Laurent Jacob
@laurentjacob.bsky.social
Reposted by Laurent Jacob
Happy to share STORIES out now on Nature Methods
STORIES learns cell fate landscapes from spatial tramscripromics data profiled at several time points, thus allowing prediction of future cell states.
Led by Geert-Jan Huizing and Jules Samaran
www.nature.com/articles/s41...
@pasteur.fr
STORIES learns cell fate landscapes from spatial tramscripromics data profiled at several time points, thus allowing prediction of future cell states.
Led by Geert-Jan Huizing and Jules Samaran
www.nature.com/articles/s41...
@pasteur.fr
STORIES: learning cell fate landscapes from spatial transcriptomics using optimal transport - Nature Methods
By learning a differentiation potential using an optimal transport-based approach, STORIES models and infers cell fate trajectories using spatiotemporal omics data.
www.nature.com
November 4, 2025 at 7:25 AM
Happy to share STORIES out now on Nature Methods
STORIES learns cell fate landscapes from spatial tramscripromics data profiled at several time points, thus allowing prediction of future cell states.
Led by Geert-Jan Huizing and Jules Samaran
www.nature.com/articles/s41...
@pasteur.fr
STORIES learns cell fate landscapes from spatial tramscripromics data profiled at several time points, thus allowing prediction of future cell states.
Led by Geert-Jan Huizing and Jules Samaran
www.nature.com/articles/s41...
@pasteur.fr
Very happy about this work on phylogenetic neural inference, led by @lblassel.bsky.social :)
We’re very excited to finally share our latest work:
Phyloformer 2, a deep end-to-end phylogenetic reconstruction method: arxiv.org/abs/2510.12976
Using neural posterior estimation, it outperforms Phyloformer 1 and maximum-likelihood methods under simple and complex evolutionary models.
🧵1/17
Phyloformer 2, a deep end-to-end phylogenetic reconstruction method: arxiv.org/abs/2510.12976
Using neural posterior estimation, it outperforms Phyloformer 1 and maximum-likelihood methods under simple and complex evolutionary models.
🧵1/17
October 17, 2025 at 5:27 AM
Very happy about this work on phylogenetic neural inference, led by @lblassel.bsky.social :)
Reposted by Laurent Jacob
October 17 is your last chance to register for the 2nd conference on Machine Learning for Evolutionary Genomics Data (Dec 8-12), in the French Alps at legend2025.sciencesconf.org
The conference talks are online at legend2025.sciencesconf.org/data/book_le...
The conference talks are online at legend2025.sciencesconf.org/data/book_le...
legend2025 : Machine Learning for Evolutionary Genomics Data - Sciencesconf.org
Evolutionary genomics and population genetics investigate patterns of genetic diversity between species or between populations within a species and play a fundamental role in many aspects, from theoretical facets of evolution to practical ones, such as conservation genetics and biomedical sciences.
legend2025.sciencesconf.org
October 13, 2025 at 11:24 AM
October 17 is your last chance to register for the 2nd conference on Machine Learning for Evolutionary Genomics Data (Dec 8-12), in the French Alps at legend2025.sciencesconf.org
The conference talks are online at legend2025.sciencesconf.org/data/book_le...
The conference talks are online at legend2025.sciencesconf.org/data/book_le...
Reposted by Laurent Jacob
Ca n'est pas si souvent, un article publié dans Nature met ma communauté à l'honneur (la bioinformatique des séquences). Je vous raconte ?
www.nature.com/articles/d41...
www.nature.com/articles/d41...
‘Google for DNA’ brings order to biology’s big data
MetaGraph compresses vast data archives into a search engine for scientists, opening up new frontiers of biological discovery.
www.nature.com
October 9, 2025 at 3:00 PM
Ca n'est pas si souvent, un article publié dans Nature met ma communauté à l'honneur (la bioinformatique des séquences). Je vous raconte ?
www.nature.com/articles/d41...
www.nature.com/articles/d41...
