impossible to get to 100%),

This also shows that @typst.app is already a viable alternative to LaTeX for top conferences in ML!

Stay tuned 👀 More combinatorics is coming

agtools: a software framework to manipulate assembly graphs https://www.biorxiv.org/content/10.1101/2025.09.14.676178v1

One of my favorite things to consider is that the pigeons we see in cities are abandoned information infrastructure

How many chromosomes can an animal have? In our paper out now in @currentbiology.bsky.social we show that the Atlas blue butterfly has 229 chromosome pairs- the highest in diploid Metazoa! These arose by rapid autosome fragmentation while sex chromosomes stayed intact. www.cell.com/current-biol...

I'm so hyped by the mega-throughput era of sequencing!

I sincerely appreciate the opportunity to visit @ebi.embl.org (thanks to the @embl.org Sabbatical fellowship). The guidance and support I received from Zam (@zaminiqbal.bsky.social), John (@bacpop.org) and other colleagues have been immensely valuable! You changed my career！❤️

Studies reveal how risky play can benefit child development go.nature.com/42622Ez

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 academic community has looked at how artificial-intelligence tools help researchers to write papers, but not how they distort the literature scientists choose to cite, says Zhicheng Lin go.nature.com/45X3Imr

minimap2.com is potentially a phishing site. Please don't use anything from that website. github.com/lh3/minimap2...

Yohan Hernandez-Courbevoie chaired by Maxime Crochemore just before presenting REINDEER2 at #SPIRE2025 in London

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler! Nanopore's getting accurate, but 1. Can this lead to better metagenome assemblies? 2. How, algorithmically, to leverage them? with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social 1 / N

Achievement unlocked: defend your habilitation thesis on the same day than your partner. That was quite a science + celebration day, thanks to all involved 💙✨

Now published in GigaScience with minor improvements: academic.oup.com/gigascience/... * Download: zenodo.org/records/1490... * More info: github.com/lh3/panmask

A wonderful day for @bonsaiseqbioinfo.bsky.social, with @camillemrcht.bsky.social's and @npmalfoy.bsky.social's HDR defenses. Congrats for the amazing work! It's a great chance for the team to have you both!

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵 Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open. doi.org/10.1101/2024...

Posts about research on Bluesky receive substantially more attention than similar posts on X, formerly called Twitter go.nature.com/45Ftiw4

Wow, more than 2.4M of assembled bacteria in the new release of ABT! We plan to index these using our efficient colored De Bruijn graph index, Fulgor. We recently conducted experiments with nearly 1M genomes…getting there :) www.biorxiv.org/content/10.1...

The conjecture that every convex polyhedron is Rupert is settled in the negative! The convex body in the image cannot pass straight through a hole inside itself. arxiv.org/abs/2508.18475 #Mathematics #Geometry #MathSky

At scale, the way that we store (and process) data matters! Many may think that the way we keep data, the file formats we adopt, and the way that we compress data are unimportant details, but they are, in fact, critical considerations to allow science to move forward at scale!

Finally printed and submitted my thesis :) You may call me Dr. now 🎓 curiouscoding.nl/thesis.pdf

A tiny silly fun thing in the midst of all the chaos... We're on the hunt for a mate for Ned, a 1 in 40,000 left-spiralling snail. www.nzgeo.com/stories/lets...

skani v0.3.0 is released. github.com/bluenote-157... - 30-40% potential reduction in memory with approximately the same runtime. - Breaking changes to indexing and searching databases Calculate ANI for contigs, genomes -- even search > 140k genomes. Pre-indexed GTDB-R226 available for download.

" @pacbio.bsky.social #HiFi #metagenomic assembly achieves a level of precision approaching that of isolated genomes derived from the same sample. This benchmarking establishes HiFi as a robust approach for generating #MAGs rivaling isolated genome quality." onlinelibrary.wiley.com/doi/full/10....

Because, as I learned early on in academic research, unfortunately, great ideas exist in relative obscurity all too often. Sometimes, they are rediscovered at a time where they catch on, other times not.

Nearly one-third of all retracted papers at PLoS ONE can be traced back to just 45 researchers who served as editors at the journal go.nature.com/4frnv04

Another great piece in @quantamagazine.bsky.social, this time on new surprising algorithms for shortest paths. With quotes from BARC head and shortest path grand-old-man Mikkel Thorup

🧬🖥️ I am strongly of the opinion that bioinformatics needs to move away entirely from text-based and "loosely" structured file formats for essentially any type of data. File formats should be binary-first, and designed for *correct* and *efficient* machine parsing 1/3

Trans people are now banned from UPenn, Harvard, Brown, Cornell, Columbia, intntnl track & field, the Olympics, chess, darts, most federal jobs, the US military & intelligence services, federal facilities, public bathrooms in most states, & many local sports. Seems bad! Let me know what I missed!

I clicked on the link before reading the whole title XD

Snappy: de novo identification of DNA methylation sites based on Oxford Nanopore reads https://www.biorxiv.org/content/10.1101/2025.08.03.668330v1

I talk a lot about Rust for building high-perf (& even non-perf critical) software, & scientific software in particular. I often discuss what's interesting to me, but wanted to offer the chance to those interested for me to answer their questions about Rust in science. Fire away with questions!🧬🖥️

Generalizable direct protein sequencing with InstaNexus https://www.biorxiv.org/content/10.1101/2025.07.25.666861v1

Scalable, fast and accurate differential gene expression testing from millions of cells of multiple patients https://www.biorxiv.org/content/10.1101/2025.07.24.666556v1

First example of a laser cavity in the animal kingdom! Cool stuff from Rachel Berkowitz at @science.org

Postdoc in genomics? want to run your own lab - own direction, own vision? Want to blend AI, genomics in yet clever ways? Want to work in an English speaking institute, situated in beautiful Heidelberg - home of the oldest university in Germany with a vibrant academic culture? Check this out 👇

Rust was once again named the most admired programming language in the Stack Overflow #DevSurvey! 🦀 Great to see Cargo, Rust’s package manager, also mentioned as one of the most loved tools—a strong signal that thoughtful, dependable tooling matters.

A fascinating explanation for the record-breaking size of the lungfish genome.

Congratulations to Rayan Chiki, (Institut Pasteur) head of the “Sequence Bioinformatics” unit, for securing the ERC Proof of Concept 2025 for his project ENZYMINER! 👏 ‪@rayan.chiki.bsky.social #Bioinformatics

Early bird applications for the Workshop on Genomics 2026 are still open until the 1st of August, we have a few spots left! Do not miss the chance to get a discount! 🙆🏽‍♀️ #evomics2026 Apply here: evomics.org/apply-worksh...

🌟 Exciting news! We’re launching three fully-funded postdoc positions for "New Horizons for Synthetic Phages” Join us in tackling antimicrobial resistance with cutting-edge synthetic biology + AI bioinformatics. Based at Flinders Uni in vibrant Adelaide. 👇 Read on for details! #Phage

For the first time, large language models performed on a par with gold medallists in the International Mathematical Olympiad go.nature.com/3IKrtVs

Sex at birth may not be purely random, according to a new #ScienceAdvances study. Instead, each family’s likelihood of having only male or only female children is a “weighted coin toss” influenced by maternal age and genetics. scim.ag/3ILwz3O