Nikolas Stefanidis
@nikolasstefanidis.bsky.social
PhD student in the Tsakiridis lab - Computational modelling of nervous system development
Reposted by Nikolas Stefanidis
Some beautiful green-fluorescent-protein (GFP)-expressing larval brains and neurons generated by my undergraduate students last week. A special shout-out for anyone who spots the neuromuscular junctions.
November 22, 2025 at 7:47 PM
Some beautiful green-fluorescent-protein (GFP)-expressing larval brains and neurons generated by my undergraduate students last week. A special shout-out for anyone who spots the neuromuscular junctions.
Reposted by Nikolas Stefanidis
Reposted by Nikolas Stefanidis
Attempt number seven at uploading this video of intermediate filaments in an enormous COS7 cell. I have a feeling the BlueSky compression will not do it any favors.
November 21, 2025 at 3:54 AM
Attempt number seven at uploading this video of intermediate filaments in an enormous COS7 cell. I have a feeling the BlueSky compression will not do it any favors.
Reposted by Nikolas Stefanidis
Reposted by Nikolas Stefanidis
Always ask yourself:
“What evidence would convince me that I’m wrong?”
If the answer is, “nothing,” then you are not adhering to the rules of science or logic.
thelogicofscience.com/2019/03/05/h...
“What evidence would convince me that I’m wrong?”
If the answer is, “nothing,” then you are not adhering to the rules of science or logic.
thelogicofscience.com/2019/03/05/h...
How not to science: Lessons from flat earthers and climate change deniers
Science is an amazingly powerful tool for disentangling fact and fiction. When done correctly, it is a systematic, objective, unbiased, and self-correcting method for understanding our universe. Un…
thelogicofscience.com
November 17, 2025 at 12:58 PM
Always ask yourself:
“What evidence would convince me that I’m wrong?”
If the answer is, “nothing,” then you are not adhering to the rules of science or logic.
thelogicofscience.com/2019/03/05/h...
“What evidence would convince me that I’m wrong?”
If the answer is, “nothing,” then you are not adhering to the rules of science or logic.
thelogicofscience.com/2019/03/05/h...
Reposted by Nikolas Stefanidis
⏰ Deadline in two weeks! ⏰
Work at the interface of biology + computation to build a virtual human embryo to predict developmental success and failure.
Happy to answer questions!
Work at the interface of biology + computation to build a virtual human embryo to predict developmental success and failure.
Happy to answer questions!
November 17, 2025 at 1:41 PM
⏰ Deadline in two weeks! ⏰
Work at the interface of biology + computation to build a virtual human embryo to predict developmental success and failure.
Happy to answer questions!
Work at the interface of biology + computation to build a virtual human embryo to predict developmental success and failure.
Happy to answer questions!
Reposted by Nikolas Stefanidis
Next Monday, we welcome @cshambaugh.bsky.social from the University of Oregon in our ROTO Lecture Series who will talk about dialectical biology. Just register via the link and join the talk and discussion at 4pm (CET): rotorub.wordpress.com/roto-lecture...
#HPBio #PhilSci #HistSci
#HPBio #PhilSci #HistSci
November 17, 2025 at 2:43 PM
Next Monday, we welcome @cshambaugh.bsky.social from the University of Oregon in our ROTO Lecture Series who will talk about dialectical biology. Just register via the link and join the talk and discussion at 4pm (CET): rotorub.wordpress.com/roto-lecture...
#HPBio #PhilSci #HistSci
#HPBio #PhilSci #HistSci
Reposted by Nikolas Stefanidis
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 Nikolas Stefanidis
Next Monday, we'll have our first reading group session in this semester. We'll discuss "The epistemic superiority of experiment to simulation" by Sherrilyn Roush: link.springer.com/article/10.1...
Wanna join the discussion at 4pm CET? Just write an e-mail to jan.baedke[at]rub.de!
