New preprint from my team! Led by @jkobject.com "scPRINT-2: Towards the next-generation of cell foundation models and benchmarks" We perform an additive benchmark of single-cell Foundation Models (scFMs) and we present scPRINT-2 pre-trained on 350 million cells 📝 www.biorxiv.org/content/10.6...

🧑‍🎄🎄 Christmas Foundation Model Release: scPRINT-2 **One-liner:** a **20M-active-param** single-cell foundation model trained on **350M cells / 16 species / 300 tissues / 500 cell types**. 1/6

#ResultatScientifique🔎| Une nouvelle méthode permet de prédire comment les cellules évoluent et se différencient dans le temps et l’espace. 💻 ✍️ @cantinilab.bsky.social et @gabrielpeyre.bsky.social 📕 @naturemethods | buff.ly/XJlsK5P

🔬 Call to create junior research groups at the Institut Pasteur Focus: Infectious diseases, host-microbe interactions, vaccines Special interest: AI methodologies 📅 Deadline: Feb 9, 2026 👥 2-12 years post-PhD Apply now 📝 research.pasteur.fr/en/call/crea... #JobOpportunity #Research

There a is a joint call between @pasteur.fr and @cnrsbiologie.bsky.social for a mid career group leader position in AI and genomics (or molecular biology). Don't hesistate to spread the word if you know anyone relevant. research.pasteur.fr/en/call/mid-...

The INCEPTION is organizing its Annual Symposium. This year is about GWAS & beyond! We're happy to have @bpasaniuc.bsky.social, @caina89.bsky.social, Iuliana Ionita-Laza , Sriram Sankararaman, and others, who will talk about tools for understanding the genetic determinants of complex diseases

By learning a differentiation potential using an optimal transport-based approach, STORIES models and infers cell fate trajectories using spatiotemporal omics data. @gabrielpeyre.bsky.social @cantinilab.bsky.social www.nature.com/articles/s41...

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

Don't miss the upcoming DBC seminar by @juliosaezrod.bsky.social, head of Research at EMBL-EBI's! (on Friday 24 october at 2pm in Auditorium Jules Bordet for those at Pasteur). Julio will present works on knowledge-based machine learning to extract disease mechanisms from spatial multi-omics data.

CIRCE out on biorxiv, give it a try for inferring peak co-accessibility networks from large single-cell data!

Very happy to introduce jsPCA, a fast and interpretable computational framework for spatial transcriptomics that simultaneously identifies spatial domains and variable genes across multi-slice and multi-sample data.

We (with @nicolasdray.bsky.social @zenlabpasteur.bsky.social) are happy to release officially FishFeats, our #napari plugin to streamline 3D smFish/RNA quantification! 🎊 Available here: github.com/gletort/Fish... user documentation: gletort.github.io/FishFeats/

1 To predict the behaviour of a primate, would you rather base your guess on a closely related species or one with a similar brain shape? We looked at brains & behaviours of 70 species, you’ll be surprised! 🧵Thread on our new preprint with @r3rt0.bsky.social , doi.org/10.1101/2025...

GRN inference algorithms often build on prior knowledge of e.g. TF binding. Build up-to-date priors with our new tool SPONGE, now out in Bioinformatics: academic.oup.com/bioinformati...

MOTL is finally out in Genome Biology! Work led by David Hirst and @anaisbaudot.bsky.social If you are interested in multi-omics matrix factorization when few samples are available (e.g. rare diseases), have a look at it! #multiomics #machinelearning #transferlearning

Going back to Paris after four days of awesome science! Really happy to have contributed to #ISMBECCB2025 with a keynote talk in the @netbio.bsky.social. Thanks again @anaisbaudot.bsky.social and all #NetBio commitee for the invitation! @institutpasteur.bsky.social #singlecell #AI #netbio

🚨 We're hiring! NCMBM @ncmbm.bsky.social is looking for 2 new group leaders to join our vibrant research community. Ready to build your own group with strong support and a solid startup package? Interested and attending #ISMBECCB2025? Let’s connect! 🔗 www.jobbnorge.no/en/available...

🚨 Excited to announce our first keynote for #NetBio 2025: Laura Cantini (@cantinilab.bsky.social)! She is sharing cutting-edge work on multi-modal learning for single-cell data integration, tackling how to combine diverse omics and spatial data to unlock new insights into cellular heterogeneity.

Flying to Liverpool for #ISMBECCB2025 @iscb.bsky.social. This year the lab is well represented with @jkobject.com presenting scPRINT in #MLCSB, Jules presenting two posters at #MLCSB: scConfluence and STORIES. I will finally, give a keynote at #NETBIO. Come to see us at the conference!

Fantastic opportunity to launch your research group following the @embl.org model in a great environment with a solid startup package and access to state-of-the-art resources. Join us at the @ncmbm.bsky.social, part of the @nordicembl.bsky.social, at @uio.no Feel free to reach out if you have Qs.

