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
Pinned
Dagmar Iber & CoBi
@iberd.bsky.social
· Jun 11
PhD Position - 3D Cell-Based Tissue Simulation Framework
jobs.ethz.ch
Are you a C++ expert and interested in making 3D cell-based tissue simulations with #SimuCell3D ever more powerful? Please apply and join us as #Master student, #PhD student or #Post-Doc!!
jobs.ethz.ch/job/view/JOP...
jobs.ethz.ch/job/view/JOP...
x.com/DagmarIber/s...
jobs.ethz.ch/job/view/JOP...
jobs.ethz.ch/job/view/JOP...
x.com/DagmarIber/s...
Reposted by Dagmar Iber & CoBi
"Within the competition to bring this field to a new level, SimuCell3D is remarkable and will mark a clear evolution of the topic."
🥁That’s what the committee said about this #SIBRemarkableOutputs 2024
👉Discover the output: tinyurl.com/53arz2rz
@iberd.bsky.social
🥁That’s what the committee said about this #SIBRemarkableOutputs 2024
👉Discover the output: tinyurl.com/53arz2rz
@iberd.bsky.social
September 18, 2025 at 2:04 PM
"Within the competition to bring this field to a new level, SimuCell3D is remarkable and will mark a clear evolution of the topic."
🥁That’s what the committee said about this #SIBRemarkableOutputs 2024
👉Discover the output: tinyurl.com/53arz2rz
@iberd.bsky.social
🥁That’s what the committee said about this #SIBRemarkableOutputs 2024
👉Discover the output: tinyurl.com/53arz2rz
@iberd.bsky.social
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.
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)
Let me add our paper to this review of mechanical drivers of NT folding.
We showed that mammalian spinal #neuraltube folding is primarily driven by #mesoderm expansion and #zippering. #Hingepoints emerge as a result of these extrinsic forces.
www.pnas.org/doi/10.1073/...
x.com/DagmarIber/s...
We showed that mammalian spinal #neuraltube folding is primarily driven by #mesoderm expansion and #zippering. #Hingepoints emerge as a result of these extrinsic forces.
www.pnas.org/doi/10.1073/...
x.com/DagmarIber/s...
June 21, 2025 at 9:41 AM
Let me add our paper to this review of mechanical drivers of NT folding.
We showed that mammalian spinal #neuraltube folding is primarily driven by #mesoderm expansion and #zippering. #Hingepoints emerge as a result of these extrinsic forces.
www.pnas.org/doi/10.1073/...
x.com/DagmarIber/s...
We showed that mammalian spinal #neuraltube folding is primarily driven by #mesoderm expansion and #zippering. #Hingepoints emerge as a result of these extrinsic forces.
www.pnas.org/doi/10.1073/...
x.com/DagmarIber/s...
Reposted by Dagmar Iber & CoBi
Epithelial tissues are well-known to invade free space and stop proliferation at confluency.
Do we know what regulates cell proliferation spatially and temporally?
🧵by @dedenonmathieu.bsky.social
Do we know what regulates cell proliferation spatially and temporally?
🧵by @dedenonmathieu.bsky.social
June 15, 2025 at 1:24 PM
Epithelial tissues are well-known to invade free space and stop proliferation at confluency.
Do we know what regulates cell proliferation spatially and temporally?
🧵by @dedenonmathieu.bsky.social
Do we know what regulates cell proliferation spatially and temporally?
🧵by @dedenonmathieu.bsky.social
Are you a C++ expert and interested in making 3D cell-based tissue simulations with #SimuCell3D ever more powerful? Please apply and join us as #Master student, #PhD student or #Post-Doc!!
jobs.ethz.ch/job/view/JOP...
jobs.ethz.ch/job/view/JOP...
x.com/DagmarIber/s...
jobs.ethz.ch/job/view/JOP...
jobs.ethz.ch/job/view/JOP...
x.com/DagmarIber/s...
PhD Position - 3D Cell-Based Tissue Simulation Framework
jobs.ethz.ch
June 11, 2025 at 11:30 AM
Are you a C++ expert and interested in making 3D cell-based tissue simulations with #SimuCell3D ever more powerful? Please apply and join us as #Master student, #PhD student or #Post-Doc!!
jobs.ethz.ch/job/view/JOP...
jobs.ethz.ch/job/view/JOP...
x.com/DagmarIber/s...
jobs.ethz.ch/job/view/JOP...
jobs.ethz.ch/job/view/JOP...
x.com/DagmarIber/s...
Reposted by Dagmar Iber & CoBi
SimuCell3D … for simulating tissue mechanics with cell polarization. @iberd.bsky.social
Dimension: 3D
Software language: C++
Download: git.bsse.ethz.ch/iber/Publica...
bsky.app/profile/epim...
Dimension: 3D
Software language: C++
Download: git.bsse.ethz.ch/iber/Publica...
bsky.app/profile/epim...
June 8, 2025 at 7:01 AM
SimuCell3D … for simulating tissue mechanics with cell polarization. @iberd.bsky.social
Dimension: 3D
Software language: C++
Download: git.bsse.ethz.ch/iber/Publica...
bsky.app/profile/epim...
