Dagmar Iber & CoBi

🎉 Our paper is out in Cell Systems @cp-cellsystems.bsky.social ! How does an embryo build an energy-efficient fractal lung before the first breath? 📄 doi.org/10.1016/j.ce... 🧵 bsky.app/profile/iberd.bsky.social/post/3lfrdth6k4c22 @maltemederacke.bsky.social @kevinyamauchi.bsky.social

Local mechanical forces — not a genetic programme — explain the fractal architecture of the lung. Uniform shear stress, hoop stress & equal pressure drops: three simple physical rules that build the whole tree, from embryo to adult, mouse to human. 🐭🧑‍⚕️ The same rules explain COPD remodelling. 🫁

Thrilled to see our #DCM paper out in @cp-newton.bsky.social! 🎉 How do cells self-organize into complex patterns so quickly during development? We show that #directed #cell #migration — chemotaxis, durotaxis, differential adhesion — is a surprisingly fast & versatile patterning engine. 🧵👇

🧰 New tool alert! ⚙️ #MorphoGrad, an open-source toolbox for simulating reaction–diffusion systems in 1D and 2D tissues, with cell-to-cell parameter heterogeneity & graphical user interface. No heavy coding required. Explore complex morphogen gradient models interactively. doi.org/10.1016/j.xp...

Smaller cells widen the #transition #zone. The tradeoff between morphogen gradient precision and transition zone sharpness may explain why epithelial cell diameters don't shrink further in developing tissues. 🧵 Thread: bsky.app/profile/iber... 📄 Paper: www.biorxiv.org/content/10.6...

🧰 New tool alert! ⚙️ #MorphoGrad, an open-source toolbox for simulating reaction–diffusion systems in 1D and 2D tissues, with cell-to-cell parameter heterogeneity & graphical user interface. No heavy coding required. Explore complex morphogen gradient models interactively. doi.org/10.1016/j.xp...

#Morphogen gradients are more precise in 2D than in 1D tissues — especially when cells are narrow. 🧵 Thread: x.com/DagmarIber/s... 📄 Paper: doi.org/10.1016/j.is...

🧰 New tool alert! ⚙️ #MorphoGrad, an open-source toolbox for simulating reaction–diffusion systems in 1D and 2D tissues, with cell-to-cell parameter heterogeneity & graphical user interface. No heavy coding required. Explore complex morphogen gradient models interactively. doi.org/10.1016/j.xp...

#MorphoGrad runs the simulations behind several of our papers on morphogen gradient precision. Here's what we found: 👇

🧰 New tool alert! ⚙️ #MorphoGrad, an open-source toolbox for simulating reaction–diffusion systems in 1D and 2D tissues, with cell-to-cell parameter heterogeneity & graphical user interface. No heavy coding required. Explore complex morphogen gradient models interactively. doi.org/10.1016/j.xp...

🔬⚙️💻 Excited to share #OptiCell3D, our new image-based framework for inferring cell mechanical properties with high precision from 3D microscopy. www.biorxiv.org/content/10.6... #ComputationalBiology #CellBiology #Biophysics #OpenSource

The @ethz.ch Animal Facility featured our work on how the lung gets its energy-efficient shape and how it remodels in disease like COPD 🐭🫁 — as part of their spotlight on responsible animal research. 🧵(1/4)

We're fully committed to 3Rs: ♻️ Replace – comp models & simulations go beyond what animal data alone could reveal 📉 Reduce – just 7 pregnant females (severity degree 0) & reuse of 20-year-old datasets instead of new experiments 🔬 Refine – SkelePlex & our pipeline extract max insight from min data

The @ethz.ch Animal Facility featured our work on how the lung gets its energy-efficient shape and how it remodels in disease like COPD 🐭🫁 — as part of their spotlight on responsible animal research. 🧵(1/4)

What determines the sharpness of cell fate boundaries in gradient-based patterning? We quantified #transition #zone #widths (TZW) across seven progenitor domain boundaries spanning the entire dorsal-ventral axis of the developing #mouse #neural #tube. Preprint: doi.org/10.64898/202... 🧵 1/6

By matching simulations with measurement of #TZW & #positional #error, we inferred kinetic and readout noise levels - and found them in the reported range. This further supports that reliable long-range morphogen patterning is feasible with physiological noise levels: x.com/DagmarIber/s... 🧵 5/6

What determines the sharpness of cell fate boundaries in gradient-based patterning? We quantified #transition #zone #widths (TZW) across seven progenitor domain boundaries spanning the entire dorsal-ventral axis of the developing #mouse #neural #tube. Preprint: doi.org/10.64898/202... 🧵 1/6

Our theoretical & computational analysis shows that #TZW is primarily set by #noise in the #cellular #readout process, not by fluctuations in the morphogen gradient itself. For exponential gradients, a noisy readout threshold naturally yields a position-independent TZW. 🧵 3/6

What determines the sharpness of cell fate boundaries in gradient-based patterning? We quantified #transition #zone #widths (TZW) across seven progenitor domain boundaries spanning the entire dorsal-ventral axis of the developing #mouse #neural #tube. Preprint: doi.org/10.64898/202... 🧵 1/6

Out now: Simulating Organogenesis in #COMSOL: Tissue Patterning with Directed Cell Migration We provide a detailed walkthrough of how to implement #DCM partial integro-differential equation models - enabling accessible simulations of tissue patterning and morphogenesis. arxiv.org/pdf/2509.08930

The goal: make it easier for others to reproduce and extend these models within COMSOL. We hope this serves as a generalizable reference for simulating collective cell behavior and pattern formation. arxiv.org/pdf/2509.08930

Out now: Simulating Organogenesis in #COMSOL: Tissue Patterning with Directed Cell Migration We provide a detailed walkthrough of how to implement #DCM partial integro-differential equation models - enabling accessible simulations of tissue patterning and morphogenesis. arxiv.org/pdf/2509.08930

Our paper "Morphogen gradients can convey position and time in growing tissues" is now out in Newton ‪@cp-newton.bsky.social‬ Quite fitting to see this novel idea that morphogen gradients not only encode position, but can also time & synchronise development over long distances out in a new journal.