Hallou Lab
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halloulab.bsky.social
Hallou Lab
@halloulab.bsky.social
Group of Adrien Hallou @kiroxford.bsky.social @ox.ac.uk
Biophysics & spatial biology of cell fate decisions & tissue dynamics
Alumnus @cam.ac.uk‬ & @normalesup.bsky.social
Franco-British Young Leader 2024 🇨🇵🇬🇧
Pinned
Celebrating the 1st anniversary [email protected] @KirOxford @uniofoxford.bsky.social 🥳🍾!! So grateful to be working with these amazing young scientists !
Watch this space in the next few weeks for:
- Exciting new science ⚙️🧬💻🔬
- An official lab picture (minus🍕🍻😆)
- Job openings 😉
Reposted by Hallou Lab
Very happy to share video of 1st lecture @college-de-france.fr on Biological computation 😊. I defend the necessity to access Algorithmic & Computational levels of analysis in cell & developmental biol. proposed by David Marr in neuroscience. Logic & Function matter 🤩.
Video: tinyurl.com/55yejk5f
Qu’est-ce que l’information biologique (suite) ? (1) - Thomas Lecuit (2025-2026)
Enseignement 2025-2026 : Qu’est-ce que l’information biologique (suite) ? Cours du 20 décembre 2025 : Introduction : approche computationelle du vivant Professeur : Thomas Lecuit Chaire Dynamiques du vivant Retrouvez les enregistrements audios et vidéos du cycle : https://www.college-de-france.fr/fr/agenda/cours/qu-est-ce-que-information-biologique Tous les enseignements du Pr Thomas Lecuit : https://www.college-de-france.fr/chaire/thomas-lecuit-dynamiques-du-vivant-chaire-statutaire https://www.youtube.com/playlist?list=PLOj9pZ2YNGZ84uMY6DhPnqpL1rq5qNAVJ Le Collège de France est une institution de recherche fondamentale dans tous les domaines de la connaissance et un lieu de diffusion du « savoir en train de se faire » ouvert à tous. Les cours, séminaires, colloques sont enregistrés puis mis à disposition du public sur le site internet du Collège de France. Découvrez toutes les ressources du Collège de France : https://www.college-de-france.fr Soutenir le Collège de France : https://www.fondation-cdf.fr/faire-un-don Suivez-nous sur : Threads : https://www.threads.net/@collegedefrance Bluesky : https://bsky.app/profile/college-de-france.fr Facebook : https://www.facebook.com/College.de.France Instagram : https://www.instagram.com/collegedefrance LinkedIn : https://fr.linkedin.com/company/coll%C3%A8gedefrance
tinyurl.com
November 24, 2025 at 9:42 AM
En route to Lyon, capital of French gastronomy 🍽️🍷, and stem cell research🔬🧫🧬(for this week)!

Very excited to participate to the 7th #FSSCR Meeting and present our most recent work on spatial #mechanomics!

Thank you @bardinlab.bsky.social @jdevos.bsky.social & to all organisers for the invitation!
The 7th #FSSCR Annual Meeting is starting today!
Welcome to all of you.
✨🔬 Exciting #StemCell science ahead!
Lyon, Nov 17–19, 2025

Full program here 🫵
buff.ly/kLeH5ET
November 17, 2025 at 10:49 AM
Reposted by Hallou Lab
A lovely example of the interplay of morphogen dynamics, tissue mechanics, cell mechanics and signal transduction at the most crucial stage of embryogenesis. And a good example of why talk of development being "programmed" into the genome is simply the wrong language.
www.cell.com/cell-stem-ce...
Crosstalk between tissue mechanics and BMP4 signaling regulates symmetry breaking in human gastrula models
Brivanlou and colleagues used optogenetics to spatially control BMP4 expression in human stem cell models across different mechanical regimes. By combining these experiments with mathematical modeling...
www.cell.com
November 6, 2025 at 8:56 PM
Reposted by Hallou Lab
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: 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
Reposted by Hallou Lab
Really excited to present the results of a fantastic collaboration with Jesse Veenvliet @jesseveenvliet.bsky.social @mpi-cbg.de @poldresden.bsky.social 🤩

We find a unique mechanism for body axis elongation in mammals, different from other vertebrate species

➡️ www.biorxiv.org/content/10.1...
October 28, 2025 at 8:25 AM
Reposted by Hallou Lab
I am absolutely delighted to share the invited speakers for our upcoming @bsdb.bsky.social "Molecules to Morphogenesis" meeting!

Registration and abstract submission is now open - join us!

bsdb.org/meetings/

March 23-26, 2026 - UK
October 23, 2025 at 5:25 PM
Reposted by Hallou Lab
1/ 🎉Excited to share our new preprint @vignjeviclab.bsky.social @davidbrueckner.bsky.social :

"Self-organization of tumor heterogeneity and plasticity"
biorxiv.org/content/10.1...