#HPBio #PhilSci
Wanna join the discussion at 4pm CET? Just write an e-mail to jan.baedke[at]rub.de!
#HPBio #PhilSci
November 10, 2025 at 3:07 PM
Next Monday, we'll have our first reading group session in this semester. We'll discuss "The epistemic superiority of experiment to simulation" by Sherrilyn Roush: link.springer.com/article/10.1...
Wanna join the discussion at 4pm CET? Just write an e-mail to jan.baedke[at]rub.de!
#HPBio #PhilSci
Wanna join the discussion at 4pm CET? Just write an e-mail to jan.baedke[at]rub.de!
#HPBio #PhilSci
Reposted by Nikolas Stefanidis
How can we organize current theoretical approaches for developmental biology - from information to dynamical systems & GRNs - into a common framework?
We propose to think along Marr's 3 levels: computational problem, algorithm, implementation
Check out our review:
arxiv.org/abs/2510.24536
We propose to think along Marr's 3 levels: computational problem, algorithm, implementation
Check out our review:
arxiv.org/abs/2510.24536
November 10, 2025 at 6:46 AM
How can we organize current theoretical approaches for developmental biology - from information to dynamical systems & GRNs - into a common framework?
We propose to think along Marr's 3 levels: computational problem, algorithm, implementation
Check out our review:
arxiv.org/abs/2510.24536
We propose to think along Marr's 3 levels: computational problem, algorithm, implementation
Check out our review:
arxiv.org/abs/2510.24536
Reposted by Nikolas Stefanidis
🧠✨ Genetic Tools Atlas 3.0 is here!
The GTA now has an additional 750 datasets, including 80+ mouse whole-brain light sheet microscopy images as well as the first macaque datasets.
🔗 https://portal.brain-map.org/genetic-tools/genetic-tools-atlas
#neuroskyence
The GTA now has an additional 750 datasets, including 80+ mouse whole-brain light sheet microscopy images as well as the first macaque datasets.
🔗 https://portal.brain-map.org/genetic-tools/genetic-tools-atlas
#neuroskyence
November 2, 2025 at 3:46 PM
🧠✨ Genetic Tools Atlas 3.0 is here!
The GTA now has an additional 750 datasets, including 80+ mouse whole-brain light sheet microscopy images as well as the first macaque datasets.
🔗 https://portal.brain-map.org/genetic-tools/genetic-tools-atlas
#neuroskyence
The GTA now has an additional 750 datasets, including 80+ mouse whole-brain light sheet microscopy images as well as the first macaque datasets.
🔗 https://portal.brain-map.org/genetic-tools/genetic-tools-atlas
#neuroskyence
Reposted by Nikolas Stefanidis
"Kaboom!"/"Extinction, Fast and Slow"
Director emerita Lorraine Daston is featured in the current issue of @lrb.co.uk and on The LRB Podcast 🌋
"Extinction is a protracted, uneven process, and hard to square with our mental picture of abrupt catastrophe."
🗞️ bit.ly/3L72ddi
🎧 bit.ly/4huQXd
#HistSci
Director emerita Lorraine Daston is featured in the current issue of @lrb.co.uk and on The LRB Podcast 🌋
"Extinction is a protracted, uneven process, and hard to square with our mental picture of abrupt catastrophe."
🗞️ bit.ly/3L72ddi
🎧 bit.ly/4huQXd
#HistSci
Lorraine Daston · Kaboom! Slow-Motion Extinction
Historians who address such topics as extinction, which straddle the history of humans and of the Earth, face the...
bit.ly
October 28, 2025 at 3:07 PM
"Kaboom!"/"Extinction, Fast and Slow"
Director emerita Lorraine Daston is featured in the current issue of @lrb.co.uk and on The LRB Podcast 🌋
"Extinction is a protracted, uneven process, and hard to square with our mental picture of abrupt catastrophe."
