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
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
Reposted by Antoine Limasset
The morning session concluded with a talk by Megan Le: DeKnot—Local haplotype-resolved assembly with k-syncmer-
based multiplex De Bruijn graphs
The goal is to perform local haplotype assembly by iteratively growing lists of k’ consecutive closed syncmers.
based multiplex De Bruijn graphs
The goal is to perform local haplotype assembly by iteratively growing lists of k’ consecutive closed syncmers.
November 6, 2025 at 6:46 PM
The morning session concluded with a talk by Megan Le: DeKnot—Local haplotype-resolved assembly with k-syncmer-
based multiplex De Bruijn graphs
The goal is to perform local haplotype assembly by iteratively growing lists of k’ consecutive closed syncmers.
based multiplex De Bruijn graphs
The goal is to perform local haplotype assembly by iteratively growing lists of k’ consecutive closed syncmers.
Reposted by Antoine Limasset
Haonan Wu gives a talk on "A k-mer-based estimator of the substitution rate between repetitive sequences"
www.biorxiv.org/content/10.1...
This work tackles the issue of Mash which ignores repeats in the genome, providing better distance estimation #GI2025
www.biorxiv.org/content/10.1...
This work tackles the issue of Mash which ignores repeats in the genome, providing better distance estimation #GI2025
November 6, 2025 at 4:38 PM
Haonan Wu gives a talk on "A k-mer-based estimator of the substitution rate between repetitive sequences"
www.biorxiv.org/content/10.1...
This work tackles the issue of Mash which ignores repeats in the genome, providing better distance estimation #GI2025
www.biorxiv.org/content/10.1...
This work tackles the issue of Mash which ignores repeats in the genome, providing better distance estimation #GI2025
Reposted by Antoine Limasset
I am happy to share our new preprint introducing MADRe - a pipeline for Metagenomic Assembly-Driven Database Reduction, enabling accurate and computationally efficient strain-level metagenomic classification.
🔗https://www.biorxiv.org/content/10.1101/2025.05.12.653324v1
1/9
🔗https://www.biorxiv.org/content/10.1101/2025.05.12.653324v1
1/9
May 16, 2025 at 8:37 AM
I am happy to share our new preprint introducing MADRe - a pipeline for Metagenomic Assembly-Driven Database Reduction, enabling accurate and computationally efficient strain-level metagenomic classification.
🔗https://www.biorxiv.org/content/10.1101/2025.05.12.653324v1
1/9
🔗https://www.biorxiv.org/content/10.1101/2025.05.12.653324v1
1/9
Reposted by Antoine Limasset
Thread on #GI2025 's second day! 👇🏻
Second day of Genome Informatics #GI2025 began with the session “Genome Assembly and Sequence Algorithms" Yun William Yu presented “Average-case Analysis of Seed-Chain-Extend under Random Mutations"
genome.cshlp.org/content/33/7/1175
providing theoretical guarantees for the popular seed-chain-extend
genome.cshlp.org/content/33/7/1175
providing theoretical guarantees for the popular seed-chain-extend
November 6, 2025 at 5:53 PM
Thread on #GI2025 's second day! 👇🏻
This!
I am continuously surprised to hear fellow colleagues say that LLMs are trash/useless for programming, while they have radically changed the way I work over the last years. Tasks that used to take a day can now be done in minutes while I fetch a drink.
I am continuously surprised to hear fellow colleagues say that LLMs are trash/useless for programming, while they have radically changed the way I work over the last years. Tasks that used to take a day can now be done in minutes while I fetch a drink.
I think I understand how it can be that LLMs are both exceptionally good and quite terrible at programming. It's because there are two entirely different skillsets that we both call "good at programming." LLMs have only one of them.
blog.genesmindsmachines.com/p/llms-excel...
blog.genesmindsmachines.com/p/llms-excel...
LLMs excel at programming—how can they be so bad at it?
My explanation for the mystery of why LLMs can be both exceptionally good and quite terrible at programming.
blog.genesmindsmachines.com
November 7, 2025 at 10:21 AM
This!
