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Laura Cantini @cantinilab.bsky.social · 8d

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 · 8d

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

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Reposted by Laura Cantini

Paul Villoutreix @paulvilloutreix.bsky.social · 19d

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.

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Reposted by Laura Cantini

Gaëlle Letort @gaellel.bsky.social · Sep 4

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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Reposted by Laura Cantini

katja heuer @k4tj4.bsky.social · Jul 27

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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...

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Reposted by Laura Cantini

Mariike Kuijjer @mkuijjer.bsky.social · Jul 28

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

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Laura Cantini @cantinilab.bsky.social · Jul 26

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 · Jul 26

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...

MOTL: enhancing multi-omics matrix factorization with transfer learning - Genome Biology

Joint matrix factorization is popular for extracting lower dimensional representations of multi-omics data but loses effectiveness with limited samples. Addressing this limitation, we introduce MOTL (...

link.springer.com

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Laura Cantini @cantinilab.bsky.social · Jul 24

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 · Jul 22

🚨 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.

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Reposted by Laura Cantini

Anthony Mathelier @amathelier.bsky.social · Jul 22

🚨 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

www.jobbnorge.no

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Reposted by Laura Cantini

NetBio COSI @netbio.bsky.social · Jul 22

🚨 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.

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Laura Cantini @cantinilab.bsky.social · Jul 20

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...

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...

www.nature.com

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Laura Cantini @cantinilab.bsky.social · Jul 20

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!

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Reposted by Laura Cantini

Anthony Mathelier @amathelier.bsky.social · Jul 3

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.

Norwegian Centre for Molecular Biosciences and Medicine (NCMBM) @ncmbm.bsky.social · Jun 30

📣 We’re recruiting 1-2 Group Leaders! NCMBM is looking for early-career researchers ready to establish their independent research groups!

🧬 With an attractive start-up package, help us shape the future of molecular biosciences and medicine in 🇳🇴 and be part of the @nordicembl.bsky.social!

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Reposted by Laura Cantini

Nature Reviews Nephrology @natrevneph.nature.com · Jun 19

Leveraging data as a patient–scientist: frustrations and opportunities

Nature Reviews Nephrology, Published online: 19 June 2025; doi:10.1038/s41581-025-00968-9The transition from data scientist to patient–scientist has given me new perspectives into clinical research and strengthened my commitment to open science. Although limitations on data availability have led to frustration, collaboration bodes well for a future in which patients will have access to more personalized information.

www.nature.com

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Laura Cantini @cantinilab.bsky.social · Jun 4

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

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Reposted by Laura Cantini

NetBioMed 2025 @netbiomed2025.bsky.social · Jun 2

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

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Reposted by Laura Cantini

NetBioMed 2025 @netbiomed2025.bsky.social · Jun 2

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

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Reposted by Laura Cantini

NetBioMed 2025 @netbiomed2025.bsky.social · Jun 2

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

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Reposted by Laura Cantini

NetBioMed 2025 @netbiomed2025.bsky.social · Jun 2

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

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Reposted by Laura Cantini

NetBioMed 2025 @netbiomed2025.bsky.social · Jun 2

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!

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Reposted by Laura Cantini

NetBioMed 2025 @netbiomed2025.bsky.social · Jun 2

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

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Reposted by Laura Cantini

NetBioMed 2025 @netbiomed2025.bsky.social · Jun 2

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

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Reposted by Laura Cantini

Vera Pancaldi @verapancaldi.bsky.social · Jun 1

@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!

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Laura Cantini @cantinilab.bsky.social · May 19

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...

CNRS Biologie @cnrsbiologie.bsky.social · May 17

#RésultatScientifique 🔎 Une IA pour lire le langage des cellules ! 🧬

Grâce à scPRINT, des chercheurs décryptent les réseaux de gènes qui contrôlent les états cellulaires à partir de millions de données single-cell.

buff.ly/XMcDog0

scPRINT : le premier modèle d'IA français pour déchiffrer les réseaux génétiques

Chaque cellule est un véritable monde moléculaire.

www.insb.cnrs.fr

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Laura Cantini @cantinilab.bsky.social · May 19

Happy to contribute to this wonderful meeting!

Thanks to @silviagrigolon.bsky.social @hugowioland.bsky.social and all co-organizers for the invitation !

Hugo Wioland @hugowioland.bsky.social · May 15

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

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

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Reposted by Laura Cantini

Hugo Wioland @hugowioland.bsky.social · May 15

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

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