Antoine Limasset
@npmalfoy.bsky.social
CNRS researcher in bioinformatics
Lille, France (Bonsai team).
I develop efficient computational methods to analyze massive sequencing data, creating scalable tools for genomics, transcriptomics, and metagenomics.
https://malfoy.github.io/
Lille, France (Bonsai team).
I develop efficient computational methods to analyze massive sequencing data, creating scalable tools for genomics, transcriptomics, and metagenomics.
https://malfoy.github.io/
Reposted by Antoine Limasset
“Today, AI advocates do not merely assume automation is necessary; they aggressively proselytize their faith, thereby paving the way for techno-fascism.” — @olivia.science
www.project-syndicate.org/commentary/a...
www.project-syndicate.org/commentary/a...
AI Is Hollowing Out Higher Education
Olivia Guest & Iris van Rooij urge teachers and scholars to reject tools that commodify learning, deskill students, and promote illiteracy.
www.project-syndicate.org
October 17, 2025 at 10:59 PM
“Today, AI advocates do not merely assume automation is necessary; they aggressively proselytize their faith, thereby paving the way for techno-fascism.” — @olivia.science
www.project-syndicate.org/commentary/a...
www.project-syndicate.org/commentary/a...
Reposted by Antoine Limasset
“There were some cells in there that were very messed up”
In a technological tour-de-force, researchers have sequenced the whole genomes of more than 100 individual cells from one 74-year-old man
go.nature.com/4rvXH8Y
In a technological tour-de-force, researchers have sequenced the whole genomes of more than 100 individual cells from one 74-year-old man
go.nature.com/4rvXH8Y
We are all mosaics: vast genetic diversity found between cells in a single person
Nature - Technical advances allow researchers to trace the genetic changes that occur over time.
go.nature.com
November 29, 2025 at 4:36 PM
“There were some cells in there that were very messed up”
In a technological tour-de-force, researchers have sequenced the whole genomes of more than 100 individual cells from one 74-year-old man
go.nature.com/4rvXH8Y
In a technological tour-de-force, researchers have sequenced the whole genomes of more than 100 individual cells from one 74-year-old man
go.nature.com/4rvXH8Y
Reposted by Antoine Limasset
I'm continuously impressed with how just how good the Rust ecosystem is. Whenever I look for a crate or a CLI utility that does what I want, 95% of the time I find it.
And the rest of the time, the components are right there for me to build it.
And the rest of the time, the components are right there for me to build it.
November 28, 2025 at 3:12 PM
I'm continuously impressed with how just how good the Rust ecosystem is. Whenever I look for a crate or a CLI utility that does what I want, 95% of the time I find it.
And the rest of the time, the components are right there for me to build it.
And the rest of the time, the components are right there for me to build it.
Reposted by Antoine Limasset
Our Ensembl 2026 paper is out!
Learn about 1,900+ new genomes, expanded pangenome support, new regulation interfaces, and what’s coming in our 2026 releases.
doi.org/10.1093/nar/gkaf1239
Learn about 1,900+ new genomes, expanded pangenome support, new regulation interfaces, and what’s coming in our 2026 releases.
doi.org/10.1093/nar/gkaf1239
Ensembl 2026
Abstract. The Ensembl project (https://www.ensembl.org) is a public and open resource providing access to genomes, annotations, high-quality tools, and met
academic.oup.com
November 28, 2025 at 4:30 PM
Our Ensembl 2026 paper is out!
Learn about 1,900+ new genomes, expanded pangenome support, new regulation interfaces, and what’s coming in our 2026 releases.
doi.org/10.1093/nar/gkaf1239
Learn about 1,900+ new genomes, expanded pangenome support, new regulation interfaces, and what’s coming in our 2026 releases.
doi.org/10.1093/nar/gkaf1239
Reposted by Antoine Limasset
"An old saying about such follies is that “six months in the lab can you save you an afternoon in the library”; here we may have wasted a trillion dollars and several years to rediscover what cognitive science already knew."
garymarcus.substack.com/p/a-trillion...
garymarcus.substack.com/p/a-trillion...
