Very excited to share our latest paper, in which we developed an approach to answer a central question: Is cell fate more dependent on a cell lineage or a cell direct neighbors?

Surprisingly, when analyzing single cell trajectories, we showed that C. elegans exhibit both

Are you passionate about the mathematics of data science, computational geometry and topology and want to apply your skills to a beautiful biological question?

Come do a PhD with us!

You will help us understand of how boundaries are established and maintained in early heart development.

Congratulations to Dr @baalberti.bsky.social !! 🎉
And many thanks to his jury members @randersson.bsky.social @arnausebe.bsky.social @olivier-gandrillon.mastodon.social.ap.brid.gy Marie Sémon Anouck Necsulea and co-supervizor @paulvilloutreix.bsky.social

It was an honor to present my work to @arnausebe.bsky.social nausebe.bsky.social , @randersson.bsky.social ersson.bsky.social, Marie Sémon, Anamaria Necsulea, and @olivier-gandrillon.mastodon.social.ap.brid.gy

A big thank you to the two teams I worked with, under the supervision of @yghavi.bsky.social and @paulvilloutreix.bsky.social. Thank you all for your support over the years. Now I can relax until the next step!

It's done! I am now a PhD for real!

I defended my PhD thesis last week and what an incredible day it was. I am very grateful to all the members of @igflyon.bsky.social who made these last 4 years and 8 months so memorable. I will cherish all these memories 😊

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.

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

Promoter-proximal gatekeepers restrict pleiotropic enhancer inputs to achieve tissue specificity Developmental enhancers are central regulatory elements that can activate multiple genes, yet how they selectively regulate one gene over its neighbours remains unclear. Using the Drosophila twist E3 ...

Ever wondered what drives enhancer-promoter specificity? Why would an enhancer activate one gene rather than another neighboring one?

Check our latest preprint, led by @mmasoura.bsky.social, to find out!
www.biorxiv.org/content/10.1...

Merci au @cnrsbiologie.bsky.social de mettre en avant notre travail! @baalberti.bsky.social @paulvilloutreix.bsky.social
@igflyon.bsky.social @ensdelyon.bsky.social

🚨 Our paper is out! 🚨
Check how spatial-scERA can predict enhancer activity in a virtual Drosophila embryo.
Very proud of this first step in the research world published in @narjournal.bsky.social
Thanks to @yghavi.bsky.social, @paulvilloutreix.bsky.social and all the scientists who made it real!