Luca Braccioli Lab @ UU
@bracciolilab.bsky.social
Exploring the interplay between gene regulation and tissue-tissue interactions in stem cell-based embryo models.
Reposted by Luca Braccioli Lab @ UU
Here is a copy of last year's Twitter thread explaining our preprint - jump to (21) for the new stuff 👀
Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function
now revised and journal accepted at www.science.org/doi/10.1126/...
🧵👇
Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function
now revised and journal accepted at www.science.org/doi/10.1126/...
🧵👇
November 27, 2025 at 9:59 PM
Here is a copy of last year's Twitter thread explaining our preprint - jump to (21) for the new stuff 👀
Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function
now revised and journal accepted at www.science.org/doi/10.1126/...
🧵👇
Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function
now revised and journal accepted at www.science.org/doi/10.1126/...
🧵👇
🧩 What breaks when you remove DNA loop extrusion?
Gastruloids show it: not lineage decisions… but morphogenesis.
That’s our contribution to www.science.org/doi/10.1126/...
Huge thanks to the amazing @karissalhansen.bsky.social + @elphegenoralab.bsky.social for leading this fantastic work 🙌
Gastruloids show it: not lineage decisions… but morphogenesis.
That’s our contribution to www.science.org/doi/10.1126/...
Huge thanks to the amazing @karissalhansen.bsky.social + @elphegenoralab.bsky.social for leading this fantastic work 🙌
(5) But can embryonic cell types properly emerge even when loop extrusion is prevented?
Unambiguous gastruloid experiments by
@bracciolilab.bsky.social
in
@dewitlab.bsky.social
: YES, they clearly can.
Even though morphogenesis, which is normally very stereotypical, is pretty screwed up.
Unambiguous gastruloid experiments by
@bracciolilab.bsky.social
in
@dewitlab.bsky.social
: YES, they clearly can.
Even though morphogenesis, which is normally very stereotypical, is pretty screwed up.
November 28, 2025 at 8:57 AM
🧩 What breaks when you remove DNA loop extrusion?
Gastruloids show it: not lineage decisions… but morphogenesis.
That’s our contribution to www.science.org/doi/10.1126/...
Huge thanks to the amazing @karissalhansen.bsky.social + @elphegenoralab.bsky.social for leading this fantastic work 🙌
Gastruloids show it: not lineage decisions… but morphogenesis.
That’s our contribution to www.science.org/doi/10.1126/...
Huge thanks to the amazing @karissalhansen.bsky.social + @elphegenoralab.bsky.social for leading this fantastic work 🙌
Reposted by Luca Braccioli Lab @ UU
IT'S HAPPENING! 💥 I'm psyched to launch the collaboration between @qedscience.bsky.social & @openrxiv.bsky.social @biorxivpreprint.bsky.social! Preprint + q.e.d = your science is out there, and anyone can appreciate it. Let's care about making discoveries, and not on “getting published” (1/3) 👇
November 6, 2025 at 2:49 PM
IT'S HAPPENING! 💥 I'm psyched to launch the collaboration between @qedscience.bsky.social & @openrxiv.bsky.social @biorxivpreprint.bsky.social! Preprint + q.e.d = your science is out there, and anyone can appreciate it. Let's care about making discoveries, and not on “getting published” (1/3) 👇
Reposted by Luca Braccioli Lab @ UU
Daniel Kahneman's imaginary sabbatical in a fly lab continues...this time: The art of letting go.
Have you felt the pain of stopping while standardising a new method? Or letting go of a project? When to stop, when to persist?
Have a read @the-node.bsky.social
thenode.biologists.com/the-kahneman...
Have you felt the pain of stopping while standardising a new method? Or letting go of a project? When to stop, when to persist?
Have a read @the-node.bsky.social
thenode.biologists.com/the-kahneman...
The Kahneman Chronicles: Lessons from a Fly Lab - the Node
The Kahneman Chronicles #2: Loss Aversion and the Art of Quitting Daniel Kahneman (1934-2024) was a legendary psychologist who revolutionized our
thenode.biologists.com
October 26, 2025 at 10:23 PM
Daniel Kahneman's imaginary sabbatical in a fly lab continues...this time: The art of letting go.
Have you felt the pain of stopping while standardising a new method? Or letting go of a project? When to stop, when to persist?
Have a read @the-node.bsky.social
thenode.biologists.com/the-kahneman...
Have you felt the pain of stopping while standardising a new method? Or letting go of a project? When to stop, when to persist?
Have a read @the-node.bsky.social
thenode.biologists.com/the-kahneman...
