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Laurent Jacob

@laurentjacob.bsky.social
320 followers 240 following 33 posts

Researcher in statistics and machine learning for genomics laurent-jacob.github.io

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Reposted by Laurent Jacob
Tanja Stadler @tanjastadler.bsky.social · 15/09/2026
🚀 Interested in joining our Computational Evolution group at ETH Zürich in Basel @bsse.ethz.ch as a Postdoc? We will be hosting ETH AI Center's Postdoc Fellows on AI x evolution, AI x single cell biology as well as AI x public health. Apply now 👉 ai.ethz.ch/apply Deadline: Oct 27, 2026
ai.ethz.ch
Fellowship Programs
The application portal for the ETH AI Center Fellowship Programs is now closed. The deadline for submitting reference letters is 23:59 CET on November 14, 2025.
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Janani Durairaj (Jay) @ninjani.bsky.social · 16/09/2026
The PhD and Postdoc application links are now live! Come join me at UNIL to work on deep learning for protein structure, interactions & design. pickybinders.org#open-positions
career5.successfactors.eu
Career Opportunities: PhD student position in deep learning for enzyme structure & catalysis (22980)
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Megan Smith @snaildit.bsky.social · 19/06/2026
I’m also recruiting a postdoc to work on an NSF-funded project focused on using machine learning for population genetic inference. Would love to talk to anyone who is interested! (Official ad to come soon).
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Pierre Peterlongo @pierrepeterlongo.bsky.social · 03/06/2026
🌎 🧬 🖥️ logan-search.org the tool to query all SRA sequences (Dec 2023 snapshot) — just got major updates. Here's what's new. 🧵 1/12
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Laurent Jacob @laurentjacob.bsky.social · 03/06/2026
cc @fbaumdicker.bsky.social @bastien-boussau.bsky.social @stamatak.bsky.social @burakyelmen.bsky.social @cc7740.bsky.social @johnlees.bacpop.org @eyesrobson.bsky.social @lblassel.bsky.social @emordret.bsky.social @phylogenetrips.bsky.social
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Laurent Jacob @laurentjacob.bsky.social · 03/06/2026
The video recordings of the legend 2025 conference held last December on machine learning for evolutionary genomics are now online ! Feel free to have a look if you missed the conference. www.canal-u.tv/chaines/lisn...
The legend 2025 conference logo showing a legendary being holding a tree in the palm of their hand, with snowy mountains in the background.
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Reposted by Laurent Jacob
Burak Yelmen @burakyelmen.bsky.social · 16/01/2026
Hello all, we are looking for PhD candidates. Details are in the document below. Please feel free to spread the word. Thank you!
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Laurent Jacob @laurentjacob.bsky.social · 19/12/2025
We had a great time at the legend 2025 conference. Thanks to all participants for making it to Aussois, and see you in Spring 2027 for the next edition!
Group picture of participants to the legend 2025 conference in front of the Centre Paul Langevin at Aussois.
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Reposted by Laurent Jacob
Burak Yelmen @burakyelmen.bsky.social · 18/12/2025
Excited to announce a new 5-year project on developing generative models for complex trait genomics. I’m now looking for PhD candidates with CS, ML, stats or bioinformatics backgrounds. I’d very much appreciate it if you could spread the word. Contact: burak.yelmen@ut.ee
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Reposted by Laurent Jacob
John Lees @johnlees.bacpop.org · 15/12/2025
We're organising a microbes & deep learning session at SMBE next year -- looking forward to seeing your abstracts!
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Laurent Jacob @laurentjacob.bsky.social · 05/12/2025
legend 2025 will be next Tuesday/Wednesday/Thursday. The detailed program is on legend2025.sciencesconf.org?lang=en If you are not attending the conference you can still follow the presentations online (Zoom links are on the website).
legend2025.sciencesconf.org
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.
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Reposted by Laurent Jacob
Laura Cantini @cantinilab.bsky.social · 04/11/2025
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
nature.com
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.