The decisions for LEGEND are out: legend2025.sciencesconf.org/data/book_le...
I'm really looking forward to hearing these 21 exciting presentations (and additional 30 posters) next December.
If you want to attend too, registration is open until October 17th through legend2025.sciencesconf.org
I'm really looking forward to hearing these 21 exciting presentations (and additional 30 posters) next December.
If you want to attend too, registration is open until October 17th through legend2025.sciencesconf.org
![Exploring the space of self-reproducing RNA using generative models, Martin Weigt
Exploring the archaic introgression landscape of admixed populations through
joint ancestry inference, Jazeps Medina Tretmanis [et al.]
Predicting natural variation in the yeast phenotypic landscape with machine
learning, Sakshi Khaiwal [et al.]
Phylodynamic modeling with unsupervised Bayesian neural networks, Marino
Gabriele [et al.]
Likelihood-free inference of phylogenetic tree posterior distributions, Luc Blas-
sel [et al.]
Generative continuous time model reveals epistatic signatures in protein evolu-
tion, Barrat-Charlaix Pierre
Neural posterior estimation for high-dimensional genomic data from complex pop-
ulation genetic models, Jiseon Min [et al.]
A differentiable model for detecting diversifying selection directly from alignments
in large-scale bacterial datasets, Leonie Lorenz [et al.]
Detecting interspecific positive selection using transformers, Charlotte West [et al.]
Predicting Multiple Sequence Alignment Uncertainty via Machine Learning, Lucia
Martin-Fernandez [et al.]
Graph Neural Networks for Likelihood-Free Inference in Diversification Mod-
els, Amélie Leroy [et al.]
Popformer: learning general signatures of genetic variation and natural selection
with a self-supervised transformer, Leon Zong [et al.]](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:7x5c6ifrcznmg4mzhfuc2a6r/bafkreidur7bz43o2jhwr4gbt36awozawqthbkkfeszxjkxf4kvhyh7q6du@jpeg)
![PRIVET: PRIVacy metric based on Extreme value Theory, Antoine Szatkownik [et
al.]
Generative models for inferring the evolutionary history of the malaria vector
Anopheles gambiae, Amelia Eneli [et al.]
Language Models Outperform Supervised-Only Approaches for Conserved Ele-
ment Comprehension, Eyes Robson [et al.]
Identification and Classification of Orphan Genes, Spurious Orphan Genes, and
Conserved Genes from the human microbiome, Chen Chen
Neural Simulation-based inference of demography and selection, Francisco De
Borja Campuzano Jiménez [et al.]
Species Identification and aDNA Read Mapping Using k-mer Embeddings, Filip
Thor [et al.]
Contrastive Learning for Population Structure and Trait Prediction, Filip Thor [et
al.]
Protein and genomic language models chart a vast landscape of antiphage de-
fenses, Mordret Ernest
The Phylogenomics and Sparse Learning of Trait Innovations, Gaurav Diwan [et
al.]](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:7x5c6ifrcznmg4mzhfuc2a6r/bafkreig4akadduemzbit67bv7jnr7x2ircwiriykabg2imuf3phy6hhube@jpeg)
October 8, 2025 at 11:04 AM
The decisions for LEGEND are out: legend2025.sciencesconf.org/data/book_le...
I'm really looking forward to hearing these 21 exciting presentations (and additional 30 posters) next December.
If you want to attend too, registration is open until October 17th through legend2025.sciencesconf.org
I'm really looking forward to hearing these 21 exciting presentations (and additional 30 posters) next December.
If you want to attend too, registration is open until October 17th through legend2025.sciencesconf.org
Reposted by Laurent Jacob
Only a few hours left to submit your abstract for a talk at the Machine Learning in Evolutionary Genomics conference in December in Aussois in the French alps!
