Laura Cantini

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

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...

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

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 poster of the Physics & Life days, division of the French Physical Society.

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

Bonsai: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data Single-cell omics methods promise to revolutionize our understanding of gene regulatory processes during cell differentiation, but analysis of such data continues to pose a major challenge. Apart from...

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