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

Great program, amazing scientists and beautiful facilities!! I visited for 6 months in 2023, a unique place in Europe at the intersection of maths, computer science and developmental biology

🧬 Excited to share Nicheformer out now in Nature Methods! A transformer foundation model linking single-cell & spatial omics, learning spatial context from gene expression to map tissue organization. Led by Ale Tejada & Anna Schaar 👏 👉 www.nature.com/articles/s41...

Thrilled to share my main postdoc work with @jamesbriscoe.bsky.social We used genomic barcoding + scRNAseq in chick & human embryos to reveal a lineage architecture that reshapes how we understand neural tube development & cell fate decisions 🧵👇 www.biorxiv.org/content/10.1...

Had a very nice time visiting Granada for the annual heart ICDAR meeting! We presented Harshit Pateria's current work in collaboration with Robert Kelly following up from our recent publication on the second heart field www.nature.com/articles/s41...

Wow @gioelelamanno.bsky.social & @giodang.bsky.social

Pleasure to announce the program of my new series of lectures at the College de France in Nov-Dec. Continuing on the theme of Biological information. I will focus on the computational aspects, building on David Marr's tri-level of analysis in biological systems. YouTube link sent when it starts.

🤩👍🏼💪🏼 Meet #TopoSPAM - a high-performance simulation platform for biological morphogenesis with a friendly Python interface. @tudresden.bsky.social @csbdresden.bsky.social @mpi-cbg.de. Solve both continuous and discrete active mechanics! Released today: arxiv.org/abs/2509.24905

Very elegant and efficient methodology to recover spatial patterns from multi-modal spatial datasets 👌!! Many congratulations @paulvilloutreix.bsky.social and to all authors👏😀!!

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.

Are digits modified fins, or evolutionary innovations? Read how we tackled this old question from a new angle🧪 A story with @chasebolt.bsky.social, @homeobox.bsky.social and myself, coordinated by @denisduboule.bsky.social from @college-de-france.fr and published in @nature.com today! #InHoxWeTrust

Very happy to share MODIS - a new Multi-Omics Data Integration method for Small and unpaired datasets! We solve a long-standing problem in the field: how to perform data integration for small unpaired datasets Our solution: learning with class imbalance on both reference and target datasets!

#PressRelease 🗞️ The 2025 CNRS Gold Medal has been awarded to Stéphane Mallat, recognised the world over for his research on mathematics applied to signal processing and artificial intelligence. 👉 cnrs.fr/en/press/bet... #CNRStalents 🏅

Springboard for an international scientific career! 🧬🧪🔭⚛️🧠🌱 Call for #MaxPlanckResearchGroups launched; applications are possible until October 14, 2025 www.mpg.de/max-planck-r... #ScienceCareer

Become a Theory Fellow at Janelia. 🔍 Use computation & theory to tackle biological problems. 🖥️ Leverage state-of-the-art computational infrastructure 🤝 Collaborate across scientific disciplines Apply by Nov. 3 @ https://janelia.link/theoryfellowprogram

Are you an AI expert who wants to stay in academia and change the world by understanding the most complex things we know - living organisms? Want to lead your own group, based in Heidelberg DE, working language English? @embl.org is hiring in AI embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

Places available in our online courses this autumn: @embo.org Project Management (17-19.09), Negotiation for Scientists (18-19.09), Lab Leadership for Postdocs (07-09.10) and for Group Leaders (04-06.11) + Self-Leadership (14-16.10). Register now: www.embolableadership.org/our-courses/ #EMBOLabLead

Dresden researchers @paveltomancak.bsky.social @bruvellu.bsky.social, Carl Modes, @cuencam15.bsky.social ‬ & colleagues published in @nature.com that a tissue fold in fruit fly embryos buffers mechanical stresses & may have evolved in response to mechanical forces. www.mpi-cbg.de/news-outreac...

📢We're #hiring Group Leaders! Apply to lead a lab at Janelia & advance biology using theory, computational modeling & machine learning. 🔹5-year renewable appointment 🔹Pioneer new tools & approaches 🔹Collaborate across disciplines Apply by Nov. 4👉 https://janelia.link/groupleader

🧬🔬🧪 🎉 Our team at @czbiohub is thrilled to share TWO companion papers out today in @NatureMethods! 📦 Ultrack — robust, scalable nD cell tracking 🌐 inTRACKtive — a beautiful, open-source web viewer for lineage exploration Let’s dive in! 👇 www.nature.com/articles/s41... www.nature.com/articles/s41...

We’re looking for curious, innovative science leaders at EMBL Heidelberg! 🔬🧬🦠 Join a vibrant, interdisciplinary community where collaboration and innovation are nurtured at all levels. Take a look at these four open positions 👇

🌐 EMBL’s new initiative is set to transform life science research through full AI integration – from genomics to drug discovery. 💡 Funding from the Hector Foundation is dedicated to attracting interdisciplinary talent, boosting infrastructure, training, & innovation. www.embl.org/news/connect...

