Dagmar Iber & CoBi
@iberd.bsky.social
Computational Biology @ETH: data-driven modeling & simulation of emerging phenomena in development & disease https://bsse.ethz.ch/cobi https://youtube.com/@cobi-ethz
Paper & poster are available on the COMSOL conference website: www.comsol.com/paper/direct...
November 5, 2025 at 4:13 PM
Paper & poster are available on the COMSOL conference website: www.comsol.com/paper/direct...
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
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
September 12, 2025 at 5:23 AM
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
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.
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.
August 25, 2025 at 10:23 AM
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.
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.
2. Dynamic #attraction #zones
Spatially varying cell attraction that changes with tissue growth can guide migrating cells, leading to precise large-scale patterning.
This mimics how tissues form rings, bands, or layered structures in vivo.
👇Thread 🧵(9/11)
Spatially varying cell attraction that changes with tissue growth can guide migrating cells, leading to precise large-scale patterning.
This mimics how tissues form rings, bands, or layered structures in vivo.
👇Thread 🧵(9/11)
July 30, 2025 at 7:00 AM
2. Dynamic #attraction #zones
Spatially varying cell attraction that changes with tissue growth can guide migrating cells, leading to precise large-scale patterning.
This mimics how tissues form rings, bands, or layered structures in vivo.
👇Thread 🧵(9/11)
Spatially varying cell attraction that changes with tissue growth can guide migrating cells, leading to precise large-scale patterning.
This mimics how tissues form rings, bands, or layered structures in vivo.
👇Thread 🧵(9/11)
We identify two mechanisms for guiding pattern orientation:
1. #Anisotropic #attraction
Cells pulling or migrating more strongly in one direction form aligned stripe-like patterns—e.g., during directional tissue growth.
👇Thread 🧵(8/11)
1. #Anisotropic #attraction
Cells pulling or migrating more strongly in one direction form aligned stripe-like patterns—e.g., during directional tissue growth.
👇Thread 🧵(8/11)
July 30, 2025 at 7:00 AM
We identify two mechanisms for guiding pattern orientation:
1. #Anisotropic #attraction
Cells pulling or migrating more strongly in one direction form aligned stripe-like patterns—e.g., during directional tissue growth.
👇Thread 🧵(8/11)
1. #Anisotropic #attraction
Cells pulling or migrating more strongly in one direction form aligned stripe-like patterns—e.g., during directional tissue growth.
👇Thread 🧵(8/11)
#DCM naturally leads to unoriented patterns—spots, labyrinths—similar to Turing-like systems.
But biological tissues often require oriented patterns to fulfill specific functions.
Can DCM produce stripes, too?
👇Thread 🧵(7/11)
But biological tissues often require oriented patterns to fulfill specific functions.
Can DCM produce stripes, too?
👇Thread 🧵(7/11)
July 30, 2025 at 7:00 AM
#DCM naturally leads to unoriented patterns—spots, labyrinths—similar to Turing-like systems.
But biological tissues often require oriented patterns to fulfill specific functions.
Can DCM produce stripes, too?
👇Thread 🧵(7/11)
But biological tissues often require oriented patterns to fulfill specific functions.
Can DCM produce stripes, too?
👇Thread 🧵(7/11)
Three key parameters drive the emergence and morphology of patterns:
• Initial density of motile cells
• Intercellular attraction strength
• Cell sensing radius
👇Thread 🧵(6/11)
• Initial density of motile cells
• Intercellular attraction strength
• Cell sensing radius
👇Thread 🧵(6/11)
July 30, 2025 at 7:00 AM
Three key parameters drive the emergence and morphology of patterns:
• Initial density of motile cells
• Intercellular attraction strength
• Cell sensing radius
👇Thread 🧵(6/11)
• Initial density of motile cells
• Intercellular attraction strength
• Cell sensing radius
👇Thread 🧵(6/11)
We developed a mathematical framework that represents a wide range of #DCM cues, e.g., chemotaxis, durotaxis, haptotaxis & a general Finite Element Method #FEM:
👉 1D, 2D, 3D
👉 arbitrary geometries & boundary conditions
👉 isotropic & anisotropic interactions
👉 fast, large-scale simulations
🧵(4/11)
👉 1D, 2D, 3D
👉 arbitrary geometries & boundary conditions
👉 isotropic & anisotropic interactions
👉 fast, large-scale simulations
🧵(4/11)
July 30, 2025 at 7:00 AM
During embryonic development, cellular tissues transition from uniform starting conditions into robust spatial patterns.