I am continuously surprised to hear fellow colleagues say that LLMs are trash/useless for programming, while they have radically changed the way I work over the last years. Tasks that used to take a day can now be done in minutes while I fetch a drink.
I am continuously surprised to hear fellow colleagues say that LLMs are trash/useless for programming, while they have radically changed the way I work over the last years. Tasks that used to take a day can now be done in minutes while I fetch a drink.
Reposted by Antoine Limasset
Our method for genome size estimation from long-read overlaps is now published 🥳
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Genome size estimation from long read overlaps
AbstractMotivation. Accurate genome size estimation is an important component of genomic analyses such as assembly and coverage calculation, though existin
academic.oup.com
November 7, 2025 at 3:19 AM
Our method for genome size estimation from long-read overlaps is now published 🥳
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Reposted by Antoine Limasset
Man; @typst.app is so good! That's all; that's the skeet.
November 5, 2025 at 4:07 PM
Man; @typst.app is so good! That's all; that's the skeet.
Reposted by Antoine Limasset
The New York Times quickly sending out Douthat to argue that Mamdani’s victory doesn’t really matter is so predictable it borders on self-parody.
Remember, folks: Every time the Right wins an election, it’s an undeniable expression of the will of the people. If a lefty wins, it’s just a blip.
Remember, folks: Every time the Right wins an election, it’s an undeniable expression of the will of the people. If a lefty wins, it’s just a blip.
Opinion | Mamdani’s Victory Is Less Significant Than You Think
www.nytimes.com
November 5, 2025 at 5:27 PM
The New York Times quickly sending out Douthat to argue that Mamdani’s victory doesn’t really matter is so predictable it borders on self-parody.
Remember, folks: Every time the Right wins an election, it’s an undeniable expression of the will of the people. If a lefty wins, it’s just a blip.
Remember, folks: Every time the Right wins an election, it’s an undeniable expression of the will of the people. If a lefty wins, it’s just a blip.
Reposted by Antoine Limasset
The number of Chinese scientists taking on leadership roles in international science projects is growing rapidly
go.nature.com/4hJH0Cd
go.nature.com/4hJH0Cd
Chinese scientists increasingly lead joint projects with the UK, US and Europe
Although China needs to strengthen its leadership in artificial intelligence, semiconductors and energy, say researchers.
go.nature.com
November 5, 2025 at 12:02 PM
The number of Chinese scientists taking on leadership roles in international science projects is growing rapidly
go.nature.com/4hJH0Cd
go.nature.com/4hJH0Cd
Reposted by Antoine Limasset
Des ERC mais en deux mois je ne peux pas avoir un badge d'accès pour un chercheur international qui a obtenu une chaire. "C'est compliqué". Quand je vais à Cambridge comme invitée, ils savent que j'arrive et j'ai un badge en une demi seconde. Fin de la blague.
November 1, 2025 at 11:24 AM
Des ERC mais en deux mois je ne peux pas avoir un badge d'accès pour un chercheur international qui a obtenu une chaire. "C'est compliqué". Quand je vais à Cambridge comme invitée, ils savent que j'arrive et j'ai un badge en une demi seconde. Fin de la blague.
Reposted by Antoine Limasset
I have been writing for years about the fact that we are not ready for the destruction of costly signalling mechanisms. Writing used to be a way of measuring effort, ability and diligence. We still have no easy substitute
Now this paper confirms that cover letters have lost their value as predictor
Now this paper confirms that cover letters have lost their value as predictor
November 5, 2025 at 1:48 AM
I have been writing for years about the fact that we are not ready for the destruction of costly signalling mechanisms. Writing used to be a way of measuring effort, ability and diligence. We still have no easy substitute
Now this paper confirms that cover letters have lost their value as predictor
Now this paper confirms that cover letters have lost their value as predictor
Reposted by Antoine Limasset
Une Erc ? quand la simple signature d'une convention et d'un bon de commande pour publication me donne des insomnies et m'oblige à faire le siège des bureaux pendant 6 mois . Apparemment, c'est le cœur de mon métier. Impression de vivre dans la maison des fous d'Asterix.
