It's that time of the year on the campus (feat Zora)
11.03.2026 17:33
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It's that time of the year on the campus (feat Zora)
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...
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
Pretty unpredictable this year and I'm here for it
Capture d'écran du tweet cité, à savoir : https://twitter.com/LeFigaroTV/status/2027067641651695678
Quelle déchéance, morale comme intellectuelle.
Dans les écoles et les crèches de ma commune, j’exige que mes futur·es élu·es s’engagent à inscrire les enfants sans discrimination, ni pénalité. et ce quelle que soit leur situation administrative ou familiale.
👉️ J’interpelle mes candidat·es : municipales-2026.nosservicespublics.fr
IA générative ou pas, les États-Unis de Puritanie (comme j'aime bien les appeler) sont en train d'imposer à la planète entière leur vision de ce qui est acceptable ou pas, «safe for work» ou pas, et c'est plutôt problématique pour qui ne partage pas ces normes et jugements.
Presentation of scientific work on De Bruijn Graphs applied to the processing of sequencing data in the context of biology. The picture was taken in the conference room of the University of Venice, where a screen displays a slide that introduces De Bruijn Graphs, with the speaker standing in front of it. Being the screen is a large renaissance painting that spans from the floor to the roof.
I had the occasion of presenting nice results about the detection of biological events in De Bruijn Graph at #DSB2026, in the context of my PhD work on #Vizitig !
Thanks to the organizers and colleagues for this amazing and super-inspiring event (and @camillemrcht.bsky.social for the picture).
That's amazing. Yes we are blessed to present in such spaces.
Thanks to the well known powerhouses @imartayan.bsky.social @curiouscoding.nl
Were you aware that these are available for the community:
- an efficient fasta/q parser in Rust
- a quick rolling hash library
- a minimizer library
All in Rust 🦀
A satisfying slide 😊
Federico Martín Aramburú
Éric Casado-Lopez
Emine Kara
Aburrahman Kizil
Sirin Ayd
Angela Rostas
Djamel Bendjaballah
Hichem Miraoui
Ismaël Aali
Ces personnes ont été assassinées par l'extrême droite entre 2022 et 2025 et n'ont reçu aucune minute de silence à l'Assemblée nationale.
How would you design a *multithreaded*, *concurrent* & *dynamic* hash table if you are focused specifically on common k-mer workloads, where streaming query & insertion are common? Jamshed, Prashant and I explore this in kache-hash, a cache-friendly k-mer hash table!
www.biorxiv.org/content/10.6...
Logo MERIT SFBI
📌 Enquête MERIT-SFBI sur les conditions de travail des bioinformaticien·ne·s dans les instituts de recherche, universités, établissements d’enseignement et recherche, secteur associatif ou privé
📎 framaforms.org/enquete-meri...
⏳ temps estimé : 20 minutes
📅 date limite de réponse : 31/03/2026
Off to a promising #DSB2026
As my friend says, should we separate the man from the bitvector? Thoughts ladies?
"Have your best babies" n’est plus de la SF : c’est le marketing de la sélection embryonnaire aux US.
La montée de l’eugénisme libertarien est un projet politique contre l’école et la solidarité - partout dans le monde.
Analyse du lien avec la "génétique du QI" ici 👇
rogueesr.fr/techno-fasci...
no foreign foe has ever dreamed of being able to sack and pillaging this country the way Trump admin and its congressional and scotus enablers do every day.
Et encore une personne en "zrr positive sous réserve" pour qui on me dit de laisser tomber. Mail aux syndicats bienvenu ce soir. Vous devriez faire pareil. Gardons trace.
"They go to the breeding gulags.” what the heck did I just watch
Les données biologiques de 20 000 enfants récupérées par des pseudo-scientifiques racistes
next.ink/223756/les-d...
Je reviens avec @jeremie-n.bsky.social et Hervé Perdry sur la récupération de données par Lasker, Kirkegaard and co mais aussi sur le racisme qui s'insinue dans la recherche
Ça ne sert pas a grand chose visiblement car le déni de démocratie est puissant! Mais tant pis. J'ai resigné quand même 👇
petitions.assemblee-nationale.fr/initiatives/...
What's the best place to look up current estimates of how many truncated/non-functional genes each of us have? there was a paper from @dgmacarthur.bsky.social and co around 2014 that had an estimate from the 1000 genomes project (around 40 per person?), but I guess we have better estimates now.
Looks like ravioles?
How do bacterial pangenomes evolve, what controls their dynamics, why do they exist?
Fitting a mechanistic model to 450 species from allthebacteria.org suggesting fast vs slow gene exchange (i.e. amount of MGEs) is a major differentiating factor, correlated with phylogeny rather than lifestyle
Really cool Sam
At long last, my final PhD chapter is out: we developed a novel evolutionary simulator of bacterial pangenomes, Pansim, fitting it to data from >600K genomes using a likelihood-free framework, PopPUNK-mod, to explore neutral and adaptive pangenome dynamics www.biorxiv.org/content/10.6...
Not this year, too many things already :(
Anyone in my circles attending IGGSy?
July 5-9 in super pretty Ascona, Ticino, Switzerland.
Honestly, you should go just for the views.
iggsy.org