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
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...
Reposted by Antoine Limasset
En pleine désillusion sur les réalités des écoles d'ingénieur, je me dis qu'en fait j'aime bien la biologie au détour d'une sortie ornithologique à Guérande.
November 24, 2025 at 9:32 AM
En pleine désillusion sur les réalités des écoles d'ingénieur, je me dis qu'en fait j'aime bien la biologie au détour d'une sortie ornithologique à Guérande.
Wow I totally forgot about this """hype""", I'm curious to see the NFT one XD
Turns out interest in Metaverse had about a ~9 month half life.
November 24, 2025 at 10:11 AM
Wow I totally forgot about this """hype""", I'm curious to see the NFT one XD
Reposted by Antoine Limasset
I knew early on I wanted to work with computers, but because of dyslexia I ended up in a lower-tier German school. The career office said a tech job wasn’t realistic. I ignored that, took a convoluted path into university, discovered bioinformatics, got hooked on algorithms&proteins, and became a PI
November 24, 2025 at 2:42 AM
I knew early on I wanted to work with computers, but because of dyslexia I ended up in a lower-tier German school. The career office said a tech job wasn’t realistic. I ignored that, took a convoluted path into university, discovered bioinformatics, got hooked on algorithms&proteins, and became a PI
Reposted by Antoine Limasset
#SEQBIM2025 is about to start, Bonsai presents 4 works this year in Nantes seqbim.cnrs.fr/seqbim-2025/...
seqbim.cnrs.fr
November 24, 2025 at 9:10 AM
#SEQBIM2025 is about to start, Bonsai presents 4 works this year in Nantes seqbim.cnrs.fr/seqbim-2025/...
Reposted by Antoine Limasset
Colored graphs (+abundances), low density minimizers and quick sequence parse 🚀
#SEQBIM2025 is about to start, Bonsai presents 4 works this year in Nantes seqbim.cnrs.fr/seqbim-2025/...
seqbim.cnrs.fr
November 24, 2025 at 9:14 AM
Colored graphs (+abundances), low density minimizers and quick sequence parse 🚀
Reposted by Antoine Limasset
I'm feeling very grateful to welcome two new women computer scientists in the lab, Klára Sladeckova who was previously at Comenius Univ and Lore Depuydt from Ghent. They will work as PhD student and postdoc in projects co-led by Simon Puglisi. Europe at its best 👌🏻
November 24, 2025 at 9:19 AM
I'm feeling very grateful to welcome two new women computer scientists in the lab, Klára Sladeckova who was previously at Comenius Univ and Lore Depuydt from Ghent. They will work as PhD student and postdoc in projects co-led by Simon Puglisi. Europe at its best 👌🏻
Reposted by Antoine Limasset
Billi: Provably Accurate and Scalable Bubble Detection in Pangenome Graphs https://www.biorxiv.org/content/10.1101/2025.11.21.689636v1
November 23, 2025 at 12:46 AM
Billi: Provably Accurate and Scalable Bubble Detection in Pangenome Graphs https://www.biorxiv.org/content/10.1101/2025.11.21.689636v1
Reposted by Antoine Limasset
Imagine, if you will, that NASA updated its website to suggest gravity might not exist, prompting CalTech and CERN to release statements saying, "With great sadness, we can no longer recommend listening to NASA."
This is what's happening in epidemiology.
This is what's happening in epidemiology.
November 21, 2025 at 8:58 PM
Imagine, if you will, that NASA updated its website to suggest gravity might not exist, prompting CalTech and CERN to release statements saying, "With great sadness, we can no longer recommend listening to NASA."
This is what's happening in epidemiology.
This is what's happening in epidemiology.
Reposted by Antoine Limasset
The joke is that you have a software security problem, you use cryptography to solve it, now you have two problems: a software security problem and a key management problem.
November 22, 2025 at 2:50 PM
The joke is that you have a software security problem, you use cryptography to solve it, now you have two problems: a software security problem and a key management problem.
Reposted by Antoine Limasset
Courrier de la Direction générale de la recherche et de l'innovation pour diffusion d'un sondage IFOP « sur les perceptions, les expériences et les dynamiques de l'anti-sémitisme » dans l'ESR finissant par des renseignements sur les opinions politiques des sondé.e.s 1/2
rogueesr.fr/wp-content/u...
rogueesr.fr/wp-content/u...
