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Alex Plum

@alex-plum.bsky.social
625 followers 475 following 8 posts

Physics PhD Candidate w/ @mattiaserra.bsky.social @UCSD Dynamical Systems | Information Theory | Origins alexplum.com

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Reposted by Alex Plum
Susie Wopat @suewop.bsky.social · 03/09/2026
This was a particularly special #morpho26 course with this amazing group of scientists (aka team M&Ms)! Thanks to course organizers @roederlab.bsky.social + @streichan.bsky.social, as well as @kitp-ucsb.bsky.social for providing a fun + creative environment to tackle quantitative bio questions 💭
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Mattia Serra @mattiaserra.bsky.social · 05/08/2026
Preprint📣: Living tissues can exhibit odd mechanics without chirality. Our minimal model shows that orientational order can generate an odd modulus—inferable from experiments—and reproduces flows & stress localization around 1/2 defects. @sreejithsanthosh.bsky.social www.biorxiv.org/content/10.6...
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David Brückner @davidbrueckner.bsky.social · 20/07/2026
Our paper on nonlocal decoding is now out in @physrevlett.aps.org! See below for a thread about the preprint 🧵 👉 journals.aps.org/prl/abstract...
journals.aps.org
Nonlocal Decoding of Positional and Correlational Information during Development
In many developmental systems, cells differentiate into a tissue by reading out morphogen concentration fields, a process fundamentally limited by noise. How much can the precision of this process be ...
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Carl T. Bergstrom @carlbergstrom.com · 04/07/2026
1. A bit of evolutionary biology. I'm really intrigued by a new perspective piece from Steve Frank that explores connections between how natural selection creates systems that generalize and recent work in machine learning about the surprising capabilities of massively overparameterized systems.
academic.oup.com
Generalization as the great leap in evolvability: insights from machine learning
Abstract. Natural selection encodes learned information in the genome. Learned solutions may be tuned specifically to past challenges, failing in altered e
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Heemskerk Lab @heemskerklab.bsky.social · 18/05/2026
New preprint! We show that cell fate can be predicted from a snapshot of combinatorial signaling — and the underlying map is a single angle in signaling space. Work by first authors Bassit Fijabi and Seth Teague and collaboration with @davidbrueckner.bsky.social. www.biorxiv.org/content/10.6...
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Alex Plum @alex-plum.bsky.social · 11/05/2026
Unexpected used book store find!
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Mattia Serra @mattiaserra.bsky.social · 21/04/2026
📢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...
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Mattia Serra @mattiaserra.bsky.social · 07/04/2026
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!
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Aissam Ikmi @aikmi.bsky.social · 20/03/2026
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
cell.com
Deciphering mechanical determinants of morphological evolution
A comparative analysis of cnidarian larval morphogenesis combined with active surface theory identifies a set of mesoscale mechanical modules that predict species-specific shapes. Manipulating these m...
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James Briscoe @jamesbriscoe.bsky.social · 06/03/2026
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
biorxiv.org
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Quanta Magazine @quantamagazine.org · 27/02/2026
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-...
quantamagazine.org
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.
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David Brückner @davidbrueckner.bsky.social · 05/01/2026
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
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Vishank Jain-Sharma @vishankjs.bsky.social · 24/12/2025
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...
nature.com
DynamicAtlas: a morphodynamic atlas for Drosophila development - Nature Methods
DynamicAtlas integrates fixed and live imaging data to generate a morphodynamic atlas of Drosophila development.
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James Briscoe @jamesbriscoe.bsky.social · 04/12/2025
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/...
pnas.org
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...
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Thomas Lecuit @thomaslecuit.bsky.social · 01/12/2025
Here is the link to download the pdf of my 2nd course on complexity and information during development: tinyurl.com/b7szw7v3
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Kavli Institute for Theoretical Physics @kitp-ucsb.bsky.social · 25/11/2025
Boris Shraiman points a physicist’s eye on biological quandaries news.ucsb.edu/2025/022264/... 🧪
news.ucsb.edu
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.
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Cambridge Morphogenesis Seminar Series @cammorphoseries.bsky.social · 21/11/2025
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! :)
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Kavli Institute for Theoretical Physics @kitp-ucsb.bsky.social · 19/11/2025
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)
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epithelial mechanics fan club @epimechfc.bsky.social · 15/11/2025
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
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Greg Priest @gregpriest.bsky.social · 08/11/2025
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
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epithelial mechanics fan club @epimechfc.bsky.social · 02/11/2025
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.
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Rikki Garner @rikkigarner.bsky.social · 23/10/2025
Happy to share that this work is now published in @biophysj.bsky.social! doi.org/10.1016/j.bp...
