New preprint. I've been chewing on why bacteria have pangenomes for years. Most species carry a distributed gene pool far larger than any one genome holds. E. coli has ~163,000 rare genes across the species. Each individual cell carries about 5,000. Why? A 🧵👇

They delayed the deadline ;P.

72 hours until the WABI deadline and then the conference season can finally start... I'm so ready for a break

Me in group meeting update: Sassy was accepted at Bioinformatics, and Barbell should be accepted soon. Me at end of group meeting update: Both Sassy and Barbell are now accepted at Bioinformatics 🎉 Who will be the first to cite? All thanks to the wonderful work of @rickbitloo.bsky.social!!!

We lost Douglas Adams 25 years ago today. This has made a lot of people very sad and has been widely regarded as a bad move.

What do you call camps where people keep disappearing and dying

Public transit apps should come with an option note. Like “hey so the transfer is a 12 minute wait but if you think you can make it and you don’t walk like a lil bitch you can try to make the one in 4 minutes. Good luck have fun bestie”

Rust 🤝 Haskell “The type signatures and this research paper should be a good starting point for the documentation”

You're probably wondering just how metric my socket set is

This is a very interesting video. After a brief intro, the first 3 minutes are a monologue starting in the English of 600AD and transitioning to modern American. Where do you start understanding it? youtu.be/842OX2_vCic?...

Reminder: bioRxiv has Contradictory and Confirmatory Results categories to encourage studies of reproducibility. Yaniv Erlich had the previous record (hours) for demonstrating irreproducibility of a paper. Now apparently we have a negative time interval 😉

Happy #EuropeDay from orbit! 🇪🇺 On 9 May, Europe Day reminds us of something our astronauts witness every day from 400 km above: a continent of remarkable diversity, bound together by shared skies 🧪🌍

What does one do when 2 people don't realize they're in the silence wagon of the train, but the 10 people between you and them are too chicken to speak up... I can volunteer, but walking over is just too much 😅 And thus we all suffer for one more hour.

PDF #1000 in my paper directory is a nice one! 1508 days since I added the first. 2/3rd a paper a day keeps the doctor away, as they say? drops.dagstuhl.de/entities/doc...

Them: “noooo you can’t just claim that ALL algorithms are afflicted by the biases and opinions of their inventors” Me, pointing at pathological behaviors of quicksort and linear memory overhead of mergesort: “biases and opinions”

🔍 New paper in Bioinformatics Advances: "Kaminari: A frugal colored index for approximate k-mer queries"  Read it here: https://doi.org/10.1093/bioadv/vbag120 Authors include: @yhhshb.bsky.social, @yoann.bsky.social, @robp.bsky.social, @pierrepeterlongo.bsky.social, @jermp.bsky.social

kuva v0.2.0 Now over 60 plots! New plot types: Gantt, Network, Waffle, Horizon, PopulationPyramid, Joint, Clustermap, ROC, PR, Lollipop, Survival, Raincloud, Slope, Venn, Parallel, Mosaic, Streamgraph, Radar, Treemap, Sunburst, Bump, Funnel, Rose, Calendar, Legend, Text github.com/Psy-Fer/kuva

Yes. Fertilizer is mostly commercially produced by the haber process, which is extremely fuel intensive (and almost exclusively fossil fuels). One of the many reasons that putting corn ethanol in gasoline is idiotic.

I hate reviewing AI-generated code (including the code I prompted). I still get annoyed waiting for the AI to 'think'. Too short to context switch, too long to stare.

All fun until one time I showed up, they didn't find me, then didn't find me with my 'other' last name, and then it turned out the booking was never confirmed and I was supposed to be at another hotel.

No horror movie has ever managed to recreate the suspense between giving your name at the hotel desk & them finding your booking.

That’s worse if you are Spanish and have two surnames, then American hotels register you with the second surname and don’t find you by your first surname.

For balls in R^n of volume 1, the radius is like √n. Surprisingly, most of the mass can be found inside a slab of width 1 around the equator. Only today did I realize that the all the cool concentration inequalities (Azuma, Hoeffding, McDiarmid) prove the same fact for the cube!

The world is now so full of ridiculous things that I struggle to deal with it all. But this is not an 'us' problem. The world really is idiotic. I made a list of things that are impossible to believe. Seeing it in writing might help you deal better with the situation. berthub.eu/articles/pos...

Fantastic (long) piece on what AU means to mathematics (and what mathematics is) So many insights. The first begins why so may people in AI research are getting obsessed with “taste”. davidbessis.substack.com/p/the-fall-o...

My contribution to the solar/farm discourse is that solar panels capture about 100x as much usable energy from the sun as corn grown for ethanol, if you include the energy cost of growing corn. Ethanol corn is effectively a very old-fashioned inefficient solar panel.

