Nikolas Stefanidis
@nikolasstefanidis.bsky.social
PhD student working with Alexander Fletcher and the Tsakiridis lab on the computational modelling of posterior nervous system development
Reposted by Nikolas Stefanidis
The world feels rough right now
So please enjoy this shrimp, filmed off Cozumel, Mexico. It may be a larval reef shrimp, but we don’t know what species or how long it lives or what it eats. The world is still full of wonder and beauty and mystery.
🎥 @pedrovalenciam scuba diver on Insta
So please enjoy this shrimp, filmed off Cozumel, Mexico. It may be a larval reef shrimp, but we don’t know what species or how long it lives or what it eats. The world is still full of wonder and beauty and mystery.
🎥 @pedrovalenciam scuba diver on Insta
January 8, 2026 at 8:20 PM
The world feels rough right now
So please enjoy this shrimp, filmed off Cozumel, Mexico. It may be a larval reef shrimp, but we don’t know what species or how long it lives or what it eats. The world is still full of wonder and beauty and mystery.
🎥 @pedrovalenciam scuba diver on Insta
So please enjoy this shrimp, filmed off Cozumel, Mexico. It may be a larval reef shrimp, but we don’t know what species or how long it lives or what it eats. The world is still full of wonder and beauty and mystery.
🎥 @pedrovalenciam scuba diver on Insta
Reposted by Nikolas Stefanidis
Another fascinating - and totally serendipitous - example of how human biological sex isn't always binary, despite executive orders that it is. In this case an XX/XY mosaic individual was a fertile female. Other XX/XY mosaics can be phenotypically male.
A fascinating case report.
The DNA of a female murder victim was genotyped and it turns out that she has been a chimera: a mixture of 46XX/46XY cell lines.
The analysis (STR-based) found:
1. The maternal chromosome was identical between the two cell lines.
www.fsigenetics.com/article/S187...
1/6
The DNA of a female murder victim was genotyped and it turns out that she has been a chimera: a mixture of 46XX/46XY cell lines.
The analysis (STR-based) found:
1. The maternal chromosome was identical between the two cell lines.
www.fsigenetics.com/article/S187...
1/6
Forensic analysis of a parthenogenetic 46, XX/46, XY congenital chimera: A case report
In forensic identification, chimerism is an extremely rare phenomenon in which DNA
samples can easily be misidentified as mixtures from two individuals. If only a single
cell population from the chime...
www.fsigenetics.com
January 6, 2026 at 10:24 PM
Another fascinating - and totally serendipitous - example of how human biological sex isn't always binary, despite executive orders that it is. In this case an XX/XY mosaic individual was a fertile female. Other XX/XY mosaics can be phenotypically male.
Reposted by Nikolas Stefanidis
⏰ Deadline Approaching! ⏰
📅 15 January 2026
Under two weeks to apply for our fully funded PhD project “Engineering an in vitro human embryo implantation platform to study pathologies arising in early pregnancy” at @sheffielduni.bsky.social. #development #endometrium #materialsscience
📅 15 January 2026
Under two weeks to apply for our fully funded PhD project “Engineering an in vitro human embryo implantation platform to study pathologies arising in early pregnancy” at @sheffielduni.bsky.social. #development #endometrium #materialsscience
January 6, 2026 at 2:02 PM
⏰ Deadline Approaching! ⏰
📅 15 January 2026
Under two weeks to apply for our fully funded PhD project “Engineering an in vitro human embryo implantation platform to study pathologies arising in early pregnancy” at @sheffielduni.bsky.social. #development #endometrium #materialsscience
📅 15 January 2026
Under two weeks to apply for our fully funded PhD project “Engineering an in vitro human embryo implantation platform to study pathologies arising in early pregnancy” at @sheffielduni.bsky.social. #development #endometrium #materialsscience
Reposted by Nikolas Stefanidis
Fuse it or lose it: cell fusion drives developmental progression
This Research Highlight showcases work by Owen Funk, Daniel Levy and David Fay:
journals.biologists.com/dev/article/...
This Research Highlight showcases work by Owen Funk, Daniel Levy and David Fay:
journals.biologists.com/dev/article/...