September 22, 2025 at 2:46 PM
Only a few hours left to submit your abstract for a talk at the Machine Learning in Evolutionary Genomics conference in December in Aussois in the French alps!
Reposted by Laurent Jacob
#MLCB2025 is tomorrow & Thursday with a fantastic lineup of keynotes & contributed talks www.mlcb.org/schedule. We'll be livestreaming through our YouTube channel www.youtube.com/@mlcbconf. Thanks to www.corteva.com, instadeep.com, the Simons Center at CSHL & NYGC for generous support!
MLCB - Schedule
The in-person component will be held at the New York Genome Center, 101 6th Ave, New York, NY 10013.
www.mlcb.org
September 10, 2025 at 12:16 AM
#MLCB2025 is tomorrow & Thursday with a fantastic lineup of keynotes & contributed talks www.mlcb.org/schedule. We'll be livestreaming through our YouTube channel www.youtube.com/@mlcbconf. Thanks to www.corteva.com, instadeep.com, the Simons Center at CSHL & NYGC for generous support!
Reposted by Laurent Jacob
Achievement unlocked: defend your habilitation thesis on the same day than your partner. That was quite a science + celebration day, thanks to all involved 💙✨
September 5, 2025 at 4:51 PM
Achievement unlocked: defend your habilitation thesis on the same day than your partner. That was quite a science + celebration day, thanks to all involved 💙✨
Reposted by Laurent Jacob
🌎👩🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
September 3, 2025 at 8:39 AM
🌎👩🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
The call for abstract for LEGEND is now open:
legend2025.sciencesconf.org
It will close on September 22nd (oral presentations) and October 1st (posters).
Send us your best work on Machine Learning for Evolutionary Genomics and come discuss it with us in the French Alps next December!
legend2025.sciencesconf.org
It will close on September 22nd (oral presentations) and October 1st (posters).
Send us your best work on Machine Learning for Evolutionary Genomics and come discuss it with us in the French Alps next December!
September 2, 2025 at 6:51 AM
The call for abstract for LEGEND is now open:
legend2025.sciencesconf.org
It will close on September 22nd (oral presentations) and October 1st (posters).
Send us your best work on Machine Learning for Evolutionary Genomics and come discuss it with us in the French Alps next December!
legend2025.sciencesconf.org
It will close on September 22nd (oral presentations) and October 1st (posters).
Send us your best work on Machine Learning for Evolutionary Genomics and come discuss it with us in the French Alps next December!
Reposted by Laurent Jacob
#TalentCNRS 🥉| Flora Jay, entre génomes synthétiques et récits évolutifs, reçoit la médaille de bronze du CNRS.
➡️ www.ins2i.cnrs.fr/fr/cnrsinfo/...
🤝 @lisnlab.bsky.social @cnrs-paris-saclay.bsky.social
➡️ www.ins2i.cnrs.fr/fr/cnrsinfo/...
🤝 @lisnlab.bsky.social @cnrs-paris-saclay.bsky.social
July 21, 2025 at 12:01 PM
#TalentCNRS 🥉| Flora Jay, entre génomes synthétiques et récits évolutifs, reçoit la médaille de bronze du CNRS.
➡️ www.ins2i.cnrs.fr/fr/cnrsinfo/...
🤝 @lisnlab.bsky.social @cnrs-paris-saclay.bsky.social
➡️ www.ins2i.cnrs.fr/fr/cnrsinfo/...
🤝 @lisnlab.bsky.social @cnrs-paris-saclay.bsky.social
Reposted by Laurent Jacob
Preprint alert! 🦌
Our new abundance index, REINDEER2, is out!
It's cheap to build and update, offers tunable abundance precision at kmer level, and delivers very high query throughput.
Short thread!
www.biorxiv.org/content/10.1...
github.com/Yohan-Hernan...
Our new abundance index, REINDEER2, is out!
It's cheap to build and update, offers tunable abundance precision at kmer level, and delivers very high query throughput.
