Yoann Dufresne (PhD)
@yoann.bsky.social
Bioinformatics and Computer Science account of Yoann Dufresne. Researcher & teacher at @univlille.bsky.social.
Alternative controleur game dev account : @collectifartefact.bsky.social
Personal account : @docteursid.bsky.social
Alternative controleur game dev account : @collectifartefact.bsky.social
Personal account : @docteursid.bsky.social
Reposted by Yoann Dufresne (PhD)
I implemented a CPU and RAM.
In Javascript.
For a blog.
In Javascript.
For a blog.
September 24, 2025 at 4:11 PM
I implemented a CPU and RAM.
In Javascript.
For a blog.
In Javascript.
For a blog.
Some days are harder than others. But at least today was a beautiful sunrise with the Moon and Venus
September 19, 2025 at 3:58 PM
Some days are harder than others. But at least today was a beautiful sunrise with the Moon and Venus
Reposted by Yoann Dufresne (PhD)
@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...
www.youtube.com/watch?v=35Yg...
Conway-Bromage-Lyndon (CBL): an exact, dynamic... - Igor Martayan - HiTSeq - ISMB 2024
YouTube video by ISCB
www.youtube.com
March 11, 2025 at 5:51 AM
@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...
www.youtube.com/watch?v=35Yg...
Reposted by Yoann Dufresne (PhD)
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.
🔬 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.
January 14, 2025 at 9:10 AM
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.
🔬 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 !
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.
🔬 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.
January 16, 2025 at 10:06 AM
Welcome to institut Pasteur !
Reposted by Yoann Dufresne (PhD)
Merry lexicographic minimiz... Christmas arxiv.org/abs/2412.17492
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 -...
arxiv.org
December 24, 2024 at 1:04 PM
Merry lexicographic minimiz... Christmas arxiv.org/abs/2412.17492
Reposted by Yoann Dufresne (PhD)
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
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...
youtube.com
December 20, 2024 at 1:04 PM
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
Reposted by Yoann Dufresne (PhD)
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...
Let me know if you want to use this :)
curiouscoding.nl/posts/fast-m...
December 17, 2024 at 2:37 PM
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...
Let me know if you want to use this :)
curiouscoding.nl/posts/fast-m...
Reposted by Yoann Dufresne (PhD)
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!
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!
December 13, 2024 at 4:46 AM
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!
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!
Reposted by Yoann Dufresne (PhD)
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.
Movi: A fast and cache-efficient full-text pangenome index
Biocomputational method; Classification of bioinformatical subject; Genomic analysis
www.cell.com
December 11, 2024 at 4:48 PM
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!
December 11, 2024 at 2:52 PM
Congratulations @epcrocha.bsky.social for your CNRS silver medal!
(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
[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
December 2, 2024 at 12:29 PM
(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
[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
This is now :)
The Primer Method seminar continue! This morning, we'll have @yoann.bsky.social n.bsky.social who will discuss about computing and querying de Bruijn Graph, including how to transform raw sequence data into k-mer sets, and common ways to store and index sets for queries.
Bluesky
n.bsky.social
December 2, 2024 at 9:22 AM
This is now :)
Reposted by Yoann Dufresne (PhD)
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!
November 25, 2024 at 11:08 AM
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!
Reposted by Yoann Dufresne (PhD)
🧬🔍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
🏔️ logan-search.org 🏔️
#Genomics #Bioinformatics #OpenScience
November 11, 2024 at 7:29 PM
🧬🔍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
🏔️ logan-search.org 🏔️
#Genomics #Bioinformatics #OpenScience
Reposted by Yoann Dufresne (PhD)
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 !
February 9, 2024 at 2:42 PM
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 !
Matinée réparation de gameboys pockets 🎮
August 21, 2023 at 7:35 AM
Matinée réparation de gameboys pockets 🎮