November 5, 2025 at 6:46 AM
Une Erc ? quand la simple signature d'une convention et d'un bon de commande pour publication me donne des insomnies et m'oblige à faire le siège des bureaux pendant 6 mois . Apparemment, c'est le cœur de mon métier. Impression de vivre dans la maison des fous d'Asterix.
Reposted by Antoine Limasset
Academics in Assyria in the 7th c BC complain that admin is preventing them from doing research and teaching
November 3, 2025 at 10:04 AM
Academics in Assyria in the 7th c BC complain that admin is preventing them from doing research and teaching
Reposted by Antoine Limasset
You're not afraid of "killer AI" and "robot overlords," you're afraid of white supremacy, ableism, patriarchy, hegemony, extractivism, kyriarchy, and capitalism.
I've said it before and I'll say it over and over and over and over and over and over and over and over and over and opver and over and over and over and over and ove and over and over and over and over and ovr and over and over andover and over and over and over and over and over and ovber again:
April 3, 2024 at 6:48 PM
You're not afraid of "killer AI" and "robot overlords," you're afraid of white supremacy, ableism, patriarchy, hegemony, extractivism, kyriarchy, and capitalism.
Reposted by Antoine Limasset
Stay tuned: We are now running Metapuccino on SRA’s 1 million human transcriptomes.
November 2, 2025 at 10:14 AM
Stay tuned: We are now running Metapuccino on SRA’s 1 million human transcriptomes.
Reposted by Antoine Limasset
www.biorxiv.org/cgi/content/...
What’s behind Metapuccino? ☕️, by PhD student Fiona Hak, @camillemrcht.bsky.social and Melina Gallopin. A thread 👇
What’s behind Metapuccino? ☕️, by PhD student Fiona Hak, @camillemrcht.bsky.social and Melina Gallopin. A thread 👇
Metappuccino: Large Language Model-driven Reconstruction of Sequence Read Archive Metadata for Cancer Research
Motivation: High-throughput RNA-sequencing has significantly advanced transcriptomic profiling in oncology. Millions of RNA-seq datasets have accumulated in public databases such as the Sequence Read ...
www.biorxiv.org
November 2, 2025 at 10:14 AM
www.biorxiv.org/cgi/content/...
What’s behind Metapuccino? ☕️, by PhD student Fiona Hak, @camillemrcht.bsky.social and Melina Gallopin. A thread 👇
What’s behind Metapuccino? ☕️, by PhD student Fiona Hak, @camillemrcht.bsky.social and Melina Gallopin. A thread 👇
It has begun
arXiv will no longer accept review articles and position papers unless they have been accepted at a journal or a conference and complete successful peer review.
This is due to being overwhelmed by a hundreds of AI generated papers a month.
Yet another open submission process killed by LLMs.
This is due to being overwhelmed by a hundreds of AI generated papers a month.
Yet another open submission process killed by LLMs.
Attention Authors: Updated Practice for Review Articles and Position Papers in arXiv CS Category – arXiv blog
blog.arxiv.org
November 2, 2025 at 1:25 PM
It has begun
Reposted by Antoine Limasset
Metappuccino: Large Language Model-driven Reconstruction of Sequence Read Archive Metadata for Cancer Research https://www.biorxiv.org/content/10.1101/2025.10.31.685769v1
November 1, 2025 at 12:47 PM
Metappuccino: Large Language Model-driven Reconstruction of Sequence Read Archive Metadata for Cancer Research https://www.biorxiv.org/content/10.1101/2025.10.31.685769v1
Reposted by Antoine Limasset
My algorithmic friends (@camillemrcht.bsky.social) doing LLM stuff : www.biorxiv.org/content/10.1...! And also, screaming last names in the author list ;P. Given my level of trust in Camille, though, perhaps it's time for me to engage more seriously with these models in research...