A trillion dollars is a terrible thing to waste
The machine learning community is finally waking up to the madness, but the detour of the last few years has been costly.
garymarcus.substack.com
November 28, 2025 at 9:41 AM
"An old saying about such follies is that “six months in the lab can you save you an afternoon in the library”; here we may have wasted a trillion dollars and several years to rediscover what cognitive science already knew."
garymarcus.substack.com/p/a-trillion...
garymarcus.substack.com/p/a-trillion...
Reposted by Antoine Limasset
I worry that systems ignoring the reality of AI use by pretending it is not happening are letting the worst versions of AI use win by default. We need policies that mitigate the worst harm & take advantage of the gains, like Josh Gans proposes for peer review joshuagans.substack.com/p/what-to-do...
November 27, 2025 at 5:19 PM
I worry that systems ignoring the reality of AI use by pretending it is not happening are letting the worst versions of AI use win by default. We need policies that mitigate the worst harm & take advantage of the gains, like Josh Gans proposes for peer review joshuagans.substack.com/p/what-to-do...
Reposted by Antoine Limasset
mim: A lightweight auxiliary index to enable fast, parallel, gzipped FASTQ parsing https://www.biorxiv.org/content/10.1101/2025.11.24.690271v1
November 27, 2025 at 5:46 PM
mim: A lightweight auxiliary index to enable fast, parallel, gzipped FASTQ parsing https://www.biorxiv.org/content/10.1101/2025.11.24.690271v1
Reposted by Antoine Limasset
Pour la dernière année j'ai eu l'honneur d'être membre du jury du prix de thèse de la Société informatique de France et j'ai encore une fois été impressionné par la très haute qualité des travaux qui lui ont été soumis.
November 27, 2025 at 6:23 PM
Pour la dernière année j'ai eu l'honneur d'être membre du jury du prix de thèse de la Société informatique de France et j'ai encore une fois été impressionné par la très haute qualité des travaux qui lui ont été soumis.
Reposted by Antoine Limasset
Because it builds off of zran and the prototype was a class project in my CMSC 701 last year. Don't worry; @curiouscoding.nl and I are working on carcinization !
November 27, 2025 at 5:34 PM
Because it builds off of zran and the prototype was a class project in my CMSC 701 last year. Don't worry; @curiouscoding.nl and I are working on carcinization !
Reposted by Antoine Limasset
Woot! The mim preprint is live now. www.biorxiv.org/content/10.1...
Happy Thanksgiving!
Cc @curiouscoding.nl
Happy Thanksgiving!
Cc @curiouscoding.nl
mim: A lightweight auxiliary index to enable fast, parallel, gzipped FASTQ parsing
The FASTQ file format is the lingua franca of primary data distribution and processing across most of bioinformatics. Over time, the compression, storage, transmission, and decompression of gzip compr...
www.biorxiv.org
November 27, 2025 at 5:22 PM
Woot! The mim preprint is live now. www.biorxiv.org/content/10.1...
Happy Thanksgiving!
Cc @curiouscoding.nl
Happy Thanksgiving!
Cc @curiouscoding.nl
Reposted by Antoine Limasset
What can researchers do if they suspect that their manuscripts have been peer reviewed using AI?
go.nature.com/4pxUNyD
go.nature.com/4pxUNyD
Major AI conference flooded with peer-reviews written fully by AI
Controversy has erupted after 21% of manuscript reviews for an international AI conference were found to be generated by artificial intelligence.
go.nature.com
November 27, 2025 at 12:16 PM
What can researchers do if they suspect that their manuscripts have been peer reviewed using AI?
