Modeling embryo & tissue morphogenesis combining physics and computer science @CbiToulouse
Toulouse, France
Based in France
- Tweets 198
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Huge thanks to all co-authors & collaborators!
Thanks @ebardot for his kind highlight in Nat Cell Biol shorturl.at/Sq1f4
@CNRSbiologie
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A central result: cadherin-dependent adhesion contributes significantly to cell-cell tension in C. elegans, with a highly non-linear, Hill-like dependence. Adhesion is not just a small correction to contractility.
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Inside the eggshell, the model predicts morphogenesis quantitatively: anterior compaction is driven by rising cell-medium tension, while P2’s early exclusion reflects high cell-cell contact tension.
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To calibrate inferred tensions, we combined AFM measurements with cortical myosin intensity. AB-lineage cells are more tense than P-lineage cells, and tension rises dynamically through the cell cycle.
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We combined live imaging, contact-angle measurements and tension inference to reconstruct relative surface tensions, then used a 3D active foam model to predict embryo shape over time.
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The early C. elegans embryo is not mechanically uniform.
Removing the eggshell, one can observe that at the 4-cell stage, ABa, ABp and EMS compact together, while P2 initially remains partly excluded — revealing dynamic, lineage-specific mechanics.
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Very happy to have this work finally published! How do embryos sculpt their shape? We map the contractile & adhesive forces shaping early C. elegans embryos.
With K. Yamamoto @Kazu_YAMAMOTO4 G. Charras' lab and my team
shorturl.at/xv7G51/6
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Very glad to see this great transatlantic collaborative work published in NCB 🎉!
nature.com/articles/s41556-0…
Congratulations to all authors: @Henry_de_belly, @andreu_gallen, Eric neiva, @OWeinerLab
Funding from MSCA @EU_Commission & @CNRSbiologie
Very excited to be sharing our new paper, just out in Nature Cell Biology! nature.com/articles/s41556-0…
The big question we investigate: How do migrating cells put their front 🔴 and back 🔵 in the right place?
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A true computational tour de force by Eric Neiva during his Marie Skłodowska-Curie postdoctoral fellowship in the team, now published in Journal Computational Physics: urlr.me/AuzK86
Congratulations, Eric!
@CNRSbiologie
Grateful to @EU_Commission for funding support
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We hope VertAX can help make inverse problems & differential programming more accessible in tissue mechanics.
Thanks to @appasqui, @MaxenceErnoult, Italian colleagues, & other members of the team for this collaboration.
Comments very welcome.
Code github.com/VirtualEmbryo/Ver…
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Beyond synthetic benchmarks, we show applications to mechanical parameter inference from microscopy images and to inverse design problems in epithelial tissues. 4/5
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We benchmark three strategies for bilevel optimization in vertex models: automatic differentiation, implicit differentiation, and equilibrium propagation.
This gives a practical comparison of their accuracy, speed, and memory trade-offs. 3/5
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VertAX unifies forward modeling and inverse modeling in the same framework.
It lets users define custom energy functions and cost functions in pure Python, while leveraging bilevel optimization & JAX for differentiation, JIT compilation, and GPU acceleration. 2/5
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How can we learn tissue mechanics directly from patterns and images?
In our new preprint, we introduce VertAX, a differentiable vertex-model framework in JAX for simulating epithelia, inferring parameters, and designing target tissue behaviors.
shorturl.at/PUzT0
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Turlier lab retweeted
If you think the next big idea in your field will come from inside the field, you're probably wrong.
ALT https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-01985-6
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Conference Alert🚨 16-21 Feb 2025
From Soft Matter to Biophysics @ Les Houches FR
t.ly/GXhPL
Apply by Dec 15 to explore the latest in soft matter & biophysics, focusing on functional materials & synthetic biology!
@karen_alim
@Karin__Jacobs
@MartinLenz
@HerveTurlier
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Registrations are open for the Qlife Quantitative Biology spring school on Cell Dynamics in Developmental System March 3-April 04 2025. Great line of talks, lectures and hands-on practicals on omics, image analysis, modeling and inference: shorturl.at/Ygthh
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Turlier lab retweeted
We recapitulate our findings in a mathematical model and show that this creates a feedback loop, where the front and back communicate through mechanical signals. @virtual_embryo @andreu_gallen
It ensures that the cell can move forward in a coordinated way.
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Thanks to all speakers @MarinoArroyo2 @AnjaGeitmann @AlainGoriely Jessica Zhang @aland_lab @GabriellaBioMec Arezki Boudaoud Christophe Godin, Brendan Lane, Robert Nürnberg, Padmini Rangamani, Arnold Reusken, Axel Voigt, Sara Zahedi, Roman Vetter
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