This is now published in Genome Research (doi.org/10.1101/gr.2...). Thank you everyone for your feedback and also the anonymous reviewers who helped to greatly improve the paper. I hope this becomes a useful resource for the community.

One of my favorite quotes about quality is: "Quality can not be inspected into a product or service; it must be built into it" - W. Edwards Deming One implication of this is that tests or code review do not create quality. The code author needs to care about code quality *as they are coding*

A GitHub for maintainers - Giving dependencies the same treatment the fork got nesbitt.io/2026/05/02/a...

Anyone who thinks English is a great language for specifying a desired algorithm has never read a type theory paper

Want oprukkend fascisme vind je niet alleen in de geschiedenisboeken. We zien het opnieuw voor onze ogen gebeuren. En opnieuw zullen we moeten opstaan en ons samen verzetten.

‘The problem is that LLMs inherently lack the virtue of laziness. Work costs nothing to an LLM. LLMs do not feel a need to optimize for their own (or anyone’s) future time, and will happily dump more and more onto a layercake of garbage. Left unchecked, LLMs will make systems larger, not better’

As one part of this thread, I do think "do consulting" is the most direct path today to "do OSS as a meaningful part of your workday". Time spent doing OSS as a consultant is an excellent way to help keep skills sharp/up to date, an excellent means of meeting people, and as a meaningful portfolio.

Been training for this moment my whole life.

A billiard knot is a path in a mirror polyhedron that realizes a knot by reflected lightrays. Not every knot is realizable in a cube, but every knot is a billiard knot in some convex right prism. arxiv.org/abs/1106.5600 mathoverflow.net/questions/38... #MathSky #Mathematics #Geometry #Knots 🧪

The RECOMB-Seq 2026 program is now available! Join us May 24–25 in Thessaloniki, Greece, for two days of cutting-edge biological sequence analysis, with keynotes by Camille Marchet (CNRS) and Manolis Kellis (MIT). Full schedule: recomb-seq.github.io/seq2026/prog... #RECOMBseq

Need a user-wide PR template containing: "Please motivate, in your own words, why this PR solves the problem." and "How much wall time did _you_ spend on this? I will spend at most half of that."

Was asked to give a P99 talk again this year 🤗 You'll hear all about the new SimdQuickHeap!

Oh btw, I'm teaching some lectures in Advanced Data Structures currently! So far covered models of computation, rank & select, and Elias-Fano. Not sure the slides without figs/examples are super useful, but anyway they are here: curiouscoding.nl/teaching/ (final slides have pics of the blackboard)

Every single time I need the Stirling approximation of the binomial (most recently a few days back), I am disappointed it's not there. And that's the main reason I keep visiting the page 🫤

New preprint: The SimdQuickHeap is the fastest priority queue by far! 2x faster than a radix heap and up to 10x faster than binary heaps. arxiv.org/abs/2604.25681 with Marvin Williams and Johannes Breitling:

Fantastiche column over de uiterst-rechtse meuk die van ochtend tot avond de Nederlandse talkshows domineert… al jaren lang!

me: morning' gemini: That's it. That's the "smoking gun" ## The "Void Context Clue" Because this conversation is empty, I assumed it was the start of a new day. ## The "Greeting Revelation" When I attended to the token "morning", it confirmed the time of day. ## The "Hanging Single Quote" ...

Nothing incredible novel, but a short 🧵 thread about MGFs, their use, and why I love Taylor series. Say you want to compute the moments of a r.v. X, which is "sufficiently well-behaved" (in some rigorous sense). That is, 𝔼[Xⁿ], for some integer(s) n≥0 of your choosing. How do you proceed?

It's finally time to announce the opening talk of the RustWeek 2026 main track! 2026.rustweek.org/talks/taylor/ Don't forget to buy your tickets, before they run out!

HERRO has been published in @nature.com nature.com/articles/s41.... This achievement is a result of the great work by Dominik Stanojevic, with contributions from Dehui Lin, @sergeynurk.bsky.social, and Paola Florez de Sessions Welcome to the era of high-quality genome assemblies supported by AI.

It is strange how the world can cooperate to get oil through the Iranian blockade at the Strait of Hormuz but still aren't able to get food through the US and Israeli blockade of Gaza and Cuba. International law is not optional Let's call it what it is: weaponized international law.

It's funny that algo folks still like to talk about linked lists. But these days we avoid them like the plague because they thrash caches and prefetchers. In the 16-bit era, we didn't have either of those things, so linked lists made a decent amount of sense. But it's been 30 years! Re-evaluate!

you used to spend a day messing with your neovim config, feel self conscious, then get back to work now people are spending weeks on some hyper customized coding agent workflow that definitely is worse than vanilla but they can talk about it like they're ahead of the game

According to the Lebanese National News Agency, these panels supply the town with electricity, which is needed for its water supply, and Israel destroyed homes, roads and olive trees as well.