go.nature.com/4pxUNyD
go.nature.com/4pxUNyD
Reposted by Antoine Limasset
Comparative metagenomics using pan-metagenomics graphs https://www.biorxiv.org/content/10.1101/2025.11.24.690211v1
November 26, 2025 at 10:46 PM
Comparative metagenomics using pan-metagenomics graphs https://www.biorxiv.org/content/10.1101/2025.11.24.690211v1
Reposted by Antoine Limasset
Optimized k-mer search across millions of bacterial genomes on laptops https://www.biorxiv.org/content/10.1101/2025.11.23.690050v1
November 26, 2025 at 4:47 PM
Optimized k-mer search across millions of bacterial genomes on laptops https://www.biorxiv.org/content/10.1101/2025.11.23.690050v1
Reposted by Antoine Limasset
US national laboratories have been instructed to broaden access to their data sets to accelerate research as part of the federal government's AI platform
go.nature.com/4p3KzX3
go.nature.com/4p3KzX3
Trump's AI ‘Genesis Mission': what are the risks and opportunities?
National laboratories have been instructed to broaden access to their data sets to accelerate research as part of the federal government's AI platform. But who stands to benefit?
go.nature.com
November 26, 2025 at 4:36 PM
US national laboratories have been instructed to broaden access to their data sets to accelerate research as part of the federal government's AI platform
go.nature.com/4p3KzX3
go.nature.com/4p3KzX3
Reposted by Antoine Limasset
OH. MY. GOD. TYPST IS SO SMOOOOOTHHH.
100ms recompiles on save, by the time my eyes move from Emacs to pdf viewer it's already updated. I'm literally too slow to even see it update.
Also, this is why escape now maps to save. Saving allll the time. And Lshift-># (alongside much older Rshift->$).
100ms recompiles on save, by the time my eyes move from Emacs to pdf viewer it's already updated. I'm literally too slow to even see it update.
Also, this is why escape now maps to save. Saving allll the time. And Lshift-># (alongside much older Rshift->$).
Unrelated to mim itself, but this is also the first preprint I've prepared in @typst.app rather than LaTeX. It was soooo much nicer. Folks; what are we doing? Why don't our journals accept manuscript sources in Typst!
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
November 25, 2025 at 2:43 PM
OH. MY. GOD. TYPST IS SO SMOOOOOTHHH.
100ms recompiles on save, by the time my eyes move from Emacs to pdf viewer it's already updated. I'm literally too slow to even see it update.
Also, this is why escape now maps to save. Saving allll the time. And Lshift-># (alongside much older Rshift->$).
100ms recompiles on save, by the time my eyes move from Emacs to pdf viewer it's already updated. I'm literally too slow to even see it update.
Also, this is why escape now maps to save. Saving allll the time. And Lshift-># (alongside much older Rshift->$).
Reposted by Antoine Limasset
You know, we’ve got a saying
November 26, 2025 at 8:25 AM
You know, we’ve got a saying
Reposted by Antoine Limasset
LoL-align: sensitive and fast probabilistic protein structure alignment https://www.biorxiv.org/content/10.1101/2025.11.24.690091v1
November 26, 2025 at 2:46 AM
LoL-align: sensitive and fast probabilistic protein structure alignment https://www.biorxiv.org/content/10.1101/2025.11.24.690091v1
Reposted by Antoine Limasset
One last point: AI conferences are now so massive that genuine discovery is getting lost. It might be time for a specialised AI-in-biology conference with a tighter scope.
November 26, 2025 at 5:57 AM
One last point: AI conferences are now so massive that genuine discovery is getting lost. It might be time for a specialised AI-in-biology conference with a tighter scope.
Reposted by Antoine Limasset
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
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
github.com
November 25, 2025 at 2:13 PM
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
@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 !
Can't wait to see what comes out of it @robp.bsky.social @camillemrcht.bsky.social !
November 25, 2025 at 1:42 PM
@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 !
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
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
November 25, 2025 at 1:03 PM
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
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
Reposted by Antoine Limasset
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.
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.
November 23, 2025 at 3:29 PM
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.
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 those who missed it, the introduction thread of REINDEER2
bsky.app/profile/npma...
November 24, 2025 at 12:41 PM
Yohan Hernandez–Courbevoie presenting REINDEER2 at Seqbim!
For those who missed it, the introduction thread of REINDEER2
bsky.app/profile/npma...
For those who missed it, the introduction thread of REINDEER2
bsky.app/profile/npma...