Laura Cantini
@cantinilab.bsky.social
PI of the machine learning for Integrative genomics lab @pasteur.fr and @CNRS.bsky.social
#NewPI #DiversityEqualityInclusion
Single-cell, multi-omics, machine learning
#NewPI #DiversityEqualityInclusion
Single-cell, multi-omics, machine learning
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/Offres/Docto...
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
emploi.cnrs.fr
January 30, 2026 at 9:28 AM
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/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
📜 Paper: lnkd.in/eJ8SfFNH
💻 Code: lnkd.in/e-qx2iNp
lnkd.in
January 29, 2026 at 2:38 PM
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
📜 Paper: lnkd.in/eJ8SfFNH
💻 Code: lnkd.in/e-qx2iNp
Reposted by Laura Cantini
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
Submit your contribution by March 3rd: shorturl.at/WC6U3
#NetSci2026 #NetBioMed2026
netbiomed-symposium.github.io
January 23, 2026 at 2:15 PM
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
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...
See the announcement for all details emploi.cnrs.fr/Offres/CDD/U...
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
emploi.cnrs.fr
January 21, 2026 at 3:51 PM
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...
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...
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...
December 17, 2025 at 2:53 PM
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...
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...
Reposted by Laura Cantini
🧑🎄🎄 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
**One-liner:** a **20M-active-param** single-cell foundation model trained on **350M cells / 16 species / 300 tissues / 500 cell types**.
1/6
December 16, 2025 at 7:48 PM
🧑🎄🎄 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
**One-liner:** a **20M-active-param** single-cell foundation model trained on **350M cells / 16 species / 300 tissues / 500 cell types**.
1/6
Reposted by Laura Cantini
#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
✍️ @cantinilab.bsky.social et @gabrielpeyre.bsky.social
📕 @naturemethods | buff.ly/XJlsK5P
www.insb.cnrs.fr
December 11, 2025 at 4:30 PM
#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
✍️ @cantinilab.bsky.social et @gabrielpeyre.bsky.social
📕 @naturemethods | buff.ly/XJlsK5P
Reposted by Laura Cantini
🔬 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
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
December 8, 2025 at 8:53 AM
🔬 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
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
Reposted by Laura Cantini
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/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
November 27, 2025 at 1:38 PM
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/en/call/mid-...
Reposted by Laura Cantini
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
November 24, 2025 at 7:05 AM
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
Reposted by Laura Cantini
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...
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.
www.nature.com
November 6, 2025 at 4:07 PM
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...
www.nature.com/articles/s41...
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 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.
www.nature.com
November 4, 2025 at 7:25 AM
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 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
Reposted by Laura Cantini
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.
October 15, 2025 at 9:34 AM
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 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
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
September 30, 2025 at 3:39 PM
CIRCE out on biorxiv, give it a try for inferring peak co-accessibility networks from large single-cell data!
Reposted by Laura Cantini
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.
September 19, 2025 at 6:50 AM
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.
Reposted by Laura Cantini
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/
Available here: github.com/gletort/Fish... user documentation: gletort.github.io/FishFeats/
September 4, 2025 at 4:07 PM
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/
Available here: github.com/gletort/Fish... user documentation: gletort.github.io/FishFeats/
Reposted by Laura Cantini
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...
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...
July 27, 2025 at 5:26 PM
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...
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...
Reposted by Laura Cantini
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
July 28, 2025 at 9:46 AM
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
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
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...
🧬 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
July 26, 2025 at 10:55 AM
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
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
Thanks again @anaisbaudot.bsky.social and all #NetBio commitee for the invitation!
@institutpasteur.bsky.social #singlecell #AI #netbio
🚨 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.
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.
July 24, 2025 at 8:47 AM
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
Thanks again @anaisbaudot.bsky.social and all #NetBio commitee for the invitation!
@institutpasteur.bsky.social #singlecell #AI #netbio
Reposted by Laura Cantini
🚨 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...
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
July 22, 2025 at 6:12 AM
🚨 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...
Interested and attending #ISMBECCB2025? Let’s connect!
🔗 www.jobbnorge.no/en/available...
Reposted by Laura Cantini
🚨 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.
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.
July 22, 2025 at 10:49 AM
🚨 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.
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.
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!
July 20, 2025 at 2:05 PM
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!
Reposted by Laura Cantini
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.
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.
📣 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!
🧬 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!
July 3, 2025 at 10:24 AM
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.
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.