Dimension: 3D
Software language: C++
Download: git.bsse.ethz.ch/iber/Publica...
bsky.app/profile/epim...
🚀 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...
Reposted by Dagmar Iber & CoBi
🚨 We are thrilled to announce our amazing list of keynote speakers!!
@PCusachs
@GeorgHalder
@hirashima0203.bsky.social
@iberd.bsky.social
@johannaivaska.bsky.social
@gijsjekoenderink.bsky.social
@laurentnguyen.com
@renkawitzteam.bsky.social
@Sixt_Lab
...
@PCusachs
@GeorgHalder
@hirashima0203.bsky.social
@iberd.bsky.social
@johannaivaska.bsky.social
@gijsjekoenderink.bsky.social
@laurentnguyen.com
@renkawitzteam.bsky.social
@Sixt_Lab
...
February 4, 2025 at 7:30 AM
🚨 We are thrilled to announce our amazing list of keynote speakers!!
@PCusachs
@GeorgHalder
@hirashima0203.bsky.social
@iberd.bsky.social
@johannaivaska.bsky.social
@gijsjekoenderink.bsky.social
@laurentnguyen.com
@renkawitzteam.bsky.social
@Sixt_Lab
...
@PCusachs
@GeorgHalder
@hirashima0203.bsky.social
@iberd.bsky.social
@johannaivaska.bsky.social
@gijsjekoenderink.bsky.social
@laurentnguyen.com
@renkawitzteam.bsky.social
@Sixt_Lab
...
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...
Thoughtful perspective by Alexander Mietke on our recent work on #bladdercancer @naturephysics.bsky.social : www.nature.com/articles/s41...
January 23, 2025 at 8:08 PM
Thoughtful perspective by Alexander Mietke on our recent work on #bladdercancer @naturephysics.bsky.social : www.nature.com/articles/s41...
How does an #embryo build an energy-efficient #fractal #lung in time for the first breath at birth? 🫁
Discover the mechanical forces shaping the bronchial tree in our latest preprint: #LungDevelopment #Mechanobiology
doi.org/10.1101/2025...
👇Thread 🧵(1/9)
Discover the mechanical forces shaping the bronchial tree in our latest preprint: #LungDevelopment #Mechanobiology
doi.org/10.1101/2025...
👇Thread 🧵(1/9)
January 15, 2025 at 8:27 AM
How does an #embryo build an energy-efficient #fractal #lung in time for the first breath at birth? 🫁
Discover the mechanical forces shaping the bronchial tree in our latest preprint: #LungDevelopment #Mechanobiology
doi.org/10.1101/2025...
👇Thread 🧵(1/9)
Discover the mechanical forces shaping the bronchial tree in our latest preprint: #LungDevelopment #Mechanobiology
doi.org/10.1101/2025...
👇Thread 🧵(1/9)
Our paper "Morphometry and mechanical instability at the onset of epithelial bladder cancer" is now out in
@naturephysics.bsky.social :
rdcu.be/d5rTP
#BladderCancer #Cancer #Tumor #Biomechanics #Morphometry #ComputationalModeling
@naturephysics.bsky.social :
rdcu.be/d5rTP
#BladderCancer #Cancer #Tumor #Biomechanics #Morphometry #ComputationalModeling
Morphometry and mechanical instability at the onset of epithelial bladder cancer
Nature Physics - Carcinoma subtypes are normally linked to specific genetic alterations, but tissue mechanical changes also play a role. Now, aberrant morphologies resembling bladder carcinoma are...
rdcu.be
January 7, 2025 at 12:00 PM
Our paper "Morphometry and mechanical instability at the onset of epithelial bladder cancer" is now out in
@naturephysics.bsky.social :
rdcu.be/d5rTP
#BladderCancer #Cancer #Tumor #Biomechanics #Morphometry #ComputationalModeling
@naturephysics.bsky.social :
rdcu.be/d5rTP
#BladderCancer #Cancer #Tumor #Biomechanics #Morphometry #ComputationalModeling
We are looking for a #PostDoc with experience in #BioImage Analysis @ETH in #Basel, CH.
Our mission: translate image-derived insights into mechanistic models of development & disease #lightsheet #ultrasound #CT
www.jobs.ethz.ch/job/view/JOP...
Our mission: translate image-derived insights into mechanistic models of development & disease #lightsheet #ultrasound #CT
www.jobs.ethz.ch/job/view/JOP...
Post-Doc Position: Bio-Image Analysis
www.jobs.ethz.ch
December 9, 2024 at 7:46 AM
We are looking for a #PostDoc with experience in #BioImage Analysis @ETH in #Basel, CH.
Our mission: translate image-derived insights into mechanistic models of development & disease #lightsheet #ultrasound #CT
www.jobs.ethz.ch/job/view/JOP...
Our mission: translate image-derived insights into mechanistic models of development & disease #lightsheet #ultrasound #CT
www.jobs.ethz.ch/job/view/JOP...