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Laurent Jacob @laurentjacob.bsky.social · 17/10/2025
Very happy about this work on phylogenetic neural inference, led by @lblassel.bsky.social :)
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Reposted by Laurent Jacob
Alexis Stamatakis @stamatak.bsky.social · 13/10/2025
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.sciencesconf.org
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.
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Camille Marchet ⚡ @camillemrcht.bsky.social · 09/10/2025
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...
nature.com
‘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.
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Laurent Jacob @laurentjacob.bsky.social · 08/10/2025
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.]
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Franz Baumdicker @fbaumdicker.bsky.social · 22/09/2025
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!
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Reposted by Laurent Jacob
David A Knowles @davidaknowles.bsky.social · 10/09/2025
#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.org
MLCB - Schedule
The in-person component will be held at the New York Genome Center, 101 6th Ave, New York, NY 10013.
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Reposted by Laurent Jacob
Camille Marchet ⚡ @camillemrcht.bsky.social · 05/09/2025
Achievement unlocked: defend your habilitation thesis on the same day than your partner. That was quite a science + celebration day, thanks to all involved 💙✨
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Reposted by Laurent Jacob
Rayan Chikhi @rayanchikhi.bsky.social · 03/09/2025
🌎👩‍🔬 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...
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Laurent Jacob @laurentjacob.bsky.social · 02/09/2025
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
legend2025 : Machine Learning for Evolutionary Genomics Data - Sciencesconf.org
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Reposted by Laurent Jacob
CNRS Sciences informatiques @cnrsinformatics.bsky.social · 21/07/2025
#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
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Reposted by Laurent Jacob
Antoine Limasset @npmalfoy.bsky.social · 19/06/2025
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...
biorxiv.org
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Laurent Jacob @laurentjacob.bsky.social · 18/06/2025
Registration is now open! The 580€ include housing and all meals. We will close on October 17th or when reaching 80 participants.
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Yun S. Song @yun-s-song.bsky.social · 06/06/2025
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
Home - ProbGen 2026
Your Site Description
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Laurent Jacob @laurentjacob.bsky.social · 02/06/2025
Merci à @cnrs-rhoneauvergne.bsky.social et @astropierre.com pour cette interview sur mes travaux en IA pour la génomique évolutive!
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Laurent Jacob @laurentjacob.bsky.social · 03/04/2025
There is a nice example in @stephaneguindon.bsky.social's Ph.D thesis p.55 theses.hal.science/tel-00843343...
theses.hal.science
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Laurent Jacob @laurentjacob.bsky.social · 03/04/2025
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.
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Laurent Jacob @laurentjacob.bsky.social · 03/04/2025
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.
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Laurent Jacob @laurentjacob.bsky.social · 12/03/2025
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
Phyloformer: Fast, accurate and versatile phylogenetic reconstruction with deep neural networks
Abstract. Phylogenetic inference aims at reconstructing the tree describing the evolution of a set of sequences descending from a common ancestor. The high
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Laurent Jacob @laurentjacob.bsky.social · 24/02/2025
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.
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Laurent Jacob @laurentjacob.bsky.social · 24/02/2025
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.
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Laurent Jacob @laurentjacob.bsky.social · 24/02/2025
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.
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Laurent Jacob @laurentjacob.bsky.social · 24/02/2025
Anne-Florence Bitbol from EPFL will give a keynote presentation on "Coevolution-aware language models".
A headshot of Dr Anne-Florence Bitbol.
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Laurent Jacob @laurentjacob.bsky.social · 24/02/2025
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.
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Camila Duitama @camiladuitama.bsky.social · 04/02/2025
🧬 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
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
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Francis Bach @bachfrancis.bsky.social · 21/12/2024
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...
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Raphael Gottardo @rgottardo.bsky.social · 24/11/2024
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
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Laurent Jacob @laurentjacob.bsky.social · 26/11/2024
Hi Raphael, thanks for putting this together, I'll be happy to be in the list if you think it makes sense :)
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Laurent Jacob @laurentjacob.bsky.social · 24/06/2024
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.
