@npmalfoy
CNRS researcher in bioinformatics Lille, France (Bonsai team). I develop efficient computational methods to analyze massive sequencing data, creating scalable tools for genomics, transcriptomics, and metagenomics. https://malfoy.github.io/
“We were aware that we might have a similar situation this year,” the Ig Nobel founder said after Trump's border policies prompted 4/10 winning teams to decline traveling in 2025. "Then the situation got far worse.”
Read about the Igs' decision to move abroad @science.org: tinyurl.com/3kfrdh7y
It's that time of the year on the campus (feat Zora)
I've been wanting to do a big refactor and build system update for salmon for a looong time. I finally got around to it, and updated the backend index to use the newest SSHash while I was at it : github.com/COMBINE-lab/... (also with native ARM support & on bioconda!)
Tout se perd
New chromosome-level assembly for the parthenogenetic nematode Acrobeloides nanus in collaboration with @worm-lab.bsky.social @phylewgenetics.bsky.social @sangerinstitute.bsky.social
See ENA PRJEB83609
1/ Our paper on Multi-Context Seeds is now out, with @tolyan.bsky.social spearheading the work and contributions from Nicolas and @marcelm.net. We introduce a new seeding concept that improves read alignment accuracy while maintaining speed.
link.springer.com/article/10.1...
I think their plan is that they still have orders of magnitude inference improvement in sight so they will be able to keep this kind of subscription in the future while the adoption war is happening right now and they know this is usually a winner takes all
RNA-seq analysis in seconds using GPUs https://www.biorxiv.org/content/10.64898/2026.03.04.709526v1
kallisto sped up RNA-seq quantification by 50x. Now another 50x speedup... quantify hundreds of millions of reads in a few seconds.
This seems too good to be true. But it's true!
Incredible accomplishment by @pmelsted.bsky.social.
Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data.
The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k...
Figure 1 shows they key result
Dear @anthropic.com, my lab builds a lot of OSS for genomics (github.com/COMBINE-lab). While we lack the widespread OSS market of popular NPM packages, pieces of our software are critical in biomedical research. Please consider extending your Claude Max offer to such labs!
Very interesting issue!
Contemplating migrating repos to Codeberg again, again facing the issue of CI infra. Is there any solution that offers even a fraction of what GitHub gives public repos *for free*? I can't afford this much cloud credit, nor a server (thanks Nvidia).
I may play around a bit more tonight, but this is a good checkpoint: github.com/COMBINE-lab/.... All features implemented, unit and integration tests, dedicated aarch64 & avx2 backends, a driver CLI! Still a bit slower than the C version, but we're closing the gap quick!
I still think that you hit a wall at some point because of the codebase size because of the limited context size(always the same issue)
Trying an experiment. I want to use WFA2-lib in Rust. But, I don't want bindings (I am so *over* having C or C++ deps in by build chain). So, I'm going to make a Rust native port with Claude Code. I started at 2:03PM. I'll provide an update (or an implementation) by the end of the day :).
Great to see this work out, led by Jon Rosen and co-supervised Karen Mohlke @klmohlke.bsky.social!
Connecting to some recent threads here:
This is so f**** up
After years of work, the centerpiece of my PhD is published in @natmethods.nature.com! Read it to learn about the biophysical insights we can get from single-cell data!
But first, I would like to talk a bit about RNA velocity and normalization. 1/
Monod fits biophysically motivated models to single-cell transcriptomics data, providing insights into gene expression dynamics. @goringennady.bsky.social @lpachter.bsky.social
www.nature.com/articles/s41...
Dear @anthropic.com please consider extending your Claude Max subscriptions to open science software devs! Our repos may not have as many stars as those of some of our OSS peers, but we develop critical infrastructure in focused areas, and might even benefit more from what Claude Max offers!
MetaStrainer: Accurate reconstruction of bacterial strain genotypes from short-read metagenomic samples. https://www.biorxiv.org/content/10.64898/2026.03.02.709061v1
When someone says „Scientists do not want you to know“ you can dismiss everything from there on. Scientists want you to know. They are desperate that you know. They can’t shut up about what they found out and want you to know.
The findings “should act as a wake-up call to developers on how easy it is to use LLMs to produce misleading and low-quality scientific research”
go.nature.com/4u4SBBP
I am always amazed by webassembly applications!
Curious about how hard it is to get this from existing Rust code
Point of comparison, Codex 5.3 did a nice initial conversion of ksw2 (just extz) to Rust, with reasonable eprf. It was unable to close the perf gap with C. It couldn't identify the key bottleneck. Claude Code (sonnet 4.6 even!), came in, thought for a bit, and nailed it. github.com/COMBINE-lab/...
Introducing kuva: A scientific plotting library in rust, along with cli binary with the option to plot directly into the terminal.
Feel free to drop me some feedback as an issue on the repo
github.com/Psy-Fer/kuva
crates.io/crates/kuva/...
Speedrunning Rust translation before the Butlerian Jihad?
The US is broadly a country that likes to invest in science. Even among Republicans this is true. But we are governed by an administration that is opposed to science, and is using procedural tools to limit spending and increase political control over the process.
