Laura Cantini

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**.
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#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

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...

🔬 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

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...

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-...

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

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

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.

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.

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/

Brain Surfaces of 70 primate species

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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...

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

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

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

🚨 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.

scConfluence: single-cell diagonal integration with regularized Inverse Optimal Transport on weakly connected features - Nature Communications The abundance of unpaired multimodal single-cell data drives the need for improved integration methods. Here, authors introduce scConfluence, a method combining uncoupled autoencoders with regularized...

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

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