#DCM offers a particularly fast and versatile route to spontaneously symmetry breaks and pattern formation without tissue buckling.
🧵(2/11)
#DCM offers a particularly fast and versatile route to spontaneously symmetry breaks and pattern formation without tissue buckling.
🧵(2/11)
July 30, 2025 at 7:00 AM
During embryonic development, cellular tissues transition from uniform starting conditions into robust spatial patterns.
#DCM offers a particularly fast and versatile route to spontaneously symmetry breaks and pattern formation without tissue buckling.
🧵(2/11)
#DCM offers a particularly fast and versatile route to spontaneously symmetry breaks and pattern formation without tissue buckling.
🧵(2/11)
How can cells self-organize rapidly into complex patterns during development?
Let’s explore a powerful and underappreciated mechanism: Directed Cell Migration (DCM).
Preprint @biorxivpreprint.bsky.social : doi.org/10.1101/2025...
👇Thread 🧵(1/11)
Let’s explore a powerful and underappreciated mechanism: Directed Cell Migration (DCM).
Preprint @biorxivpreprint.bsky.social : doi.org/10.1101/2025...
👇Thread 🧵(1/11)
July 30, 2025 at 7:00 AM
How can cells self-organize rapidly into complex patterns during development?
Let’s explore a powerful and underappreciated mechanism: Directed Cell Migration (DCM).
Preprint @biorxivpreprint.bsky.social : doi.org/10.1101/2025...
👇Thread 🧵(1/11)
Let’s explore a powerful and underappreciated mechanism: Directed Cell Migration (DCM).
Preprint @biorxivpreprint.bsky.social : doi.org/10.1101/2025...
👇Thread 🧵(1/11)
⚡ No plateaus here!
Classical PINNs stall. PINNverse keeps improving physics loss ∼ epoch^(-1.4) for Fisher’s equation.
Algebraic decay >> stagnation!
Classical PINNs stall. PINNverse keeps improving physics loss ∼ epoch^(-1.4) for Fisher’s equation.
Algebraic decay >> stagnation!
April 10, 2025 at 8:24 AM
⚡ No plateaus here!
Classical PINNs stall. PINNverse keeps improving physics loss ∼ epoch^(-1.4) for Fisher’s equation.
Algebraic decay >> stagnation!
Classical PINNs stall. PINNverse keeps improving physics loss ∼ epoch^(-1.4) for Fisher’s equation.
Algebraic decay >> stagnation!
📉 #PINNverse crushes parameter error — even with:
- High noise
- Terrible initial guesses
Stable & accurate where others fail (e.g., Fisher-KPP).
- High noise
- Terrible initial guesses
Stable & accurate where others fail (e.g., Fisher-KPP).
April 10, 2025 at 8:24 AM
📉 #PINNverse crushes parameter error — even with:
- High noise
- Terrible initial guesses
Stable & accurate where others fail (e.g., Fisher-KPP).
- High noise
- Terrible initial guesses
Stable & accurate where others fail (e.g., Fisher-KPP).
💥 Why is this a breakthrough?
Standard PINNs miss non-convex Pareto fronts → overfit.
#PINNverse captures the entire Pareto front → balances physics + data perfectly.
Standard PINNs miss non-convex Pareto fronts → overfit.
#PINNverse captures the entire Pareto front → balances physics + data perfectly.
April 10, 2025 at 8:24 AM
💥 Why is this a breakthrough?
Standard PINNs miss non-convex Pareto fronts → overfit.
#PINNverse captures the entire Pareto front → balances physics + data perfectly.
Standard PINNs miss non-convex Pareto fronts → overfit.
#PINNverse captures the entire Pareto front → balances physics + data perfectly.
🔑 The big idea:
Classical PINNs use weighted-sum loss → often fails.
#PINNverse reframes it as constrained optimization → unlocks better solutions.
Small change, huge impact!
Classical PINNs use weighted-sum loss → often fails.
#PINNverse reframes it as constrained optimization → unlocks better solutions.
Small change, huge impact!
April 10, 2025 at 8:24 AM
🔑 The big idea:
Classical PINNs use weighted-sum loss → often fails.
#PINNverse reframes it as constrained optimization → unlocks better solutions.
Small change, huge impact!
Classical PINNs use weighted-sum loss → often fails.
#PINNverse reframes it as constrained optimization → unlocks better solutions.
Small change, huge impact!
📊 How does #PINNverse stack up?