Short thread!
www.biorxiv.org/content/10.1...
github.com/Yohan-Hernan...
www.biorxiv.org
June 19, 2025 at 9:13 AM
Preprint alert! 🦌
Our new abundance index, REINDEER2, is out!
It's cheap to build and update, offers tunable abundance precision at kmer level, and delivers very high query throughput.
Short thread!
www.biorxiv.org/content/10.1...
github.com/Yohan-Hernan...
Our new abundance index, REINDEER2, is out!
It's cheap to build and update, offers tunable abundance precision at kmer level, and delivers very high query throughput.
Short thread!
www.biorxiv.org/content/10.1...
github.com/Yohan-Hernan...
Registration is now open!
The 580€ include housing and all meals.
We will close on October 17th or when reaching 80 participants.
The 580€ include housing and all meals.
We will close on October 17th or when reaching 80 participants.
The next LEGEND conference on machine learning for evolutionary genomics will be in Aussois (French Alps) between December 8th and 12th.
Mark your calendars and make sure your best work is ready next September when the call for abstracts opens 🙂
legend2025.sciencesconf.org
Mark your calendars and make sure your best work is ready next September when the call for abstracts opens 🙂
legend2025.sciencesconf.org
June 18, 2025 at 7:22 AM
Registration is now open!
The 580€ include housing and all meals.
We will close on October 17th or when reaching 80 participants.
The 580€ include housing and all meals.
We will close on October 17th or when reaching 80 participants.
Reposted by Laurent Jacob
The 2026 Probabilistic Modeling in Genomics (ProbGen) meeting will be held at UC Berkeley, March 25-28, 2026. We have an amazing list of keynote speakers and session chairs:
probgen2026.github.io
Please help spread the news.
probgen2026.github.io
Please help spread the news.
Home - ProbGen 2026
Your Site Description
probgen2026.github.io
June 6, 2025 at 5:52 PM
The 2026 Probabilistic Modeling in Genomics (ProbGen) meeting will be held at UC Berkeley, March 25-28, 2026. We have an amazing list of keynote speakers and session chairs:
probgen2026.github.io
Please help spread the news.
probgen2026.github.io
Please help spread the news.
Merci à @cnrs-rhoneauvergne.bsky.social et @astropierre.com pour cette interview sur mes travaux en IA pour la génomique évolutive!
Grâce à l’IA, les scientifiques disposent de nouveaux outils pour décrypter, analyser et interpréter les milliards de lettres de notre ADN🧬. Explications de Laurent Jacob chercheur en IA pour la génomique au #CQSB
À lire sur le blog #FocusSciences🎯 du CNRS 👉 lejournal.cnrs.fr/nos-blogs/fo...
À lire sur le blog #FocusSciences🎯 du CNRS 👉 lejournal.cnrs.fr/nos-blogs/fo...
L’intelligence artificielle au secours du décodage et de l’analyse du génome
lejournal.cnrs.fr
June 2, 2025 at 10:53 AM
Merci à @cnrs-rhoneauvergne.bsky.social et @astropierre.com pour cette interview sur mes travaux en IA pour la génomique évolutive!
There is a nice example in @stephaneguindon.bsky.social's Ph.D thesis p.55
theses.hal.science/tel-00843343...
theses.hal.science/tel-00843343...
theses.hal.science
April 3, 2025 at 12:30 PM
There is a nice example in @stephaneguindon.bsky.social's Ph.D thesis p.55
theses.hal.science/tel-00843343...
theses.hal.science/tel-00843343...
The design matrix of the regression should be nPairs x nBranches, and have a 1 at coordinates (i,j) such that branch j belongs to the path defined by pair i in the tree, 0 otherwise.
April 3, 2025 at 12:26 PM
The design matrix of the regression should be nPairs x nBranches, and have a 1 at coordinates (i,j) such that branch j belongs to the path defined by pair i in the tree, 0 otherwise.
