Laurent Jacob
@laurentjacob.bsky.social
290 followers 220 following 28 posts
Researcher in statistics and machine learning for genomics https://laurent-jacob.github.io/
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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.]
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!
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
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 💙✨
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...
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!
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
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
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
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.
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
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
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
laurentjacob.bsky.social
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.
laurentjacob.bsky.social
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.
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.
laurentjacob.bsky.social
Come hear about the latest advances in the field and discuss your own work at Centre Paul Langevin in beautiful Aussois.
People having breakfast in front of the Alps in the Centre Paul Langevin.
laurentjacob.bsky.social
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".
A headshot of Dr Burak Yelmen.
laurentjacob.bsky.social
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".
A headshot of Dr Claudia Solis-Lemus.
laurentjacob.bsky.social
Anne-Florence Bitbol from EPFL will give a keynote presentation on "Coevolution-aware language models".
A headshot of Dr Anne-Florence Bitbol.
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.
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
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...
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
laurentjacob.bsky.social
Hi Raphael, thanks for putting this together, I'll be happy to be in the list if you think it makes sense :)
laurentjacob.bsky.social
All this work was done by Luca Nesterenko and
@lblassel.bsky.social , assisted by P. Veber, Bastien Boussau
and myself.

The code and data are available at github.com/lucanest/Phy...

Please share if you find this interesting, and we welcome your feedback :)
A sketch summarizing the entire Phyloformer process.