Tumor heterogeneity and plasticity drive metastasis and relapse. How is tumor patterning coordinated?

A thread👇
October 16, 2025 at 9:55 PM
Reposted by Hallou Lab
Awesome talk by @halloulab.bsky.social at #EMBLSpatialBiology. May the force be with you in biophysical phenotypes of spatial transcriptomics; out now in @natmethods.nature.com: www.nature.com/articles/s41... 🧪
A computational pipeline for spatial mechano-transcriptomics - Nature Methods
The authors present a computational framework that leverages mechanical force inference and spatial transcriptomics to enable analyses of the interplay between the transcriptomic and mechanical state.
www.nature.com
October 15, 2025 at 1:58 PM
Reposted by Hallou Lab
New preprint from the lab! We discovered a transient fluidization in the basal region of human forebrains by tracking microdroplets in cerebral organoids.This “basal fluidization”, absent in gorilla and mouse, may contribute to greater surface expansion in human forebrains
1/
doi.org/10.1101/2025...
October 8, 2025 at 1:05 PM
Delighted that the Nobel Prize for Physics has been awarded to Professor John Clarke FRS, an alumnus of my old Cambridge College @darwincollegecam.bsky.social ! John was the first president of the Darwin Student Association and is the seventh Nobel Prize laureate in the College's 60-year history !
Enormous congratulations to Darwin alumnus Professor John Clarke, who has been jointly awarded the Nobel Prize for Physics.

John joined Darwin in 1965, as one of our first PhD students. He became an Honorary Fellow in 2023.

www.darwin.cam.ac.uk/news/alumnus...
October 7, 2025 at 5:39 PM
John was a true gentleman scientist. I remember how he took time to speak to me after my first talk as a postdoc @gurdoninstitute.bsky.social & his enthusiasm when he told me one morning he was excited to do his "1st single-cell experiment" while queuing behind me at the ice machine! Vale Sir John!
Very sad news, John Gurdon has died.

A developmental biologist's developmental biologist, Nobel prize winner

His work is the foundation of much of today's dev & stem cell bio.

An inspiration to many, including me. Always asking questions & wanting the answers

www.magd.cam.ac.uk/news/profess...
Professor Sir John Gurdon FRS (1933-2025) | Magdalene College
Magdalene College is deeply saddened to announce the death of Professor Sir John Gurdon FRS, who served as Master of the College from 1995 to 2002.
www.magd.cam.ac.uk
October 7, 2025 at 5:20 PM
Reposted by Hallou Lab
Latest from ours: www.cell.com/cell-reports...

This is two stories in one: a case study/cautionary tale on developing genetic tools in new organisms, and the first hint at a gene regulatory network for choanoflagellate multicellular development (which turn out to involve a Hippo/YAP/ECM loop!) A 🧵
October 5, 2025 at 10:35 AM
Reposted by Hallou Lab
Can pressure gradients persist over long timescales in animal cells? We induced intracellular pressure gradients and examined the resulting flows in single cells. We reveal surprisingly long lasting pressure gradients.

More here: elifesciences.org/reviewed-pre...
elifesciences.org
September 29, 2025 at 8:45 AM
Reposted by Hallou Lab
🧵 I've been meaning to write a #Skytorial on our recently posted prepring in which we show evidence that the Golgi 🥞 is a mechanoresponsive organelle. Extracellular mechanical forces also tune Golgi export capacity! 👉 www.biorxiv.org/content/10.1...
Mechanical forces stimulate Golgi export
Human cells face a wide range of external mechanical stimuli that vary with cell type, state, and pathological conditions. The rapidly growing field of mechanobiology investigates how cells sense and ...
www.biorxiv.org
September 22, 2025 at 5:04 PM
Reposted by Hallou Lab
How do #stemcells integrate information to coordinate fate decisions? Delighted to finally see our work showing how growth factors regulate the mechano-osmotic state of the #nucleus and #chromatin to control #pluripotency exit out! www.nature.com/articles/s41... see 🧵 👇
Mechano-osmotic signals control chromatin state and fate transitions in pluripotent stem cells - Nature Cell Biology
McCreery, Stubb et al. show that mechano-osmotic changes in the nucleus induce general transcriptional repression and prime chromatin for cell fate transitions by relieving repression of specific differentiation genes.
www.nature.com
September 29, 2025 at 4:45 PM
Reposted by Hallou Lab
So proud of the exciting story from my PhD student Jakub Sumbal on contractile fibroblasts shaping branching morphogenesis!
Fantastic collaboration with the lab of Zuzana Koledova in Prague!
@sumbalovakoledova.bsky.social

It just came out online, check it out here:
rdcu.be/eIIKD
Contractile fibroblasts form a transient niche for the branching mammary epithelium
Nature Communications - Fibroblasts represent a heterogenous cell population but how their differences reflect their plasticity and origin is not fully understood. Here, the authors map the origin...
rdcu.be
September 29, 2025 at 4:34 PM
Reposted by Hallou Lab
Absolutely delighted to host Dr Jenna Cash from @edinburgh-uni.bsky.social for our next @kiroxford.bsky.social External Seminar on Monday 29 September at 12 pm !