November 22, 2025 at 2:07 PM
Courrier de la Direction générale de la recherche et de l'innovation pour diffusion d'un sondage IFOP « sur les perceptions, les expériences et les dynamiques de l'anti-sémitisme » dans l'ESR finissant par des renseignements sur les opinions politiques des sondé.e.s 1/2
rogueesr.fr/wp-content/u...
rogueesr.fr/wp-content/u...
Reposted by Antoine Limasset
Lolz --- the mim parser (fastq parser that takes advantage of the auxiliary mim index if it is built) is actually way faster than I had been measuring. The example application was counting nucleotides, and there was false sharing in the vectors of counters used by different threads ;P.
November 21, 2025 at 5:05 PM
Lolz --- the mim parser (fastq parser that takes advantage of the auxiliary mim index if it is built) is actually way faster than I had been measuring. The example application was counting nucleotides, and there was false sharing in the vectors of counters used by different threads ;P.
Reposted by Antoine Limasset
We spent a year investigating billionaires for @washingtonpost.com.
We found: the wealthiest 100 Americans gave $1.1 billion to influence the 2024 elections — 140x more than they did in 2000. And almost all of that giving boosted Republicans.
washingtonpost.com/politics/int...
We found: the wealthiest 100 Americans gave $1.1 billion to influence the 2024 elections — 140x more than they did in 2000. And almost all of that giving boosted Republicans.
washingtonpost.com/politics/int...
November 21, 2025 at 2:56 PM
We spent a year investigating billionaires for @washingtonpost.com.
We found: the wealthiest 100 Americans gave $1.1 billion to influence the 2024 elections — 140x more than they did in 2000. And almost all of that giving boosted Republicans.
washingtonpost.com/politics/int...
We found: the wealthiest 100 Americans gave $1.1 billion to influence the 2024 elections — 140x more than they did in 2000. And almost all of that giving boosted Republicans.
washingtonpost.com/politics/int...
Reposted by Antoine Limasset
@wytamma.bsky.social : so, it took a little bit of extra time (not the flight back from the CZI meeting), but I decided to just f#&$ing do it, and the basic code to build and parse with the auxiliary fastq index is working (github.com/COMBINE-lab/...). 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 19, 2025 at 3:01 AM
@wytamma.bsky.social : so, it took a little bit of extra time (not the flight back from the CZI meeting), but I decided to just f#&$ing do it, and the basic code to build and parse with the auxiliary fastq index is working (github.com/COMBINE-lab/...). 1/2
Reposted by Antoine Limasset
Using an integrative phylogenomic approach, new research in Science reveals unprecedented phylogenomic support for sponges as the sister lineage to all other animals.
Learn more in a new #SciencePerspective: https://scim.ag/4r7SLqm
Learn more in a new #SciencePerspective: https://scim.ag/4r7SLqm
Sponging away phylogenomic incongruence
Genes with strong and consistent signals favor sponges as humans’ most distant animal relatives
scim.ag
November 19, 2025 at 8:54 PM
Using an integrative phylogenomic approach, new research in Science reveals unprecedented phylogenomic support for sponges as the sister lineage to all other animals.
Learn more in a new #SciencePerspective: https://scim.ag/4r7SLqm
Learn more in a new #SciencePerspective: https://scim.ag/4r7SLqm
Reposted by Antoine Limasset
Ethicists say AI-powered advances will threaten the privacy and autonomy of people who use mind-reading devices
go.nature.com/4r947us
go.nature.com/4r947us
Mind-reading devices can now predict preconscious thoughts: is it time to worry?
Ethicists say AI-powered advances will threaten the privacy and autonomy of people who use neurotechnology.
go.nature.com
November 19, 2025 at 10:55 AM
Ethicists say AI-powered advances will threaten the privacy and autonomy of people who use mind-reading devices
go.nature.com/4r947us
go.nature.com/4r947us
Reposted by Antoine Limasset
Et en parallèle, des formations sur « accompagner l'usage de l'IA générative dans l'enseignement ».
November 19, 2025 at 12:28 PM
Et en parallèle, des formations sur « accompagner l'usage de l'IA générative dans l'enseignement ».
Reposted by Antoine Limasset
Reposted by Antoine Limasset
Reposted by Antoine Limasset
My account's upload and bulk download access were terminated permanently in 2021 without explanation after I published *checksums* of GISAID genomes. GISAID and its SAB have since ignored a dozen emails seeking explanation.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.
On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
November 17, 2025 at 1:32 PM
My account's upload and bulk download access were terminated permanently in 2021 without explanation after I published *checksums* of GISAID genomes. GISAID and its SAB have since ignored a dozen emails seeking explanation.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.