🗞️ bit.ly/3L72ddi
🎧 bit.ly/4huQXd
#HistSci
Director emerita Lorraine Daston is featured in the current issue of @lrb.co.uk and on The LRB Podcast 🌋
"Extinction is a protracted, uneven process, and hard to square with our mental picture of abrupt catastrophe."
🗞️ bit.ly/3L72ddi
🎧 bit.ly/4huQXd
#HistSci
Reposted by Nikolas Stefanidis
Our lab studies how animals regenerate their body, e.g. how crustaceans regenerate broken legs. One of our aims is to understand if regeneration re-uses the gene networks that built the legs in the first place. Arthur Monternier, an artist in our team, captured the question in this cartoon.
October 27, 2025 at 3:25 PM
Our lab studies how animals regenerate their body, e.g. how crustaceans regenerate broken legs. One of our aims is to understand if regeneration re-uses the gene networks that built the legs in the first place. Arthur Monternier, an artist in our team, captured the question in this cartoon.
Reposted by Nikolas Stefanidis
I am absolutely delighted to share the invited speakers for our upcoming @bsdb.bsky.social "Molecules to Morphogenesis" meeting!
Registration and abstract submission is now open - join us!
bsdb.org/meetings/
March 23-26, 2026 - UK
Registration and abstract submission is now open - join us!
bsdb.org/meetings/
March 23-26, 2026 - UK
October 23, 2025 at 5:25 PM
I am absolutely delighted to share the invited speakers for our upcoming @bsdb.bsky.social "Molecules to Morphogenesis" meeting!
Registration and abstract submission is now open - join us!
bsdb.org/meetings/
March 23-26, 2026 - UK
Registration and abstract submission is now open - join us!
bsdb.org/meetings/
March 23-26, 2026 - UK
Reposted by Nikolas Stefanidis
New paper: "Modelling the prebiotic origins of regulation and agency in evolving protocell ecologies"
Happy to have participated in this work!
royalsocietypublishing.org/doi/10.1098/...
Happy to have participated in this work!
royalsocietypublishing.org/doi/10.1098/...
Modelling the prebiotic origins of regulation and agency in evolving protocell ecologies | Philosophical Transactions of the Royal Society B: Biological Sciences
How and why did natural systems develop the first mechanisms of regulation? How could they turn into adaptive agents in a minimal (though deeply meaningful) biological sense? A novel simulation platform, Araudia, has been implemented to address these ...
royalsocietypublishing.org
October 2, 2025 at 12:37 PM
New paper: "Modelling the prebiotic origins of regulation and agency in evolving protocell ecologies"
Happy to have participated in this work!
royalsocietypublishing.org/doi/10.1098/...
Happy to have participated in this work!
royalsocietypublishing.org/doi/10.1098/...
Reposted by Nikolas Stefanidis
Time for a thread!🧵 How different is the molecular organization of thylakoids in “higher” plants🌱? To find out, we teamed up with @profmattjohnson.bsky.social to dive into spinach chloroplasts with #CryoET ❄️🔬. Curious? ..Read on!
#TeamTomo #PlantScience 🧪 🧶🧬 🌾
elifesciences.org/articles/105...
1/🧵
#TeamTomo #PlantScience 🧪 🧶🧬 🌾
elifesciences.org/articles/105...
1/🧵
September 25, 2025 at 6:00 PM
Time for a thread!🧵 How different is the molecular organization of thylakoids in “higher” plants🌱? To find out, we teamed up with @profmattjohnson.bsky.social to dive into spinach chloroplasts with #CryoET ❄️🔬. Curious? ..Read on!
#TeamTomo #PlantScience 🧪 🧶🧬 🌾
elifesciences.org/articles/105...
1/🧵
#TeamTomo #PlantScience 🧪 🧶🧬 🌾
elifesciences.org/articles/105...
