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
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.
Reposted by Antoine Limasset
Reposted by Antoine Limasset
Reposted by Antoine Limasset
An AI model that is trained to use computational tools might accelerate mathematical discovery
go.nature.com/4pd11nA
go.nature.com/4pd11nA
Mathematicians put AI model AlphaProof to the test
Mathematicians use computational tools to prove theorems. An AI model that is trained to use these tools might accelerate mathematical discovery.
go.nature.com
November 17, 2025 at 9:43 AM
An AI model that is trained to use computational tools might accelerate mathematical discovery
go.nature.com/4pd11nA
go.nature.com/4pd11nA
Reposted by Antoine Limasset
Paired-end parsing now works with our lightweight, auxiliary FASTQ.gz indexing scheme! Now I hope to get some benchmarks and a preprint out soon.
November 16, 2025 at 3:33 PM
Paired-end parsing now works with our lightweight, auxiliary FASTQ.gz indexing scheme! Now I hope to get some benchmarks and a preprint out soon.
Reposted by Antoine Limasset
your dead AI mother loves you so much ❤️
November 15, 2025 at 12:50 AM
your dead AI mother loves you so much ❤️
Reposted by Antoine Limasset
Chatty for grant title brainstorming .. is off the chart this morning ... I just had to share the gem of the pile:
BUTTER-SEQ
BUTTER-SEQ
November 15, 2025 at 8:39 AM
Chatty for grant title brainstorming .. is off the chart this morning ... I just had to share the gem of the pile:
BUTTER-SEQ
BUTTER-SEQ
Reposted by Antoine Limasset
Reposted by Antoine Limasset
Congratulations to Richard Durbin on being awarded our Genetics Society Medal!
November 14, 2025 at 12:40 PM
Congratulations to Richard Durbin on being awarded our Genetics Society Medal!
Reposted by Antoine Limasset
Honoured and quite blown-over to receive this award. I have been, and continue to be, very lucky - first with great mentors, and then really prodigious students, postdocs and collaborators. Working with them has been a joy.
Congratulations to @zaminiqbal.bsky.social from @milnerevolution.bsky.social on being awarded the 2026 Mary Lyon Medal!
November 14, 2025 at 12:55 PM
Honoured and quite blown-over to receive this award. I have been, and continue to be, very lucky - first with great mentors, and then really prodigious students, postdocs and collaborators. Working with them has been a joy.
Reposted by Antoine Limasset
Reposted by Antoine Limasset
I'm not normally one to put stickers on my laptop, but these are 👨🍳💋 www.etsy.com/listing/1133...
November 12, 2025 at 11:02 PM
I'm not normally one to put stickers on my laptop, but these are 👨🍳💋 www.etsy.com/listing/1133...
Reposted by Antoine Limasset
From 97% to 99.9%. Uncover how Oxford Nanopore technologies increase in raw read accuracy is enabling discoveries such as somatic variants in the mitochondrial genome, and how researchers are taking a broader view to make discoveries that truly matter. https://bit.ly/4pmvVtN
November 12, 2025 at 7:17 PM
From 97% to 99.9%. Uncover how Oxford Nanopore technologies increase in raw read accuracy is enabling discoveries such as somatic variants in the mitochondrial genome, and how researchers are taking a broader view to make discoveries that truly matter. https://bit.ly/4pmvVtN
Reposted by Antoine Limasset
The paper is out too www.nature.com/articles/s41...
Toward security-aware portable sequencing - Nature Communications
Portable genome sequencers are revolutionizing genomic research. However, their reliance on external systems introduces new vulnerabilities that threaten the security of these sequencers. By employing...
www.nature.com
November 12, 2025 at 12:26 PM
The paper is out too www.nature.com/articles/s41...
Reposted by Antoine Limasset
Bioinformatics x cybersecurity: Christina Boucher and her colleague Sara Rampazzi uncovered a basic yet critical vulnerability in MinIONs through the MinKNOW software bioengineer.org/portable-gen...
Portable Genetic Sequencer Security Vulnerabilities Could Endanger Personal
Portable genetic sequencers, particularly those manufactured by Oxford Nanopore Technologies, have revolutionized the field of genomics, making DNA sequencing more accessible and practical across the
bioengineer.org
November 12, 2025 at 7:44 AM
Bioinformatics x cybersecurity: Christina Boucher and her colleague Sara Rampazzi uncovered a basic yet critical vulnerability in MinIONs through the MinKNOW software bioengineer.org/portable-gen...
Reposted by Antoine Limasset
The idea is to decouple the journals from the review step. They’ll still exist, but they’ll need to add other value. They’ll highlight, curate, add new perspectives. If they do a good job they can still be prestigious (like Scientific American or Wired) (1.2) 👇
November 8, 2025 at 6:02 AM
The idea is to decouple the journals from the review step. They’ll still exist, but they’ll need to add other value. They’ll highlight, curate, add new perspectives. If they do a good job they can still be prestigious (like Scientific American or Wired) (1.2) 👇
Reposted by Antoine Limasset
