Laurent Jacob
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laurentjacob.bsky.social
Laurent Jacob
@laurentjacob.bsky.social
290 followers 220 following 29 posts
Researcher in statistics and machine learning for genomics

https://laurent-jacob.github.io/
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Reposted by Laurent Jacob
cantinilab.bsky.social
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: 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
laurentjacob.bsky.social
Very happy about this work on phylogenetic neural inference, led by @lblassel.bsky.social :)
lblassel.bsky.social Luc Blassel @lblassel.bsky.social · 26d
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
A three panel figure describing the Phyloformer 2 (PF2) method. The top panel describes the architecture of the PF2 neural network. The bottom right panel describes how PF2 estimates the posterior probability of a tree given a sequence emebdding at train time. The bottom left panel describes how PF2 samples trees from the learned posterior at inference time.
October 17, 2025 at 5:27 AM
Reposted by Laurent Jacob
stamatak.bsky.social
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...
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
Reposted by Laurent Jacob
camillemrcht.bsky.social
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...
‘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
laurentjacob.bsky.social
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
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.] 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.]
October 8, 2025 at 11:04 AM
Reposted by Laurent Jacob
fbaumdicker.bsky.social
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
Reposted by Laurent Jacob
davidaknowles.bsky.social
#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
Reposted by Laurent Jacob
camillemrcht.bsky.social
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
Reposted by Laurent Jacob
rayanchikhi.bsky.social
🌎👩‍🔬 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...
September 3, 2025 at 8:39 AM
laurentjacob.bsky.social
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!
September 2, 2025 at 6:51 AM
Reposted by Laurent Jacob
cnrsinformatics.bsky.social
#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
July 21, 2025 at 12:01 PM
Reposted by Laurent Jacob
npmalfoy.bsky.social
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...
www.biorxiv.org
June 19, 2025 at 9:13 AM
laurentjacob.bsky.social
Registration is now open!

The 580€ include housing and all meals.

We will close on October 17th or when reaching 80 participants.
laurentjacob.bsky.social Laurent Jacob @laurentjacob.bsky.social · Feb 24
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
A legendary being holds a phylogenetic tree in the palm of their hand, with snowy mountains in the background.
June 18, 2025 at 7:22 AM
Reposted by Laurent Jacob
yun-s-song.bsky.social
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.
Home - ProbGen 2026
Your Site Description
probgen2026.github.io
June 6, 2025 at 5:52 PM
laurentjacob.bsky.social
Merci à @cnrs-rhoneauvergne.bsky.social et @astropierre.com pour cette interview sur mes travaux en IA pour la génomique évolutive!
cnrs-rhoneauvergne.bsky.social CNRS Rhône Auvergne @cnrs-rhoneauvergne.bsky.social · Jun 2
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...
L’intelligence artificielle au secours du décodage et de l’analyse du génome
lejournal.cnrs.fr
June 2, 2025 at 10:53 AM
laurentjacob.bsky.social
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.
March 12, 2025 at 11:49 AM
laurentjacob.bsky.social
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
A legendary being holds a phylogenetic tree in the palm of their hand, with snowy mountains in the background.
February 24, 2025 at 8:58 AM
Reposted by Laurent Jacob
camiladuitama.bsky.social
🧬 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:
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
Reposted by Laurent Jacob
bachfrancis.bsky.social
My book is (at last) out, just in time for Christmas!
A blog post to celebrate and present it: francisbach.com/my-book-is-o...
December 21, 2024 at 3:23 PM
Reposted by Laurent Jacob
rgottardo.bsky.social
Ok, I tried to create my own list of people working on developing statistical or machine learning models applied to omics data. I am sure I missed a lot of cool people. If you'd like to be added, let me know. #Stats #ML #Omics
go.bsky.app/73rcuJn
November 24, 2024 at 7:50 AM
laurentjacob.bsky.social
We just released a preprint for Phyloformer, a likelihood-free inference method for phylogenetic reconstruction: biorxiv.org/content/10.1...

Faster than distance methods like neighbor joining, it outperforms maximum likelihood methods under complex models of sequence evolution.

🧵
A logo symbolizing the Phyloformer process: it starts from an artificial neural networks and ends with a phylogeny.
June 24, 2024 at 8:24 AM
laurentjacob.bsky.social
The first LEGEND conference on Machine Learning for Evolutionary Genomics will be held on May 13-15th in Heraklion!

Keynotes by Sara Mathieson, Hélène Morlon, Pier Palamara and Tal Pupko.

Register and submit your abstract here: legend2024.sciencesconf.org
January 17, 2024 at 9:26 AM