✅ beats Nelder-Mead & classical PINNs
✅ handles noisy data & bad initial guesses
✅ tested on 4 tough benchmarks:
- Kinetic reaction ODE
- FitzHugh–Nagumo
- Fisher–KPP PDE
- Burgers’ PDE
✅ beats Nelder-Mead & classical PINNs
✅ handles noisy data & bad initial guesses
✅ tested on 4 tough benchmarks:
- Kinetic reaction ODE
- FitzHugh–Nagumo
- Fisher–KPP PDE
- Burgers’ PDE
April 10, 2025 at 8:24 AM
📊 How does #PINNverse stack up?
✅ beats Nelder-Mead & classical PINNs
✅ handles noisy data & bad initial guesses
✅ tested on 4 tough benchmarks:
- Kinetic reaction ODE
- FitzHugh–Nagumo
- Fisher–KPP PDE
- Burgers’ PDE
✅ beats Nelder-Mead & classical PINNs
✅ handles noisy data & bad initial guesses
✅ tested on 4 tough benchmarks:
- Kinetic reaction ODE
- FitzHugh–Nagumo
- Fisher–KPP PDE
- Burgers’ PDE
🚀 Introducing #PINNverse — a game-changer for parameter estimation in differential equations! 🧠💡
No forward solves. Better accuracy. Robust to noise.
Preprint: doi.org/10.48550/arX...
#SciComm #MachineLearning #InverseProblems #PINNs
No forward solves. Better accuracy. Robust to noise.
Preprint: doi.org/10.48550/arX...
#SciComm #MachineLearning #InverseProblems #PINNs
April 10, 2025 at 8:24 AM
🚀 Introducing #PINNverse — a game-changer for parameter estimation in differential equations! 🧠💡
No forward solves. Better accuracy. Robust to noise.
Preprint: doi.org/10.48550/arX...
#SciComm #MachineLearning #InverseProblems #PINNs
No forward solves. Better accuracy. Robust to noise.
Preprint: doi.org/10.48550/arX...
#SciComm #MachineLearning #InverseProblems #PINNs
What a beautiful cover for our #mechanobiology paper "Morphometry and mechanical instability at the onset of epithelial bladder cancer": doi.org/10.1038/s415... - thx @naturephysics.bsky.social !!
News & Views "Tissue wrinkles foreshadow cancer" doi.org/10.1038/s415...
News & Views "Tissue wrinkles foreshadow cancer" doi.org/10.1038/s415...
February 20, 2025 at 5:30 AM
What a beautiful cover for our #mechanobiology paper "Morphometry and mechanical instability at the onset of epithelial bladder cancer": doi.org/10.1038/s415... - thx @naturephysics.bsky.social !!
News & Views "Tissue wrinkles foreshadow cancer" doi.org/10.1038/s415...
News & Views "Tissue wrinkles foreshadow cancer" doi.org/10.1038/s415...
Pleased to share our latest review "Coordination of nephrogenesis with branching of the urinary collecting system, the vasculature and the nervous system"
authors.elsevier.com/a/1kXJ6Fzn7S...
authors.elsevier.com/a/1kXJ6Fzn7S...
January 31, 2025 at 3:07 PM
Pleased to share our latest review "Coordination of nephrogenesis with branching of the urinary collecting system, the vasculature and the nervous system"
authors.elsevier.com/a/1kXJ6Fzn7S...
authors.elsevier.com/a/1kXJ6Fzn7S...
We present a simple yet comprehensive model integrating multiple mechanical forces to guide lung development.
These principles operate during both development and disease, providing a dynamic framework to understand and predict lung remodeling processes.
👇Thread 🧵(9/9)
These principles operate during both development and disease, providing a dynamic framework to understand and predict lung remodeling processes.
👇Thread 🧵(9/9)
January 15, 2025 at 8:27 AM
We present a simple yet comprehensive model integrating multiple mechanical forces to guide lung development.
These principles operate during both development and disease, providing a dynamic framework to understand and predict lung remodeling processes.
👇Thread 🧵(9/9)
These principles operate during both development and disease, providing a dynamic framework to understand and predict lung remodeling processes.
👇Thread 🧵(9/9)
In #COPD patients, destruction of #lung #tissue leads to #remodelling of the lung tree.
Our biophysical model explains the thickening of the airway walls, potentially helping to localize affected areas, and yields quantitative #biomarkers for #PersonalizedHealth.
👇Thread 🧵(8/9)
Our biophysical model explains the thickening of the airway walls, potentially helping to localize affected areas, and yields quantitative #biomarkers for #PersonalizedHealth.
