I think we are getting a preview of what will more generally happen with the publication system at some point, we must find solutions to distinguish the data from the noise as a community

To be clear, I'm saying this being a part of the problem!

From my point of view this issue existed before rewrites (see the number of published compressors, aligner, assembler...)

Unclear why they'd do this.

Turns out that the usual NtHash is not as random as one might think?!?! At least not for minimizers.

Seq-hash (and simd-minimizers) already has this fixed by default ;)

github.com/rust-seq/seq...

I don't think the idea is to publish rewrites of existing tools with no novelty.
For example in a recent paper we proposed a new data structure and we "rewrited" an existing tool with our data structure plugged to show the gain on a practical application.

New blog post!

I use ntHash all the time to hash k-mers, yet it turns out it has some unexpected flaws (collision propagation, bias on leading zeros...). The good news: each of them can be fixed!

igor.martayan.org/posts/breaki...

Almost half of EU’s busiest flight routes are ‘hard or impossible’ to book on trains – report ‘Stone age’ system of booking cross-border rail tickets holding back climate action by consumers, says thinktank

Almost half of EU’s busiest flight routes are ‘hard or impossible’ to book on trains – report

I was investigating the genomes that I didn't manage to convert to near-complete MAGs in my assembly graph (the components in gray).

The circle on top left is actually a complete genome but with 40% completeness (both in metaMDBG and myloasm)

First complete genome loaded onto a quantum computer Researchers encode the tiny hepatitis D virus in an early step toward “quantum genomics”

The genome of the hepatitis D virus, with just 1700 bases of RNA, was squeezed onto a quantum computer.

Learn more: https://scim.ag/4mCifuv

Amazing work, as always, from @ale-campa.bsky.social! Now you can index AllTheBacteria v2 (sans dustbin and unknown) in only 130G. It’s always a pleasure to work with @jermp.bsky.social and @ale-campa.bsky.social, and I’m very excited for where Fulgor is going next!

Two more days to submit your abstract for a short talk or poster at RECOMB-Seq 2026. See instructions at recomb-seq.github.io/seq2026/call...

With @jermp.bsky.social & @robp.bsky.social, we have just released Fulgor v4.1.0 (also on bioconda! bioconda.github.io/recipes/fulg...).
Here's what's new, and what's to come. 🧵 (1/6)

Don't be shy to take on a little two-week side project. These five months will be the most precious three years of your academic journey.

Like we very explicitly flag forks on GitHub we should have very clear indication of rewrites and/or the fact the repo is somewhat local/WIP/experimental

GitHub - henriksson-lab/rustification Contribute to henriksson-lab/rustification development by creating an account on GitHub.

They explain their motivation to do so here and I'm somewhat sensible to their arguments while I agree that the names collision is indeed an issue that we will need to handle soon to avoid getting flooded
github.com/henriksson-l...

hilarious side effect here: execs getting advice from models whose training data is skewed specifically toward *failed businesses*

This is from 7 years ago (merenlab.org/2019/02/24/f...). We are talking about the same things today. We will be talking about the same things 7 years from now. There is no one to blame for this apart from ourselves. I find it very depressing.

Agree with this great thread as a whole. However in my niche where the search space is gargantuan LLM can implement and try an explosive amount of solution. Then the human only has to focus the interesting ones (a very tiny subset) according to a (non LLM) benchmark

With all the cuts to research funding in European countries, everyone is turning to the ERC...

The ERC should be a source of supplementary funding, not a substitute.

Every country in Europe must invest in basic research and increase its budgets!!!!

ERC : "We're overwhelmed with funding request, it's becoming unmanageable. We need to find a way to reduce the number of applications."

French Government: "You need to go get the money from Europe, you bunch of losers!"

🫣

bIvangpu' 'e' yIvangQo'!

Announcing Rust 1.95.0 | Rust Blog Empowering everyone to build reliable and efficient software.

Rust 1.95!

* IF-LET GUARDS; LFG!!!!
* compile-time `cfg_select!`
* a bunch of stabilizations

blog.rust-lang.org/2026/04/16/R...

Are review papers in the scope of the SPIRE conference?(asking for a friend)

🧬 Preprint update with @worm-lab.bsky.social !

If you are aiming for a phased assembly, should you sequence @pacbio.bsky.social HiFi or @nanoporetech.com R10 reads? Whichever you have easier access to!

The real question is: which assembler should you use based on your data? (1/2)
#genomes

AI models ‘subliminally’ transmit biases when training other systems Using artificial-intelligence to teach other models can be cheaper and faster than building them from scratch, but this approach can introduce dangerous traits.

Data generated by AI models can contain subliminal signals that ‘teach’ other LLMs particular traits and biases

go.nature.com/483Kkor

Fast and accurate multiple-protein-sequence alignment at scale with FAMSA2 www.nature.com/articles/s41... 🧬💻🧪 rdcu.be/fdw40

Quantum mechanics has gone from a theory in test to becoming the foundation of new technologies.

Learn more in a 2025 #SciencePerspective that looked at 100 years of quantum mechanics: https://scim.ag/3Qvgi6M

Fast and accurate multiple-protein-sequence alignment at scale with FAMSA2 - Nature Biotechnology FAMSA2 accurately aligns millions of protein sequences at high speed.

10 years after the first FAMSA paper, its successor is now published in Nat Biotech! We believe that FAMSA2 can enable analyses of large protein collections that were previously unattainable. Thank you, Andrzej and Cedric, for great collaboration
www.nature.com/articles/s41...