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Laurent Jacob @laurentjacob.bsky.social · 24/06/2024
In all these experiments, and regardless of model complexity, Phyloformer run on a GPU was the fastest method. About two orders of magnitude faster than IQtree, and even twice faster than FastME.
A plot comparing the speed of all methods.
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Laurent Jacob @laurentjacob.bsky.social · 24/06/2024
We then trained Phyloformer under a more realistic model, accounting for co-evolution. It outperformed all other methods, including IQTree/FastTree, on all metrics.
A plot comparing the error of different methods under a more complex probabilistic model of sequence evolution. Phyloformer outperforms all other methods under all metrics.
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Laurent Jacob @laurentjacob.bsky.social · 24/06/2024
More precisely, Phyloformer was very good at predicting distances, and on the Kuhner-Felsenstein metric accounting for both topology and branch lengths. Looking at the topology only (Robinson-Foulds metric), it performed less well than IQTree/FastTree, but better than FastME.
A plot stratifying the error into two terms: we perform very well for estimating evolutionary distances, less well for the topology.
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Laurent Jacob @laurentjacob.bsky.social · 24/06/2024
We first trained Phyloformer to perform inference under LG, a common model under which likelihood computation is possible. It performed much better than FastME (distance method), on par with maximum likelihood approaches (IQTree, FastTree).
A plot comparing the error made by different methods of phylogenetic inference. The distance method FastME underperforms, our method is on par with likelihood methods.
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Laurent Jacob @laurentjacob.bsky.social · 24/06/2024
Phyloformer uses self-attention to progressively share information among and between sequences. This choice makes our function invariant to the order of the input sequences (any order yields the same output phylogeny).
A visual justification of permutation invariance: two sequence alignments that are identical up to a permutation must lead to the same phylogeny.
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Laurent Jacob @laurentjacob.bsky.social · 24/06/2024
Once trained, Phyloformer provides estimates of all evolutionary distances given the sequences. But each of these distance estimates is informed by the entire set of sequence, not just the corresponding pair! We then pass them to FastME, a distance method, to obtain a tree.
The inference process of Phyloformer. We use the train network to estimate evolutionary distances from related sequences, and pass these estimates to FastME to build a phylogeny.
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Laurent Jacob @laurentjacob.bsky.social · 24/06/2024
Phyloformer is a learnable function. Its input is a set of sequences, its output is their phylogeny, represented by evolutionary distances between all pairs of sequences. We optimize this function on a large number of (phylogeny, sequences) sampled from the probabilistic model.
The process for training Phyloformer. We sample trees and sequences evolved along these trees from the model under which we want to do inference. We use these examples to train a network that predicts the parameters (evolutionary distances, equivalent to the tree) from an observation (aligned related sequences).
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Laurent Jacob @laurentjacob.bsky.social · 24/06/2024
This is where likelihood-free/simulation-based inference comes into play. Sampling trees and sequences under a probabilistic model is possible under much more complex models, for which likelihood computations would be prohibitive. It's an alternative way to access the model.
A visual justification of simulation-based and likelihood-free inference: under some probabilistic models, computing likelihoods is hard but sampling data is easy.
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Laurent Jacob @laurentjacob.bsky.social · 24/06/2024
Maximum likelihood approaches on the other hand search for the most likely tree jointly over all sequences. This makes them accurate but slow. It also restricts these approaches to simplistic models under which likelihood computations are fast enough.
A visual summary of maximum likelihood approaches for phylogenetic inference. We explore the space of phylogenetic trees to find the one making a given set of related sequences as likely as possible under a chosen probabilistic model of sequence evolution.
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Laurent Jacob @laurentjacob.bsky.social · 24/06/2024
Knowing the evolutionary distances (sum of branch lengths) between all pairs of sequences is enough to recover the tree, by hierarchical clustering. Distance methods rely on this idea, with estimates from pairs of sequences taken separately. This makes them fast but inaccurate.
A visual summary of so-called distance methods for phylogenetic inference. We start from an estimate of evolutionary distances between all pairs of sequences (sums of branch lengths between leaves in the true tree) and build a tree by hierarchical clustering.
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