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Ryan Savill @cryaaa.bsky.social · 12/09/2025
(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...
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James Briscoe @jamesbriscoe.bsky.social · 14/08/2025
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...
biorxiv.org
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...
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gserranonajera.bsky.social @gserranonajera.bsky.social · 07/08/2025
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
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Alfonso Martinez Arias @amartinezarias.bsky.social · 06/08/2025
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
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Camilla Autorino @cami-autorino.bsky.social · 11/06/2025
🔔 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 🧵⤵️
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Mattia Serra @mattiaserra.bsky.social · 09/06/2025
📣 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...
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Alex Plum @alex-plum.bsky.social · 06/06/2025
Our review on dynamical systems of fate and form in development!
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Alex Plum @alex-plum.bsky.social · 03/06/2025
@sreejithsanthosh.bsky.social developed a resource for analyzing motion on dynamic surfaces, including in morphogenesis! Tutorial and code: sreejithsanthosh.github.io/FTLEhub/FTLE...
sreejithsanthosh.github.io
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sreejithsanthosh.bsky.social @sreejithsanthosh.bsky.social · 30/05/2025
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!
sreejithsanthosh.github.io
Introduction
Welcome to your one stop solution for all your FTLE needs!
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James Briscoe @jamesbriscoe.bsky.social · 29/05/2025
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...
biorxiv.org
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...
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Suckjoon Jun’s lab at UCSD @junlab.bsky.social · 05/05/2025
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
rdcu.be
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...
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Jake Cornwall-Scoones @jcornwallscoones.bsky.social · 30/04/2025
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...
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
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Rikki Garner @rikkigarner.bsky.social · 24/04/2025
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...
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Rashmi Priya @rashmi-priya.bsky.social · 10/03/2025
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...
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James Briscoe @jamesbriscoe.bsky.social · 05/02/2025
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/...
journals.biologists.com
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...
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epithelial mechanics fan club @epimechfc.bsky.social · 26/01/2025
Chuai et al 2023 nicely tie in large scale tissue deformations to local cell behaviors like intercalations and ingression.
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Mattia Serra @mattiaserra.bsky.social · 24/01/2025
📣Check out our work led by @alex-plum.bsky.social ! We developed a mathematical framework for morphogen patterning in dynamic tissues, revealing key insights into how morphogenesis mediates cell-cell communication, morphogen compartmentalization and fate coordination. biorxiv.org/content/10.1...
Morphogenetic movements reshape cell-cell interaction ranges, quantified as Embryological Light Cones (ELCs). These ELCs are highly different from the corresponding static tissue patterning ELCs.
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Mattia Serra @mattiaserra.bsky.social · 16/01/2025
📣 Excited to receive the 💥 NSF CAREER 💥 Award. Our group is looking for PhD students and postdocs interested in the Nonlinear Dynamics and the Physics of Living Systems, with support from NSF, HFSP, and other sources. We’d appreciate your help in spreading the word! @ucsdphysci.bsky.social
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Sean Carroll @seanmcarroll.bsky.social · 20/01/2025
Mindscape 302 | Chris Kempes on the Biophysics of Evolution. Even squishy organisms are subject to the fundamental laws of nature. #MindscapePodcast www.preposterousuniverse.com/podcast/2025...
Chris Kempes
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epithelial mechanics fan club @epimechfc.bsky.social · 17/01/2025
Chuai, M., Serrano Nájera, G., Serra, M., Mahadevan, L., & Weijer, C. J. (2023). Reconstruction of distinct vertebrate gastrulation modes via modulation of key cell behaviors in the chick embryo. Science Advances, 9(1), eabn5429. doi.org/10.1126/sciadv.abn5429 #EpithelialMechanics
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epithelial mechanics fan club @epimechfc.bsky.social · 16/01/2025
Nájera, G. S., & Weijer, C. J. (2023). The evolution of gastrulation morphologies. Development, 150(7), dev200885. doi.org/10.1242/dev.200885 #EpithelialMechanicsReview
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Santa Fe Institute @sfiscience.bsky.social · 03/01/2025
🦦 Feed your intellectual curiosity & challenge your limits at SFI’s Undergraduate Complexity Research program. Pursue new research directions and walk away with an unforgettable, transformative experience. Apply by January 14: apply-sfi.smapply.org/prog/ucr2025/
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James Briscoe @jamesbriscoe.bsky.social · 12/11/2024
A stimulating workshop on the subject of Waddington Landscapes in Lyon last week, prompted me to compose some thoughts on dynamical landscapes, gene regulatory networks, and single cell transcriptomics briscoelab.org/morphogenalia/
briscoelab.org
Briscoe Lab
Developmental Dynamics of Tissue Formation
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Alex Plum @alex-plum.bsky.social · 17/11/2024
Nothing like niche books at the La Jolla farmers market for $1
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