Reposted by Luca Braccioli Lab @ UU
Ascidians (Ciona intestinalis)🪸Our distant chordate cousins! 🌊 Simple sea squirts that reveal how vertebrate body plans evolved 🧬 A key model for notochord formation, neural induction, and cell lineage mapping 📸 Video by MBL Embryology 2019 #ModelMonday #DevBio #EvoDevo
October 28, 2025 at 12:46 AM
Ascidians (Ciona intestinalis)🪸Our distant chordate cousins! 🌊 Simple sea squirts that reveal how vertebrate body plans evolved 🧬 A key model for notochord formation, neural induction, and cell lineage mapping 📸 Video by MBL Embryology 2019 #ModelMonday #DevBio #EvoDevo
Reposted by Luca Braccioli Lab @ UU
Three short talks now at #GenBio25. @bracciolilab.bsky.social discusses the ability of cells to contribute to different lineages in a gastruloid model. Luca recently published an ‘In preprints’ article in @dev-journal.bsky.social: doi.org/10.1242/dev....
October 20, 2025 at 10:57 AM
Three short talks now at #GenBio25. @bracciolilab.bsky.social discusses the ability of cells to contribute to different lineages in a gastruloid model. Luca recently published an ‘In preprints’ article in @dev-journal.bsky.social: doi.org/10.1242/dev....
Reposted by Luca Braccioli Lab @ UU
Very proud of our paper on "scrambling-by-hopping" LADs, which was just published: www.nature.com/articles/s41.... Congrats to Lise Dauban and the rest of the team – this was a real tour-de-force!
September 2, 2025 at 5:26 PM
Very proud of our paper on "scrambling-by-hopping" LADs, which was just published: www.nature.com/articles/s41.... Congrats to Lise Dauban and the rest of the team – this was a real tour-de-force!
Reposted by Luca Braccioli Lab @ UU
(1/14) I’m happy and proud to introduce: SpinePy – a framework to detect the "spine" of gastruloids and measure biological and physical signals in a local dynamic 3D coordinate system. www.biorxiv.org/content/10.1...
September 12, 2025 at 12:44 PM
(1/14) I’m happy and proud to introduce: SpinePy – a framework to detect the "spine" of gastruloids and measure biological and physical signals in a local dynamic 3D coordinate system. www.biorxiv.org/content/10.1...
Ever wondered how to get a gastruloid to grow a head?
The Bulut-Karslioğlu lab figured out that by growing different stem cell aggregates in high and low oxygen and later assembling them, you can get gastruloids with a fully formed neural tube. Check out our "In preprints": doi.org/10.1242/dev....
The Bulut-Karslioğlu lab figured out that by growing different stem cell aggregates in high and low oxygen and later assembling them, you can get gastruloids with a fully formed neural tube. Check out our "In preprints": doi.org/10.1242/dev....
In preprints: gastruloids get (a)head
A major breakthrough in the field of mammalian embryology is the development of stem-cell based embryo models. Derived from pluripotent stem cells, such as embryonic stem cells or induced pluripotent ...
doi.org
September 16, 2025 at 8:31 AM
Ever wondered how to get a gastruloid to grow a head?
The Bulut-Karslioğlu lab figured out that by growing different stem cell aggregates in high and low oxygen and later assembling them, you can get gastruloids with a fully formed neural tube. Check out our "In preprints": doi.org/10.1242/dev....
The Bulut-Karslioğlu lab figured out that by growing different stem cell aggregates in high and low oxygen and later assembling them, you can get gastruloids with a fully formed neural tube. Check out our "In preprints": doi.org/10.1242/dev....
Reposted by Luca Braccioli Lab @ UU
We are searching for an enthusiastic scientist to join our team and establish annual killifish as a model system for early developmental biology and biophysics! @embl.org @embldbunit.bsky.social
Apply here:
embl.wd103.myworkdayjobs.com/EMBL/job/Hei...
Please re-post 🙏
Apply here:
embl.wd103.myworkdayjobs.com/EMBL/job/Hei...
Please re-post 🙏
August 8, 2025 at 9:01 AM
We are searching for an enthusiastic scientist to join our team and establish annual killifish as a model system for early developmental biology and biophysics! @embl.org @embldbunit.bsky.social
Apply here:
embl.wd103.myworkdayjobs.com/EMBL/job/Hei...
Please re-post 🙏
Apply here:
embl.wd103.myworkdayjobs.com/EMBL/job/Hei...
Please re-post 🙏
Reposted by Luca Braccioli Lab @ UU
New preprint with @gfudenberg.bsky.social
We find the rate of cohesin loop extrusion in cells is set by NIPBL dosage and tunes many aspects of chromosome folding.
This provides a molecular basis for NIPBL haploinsufficiency in humans. 🧵👇
www.biorxiv.org/content/10.1...
We find the rate of cohesin loop extrusion in cells is set by NIPBL dosage and tunes many aspects of chromosome folding.
