Laurent Jacob
@laurentjacob.bsky.social
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Researcher in statistics and machine learning for genomics
https://laurent-jacob.github.io/
reposted by
Laurent Jacob
Laura Cantini
6 days ago
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
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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.
https://www.nature.com/articles/s41592-025-02855-4
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Very happy about this work on phylogenetic neural inference, led by
@lblassel.bsky.social
:)
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25 days ago
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Laurent Jacob
Alexis Stamatakis
28 days ago
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...
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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.
https://legend2025.sciencesconf.org/
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Laurent Jacob
Camille Marchet ⚡
about 1 month ago
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...
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‘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.
https://www.nature.com/articles/d41586-025-03219-w
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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
about 1 month ago
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Laurent Jacob
Franz Baumdicker
about 2 months ago
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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Laurent Jacob
David A Knowles
2 months ago
#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!
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MLCB - Schedule
The in-person component will be held at the New York Genome Center, 101 6th Ave, New York, NY 10013.
https://www.mlcb.org/schedule
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Laurent Jacob
Camille Marchet ⚡
2 months ago
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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Laurent Jacob
Rayan Chikhi
2 months ago
🌎👩🔬 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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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!
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2 months ago
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Laurent Jacob
CNRS Sciences informatiques
4 months ago
#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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Laurent Jacob
Antoine Limasset
5 months ago
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...
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https://www.biorxiv.org/content/10.1101/2025.06.16.659990v1.full.pdf
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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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5 months ago
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Laurent Jacob
Yun S. Song
5 months ago
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.
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Home - ProbGen 2026
Your Site Description
https://probgen2026.github.io
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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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5 months ago
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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.
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8 months ago
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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
9 months ago
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reposted by
Laurent Jacob
Camila Duitama
9 months ago
🧬 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:
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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
https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaf054/7997265?rss=1
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reposted by
Laurent Jacob
Francis Bach
11 months ago
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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reposted by
Laurent Jacob
Raphael Gottardo
12 months ago
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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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. 🧵
over 1 year ago
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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
almost 2 years ago
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