Two weeks ago, I had the pleasure to discuss the research activity of my team @institutpasteur.bsky.social in the panel discussion "How is AI and data-driven innovation reshaping oncology" at @parissaclay.bsky.social SPRING 2025 in @ecolepolytechnique.bsky.social #ParisSaclaySPRING #SPRING25

Kicking off our afternoon session, @cantinilab.bsky.social discusses her dual approach to capture both multi-modal dimensionality reduction and molecular network inference. She gave a very nice overview of her work! #NetBioMed2025 #NetSci2025 @verapancaldi.bsky.social

Before lunch break Elma Dervic gave us a very quick talk on how to build comorbidity networks from data. I loved her visualization through time. More amazing talks at #NetBioMed2025 after lunch, so stay tuned! #NetSci2025 @verapancaldi.bsky.social

After coffee break Anna Niarakis discusses her approach to #digitaltwins, a novel conception to treat complex human pathologies. If we haven't been able to build artificial agents capable of openended evolution, can we truly build biological digital twins? #NetSci2025 #NetBioMed2025

Now @lmrocha.bsky.social goes deeper into the #digitaltwins paradigm, discussing how to build multiscale models for this purpose. What's the temporal limit when building these complex models? Can we build something as complex as biological architectures? #NetBioMed2025 #NetSci2025

Iker Nuñez-Carpintero shows us his integrative #multilayer approach to explore rare neuromuscular disorders. Particularly he's focusing on cardiac and skeletal muscle myopathies. Join us at #NetBioMed2025, a @netsciconf.bsky.social satellite at #NetSci2025!

Kristel Van Steen kicks off our #NetBioMed2025 Satellite discussing how to use #networkscience to develop individual medical networks, going towards personalized medicine! @netsciconf.bsky.social @verapancaldi.bsky.social

Our second talk of the day corresponds to Natasa Przulj, who gave us a detailed explanation on how to use #AI techniques in order to build #complexnetworks based on multi-omics! #NetBioMed2025 #NetSci2025 @verapancaldi.bsky.social

@netsciconf.bsky.social crossing Holland on my way to Maastricht for @netbiomed2025.bsky.social Join us tomorrow at FASOS for a great day of network biomedicine talks!

Super cool to see scPRINT, work of my team led by @jkobject.com, featured by @cnrsbiologie.bsky.social To access the work www.nature.com/articles/s41...

Happy to contribute to this wonderful meeting! Thanks to @silviagrigolon.bsky.social @hugowioland.bsky.social and all co-organizers for the invitation !

Save the date for the 3rd edition of the Physics & Life days, division of the French Physical Society, October 2-3 at the Institute Jacques Monod, Paris. More info coming soon! Co-organised with Silvia Grigolon & Morgan Chabanon. @sfp-physique.bsky.social @ijmonod.bsky.social

Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social. I'm so excited about this! www.biorxiv.org/content/10.1...

Looking forward to @netbiomed2025.bsky.social @netsciconf.bsky.social thanks @verapancaldi.bsky.social and all organizers for the invitation!

How can we design #machinelearning methods able to co-analyze the numerous available #omics data and translate them into actionable biological knowledge? @cantinilab.bsky.social will answer this and other exciting questions related to single-cell data integration! #NetBioMed2025 #NetSci2025

Our new call for VIB.AI group leaders is online! Junior and senior positions available to develop innovative ML methods in biology. With professorship at CS or Medical Faculty. Deadline 14th June. DM for more info.

🚨 Two PhD positions available in the lab of @arnaumontagud.bsky.social in I2SysBio 🇪🇸. Both are related to simulations of biological tissues

📢 Exciting news! We will soon open two PhD positions at @i2sysbio.bsky.social @csic.es, in research projects in collaboration with the @bsc-cns.bsky.social. Both are related to tools to simulate biological tissues. Here’s the description of the open positions. #PhDpositions #PhDOpportunities 👇

🚨 New preprint: Topography Aware Optimal Transport for Alignment of Spatial Omics Data We present our new alignment framework TOAST www.biorxiv.org/content/10.1...

[email protected] @cantinilab.bsky.social @gabrielpeyre.bsky.social present a foundation model trained on 50 million cells, generating a meaningful gene network with zero-shot ability. #AIxBio @natcomms.nature.com www.nature.com/articles/s41...

Excited to see scPRINT published in @natcomms.nature.com ! scPRINT is a large cell model for the inference of gene networks pre-trained on 50Mcells with innovative pretraining tasks inspired from biology. Work led by @jkobject.com

📢 permanent research engineer position as leader of the Hub Algorithmics & AI pole at the Institut Pasteur. Come and join us! More details on research.pasteur.fr/en/job/perma...

Last day of our "AI for Life Sciences" course @pasteuredu.bsky.social This morning we talk about Intellectual Property & AI with Nicolas Torno and Helene Chommy from DARRI @pasteur.fr

We are welcoming applications to the 8th edition of the International Curie Course on Computational Systems Biology of Cancer, to be held in Paris, September 22-26, 2025. This year the focus will be on multimodal data analysis and network modelling to master cancer hallmarks. 👇 tinyurl.com/57d4ed2v

Final thematic session of our "AI for Life Sciences" is "AI in Neuroscience" with Jean-Baptiste Masson @pasteur.fr @pasteuredu.bsky.social

It is now time for "AI in Structural Biology" with Guillaume Bouvier: AlphaFold and beyond! Short talks by @bardiauxb.bsky.social Ludovic Sauguet Vincent Schnapka and @duyvd.bsky.social @pasteur.fr @pasteuredu.bsky.social

AI for life sciences day 2 started! @m-albert.bsky.social is now teaching AI for image analysis. Felipe Llinares from Bioptimus will then talk about LLMs, with short talks from @jkobject.com from my team and @emordret.bsky.social from @audeber.bsky.social team. @pasteur.fr @pasteuredu.bsky.social

We are back with our "AI for life sciences" course @pasteur.fr @pasteuredu.bsky.social with a deep dive into Neural Networks with @vincentmallet.bsky.social

🧬If you work with @10xgenomics.bsky.social Xenium, this might be of your interest. Our new study on Xenium exploration best practice and comparing it with other commercial platforms is now out in @naturemethods.bsky.social www.nature.com/articles/s41...