👇Thread 🧵(8/9)
January 15, 2025 at 8:27 AM
In #COPD patients, destruction of #lung #tissue leads to #remodelling of the lung tree.
Our biophysical model explains the thickening of the airway walls, potentially helping to localize affected areas, and yields quantitative #biomarkers for #PersonalizedHealth.
👇Thread 🧵(8/9)
Our biophysical model explains the thickening of the airway walls, potentially helping to localize affected areas, and yields quantitative #biomarkers for #PersonalizedHealth.
👇Thread 🧵(8/9)
After the right lung is surgically removed, bronchial trees exhibit enormous plasticity, reorganizing for energy efficiency while regenerating lost tissue volume.
⇨ Fluid–structure interactions act as powerful mechanisms for transmitting information continuously across scales.
👇Thread 🧵(7/9)
⇨ Fluid–structure interactions act as powerful mechanisms for transmitting information continuously across scales.
👇Thread 🧵(7/9)
January 15, 2025 at 8:27 AM
After the right lung is surgically removed, bronchial trees exhibit enormous plasticity, reorganizing for energy efficiency while regenerating lost tissue volume.
⇨ Fluid–structure interactions act as powerful mechanisms for transmitting information continuously across scales.
👇Thread 🧵(7/9)
⇨ Fluid–structure interactions act as powerful mechanisms for transmitting information continuously across scales.
👇Thread 🧵(7/9)
Using #SkelePlex, we show that the fractalization of the lung happens on the go during the pseudoglandular stage of lung development.
Branch morphology adapts plastically depending on tip number, illustrating how local cues drive efficient lung formation.
👇Thread 🧵(6/9)
Branch morphology adapts plastically depending on tip number, illustrating how local cues drive efficient lung formation.
👇Thread 🧵(6/9)
January 15, 2025 at 8:27 AM
Using #SkelePlex, we show that the fractalization of the lung happens on the go during the pseudoglandular stage of lung development.
Branch morphology adapts plastically depending on tip number, illustrating how local cues drive efficient lung formation.
👇Thread 🧵(6/9)
Branch morphology adapts plastically depending on tip number, illustrating how local cues drive efficient lung formation.
👇Thread 🧵(6/9)
Tracking lung remodeling has been a challenge—until now.
We developed #SkelePlex, an #opensource tool for tracking bronchial tree growth & regeneration.
Validated on:
🐭 Mouse development
🐶 Dog lung regeneration post-surgery
🧑⚕️ #COPD patient cohorts
👇Thread 🧵(5/9)
We developed #SkelePlex, an #opensource tool for tracking bronchial tree growth & regeneration.
Validated on:
🐭 Mouse development
🐶 Dog lung regeneration post-surgery
🧑⚕️ #COPD patient cohorts
👇Thread 🧵(5/9)
January 15, 2025 at 8:27 AM
Tracking lung remodeling has been a challenge—until now.
We developed #SkelePlex, an #opensource tool for tracking bronchial tree growth & regeneration.
Validated on:
🐭 Mouse development
🐶 Dog lung regeneration post-surgery
🧑⚕️ #COPD patient cohorts
👇Thread 🧵(5/9)
We developed #SkelePlex, an #opensource tool for tracking bronchial tree growth & regeneration.
Validated on:
🐭 Mouse development
🐶 Dog lung regeneration post-surgery
🧑⚕️ #COPD patient cohorts
👇Thread 🧵(5/9)
As flow rate Q depends on tip number, diameter and wall thickness adjust naturally across scales!
This universal, #scaleinvariant mechanism enables lungs to function efficiently across species—whether in mice 🐭, dogs 🐶, or humans 🧑⚕️.
👇Thread 🧵(4/9)
This universal, #scaleinvariant mechanism enables lungs to function efficiently across species—whether in mice 🐭, dogs 🐶, or humans 🧑⚕️.
👇Thread 🧵(4/9)
January 15, 2025 at 8:27 AM
As flow rate Q depends on tip number, diameter and wall thickness adjust naturally across scales!
This universal, #scaleinvariant mechanism enables lungs to function efficiently across species—whether in mice 🐭, dogs 🐶, or humans 🧑⚕️.
👇Thread 🧵(4/9)
This universal, #scaleinvariant mechanism enables lungs to function efficiently across species—whether in mice 🐭, dogs 🐶, or humans 🧑⚕️.
👇Thread 🧵(4/9)