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
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.
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
#ParisSaclaySPRING #SPRING25
June 4, 2025 at 9:04 PM
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
#ParisSaclaySPRING #SPRING25
Reposted by Laura Cantini
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
#NetBioMed2025 #NetSci2025 @verapancaldi.bsky.social
June 2, 2025 at 12:27 PM
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
#NetBioMed2025 #NetSci2025 @verapancaldi.bsky.social
Reposted by Laura Cantini
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
June 2, 2025 at 10:33 AM
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
Reposted by Laura Cantini
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
June 2, 2025 at 9:28 AM
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
Reposted by Laura Cantini
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
#NetBioMed2025 #NetSci2025
June 2, 2025 at 10:03 AM
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
#NetBioMed2025 #NetSci2025
Reposted by Laura Cantini
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!
June 2, 2025 at 10:20 AM
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!
Reposted by Laura Cantini
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
@netsciconf.bsky.social @verapancaldi.bsky.social
June 2, 2025 at 7:35 AM
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
@netsciconf.bsky.social @verapancaldi.bsky.social
Reposted by Laura Cantini
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
#NetBioMed2025 #NetSci2025 @verapancaldi.bsky.social
June 2, 2025 at 7:40 AM
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
#NetBioMed2025 #NetSci2025 @verapancaldi.bsky.social
Reposted by Laura Cantini
@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!
June 1, 2025 at 4:34 PM
@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...
To access the work www.nature.com/articles/s41...
#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
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
May 19, 2025 at 8:06 AM
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...
To access the work www.nature.com/articles/s41...