Very happy to see this out. 👏 @yinanwan.bsky.social
Bogdan Bintu and team.
Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis | free link Science www.science.org/eprint/5MHTM...
Kicking off the AI for Life Sciences course at @institutpasteur.bsky.social today! 🧬🤖
Special thanks to @bonomimax.bsky.social and Ernest Mordret for the co-organization, to the @pasteuredu.bsky.social and all the trainers.
Excited to dive into how algorithms can help us understand life!
PhD position in my team at @pasteur.fr ! The selected canddiate will work on the development of new methods combining biophysicial and machine learning modelling for single-cell multi-omics spatiotemporal data.
emploi.cnrs.fr/Offres/Docto...
New preprint from my team! led by @remitrimbour.bsky.social in collaboration with the @saezlab.bsky.social, we developped ReCoN a new method to model multicellular coordination and its underlying molecular mechanisms.
📜 Paper: lnkd.in/eJ8SfFNH
💻 Code: lnkd.in/e-qx2iNp
Did you miss us? Join us this summer at @netsciconf.bsky.social, where our excellent group of thinkers will explore the role of #NetworkMedicine across different scales!🧬🔁🏥
Submit your contribution by March 3rd: shorturl.at/WC6U3
#NetSci2026 #NetBioMed2026
netbiomed-symposium.github.io
Two postdoc positions opened in my team @pasteur.fr in Paris on the development of machine learning methods for single-cell multi-omics spatiotemporal data.
See the announcement for all details emploi.cnrs.fr/Offres/CDD/U...
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/
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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.
For more infos on the presented works
scPRINT: www.nature.com/articles/s41...
scConfluence: www.nature.com/articles/s41...
STORIES: www.biorxiv.org/content/10.1...
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
