📢Preprint: Positional information (PI) and information flows in dynamic tissues.
Our mathematical framework quantifies, from data, how the coupled stochastic dynamics of cell positions and properties preserve, degrade and generate PI. @alex-plum.bsky.social www.biorxiv.org/content/10.6...
We have postdoc openings for data-driven modeling and information flows in living systems, with a focus on embryonic development. mattiaserra.com
Requirements: PhD in Physics, Applied Math, or similar; prior exposure to biological data preferred.
Please share with potential candidates. Thank you!
Our study on shape diversity in cnidarians is now published. The final version includes extensive new data that substantially extend the original bioRxiv preprint. Congrats to everyone who contributed to this work! www.cell.com/cell/fulltex...
@embl.org
New preprint from Meri Saez & co
How much information does a developmental landscape encode?
Integrating information theory, dynamical systems & dev bio to quantify the number of signalling regimes that generate distinguishable cell fates
biorxiv.org/content/10.64898/2026.03.03.709461v1
Sometimes, the only way to build back up is to let everything fall apart. This is certainly true at the cellular level. www.quantamagazine.org/break-it-to-...
How can cells use information from neighboring cells to improve the spatial precision of morphogen patterns? 🤔
We show that cells can gain positional information by "talking" to their neighbors - how much depends critically on spatial correlations of the patterns.
buff.ly/w56OUJT
Happy to share our new work from my graduate lab: DynamicAtlas, a morphodynamic atlas of Drosophila development! We develop methods for morphological time alignment of live data. Surprisingly, we find that the kinematics of fly morphogenesis are *very* simple. Enjoy!
www.nature.com/articles/s41...
Great to see this published: Fitting dynamical landscape models to single-cell data, creating interpretable maps of cell decision making & developmental logic
Applied to neural tube patterning, we show how morphogen signals reshape landscapes and drive fate decisions
www.pnas.org/doi/10.1073/...
Here is the link to download the pdf of my 2nd course on complexity and information during development:
tinyurl.com/b7szw7v3
Next Monday, 24th November at 2:30 PM (UK), we are welcoming two ERCs: Meng Zhu @zhumeng123.bsky.social (Harvard University) and Alex Plum @alex-plum.bsky.social (University of California San Diego). Don't forget to subscribe to our mailing list to receive the Zoom link! Hope to see you all! :)
Advanced grad students + postdocs: apply for the 2026 #kitpqbio summer course, "Physical Principles of Morphogenesis in Plants and Animals," at buff.ly/OXXMKEv. Apply by Feb. 1.
Course directors Adrienne Roeder (Cornell) and Sebastian Streichan (UCSB)
Hi, I’m David Brückner @davidbrueckner.bsky.social.
I’ll take you through how cells in a tissue can use information distributed by biochemical gradients to make decisions, and how we can measure such positional information.
buff.ly/RFxVeHh
Conrad Hal Waddington was born OTD in 1905.
His “epigenetic landscape” is a diagrammatic representation of the constraints influencing embryonic development.
On his 50th birthday, his colleagues gave him a pinball machine on the model of the epigenetic landscape.
🧪 🦫🦋 🌱🐋 #HistSTM #philsci #evobio
Which features of tissue flows are most robust and how do they emerge from #EpithelialMechanics?
I’m @alex-plum.bsky.social (@mattiaserra.bsky.social group) and I’ll be sharing some papers on characterizing and controlling avian gastrulation flows.
Happy to share that this work is now published in @biophysj.bsky.social! doi.org/10.1016/j.bp...
(1/14) I’m happy and proud to introduce: SpinePy – a framework to detect the "spine" of gastruloids and measure biological and physical signals in a local dynamic 3D coordinate system. www.biorxiv.org/content/10.1...
Latest on Waddington Landscapes: Computational methods to fit dynamical landscapes directly to single cell data
Applied to neural tube patterning shows morphogen-signalling landscapes can be linearly interpolated
Connects interpretable landscape models with data
www.biorxiv.org/content/10.1...
Hi bsky!
Do embryonic tissues have backup plans🔀? Gastruloids (model of body elongation) can build an axis through different cellular mechanisms when on adherent substrates instead of free floating. A case of developmental plasticity!
w/ A. Delahaye & @bensteventon.bsky.social
shorturl.at/v01DO
What happens when you plate #gastruloids at different times on different subtstrates is that we learn about cells, pattern formation and gastrulation. Excellent experiments from G. Serrano and @bensteventon.bsky.social raising interesting questions www.biorxiv.org/content/10.1...
#CellsRUs
🔔 Proud to share the preprint of my PhD work in the Petridou group @nicolettapetridou.bsky.social @embl.org ✨
“A closed feedback between tissue phase transitions and morphogen gradients drives patterning dynamics” 🐟 🔁 📶
🔗 www.biorxiv.org/content/10.1...
#devbio #biophysics
🧵⤵️
📣 New paper out! How do thousands of cells shape the emergent geometry of the avian embryo? We identify distinct, independently controllable mechanisms that contribute to embryo size and shape. @alex-plum.bsky.social @bensteventon.bsky.social @Guillermo Serrano Najera
www.nature.com/articles/s41...
Thanks Jesse!
Our review on dynamical systems of fate and form in development!
@sreejithsanthosh.bsky.social developed a resource for analyzing motion on dynamic surfaces, including in morphogenesis!
Tutorial and code: sreejithsanthosh.github.io/FTLEhub/FTLE...
Check out our new work!
The code for performing coherent structure analysis, along with the documentation, is available at sreejithsanthosh.github.io/FTLEhub/. Please feel free to reach out if you are interested in using this analysis for kinematic data in your system!
Our latest "Dynamic Landscape Analysis of Cell Fate Decisions: Predictive Models of Neural Development From Single-Cell Data"
A rigorous mathematical foundation for Waddington's landscape to study cell fate decision making
Applied to ventral neural tube development
www.biorxiv.org/content/10.1...
Our paper on the E. coli Min system in vivo with @physicsoflifelmu.bsky.social & Judy Kim (UCSD) has been published in Nature Physics today. Tight integration of experiment and theory, and physiology and biophysics. Incredible perseverance of our young students. rdcu.be/ekIpO
Poster for a Royal Society funded workshop on “generative biology” at the interface between synthetic and developmental biology. The workshop is scheduled for 20-21 October 2025, and features the following speakers: Philip Ball, David Brückner, Francesca Ceroni, Jamie Davies, Pulin Li, Mattias Malaguti, Yolanda Schaerli, Ricard Solé, Berna Sozen, Ben Steventon, Jared Toettcher, Vikas Trivedi, Berta Verd, Sara Wickström. Places available for short talks and posters
Can using synthetic approaches to build biology help teach us the design principles of how embryos build themselves? 👷♀️🔧
If this is a question that interests you, come and share your thoughts at this Royal Society Workshop on Generative Biology
www.royalsoc.ac.uk/science-even...
In developing embryos, cells move a lot! Plenty of that movement is random. Is random cell mixing a feature or bug for tissue patterning? Turns out, it’s both! Excited to share the 1st preprint from my postdoc w/ Sean Megason @seanemcgeary.bsky.social and Allon Klein. 1/20 doi.org/10.1101/2025...
