Alex Plum

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

Break It To Make It: How Fracturing Sculpts Tissues and Organs | Quanta Magazine Growing tissues can crack, break, and dissociate to form structures that can later withstand immense forces.

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

DynamicAtlas: a morphodynamic atlas for Drosophila development - Nature Methods DynamicAtlas integrates fixed and live imaging data to generate a morphodynamic atlas of Drosophila development.

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...

Reconstructing Waddington’s landscape from data | PNAS The development of a zygote into a functional organism requires that this single progenitor cell gives rise to numerous distinct cell types. Attemp...

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

Boris Shraiman points a physicist’s eye on biological quandaries Boris Shraiman is awarded the American Physical Society’s Max Delbrück Prize in Biological Physics.

Boris Shraiman points a physicist’s eye on biological quandaries news.ucsb.edu/2025/022264/... 🧪

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...

Reconstructing Waddington's Landscape from Data The development of a zygote into a functional organism requires that this single progenitor cell gives rise to numerous distinct cell types. Attempts to exhaustively tabulate the interactions within d...

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!

Dynamic Landscape Analysis of Cell Fate Decisions: Predictive Models of Neural Development From Single-Cell Data Building a mechanistic understanding of cell fate decisions remains a fundamental goal of developmental biology, with implications for stem cell therapies, regenerative medicine and understanding dise...

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...

Robust and resource-optimal dynamic pattern formation of Min proteins in vivo Nature Physics - Oscillatory Min protein patterns prevent abnormal bacterial cell division. Now it is shown that Min pattern formation is resource efficient and involves wavelength-invariant...

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...

Stoked to present our latest, superbly led by Chris et al & @torres-sanchez.bsky.social We tackled a fundamental problem – how tissues are patterned during development – found that geometry-constrained ECM fractures pattern the myocardium in the vertebrate heart 1/n www.biorxiv.org/content/10.1...

A case for broadening our view of mechanism in developmental biology ABSTRACT. Developmental biologists can perform studies that describe a phenomenon (descriptive work) and/or explain how the phenomenon works (mechanistic work). There is a prevalent perception that mo...

ICYMI: Commentary on "mechanism" in dev bio

Ozpolat et al argue for diverse approaches to mechanism - from molecular to systems level

journals.biologists.com/dev/article/...

Chuai et al 2023 nicely tie in large scale tissue deformations to local cell behaviors like intercalations and ingression.