Please join us if you want to learn more about how the most recent spatial omics technologies can be used to understand skin biology!
On Monday 29 September, Dr Jenna Cash from the University of Edinburgh will visit us to talk about "Derailed Cellular Choreography in the Skin Ulcer Niche: Roadblocks to Repair". Our External Seminars are open to any member of the University of Oxford. Don't miss it! talks.ox.ac.uk/talks/id/743...
September 26, 2025 at 12:21 PM
Reposted by Hallou Lab
Now out in final published form - with a new title "Mechanical control of cell fate decisions in the skin epidermis" and simulations/quantifications! See below for thread of how unbalanced tensions can bias fate choices in minimal 3D models of tissues! www.nature.com/articles/s41...
Happy to share the latest work from Preeti Sahu, with Adriana Sanchez-Danes on the biomechanics of cell fate choices during tumor initiation! We implement/test a 3D vertex model with proliferation and fate choices for multilayered tissues! See 🧵 below (1/n) bit.ly/3ZXxJzk
September 26, 2025 at 2:14 PM
Absolutely delighted to host Dr Jenna Cash from @edinburgh-uni.bsky.social for our next @kiroxford.bsky.social External Seminar on Monday 29 September at 12 pm !

Please join us if you want to learn more about how the most recent spatial omics technologies can be used to understand skin biology!
On Monday 29 September, Dr Jenna Cash from the University of Edinburgh will visit us to talk about "Derailed Cellular Choreography in the Skin Ulcer Niche: Roadblocks to Repair". Our External Seminars are open to any member of the University of Oxford. Don't miss it! talks.ox.ac.uk/talks/id/743...
September 26, 2025 at 12:21 PM
Reposted by Hallou Lab
Are you interested on how regenerating tissues transit between stages? Am sharing here our work showing that during #Xenopus tail regeneration, tissue stiffening activates a Piezo1-Yap1 mechanosensitive cascade to allow wounded epithelia to transit into regenerative states!
September 23, 2025 at 7:39 PM
Reposted by Hallou Lab
Development does not happen in isolation! Material properties, geometry, stiffness, fluid flows...can all steer how development unfolds. If you’re exploring these kinds of questions, we’d love to see your work @dev-journal.bsky.social
More info below ⬇️
📢Call for papers. Submit your latest research to our upcoming special issue – The Extracellular Environment in Development, Regeneration and Stem Cells

Guest Editors: Alex Hughes and Rashmi Priya

📅 Deadline: 1 March 2026

journals.biologists.com/dev/pages/ex...

#DevBio
September 19, 2025 at 9:48 AM
Reposted by Hallou Lab
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
Reposted by Hallou Lab
We only had a very minor contribution to this story with Alexis, but definitly worth a reading for those interested by patterning, precision and refinment. Nice combining of quantitative live imaging, modeling and optogenetics to dissect vein patterning dynamics
www.cell.com/developmenta...
Signaling-dependent refinement of cell fate choice during tissue remodeling in Drosophila pupal wings
Herszterg et al. show that during morphogenesis of the Drosophila pupal wing, a wave of Notch signaling activity updates cell fates to ensure robust and precise patterning of wing veins.
www.cell.com
September 19, 2025 at 8:35 AM
Reposted by Hallou Lab
Fresh from the press💥 We asked what happens when you evolve gene regulatory networks computationally at scale. Do general principles of GRN evolution jump out? Is the process predictable? Read on to find out @prxlife.bsky.social @crick.ac.uk @ucl-ipls.bsky.social 👉 journals.aps.org/prxlife/abst...
Gene Network Organization, Mutation, and Selection Collectively Drive Developmental Pattern Evolvability and Predictability
The historical order in which mutations appear during evolution determine the evolutionary trajectory of gene regulatory networks and influence how developmental patterns change and diversify over tim...
journals.aps.org
September 16, 2025 at 7:46 PM
Reposted by Hallou Lab
We’re organizing a conference at @ijmonod.bsky.social in Paris, January 2026, in memory of M.P. Sheetz — pioneer in cell mechanics and mechanobiology, co-discoverer of kinesin, and founder of @mbisg.bsky.social. Join us to explore his legacy.

mikeinmemoriam.sciencesconf.org
September 18, 2025 at 8:50 AM