I think one way to do this is the least squares method, which gives you the set of branch lengths on your given topology such that the sum of squared differences between your given distances and the distances on the tree are minimal.
April 3, 2025 at 12:23 PM
I think one way to do this is the least squares method, which gives you the set of branch lengths on your given topology such that the sum of squared differences between your given distances and the distances on the tree are minimal.
Phyloformer is finally published in MBE! 🎉
academic.oup.com/mbe/advance-...
The thread below provides a summary of our neural network for likelihood-free phylogenetic reconstruction.
academic.oup.com/mbe/advance-...
The thread below provides a summary of our neural network for likelihood-free phylogenetic reconstruction.
March 12, 2025 at 11:49 AM
Phyloformer is finally published in MBE! 🎉
academic.oup.com/mbe/advance-...
The thread below provides a summary of our neural network for likelihood-free phylogenetic reconstruction.
academic.oup.com/mbe/advance-...
The thread below provides a summary of our neural network for likelihood-free phylogenetic reconstruction.
Come hear about the latest advances in the field and discuss your own work at Centre Paul Langevin in beautiful Aussois.
February 24, 2025 at 8:58 AM
Come hear about the latest advances in the field and discuss your own work at Centre Paul Langevin in beautiful Aussois.
Burak Yelmen from the University of Tartu will give a keynote presentation on "A perspective on generative neural networks in genomics with applications in synthetic data generation".
February 24, 2025 at 8:58 AM
Burak Yelmen from the University of Tartu will give a keynote presentation on "A perspective on generative neural networks in genomics with applications in synthetic data generation".
Claudia Solís-Lemus from the University of Wisconsin-Madison will give a keynote presentation on "The good, the bad and the ugly of deep learning in phylogenetic inference".
February 24, 2025 at 8:58 AM
Claudia Solís-Lemus from the University of Wisconsin-Madison will give a keynote presentation on "The good, the bad and the ugly of deep learning in phylogenetic inference".
Anne-Florence Bitbol from EPFL will give a keynote presentation on "Coevolution-aware language models".
February 24, 2025 at 8:58 AM
Anne-Florence Bitbol from EPFL will give a keynote presentation on "Coevolution-aware language models".
The next LEGEND conference on machine learning for evolutionary genomics will be in Aussois (French Alps) between December 8th and 12th.
Mark your calendars and make sure your best work is ready next September when the call for abstracts opens 🙂
legend2025.sciencesconf.org
Mark your calendars and make sure your best work is ready next September when the call for abstracts opens 🙂
legend2025.sciencesconf.org
February 24, 2025 at 8:58 AM
The next LEGEND conference on machine learning for evolutionary genomics will be in Aussois (French Alps) between December 8th and 12th.
Mark your calendars and make sure your best work is ready next September when the call for abstracts opens 🙂
legend2025.sciencesconf.org
Mark your calendars and make sure your best work is ready next September when the call for abstracts opens 🙂
legend2025.sciencesconf.org
Reposted by Laurent Jacob
🧬 Excited to share our latest work, MUSET 🌭, a new tool for creating abundance unitig matrices from sequencing data. It was published yesterday in Oxford Bioinformatics if you want to have a look👀 :
academic.oup.com/bioinformati...
Let's break it down:
academic.oup.com/bioinformati...
Let's break it down:
MUSET: Set of utilities for constructing abundance unitig matrices from sequencing data
AbstractSummary. MUSET is a novel set of utilities designed to efficiently construct abundance unitig matrices from sequencing data. Unitig matrices extend
academic.oup.com
February 4, 2025 at 2:47 PM
🧬 Excited to share our latest work, MUSET 🌭, a new tool for creating abundance unitig matrices from sequencing data. It was published yesterday in Oxford Bioinformatics if you want to have a look👀 :
academic.oup.com/bioinformati...
Let's break it down:
academic.oup.com/bioinformati...
Let's break it down: