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Laura Cantini

@cantinilab.bsky.social
946 followers 245 following 24 posts

PI of the machine learning for Integrative genomics lab @pasteur.fr and @CNRS.bsky.social #NewPI #DiversityEqualityInclusion Single-cell, multi-omics, machine learning

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Reposted by Laura Cantini
Jean-Yves Tinevez @jytinevez.bsky.social · 22/09/2026
I'd like to introduce a piece of work we did for the paper of @ines-ssm.bsky.social and colleagues in the lab of Chiara Zurzolo in @pasteur.fr www.nature.com/articles/s41...
nature.com
Tunneling nanotubes regulate mitochondrial homeostasis between glioblastoma and astrocytes, and between tumor cells in vivo - Nature Communications
Tunneling nanotube-like (TNT) connections allow mitochondrial exchange between tumor cells and its tumor microenvironment. Here, the authors show that TNT connections mediate bidirectional mitochondri...
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Gaëlle Letort @gaellel.bsky.social · 03/09/2026
The final version of the paper presenting our tool EpiCure is now online: journals.biologists.com/dev/article/... !! Thanks again to all collaborators in this project
journals.biologists.com
EpiCure (Epithelial Curation): a versatile and handy tool for curation of epithelial segmentation
Summary: EpiCure is a napari plugin designed to optimise epithelia segmentation and tracking curation through automatic errors detection and ergonomic correction while being easily interoperable with ...
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Levayer Lab @levayerr.bsky.social · 03/09/2026
The last version of our EpiCure tool is now out in @dev-journal.bsky.social, a user friendly Napari plugin for epithelial segmentation curation. A bit thanks to @gaellel.bsky.social for carrying all along this joint department effort (check the details below). Feel free to use it and expand it !
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Zenlabpasteur.bsky.social @zenlabpasteur.bsky.social · 07/07/2026
🚨 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...
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Jean-Yves Tinevez @jytinevez.bsky.social · 09/07/2026
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/...
insb.cnrs.fr
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Camille Berthelot @camilleberthelot.bsky.social · 10/06/2026
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...
nature.com
Alignment-free integration of single-nucleus ATAC-seq across species with sPYce - Nature Ecology & Evolution
This paper presents sPYce, a method that integrates single-nucleus ATAC-seq data across species, allowing for comparison of gene regulatory evolution across species.
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Yad Ghavi-Helm @yghavi.bsky.social · 18/05/2026
📢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!
spatial-cell-id.github.io
SCID 2026
Using Spatial OMICs to uncover cell identity during developmental processes 13-18 September 2026 Aussois, France
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Laura Cantini @cantinilab.bsky.social · 12/05/2026
📢 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!
research.pasteur.fr
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...
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Laura Cantini @cantinilab.bsky.social · 07/05/2026
🚨 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...
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Aissam Ikmi @aikmi.bsky.social · 20/03/2026
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
cell.com
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...
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Alex Schier @schierlab.bsky.social · 12/03/2026
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...
science.org
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...
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Laura Cantini @cantinilab.bsky.social · 09/03/2026
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!
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Laura Cantini @cantinilab.bsky.social · 30/01/2026
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...
emploi.cnrs.fr
Portail Emploi CNRS - Offre d'emploi - PhD (M/F) in development of machine learning methods for single-cell omics data integration
Assurez-vous que votre profil candidat soit correctement renseigné avant de postuler
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Laura Cantini @cantinilab.bsky.social · 29/01/2026
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
lnkd.in
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NetBioMed 2026 @netbiomed2026.bsky.social · 23/01/2026
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
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Laura Cantini @cantinilab.bsky.social · 21/01/2026
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...
emploi.cnrs.fr
Portail Emploi CNRS - Offre d'emploi - Two Postdoctoral (M/F) Positions in the Development of Machine Learning Methods for Single-Cell Multi-Omics Spatiotemporal Data
Assurez-vous que votre profil candidat soit correctement renseigné avant de postuler
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Laura Cantini @cantinilab.bsky.social · 17/12/2025
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...
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Jeremie Kalfon 👨‍💻🧬🤖🚀 @jkobject.com · 16/12/2025
🧑‍🎄🎄 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
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CNRS Biologie @cnrsbiologie.bsky.social · 11/12/2025
#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
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Institut Pasteur | 130 years of biomedical research @pasteur.fr · 08/12/2025
🔬 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
research.pasteur.fr
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...
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Levayer Lab @levayerr.bsky.social · 27/11/2025
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-...
research.pasteur.fr
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...
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Reposted by Laura Cantini
Computational Biology Dpt at Pasteur @pasteur-dbc.bsky.social · 24/11/2025
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
research.pasteur.fr
INCEPTION Symposium 2025 - Research
INCEPTION symposium 2025 - Focus on GWAS: paving the way for the future of genetics.
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Reposted by Laura Cantini
Nature Methods @natmethods.nature.com · 06/11/2025
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...
nature.com
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.
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Laura Cantini @cantinilab.bsky.social · 04/11/2025
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
nature.com
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.
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Computational Biology Dpt at Pasteur @pasteur-dbc.bsky.social · 15/10/2025
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.
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Laura Cantini @cantinilab.bsky.social · 30/09/2025
CIRCE out on biorxiv, give it a try for inferring peak co-accessibility networks from large single-cell data!
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Paul Villoutreix @paulvilloutreix.bsky.social · 19/09/2025
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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Gaëlle Letort @gaellel.bsky.social · 04/09/2025
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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katja heuer @k4tj4.bsky.social · 27/07/2025
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...
Brain Surfaces of 70 primate species
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Mariike Kuijjer @mkuijjer.bsky.social · 28/07/2025
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...
academic.oup.com
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
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Laura Cantini @cantinilab.bsky.social · 26/07/2025
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
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Laura Cantini @cantinilab.bsky.social · 24/07/2025
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
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Anthony Mathelier @amathelier.bsky.social · 22/07/2025
🚨 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...
jobbnorge.no
Group Leader (282908) | University of Oslo
Job title: Group Leader (282908), Employer: University of Oslo, Deadline: Monday, September 8, 2025
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NetBio COSI @netbio.bsky.social · 22/07/2025
🚨 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 · 20/07/2025
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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Anthony Mathelier @amathelier.bsky.social · 03/07/2025
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.
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Nature Reviews Nephrology @natrevneph.nature.com · 19/06/2025
nature.com
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.
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Laura Cantini @cantinilab.bsky.social · 04/06/2025
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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NetBioMed 2026 @netbiomed2026.bsky.social · 02/06/2025
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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NetBioMed 2026 @netbiomed2026.bsky.social · 02/06/2025
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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NetBioMed 2026 @netbiomed2026.bsky.social · 02/06/2025
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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NetBioMed 2026 @netbiomed2026.bsky.social · 02/06/2025
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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NetBioMed 2026 @netbiomed2026.bsky.social · 02/06/2025
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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NetBioMed 2026 @netbiomed2026.bsky.social · 02/06/2025
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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NetBioMed 2026 @netbiomed2026.bsky.social · 02/06/2025
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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Vera Pancaldi @verapancaldi.bsky.social · 01/06/2025
@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 · 19/05/2025
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...
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Laura Cantini @cantinilab.bsky.social · 19/05/2025
Happy to contribute to this wonderful meeting! Thanks to @silviagrigolon.bsky.social @hugowioland.bsky.social and all co-organizers for the invitation !
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Hugo Wioland @hugowioland.bsky.social · 15/05/2025
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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Erik van Nimwegen @erikvannimwegen.bsky.social · 09/05/2025
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...
biorxiv.org
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...
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