December 23, 2025 at 9:46 AM
Fuse it or lose it: cell fusion drives developmental progression
This Research Highlight showcases work by Owen Funk, Daniel Levy and David Fay:
journals.biologists.com/dev/article/...
This Research Highlight showcases work by Owen Funk, Daniel Levy and David Fay:
journals.biologists.com/dev/article/...
Reposted by Nikolas Stefanidis
This movie shows lysosomes (orange) and keratin (gray) in a cultured cell over 10 minutes.
December 12, 2025 at 6:20 AM
This movie shows lysosomes (orange) and keratin (gray) in a cultured cell over 10 minutes.
Super interesting read about the connections of human and AI evolution 🧬
---
What is the future of intelligence? The answer could lie in the story of its evolution www.nature.com/articles/d41...
---
What is the future of intelligence? The answer could lie in the story of its evolution www.nature.com/articles/d41...
What is the future of intelligence? The answer could lie in the story of its evolution
The advent of artificial intelligence might be just the latest stage in a guiding biological process that has produced ever more complex, mutually dependent organisms over the history of life.
www.nature.com
December 8, 2025 at 11:35 AM
Super interesting read about the connections of human and AI evolution 🧬
---
What is the future of intelligence? The answer could lie in the story of its evolution www.nature.com/articles/d41...
---
What is the future of intelligence? The answer could lie in the story of its evolution www.nature.com/articles/d41...
Reposted by Nikolas Stefanidis
Great to see this published: Fitting dynamical landscape models to single-cell data, creating interpretable maps of cell decision making & developmental logic
Applied to neural tube patterning, we show how morphogen signals reshape landscapes and drive fate decisions
www.pnas.org/doi/10.1073/...
Applied to neural tube patterning, we show how morphogen signals reshape landscapes and drive fate decisions
www.pnas.org/doi/10.1073/...
Reconstructing Waddington’s landscape from data | PNAS
The development of a zygote into a functional organism requires that this single progenitor
cell gives rise to numerous distinct cell types. Attemp...
www.pnas.org
December 4, 2025 at 6:29 AM
Great to see this published: Fitting dynamical landscape models to single-cell data, creating interpretable maps of cell decision making & developmental logic
Applied to neural tube patterning, we show how morphogen signals reshape landscapes and drive fate decisions
www.pnas.org/doi/10.1073/...
Applied to neural tube patterning, we show how morphogen signals reshape landscapes and drive fate decisions
www.pnas.org/doi/10.1073/...
Reposted by Nikolas Stefanidis
New preprint! Do you like ocean waves? We found similar waves on bacterial colonies! We found that this collective behavior, known as rippling, is nothing but surface waves on an active nematic. @princeton.edu @mpipks.bsky.social @ub.edu @icreacommunity.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
December 2, 2025 at 8:02 PM
New preprint! Do you like ocean waves? We found similar waves on bacterial colonies! We found that this collective behavior, known as rippling, is nothing but surface waves on an active nematic. @princeton.edu @mpipks.bsky.social @ub.edu @icreacommunity.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Nikolas Stefanidis
Perseverance on the move again, proceeding toward Lac de Charmes, a major science target on the plains beyond the rim
ℹ️ www.jpl.nasa.gov/news/nasas-p...
#Mars Nov. 29, 2025 - Sol 1698
Credits: NASA/JPL-Caltech 🧪🔭
ℹ️ www.jpl.nasa.gov/news/nasas-p...
#Mars Nov. 29, 2025 - Sol 1698
Credits: NASA/JPL-Caltech 🧪🔭
November 29, 2025 at 3:01 PM
Perseverance on the move again, proceeding toward Lac de Charmes, a major science target on the plains beyond the rim
ℹ️ www.jpl.nasa.gov/news/nasas-p...
#Mars Nov. 29, 2025 - Sol 1698
Credits: NASA/JPL-Caltech 🧪🔭
ℹ️ www.jpl.nasa.gov/news/nasas-p...
#Mars Nov. 29, 2025 - Sol 1698
Credits: NASA/JPL-Caltech 🧪🔭
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/🧵