🚨 New pre-print alert! 🚨 Adult neural stem cell state and fate decisions are hidden within transcriptional heterogeneity. To find out how we decoded these heterogeneities to identify a molecularly encoded quiescence cycle, check out the pre-print on bioRxiv! doi: doi.org/10.64898/202...

Congratulations to superstar and awesome colleague Gaëlle Letort @gaellel.bsky.social, bioimage analyst extraordinaire for THE CRYSTAL MEDAL OF THE CNRS 2026!!! 🥳🎉🕺🦄🥳 We work with amazing people www.insb.cnrs.fr/fr/personne/...

sPYce is now published in Nature Ecology and Evolution! sPYce is a method to integrate single-cell regulatory data across species, without requiring whole-genome alignments between species. More below ⬇️ www.nature.com/articles/s41...

📢Join us for the Spatial-Cell-ID #spatialOMICs Summer School, September 13-18th 2026, at the Centre Paul-Langevin in Aussois, in the French Alps! You can find the full scientific program, our speakers, and the application form on our website: spatial-cell-id.github.io/scid2026/ Please share!

SCID 2026

Using Spatial OMICs to uncover cell identity during developmental processes 13-18 September 2026 Aussois, France

spatial-cell-id.github.io

📢 We are recruiting! We are looking for postdoctoral researchers to join my team at @pasteur.fr (research.pasteur.fr/en/team/mach...). We develop AI methods to infer cellular dynamics and gene regulation. If you are interested, send me an email with your CV. We look forward to hearing from you!

Machine Learning for integrative genomics – Research

Single-cell high-throughput sequencing, a major breakthrough in life sciences, allows to access the integrated molecular profiles of thousands of cells in a single experiment. This abundance of data p...

research.pasteur.fr

🚨 New preprint from the lab out! Led by Jules Samaran, we present CHAMPOLLION, a new method designed for bridge integration, i.e. aligning unimodal datasets using a paired multi-omic reference. 📄 Preprint: www.biorxiv.org/content/10.6... 💻 Code: github.com/cantinilab/c...

Our study on shape diversity in cnidarians is now published. The final version includes extensive new data that substantially extend the original bioRxiv preprint. Congrats to everyone who contributed to this work! www.cell.com/cell/fulltex... @embl.org

Deciphering mechanical determinants of morphological evolution

A comparative analysis of cnidarian larval morphogenesis combined with active surface theory identifies a set of mesoscale mechanical modules that predict species-specific shapes. Manipulating these m...

cell.com

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...

Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis

Gene expression patterns underlie development, but their systematic detection in whole embryos has remained elusive. We introduce a whole-embryo imaging platform using multiplexed error-robust fluores...

science.org

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

insb.cnrs.fr

🔬 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

Creation of new junior research groups at the Institut Pasteur - Call for applications 2026 - Research

The Institut Pasteur is launching an international call to recruit new junior research group leaders leveraging cutting-edge transdisciplinary approaches to exploring infectious diseases, host-microbe...

research.pasteur.fr

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-...

Mid-career Group Leader position in AI in genomics at Institut Pasteur, Paris - Research

Institut Pasteur and the CNRS are launching a call for a mid-career group leader position in AI in genomics. We are looking for an experienced researcher (typically with > 8 years of research experien...

research.pasteur.fr

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

INCEPTION Symposium 2025 - Research

INCEPTION symposium 2025 - Focus on GWAS: paving the way for the future of genetics.

research.pasteur.fr

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...

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.

nature.com

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

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.

nature.com

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!

Rémi Trimbour - MD-PhD student@remitrimbour.bsky.social · 10mo ago

Very happy to see this work finally online 🥳 It was really interesting to write a short manuscript mixing method presentation & broader insights on data preprocessing. 📝 Thank you to my co-supervisors @cantinilab.bsky.social & @juliosaezrod.bsky.social for their feedback on this side work! 🫶 5/5

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...

SPONGE: simple prior omics network GEnerator

AbstractSummary. Gene regulatory networks modelled from experimental data can be improved through the use of prior biological knowledge, e.g. transcription

academic.oup.com

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

Anaïs Baudot@anaisbaudot.bsky.social · last yr.

Excited to share David Hirst's PhD work! 🧬 When you only have a few datasets available for multi-omics integration, for instance because you work on rare diseases, one solution is Transfer Learning. Introducing #MOTL - now available in Genome Biology! doi.org/10.1186/s130...

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

NetBio COSI@netbio.bsky.social · last yr.

🚨 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.

🚨 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...

Group Leader (282908) | University of Oslo

Job title: Group Leader (282908), Employer: University of Oslo, Deadline: Monday, September 8, 2025

jobbnorge.no