1/🧵
Reposted by Nikolas Stefanidis
🚀 Excited to share scPortrait! Led by Sophia Mädler & Niklas Schmacke w/ the Mann lab — a new @scverse tool for standardized single-cell image data. Enables ML-ready extraction, >1B cell processing, cross-omics, & cancer macrophage insights.
🔗 www.biorxiv.org/content/10.1...
🔗 www.biorxiv.org/content/10.1...
September 28, 2025 at 5:50 PM
🚀 Excited to share scPortrait! Led by Sophia Mädler & Niklas Schmacke w/ the Mann lab — a new @scverse tool for standardized single-cell image data. Enables ML-ready extraction, >1B cell processing, cross-omics, & cancer macrophage insights.
🔗 www.biorxiv.org/content/10.1...
🔗 www.biorxiv.org/content/10.1...
Reposted by Nikolas Stefanidis
Now out in final published form - with a new title "Mechanical control of cell fate decisions in the skin epidermis" and simulations/quantifications! See below for thread of how unbalanced tensions can bias fate choices in minimal 3D models of tissues! www.nature.com/articles/s41...
Happy to share the latest work from Preeti Sahu, with Adriana Sanchez-Danes on the biomechanics of cell fate choices during tumor initiation! We implement/test a 3D vertex model with proliferation and fate choices for multilayered tissues! See 🧵 below (1/n) bit.ly/3ZXxJzk
September 26, 2025 at 2:14 PM
Now out in final published form - with a new title "Mechanical control of cell fate decisions in the skin epidermis" and simulations/quantifications! See below for thread of how unbalanced tensions can bias fate choices in minimal 3D models of tissues! www.nature.com/articles/s41...
Reposted by Nikolas Stefanidis
We only had a very minor contribution to this story with Alexis, but definitly worth a reading for those interested by patterning, precision and refinment. Nice combining of quantitative live imaging, modeling and optogenetics to dissect vein patterning dynamics
www.cell.com/developmenta...
www.cell.com/developmenta...
Signaling-dependent refinement of cell fate choice during tissue remodeling in Drosophila pupal wings
Herszterg et al. show that during morphogenesis of the Drosophila pupal wing, a wave
of Notch signaling activity updates cell fates to ensure robust and precise patterning
of wing veins.
www.cell.com
September 19, 2025 at 8:35 AM
We only had a very minor contribution to this story with Alexis, but definitly worth a reading for those interested by patterning, precision and refinment. Nice combining of quantitative live imaging, modeling and optogenetics to dissect vein patterning dynamics
www.cell.com/developmenta...
www.cell.com/developmenta...
Reposted by Nikolas Stefanidis
Fresh from the press💥 We asked what happens when you evolve gene regulatory networks computationally at scale. Do general principles of GRN evolution jump out? Is the process predictable? Read on to find out @prxlife.bsky.social @crick.ac.uk @ucl-ipls.bsky.social 👉 journals.aps.org/prxlife/abst...
Gene Network Organization, Mutation, and Selection Collectively Drive Developmental Pattern Evolvability and Predictability
The historical order in which mutations appear during evolution determine the evolutionary trajectory of gene regulatory networks and influence how developmental patterns change and diversify over tim...
journals.aps.org
September 16, 2025 at 7:46 PM
Fresh from the press💥 We asked what happens when you evolve gene regulatory networks computationally at scale. Do general principles of GRN evolution jump out? Is the process predictable? Read on to find out @prxlife.bsky.social @crick.ac.uk @ucl-ipls.bsky.social 👉 journals.aps.org/prxlife/abst...
Reposted by Nikolas Stefanidis
Geometry first: how positional cues dictate fate in bilayered epithelia thenode.biologists.com/geometry-fir...
Geometry first: how positional cues dictate fate in bilayered epithelia - the Node
Behind the paper story focussed on research on early fate decisions in bilayered epithelia.
thenode.biologists.com
September 9, 2025 at 7:12 AM
Geometry first: how positional cues dictate fate in bilayered epithelia thenode.biologists.com/geometry-fir...
