Alex Plum
@alex-plum.bsky.social
Physics (Biophysics) PhD Candidate
with Mattia Serra @UCSD
Morphogenesis | Dynamical Systems | Origins
with Mattia Serra @UCSD
Morphogenesis | Dynamical Systems | Origins
Pinned
Alex Plum
@alex-plum.bsky.social
· Jun 6
📣 New review! Dynamical systems and low-dimensional geometric structures in phase space help rationalize how embryos develop form and function, from large datasets. We focus on morphogenesis, cell differentiation, and their interconnection.
@alex-plum.bsky.social
sciencedirect.com/science/arti...
@alex-plum.bsky.social
sciencedirect.com/science/arti...
Our review on dynamical systems of fate and form in development!
Reposted by Alex Plum
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! :)
November 21, 2025 at 9:46 AM
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! :)
Reposted by Alex Plum
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)
Course directors Adrienne Roeder (Cornell) and Sebastian Streichan (UCSB)
November 19, 2025 at 11:45 PM
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)
Course directors Adrienne Roeder (Cornell) and Sebastian Streichan (UCSB)
Reposted by Alex Plum
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
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
November 15, 2025 at 8:00 AM
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
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
Reposted by Alex Plum
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
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
November 8, 2025 at 4:03 PM
Reposted by Alex Plum
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.
I’m @alex-plum.bsky.social (@mattiaserra.bsky.social group) and I’ll be sharing some papers on characterizing and controlling avian gastrulation flows.
November 2, 2025 at 9:02 AM
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.
I’m @alex-plum.bsky.social (@mattiaserra.bsky.social group) and I’ll be sharing some papers on characterizing and controlling avian gastrulation flows.
Reposted by Alex Plum
Happy to share that this work is now published in @biophysj.bsky.social! doi.org/10.1016/j.bp...
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...
October 23, 2025 at 4:30 PM
Happy to share that this work is now published in @biophysj.bsky.social! doi.org/10.1016/j.bp...
Reposted by Alex Plum
(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...
September 12, 2025 at 12:44 PM
(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...
Reposted by Alex Plum
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...
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...
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...
www.biorxiv.org
August 14, 2025 at 7:53 AM
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...
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...
Reposted by Alex Plum
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
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
August 7, 2025 at 3:01 PM
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
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
Reposted by Alex Plum
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
#CellsRUs
August 6, 2025 at 3:49 PM
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
#CellsRUs
Reposted by Alex Plum
🔔 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
🧵⤵️
“A closed feedback between tissue phase transitions and morphogen gradients drives patterning dynamics” 🐟 🔁 📶
🔗 www.biorxiv.org/content/10.1...
#devbio #biophysics
🧵⤵️
June 11, 2025 at 4:47 PM
🔔 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
🧵⤵️
“A closed feedback between tissue phase transitions and morphogen gradients drives patterning dynamics” 🐟 🔁 📶
🔗 www.biorxiv.org/content/10.1...
#devbio #biophysics
🧵⤵️
Reposted by Alex Plum
📣 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...
www.nature.com/articles/s41...
June 9, 2025 at 5:00 PM
📣 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...
www.nature.com/articles/s41...
Our review on dynamical systems of fate and form in development!
📣 New review! Dynamical systems and low-dimensional geometric structures in phase space help rationalize how embryos develop form and function, from large datasets. We focus on morphogenesis, cell differentiation, and their interconnection.
@alex-plum.bsky.social
sciencedirect.com/science/arti...
@alex-plum.bsky.social
sciencedirect.com/science/arti...
June 6, 2025 at 3:27 PM
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...
Tutorial and code: sreejithsanthosh.github.io/FTLEhub/FTLE...
June 3, 2025 at 5:37 PM
@sreejithsanthosh.bsky.social developed a resource for analyzing motion on dynamic surfaces, including in morphogenesis!
Tutorial and code: sreejithsanthosh.github.io/FTLEhub/FTLE...
Tutorial and code: sreejithsanthosh.github.io/FTLEhub/FTLE...
Reposted by Alex Plum
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!
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!
May 30, 2025 at 4:26 PM
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!
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!
Reposted by Alex Plum
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...
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...
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...
www.biorxiv.org
May 29, 2025 at 12:08 PM
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...
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...
Reposted by Alex Plum
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
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...
rdcu.be
May 5, 2025 at 2:53 PM
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
Reposted by Alex Plum
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...
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...
April 30, 2025 at 7:51 AM
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...
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...
Reposted by Alex Plum
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...
April 24, 2025 at 1:19 PM
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...
Reposted by Alex Plum
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...
March 10, 2025 at 2:43 AM
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...
Reposted by Alex Plum
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/...
Ozpolat et al argue for diverse approaches to mechanism - from molecular to systems level
journals.biologists.com/dev/article/...
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...
journals.biologists.com
February 5, 2025 at 10:56 AM
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/...
Ozpolat et al argue for diverse approaches to mechanism - from molecular to systems level
journals.biologists.com/dev/article/...
Reposted by Alex Plum
Chuai et al 2023 nicely tie in large scale tissue deformations to local cell behaviors like intercalations and ingression.
January 26, 2025 at 11:42 AM
Chuai et al 2023 nicely tie in large scale tissue deformations to local cell behaviors like intercalations and ingression.
Reposted by Alex Plum
📣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...
January 24, 2025 at 5:16 PM
📣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...
Reposted by Alex Plum
📣 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
January 16, 2025 at 9:08 PM
📣 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
Reposted by Alex Plum
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...
www.preposterousuniverse.com/podcast/2025...
January 20, 2025 at 1:13 PM
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...
www.preposterousuniverse.com/podcast/2025...