Metappuccino: Large Language Model-driven Reconstruction of Sequence Read Archive Metadata for Cancer Research
Motivation: High-throughput RNA-sequencing has significantly advanced transcriptomic profiling in oncology. Millions of RNA-seq datasets have accumulated in public databases such as the Sequence Read ...
www.biorxiv.org
November 1, 2025 at 3:08 PM
My algorithmic friends (@camillemrcht.bsky.social) doing LLM stuff : www.biorxiv.org/content/10.1...! And also, screaming last names in the author list ;P. Given my level of trust in Camille, though, perhaps it's time for me to engage more seriously with these models in research...
Reposted by Antoine Limasset
I'm very happy with `sassy grep` now!
If you ever need to inspect what's in your data, please try and let me know how it goes :)
Of course, it's fast: >1GB/s when using multiple threads.
If you ever need to inspect what's in your data, please try and let me know how it goes :)
Of course, it's fast: >1GB/s when using multiple threads.
Following ish's `filter` and bqtools' `grep`, Sassy now also has initial support for grep and filter!
Grep mode shows all matches, grouped per record, and is meant for human consumption.
Filter mode prints full matching (or non-matching) records to stdout or output files.
Grep mode shows all matches, grouped per record, and is meant for human consumption.
Filter mode prints full matching (or non-matching) records to stdout or output files.
October 31, 2025 at 3:58 PM
I'm very happy with `sassy grep` now!
If you ever need to inspect what's in your data, please try and let me know how it goes :)
Of course, it's fast: >1GB/s when using multiple threads.
If you ever need to inspect what's in your data, please try and let me know how it goes :)
Of course, it's fast: >1GB/s when using multiple threads.
Reposted by Antoine Limasset
Rust 1.91.0 has been released! 🌈 🦀
This version brings you tier 1 support for aarch64-pc-windows-msvc, warnings for dangling pointers to locals, new methods on AtomicPtr, array::repeat, BTreeMap::extract_if, const TypeId::of, and more!
Check out the announcement: blog.rust-lang.org/2025/10/30/R...
This version brings you tier 1 support for aarch64-pc-windows-msvc, warnings for dangling pointers to locals, new methods on AtomicPtr, array::repeat, BTreeMap::extract_if, const TypeId::of, and more!
Check out the announcement: blog.rust-lang.org/2025/10/30/R...
Announcing Rust 1.91.0 | Rust Blog
Empowering everyone to build reliable and efficient software.
blog.rust-lang.org
October 30, 2025 at 8:21 PM
Rust 1.91.0 has been released! 🌈 🦀
This version brings you tier 1 support for aarch64-pc-windows-msvc, warnings for dangling pointers to locals, new methods on AtomicPtr, array::repeat, BTreeMap::extract_if, const TypeId::of, and more!
Check out the announcement: blog.rust-lang.org/2025/10/30/R...
This version brings you tier 1 support for aarch64-pc-windows-msvc, warnings for dangling pointers to locals, new methods on AtomicPtr, array::repeat, BTreeMap::extract_if, const TypeId::of, and more!
Check out the announcement: blog.rust-lang.org/2025/10/30/R...
Reposted by Antoine Limasset
Following ish's `filter` and bqtools' `grep`, Sassy now also has initial support for grep and filter!
Grep mode shows all matches, grouped per record, and is meant for human consumption.
Filter mode prints full matching (or non-matching) records to stdout or output files.
Grep mode shows all matches, grouped per record, and is meant for human consumption.
Filter mode prints full matching (or non-matching) records to stdout or output files.
October 30, 2025 at 11:46 PM
Following ish's `filter` and bqtools' `grep`, Sassy now also has initial support for grep and filter!
Grep mode shows all matches, grouped per record, and is meant for human consumption.
Filter mode prints full matching (or non-matching) records to stdout or output files.
Grep mode shows all matches, grouped per record, and is meant for human consumption.
Filter mode prints full matching (or non-matching) records to stdout or output files.