Reposted by Nikolas Stefanidis
The last paper from my PhD is now online! 🥳
👉 pubs.aip.org/aip/rsi/arti...
We have designed a new device based on the elastic micropillar array assay to measure the detachment forces between spread cells.
@leidenphysics.bsky.social
👉 pubs.aip.org/aip/rsi/arti...
We have designed a new device based on the elastic micropillar array assay to measure the detachment forces between spread cells.
@leidenphysics.bsky.social
September 5, 2025 at 1:11 PM
The last paper from my PhD is now online! 🥳
👉 pubs.aip.org/aip/rsi/arti...
We have designed a new device based on the elastic micropillar array assay to measure the detachment forces between spread cells.
@leidenphysics.bsky.social
👉 pubs.aip.org/aip/rsi/arti...
We have designed a new device based on the elastic micropillar array assay to measure the detachment forces between spread cells.
@leidenphysics.bsky.social
Reposted by Nikolas Stefanidis
From a spark of an idea to a funded project. The missing link? The right collaborator 🤝
But finding that expert in another department can feel like searching for a needle in a haystack
✅ At Glink, we make collaborative science easy!
🚀 Visit us at www.glink.ltd to find your next research partner
But finding that expert in another department can feel like searching for a needle in a haystack
✅ At Glink, we make collaborative science easy!
🚀 Visit us at www.glink.ltd to find your next research partner
Glink - Collaborative science made easy
Glink - Collaborative science made easy
www.glink.ltd
September 3, 2025 at 7:39 AM
From a spark of an idea to a funded project. The missing link? The right collaborator 🤝
But finding that expert in another department can feel like searching for a needle in a haystack
✅ At Glink, we make collaborative science easy!
🚀 Visit us at www.glink.ltd to find your next research partner
But finding that expert in another department can feel like searching for a needle in a haystack
✅ At Glink, we make collaborative science easy!
🚀 Visit us at www.glink.ltd to find your next research partner
Big thanks to the authors - incredibly helpful
From genes to patterns: five key dynamical systems concepts to decode developmental regulatory mechanisms url: journals.biologists.com/dev/article/...
From genes to patterns: five key dynamical systems concepts to decode developmental regulatory mechanisms url: journals.biologists.com/dev/article/...
From genes to patterns: five key dynamical systems concepts to decode developmental regulatory mechanisms
Summary: Dynamical systems theory provides a powerful quantitative and intuitive framework to understand developmental processes. This Primer brings key concepts of this framework to the ever-growing ...
journals.biologists.com
August 29, 2025 at 9:23 AM
Big thanks to the authors - incredibly helpful
From genes to patterns: five key dynamical systems concepts to decode developmental regulatory mechanisms url: journals.biologists.com/dev/article/...
From genes to patterns: five key dynamical systems concepts to decode developmental regulatory mechanisms url: journals.biologists.com/dev/article/...
Reposted by Nikolas Stefanidis
Our latest: We developed a chemo-optogenetic system for precise spatiotemporal control of morphogen production. Using dual light + small molecule control of Sonic Hedgehog production, we recapitulated neural tube patterning in vitro & measured spread of Shh
🧵
www.sciencedirect.com/science/arti...
🧵
www.sciencedirect.com/science/arti...
Investigating morphogen and patterning dynamics with optogenetic control of morphogen production
Morphogen gradients provide the patterning cues that instruct cell fate decisions during development. Here, we establish an optogenetic system for the…
www.sciencedirect.com
August 26, 2025 at 8:28 AM
Our latest: We developed a chemo-optogenetic system for precise spatiotemporal control of morphogen production. Using dual light + small molecule control of Sonic Hedgehog production, we recapitulated neural tube patterning in vitro & measured spread of Shh
🧵
www.sciencedirect.com/science/arti...
🧵
www.sciencedirect.com/science/arti...