Yoann Dufresne (PhD)

I implemented a CPU and RAM.

In Javascript.

For a blog.

Just before the sunrise. Pink and yellow colors under the moon and venus in Lille (french city)

Some days are harder than others. But at least today was a beautiful sunrise with the Moon and Venus

YouTube video by ISCB Conway-Bromage-Lyndon (CBL): an exact, dynamic... - Igor Martayan - HiTSeq - ISMB 2024

@imartayan.bsky.social pronounced my name incorrectly. Is it wrong of me to hope that generations of students and bioinformaticians to come will continue to do so?

www.youtube.com/watch?v=35Yg...

Welcome to the official Bluesky page of the Institut Pasteur!

🔬 Explore with us the frontiers of biomedical research

🧪 Follow us to uncover groundbreaking discoveries

💡 Share knowledge for global health

🌍 Join a community passionate about progress and open science.

Welcome to institut Pasteur !

On the number of $k$-mers admitting a given lexicographical minimizer The minimizer of a word of size $k$ (a $k$-mer) is defined as its smallest substring of size $m$ (with $m\leq k$), according to some ordering on $m$-mers. minimizers have been used in bioinformatics -...

Merry lexicographic minimiz... Christmas arxiv.org/abs/2412.17492

Writing in Computer Science - YouTube This is a small collection of videos for learning about how to write research papers in computer science. For now, it contains four basic lectures, with more...

Do you want to learn systematic ways in which you can revise your research papers? I've posted a short collection of 4 lectures youtube.com/playlist?lis... 1/n

I extended my fast-minimizers blogpost with the lastest results, providing proper deduplicated minimizers and super-k-mers in 1.65ns/kmer, and canonical kmers in 1.90ns/kmer. Or 5.4s and 6.4s respectively on a human genome.

Let me know if you want to use this :)

curiouscoding.nl/posts/fast-m...

Nice result to end the day (night*):
After discussions with @imartayan.bsky.social, the SIMD minimizer code now also does proper canonical (revcomp) minimizers:

~1ns/bp for fwd minis
+0.4ns/bp with collect and dedup
+0.6ns/bp with canonical hashes.

Super happy how it's only 2x slower in the end!

Movi: A fast and cache-efficient full-text pangenome index Biocomputational method; Classification of bioinformatical subject; Genomic analysis

Very excited to see Movi (by @mohsenzakeri.bsky.social) now out in iScience: www.cell.com/iscience/ful.... Movi builds on the "move structure" pangenome index, a compressed full-text index and close cousin to r-index. Compared to r-index, the move structure is simpler and more cache-efficient.

Congratulations @epcrocha.bsky.social for your CNRS silver medal!

Hopefully everything will balance in the next months.

The same for me. I'm very surprise to have a x5 increase of followers regarding my previous twitter account.

Full thread when the paper is fully online (sooon)

[INFO IMPORTANTE] Je découpe mon compte en 3:
- Pour la science (bioinfo/info) [EN]: @yoann.bsky.social
- Pour la création de jeux à controlleurs alternatifs [FR]: @collectifartefact.bsky.social
- Compte perso sans but [EN/FR]: @docteursid.bsky.social

Tomato slicing metaphore

(Francais dans la réponse)

[IMPORTANT INFO] I'm splitting my account into 3 pieces:
- For science (bioinfo/comp.sci.) [EN]: @yoann.bsky.social
- For alt ctrl game creation [FR]: @collectifartefact.bsky.social
- Personal random account [EN/FR]: @docteursid.bsky.social

It was not but I can redo the presentation in any other context ! This was basically the presentation of techniques like SSHash and why it is saving space and time.

This is now :)

The dpt started a new Primer Method session! The meeting will take place every Monday for 2 months. Today we had @hu-asch.bsky.social discussing interaction effect testing in linear models. Next week @yoann.bsky.social will talk about computing, storing and querying de Bruijn Graph from k-mer!

🧬🔍There are 50 petabases of freely-available DNA sequencing data. We introducing Logan Search which allows you to search for any DNA sequence in minutes, bringing Earth’s largest genomic resource to your fingertips.
🏔️ logan-search.org 🏔️
#Genomics #Bioinformatics #OpenScience

ping @natachatriou.bsky.social @alexandradelbot.bsky.social

Log Cabin xkcd.com/2891

@davesheik.bsky.social , in Speedrun pokemon bleu sur écran géant ?

Salut les amis du ciel bleu. Si demain vous ne faites rien entre 15h et 19h, vous êtes les bienvenus à la Tréso à Malakoff pour jouer à la gameboy avec mon asso Benji et moi. Il paraît même qu'on y fera un tournoi de Tetris avec des cable link !

Thé vert

Still too few genomic people. Maybe in a few months if we continue to give 1 invite per week

Ha par contre c'est un jeu où il faut surtout pas se spoiler. Tout doux sur les vidéos de gameplay sinon tu perd l'intérêt de l'exploitation du jeu.

Dans les jeux stylés, t'as essayé outer wilds ? Tunic s'est fait détrôné par celui-ci dans mon cœur

Si tu peux me renvoyer le code que je t'avais filé en dernier que je teste chez moi, ce serait cool.
Mon adresse email est là si besoin : github.com/yoann-dufresne

C'est un super jeu qui vaut le coup d'insister. Il est pas si dur que ca après quelques morts (sauf le boss de fin de l'enfer)