Antoine Limasset

Would you care to share the template I can't wait to write a paper in Typst !

Can't wait for the preprint!
Would the approach be compatible with zstd for example?

GitHub - COMBINE-lab/mim: A small, auxiliary index to massively improve parallel fastq parsing A small, auxiliary index to massively improve parallel fastq parsing - COMBINE-lab/mim

Ok; mim (github.com/COMBINE-lab/...) preprint submitted! Excited for folks to see it and share thoughts. The key takeaway; mim allows the quick, one-time, building of a small auxiliary index that then allows scaling gzipped FASTQ parsing linearly in # of threads. 1/2

I read RobRust minimizers at first and was in awe :D

@imartayan.bsky.social talks about Scalable comparison of long sequences at #Seqbim

Can't wait to see what comes out of it @robp.bsky.social @camillemrcht.bsky.social !

And now Florian Ingels present multiminimizers and various results about density at #Seqbim

Once again thread (I'm pretty late) incoming and for those you absolutely can't wait the preprint is already out if you want to spoil yourself :p

Timothe Rouze speak about unitigs collection at #SeqBim!

Preprint (and thread) hopefully coming soon :p

Holy shit. So Elon decides it would be nice to know what region of the world people are posting from. So they add that little feature.
2 hours later they figure out that many Trump supporters with millions of followers are posting from other countries. Surprise!
That "feature" is now gone.

Yohan Hernandez–Courbevoie presenting REINDEER2 at Seqbim!

For those who missed it, the introduction thread of REINDEER2

bsky.app/profile/npma...

For recall, the introduction thread of REINDEER2!
bsky.app/profile/npma...

En pleine désillusion sur les réalités des écoles d'ingénieur, je me dis qu'en fait j'aime bien la biologie au détour d'une sortie ornithologique à Guérande.

Wow I totally forgot about this """hype""", I'm curious to see the NFT one XD

I knew early on I wanted to work with computers, but because of dyslexia I ended up in a lower-tier German school. The career office said a tech job wasn’t realistic. I ignored that, took a convoluted path into university, discovered bioinformatics, got hooked on algorithms&proteins, and became a PI

#SEQBIM2025 is about to start, Bonsai presents 4 works this year in Nantes seqbim.cnrs.fr/seqbim-2025/...

Colored graphs (+abundances), low density minimizers and quick sequence parse 🚀

I'm feeling very grateful to welcome two new women computer scientists in the lab, Klára Sladeckova who was previously at Comenius Univ and Lore Depuydt from Ghent. They will work as PhD student and postdoc in projects co-led by Simon Puglisi. Europe at its best 👌🏻

Billi: Provably Accurate and Scalable Bubble Detection in Pangenome Graphs https://www.biorxiv.org/content/10.1101/2025.11.21.689636v1

Imagine, if you will, that NASA updated its website to suggest gravity might not exist, prompting CalTech and CERN to release statements saying, "With great sadness, we can no longer recommend listening to NASA."

This is what's happening in epidemiology.

The joke is that you have a software security problem, you use cryptography to solve it, now you have two problems: a software security problem and a key management problem.

Courrier de la Direction générale de la recherche et de l'innovation adressé aux présidentes et présidents d'université et aux présidentes et prédidents d'organismes nationaux de recherche demandant la diffusion d'un sondage IFOP

Courrier de la Direction générale de la recherche et de l'innovation pour diffusion d'un sondage IFOP « sur les perceptions, les expériences et les dynamiques de l'anti-sémitisme » dans l'ESR finissant par des renseignements sur les opinions politiques des sondé.e.s 1/2

rogueesr.fr/wp-content/u...

Lolz --- the mim parser (fastq parser that takes advantage of the auxiliary mim index if it is built) is actually way faster than I had been measuring. The example application was counting nucleotides, and there was false sharing in the vectors of counters used by different threads ;P.

We spent a year investigating billionaires for @washingtonpost.com.

We found: the wealthiest 100 Americans gave $1.1 billion to influence the 2024 elections — 140x more than they did in 2000. And almost all of that giving boosted Republicans.

washingtonpost.com/politics/int...

GitHub - COMBINE-lab/mim: A small, auxiliary index to massively improve parallel fastq parsing A small, auxiliary index to massively improve parallel fastq parsing - COMBINE-lab/mim

@wytamma.bsky.social : so, it took a little bit of extra time (not the flight back from the CZI meeting), but I decided to just f#&$ing do it, and the basic code to build and parse with the auxiliary fastq index is working (github.com/COMBINE-lab/...). 1/2

Sponging away phylogenomic incongruence Genes with strong and consistent signals favor sponges as humans’ most distant animal relatives

Using an integrative phylogenomic approach, new research in Science reveals unprecedented phylogenomic support for sponges as the sister lineage to all other animals.

Learn more in a new #SciencePerspective: https://scim.ag/4r7SLqm

Mind-reading devices can now predict preconscious thoughts: is it time to worry? Ethicists say AI-powered advances will threaten the privacy and autonomy of people who use neurotechnology.

Ethicists say AI-powered advances will threaten the privacy and autonomy of people who use mind-reading devices

go.nature.com/4r947us

Et en parallèle, des formations sur « accompagner l'usage de l'IA générative dans l'enseignement ».

Oracle’s astonishing $300bn OpenAI deal is now valued at minus $74bn [FREE TO READ] And suddenly, there may be a reverse Midas at the centre of AI’s circular economy

Big oof.

on.ft.com/4peYLvP

Is this a "I'm kidnapped" message ?

Screenshot from the rust survey showing two checked items: - Rust makes me more productive - Rust is fun to use

My account's upload and bulk download access were terminated permanently in 2021 without explanation after I published *checksums* of GISAID genomes. GISAID and its SAB have since ignored a dozen emails seeking explanation.

4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.