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
Some days are harder than others. But at least today was a beautiful sunrise with the Moon and Venus
@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...
Conway-Bromage-Lyndon (CBL): an exact, dynamic... - Igor Martayan - HiTSeq - ISMB 2024
YouTube video by ISCB
youtube.com
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.
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
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
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...
Computing random minimizers, fast
Table of Contents 1 Introduction 1.1 Results 2 Random minimizers 3 Algorithms 3.1 Problem statement Problem A: Only the set of minimizers Problem B: The minimizer of each window Problem C: Super-k-mer...
curiouscoding.nl
Ragnar {Groot Koerkamp}@curiouscoding.nl · 2y agoNice 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!
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!
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
cell.com
(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
This is now :)
Computational Biology Dpt at Pasteur@pasteur-dbc.bsky.social · 2y agoThe 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.
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
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 !