#DBfeature #Celegans🪱 Left/right asymmetrically expressed ephrin and Flamingo proteins regulate lateralized axon growth in C. elegans by Khulganaa Buyannemekh, Paul Villoutreix, Vincent Bertrand www.sciencedirect.com/science/arti...

Très fier d'avoir pu contribuer à ce beau projet!

Great collaboration with fantastic colleagues :-) @paulvilloutreix.bsky.social, @cantinilab.bsky.social, Morgane Térézol, and Matthieu Vignes.

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...

🚨 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!

Preprint alert! Want to hear more about the coolest new society on the block? You should check out our new preprint discussing @globias.bsky.social ! Hop into 🧵 for a couple quick highlights (1/x):

Spatial Transcript Omics DataBase (STOmics DB) is a comprehensive repository of literature and Datasets related to spatial transcriptomics topics, and provides convenient tools for Data analysis, search and visualization. db.cngb.org/stomics/

What a nice week at CIRM in Marseille for the workshop "Mathematics of Single-Cell Data Analysis", organized by PEPR Digital Health and PEPR MathVives. So many exciting mathematical approaches covering GRN inference, statistical testing and optimal transport. Looking forward to the next edition!

Very happy to see our paper on nested genes published! Very nice interdisciplinary collaboration with the Bertrand lab @ibdm.bsky.social - very combination of scRNASeq + smFISH to explore a fascinating question => www.sciencedirect.com/science/arti...

🥇Sham Tlili has been awarded the CNRS 2025 Bronze Medal! She studies how physical forces shape living tissues by using mouse stem cell models known as gastruloids. A unique blend of physics & biology. 🔗 Read more: www.ibdm.univ-amu.fr/sham-tlili-w...

Novel Research in Biological Artificial Intelligence: Expressions of interest and nominations for a Max Planck Director to lead research in the field of Biological Artificial Intelligence @mpi-cbg.de and @csbdresden.bsky.social. More information: www.mpi-cbg.de/news-outreac...

Pas de Wikipédia, pas de chocolat 😉.

🚨 Calling all plant modelling enthusiasts! Plant Computational Biology Workshop Open to researchers at all levels Workshop is free. Participants cover own travel, food & accommodation 📅 8-12 Sept | 💻 Talks, tools & hand-on sessions 🔗 www.slcu.cam.ac.uk/computationa... #ComputationalBiology #PlantSci

Why wait for #FluorescenceFriday if you can have a neat #zebrafish right now. (pic credit Amanda Garfield @cudevbio.bsky.social) #devbio

What is possible in the space of organs, organoids and organisms? How can synthetic biology help designing new types of tissues and even novel organs? How can cognition be engineered from scratch? Check our paper @jordiplam.bsky.social @drmichaellevin.bsky.social www.nature.com/articles/s41...

Our latest work - MODIS: Multi-Omics Data Integration for Small and Unpaired Datasets - was in Singapore for the www.lmrl.org workshop at ICLR. Congrats Daniel Lepe-Soltero!! Preprint: arxiv.org/abs/2503.18856

Our 3D study of the tumor microenvironment is finally out! Play around with the data yourself at lung-3d-browser.mdc-berlin.de (Kudos to @danilexn.bsky.social👏 ) Many thanks to Nikolaus Rajewsky lab at @mdc-bimsb.bsky.social and everyone involved, it takes a village to raise a multimodal paper!

Excited to see scPRINT published in @natcomms.nature.com ! scPRINT is a large cell model for the inference of gene networks pre-trained on 50Mcells with innovative pretraining tasks inspired from biology. Work led by @jkobject.com

New method for identifying spatially variable genes in spatial transcriptomics. We use spectral graph theory to extract 1D curves related to tissue morphology, creating a more relevant coordinate system. Improves sensitivity. with @PhillipNicol et al. www.biorxiv.org/content/10.1...

Some advertisement for a very nice science-related event in Marseille! I was in the public last year, it was great! I will be on stage this year, hopefully it will be good as well :) - on 29th of April at 5pm or 8:30 pm in Espace Julien and livestream! (In french)

Les inscriptions pour les Treize Minutes Marseille 2025 sont ouvertes ! treize.lis-lab.fr

Very elegant approach on a difficult question! Congratulations Paul @paulvilloutreix.bsky.social and to the whole team👏!!

Congrats @paulvilloutreix.bsky.social 🎉🥂https://bsky.app/profile/paulvilloutreix.bsky.social/post/3ll6oyjokrc2r

Very happy to share our new preprint "MODIS: Multi-Omics Data Integration for Small and Unpaired Datasets"! We proposed a new coupled variational auto-encoder architecture to solve the problem of data integration for small and unpaired datasets (diagonal integration) arxiv.org/abs/2503.18856

To find out more about the work, we spoke to first author Christopher De Bono, and to co-corresponding authors Stéphane Zaffran and Heather Etchevers @etche.bsky.social (Team Leaders at Marseille Medical Genetics in Aix Marseille University, France): journals.biologists.com/dev/article/...

Thank you @paulvilloutreix.bsky.social !! And to the future of 'physics-informed spatial biology' 😉!

Beautiful work, congratulations !!