This provides a molecular basis for NIPBL haploinsufficiency in humans. 🧵👇
www.biorxiv.org/content/10.1...
NIPBL dosage shapes genome folding by tuning the rate of cohesin loop extrusion
Cohesin loop extrusion is a major driver of chromosome folding, but how its dynamics are controlled to shape the genome remains elusive. Here we disentangle the contributions of the cohesin cofactors ...
www.biorxiv.org
August 16, 2025 at 3:03 AM
New preprint with @gfudenberg.bsky.social
We find the rate of cohesin loop extrusion in cells is set by NIPBL dosage and tunes many aspects of chromosome folding.
This provides a molecular basis for NIPBL haploinsufficiency in humans. 🧵👇
www.biorxiv.org/content/10.1...
We find the rate of cohesin loop extrusion in cells is set by NIPBL dosage and tunes many aspects of chromosome folding.
This provides a molecular basis for NIPBL haploinsufficiency in humans. 🧵👇
www.biorxiv.org/content/10.1...
Reposted by Luca Braccioli Lab @ UU
The Vlaming lab is expanding! If you are or know a good prospective PhD student, excited about studying transcription, please (suggest them to) apply here: www.uu.nl/en/organisat...
My biased opinion: exciting topic, super nice colleagues, and great research environment in a lovely city.
My biased opinion: exciting topic, super nice colleagues, and great research environment in a lovely city.
PhD position in Gene Regulation
Are you excited about studying the crucial process of transcription? Join our supportive, young and growing team!
www.uu.nl
August 15, 2025 at 10:22 AM
The Vlaming lab is expanding! If you are or know a good prospective PhD student, excited about studying transcription, please (suggest them to) apply here: www.uu.nl/en/organisat...
My biased opinion: exciting topic, super nice colleagues, and great research environment in a lovely city.
My biased opinion: exciting topic, super nice colleagues, and great research environment in a lovely city.
Reposted by Luca Braccioli Lab @ UU
Two new preprints from the @arjunraj.bsky.social on #gastruloids. Both excellent. Exploring the relationship between macroscopic reproducibility v microscopic heterogeneity. Stunning experiments and much to think about
biorxiv.org/content/earl...
biorxiv.org/content/earl...
biorxiv.org/content/earl...
biorxiv.org/content/earl...
July 15, 2025 at 1:28 PM
Two new preprints from the @arjunraj.bsky.social on #gastruloids. Both excellent. Exploring the relationship between macroscopic reproducibility v microscopic heterogeneity. Stunning experiments and much to think about
biorxiv.org/content/earl...
biorxiv.org/content/earl...
biorxiv.org/content/earl...
biorxiv.org/content/earl...
Reposted by Luca Braccioli Lab @ UU
Please pread the word.
We have just launched the Hubrecht International PhD Program (HIPP).
Are you looking for a PhD position in molecular and developmental biology or related subject in an international, very supportive and collaborative environment?
Then apply to the HIPP!! 👇
We have just launched the Hubrecht International PhD Program (HIPP).
Are you looking for a PhD position in molecular and developmental biology or related subject in an international, very supportive and collaborative environment?
Then apply to the HIPP!! 👇
🧬 Looking for a PhD position in molecular or developmental biology? 🔬
✉️ The Hubrecht Institute now has its very own PhD program! Applications are open and will be accepted until September 15th. Read more here 👉 www.hubrecht.eu/hipp/
✉️ The Hubrecht Institute now has its very own PhD program! Applications are open and will be accepted until September 15th. Read more here 👉 www.hubrecht.eu/hipp/
July 10, 2025 at 6:56 PM
Please pread the word.
We have just launched the Hubrecht International PhD Program (HIPP).
Are you looking for a PhD position in molecular and developmental biology or related subject in an international, very supportive and collaborative environment?
Then apply to the HIPP!! 👇
We have just launched the Hubrecht International PhD Program (HIPP).
Are you looking for a PhD position in molecular and developmental biology or related subject in an international, very supportive and collaborative environment?
Then apply to the HIPP!! 👇
Reposted by Luca Braccioli Lab @ UU
Excellent work supporting #modularity of the mammalian #embryo, a role for #hypoxia & how development exploits these features. It shows what we can learn from assemblies of #gastruloids @ spatio-temporal coordination of the modules in AP organization. Putting modules together, extremely informative
⚠️ I am really excited to share the work of Anastasios Balaskas, an excellent PhD candidate in the lab, with the wider world. Tasos made a significant advance: generating a stem cell-based embryo model that contains both posterior and anterior neural tissues of the late-stage gastrulating embryo.
June 23, 2025 at 5:51 PM
Excellent work supporting #modularity of the mammalian #embryo, a role for #hypoxia & how development exploits these features. It shows what we can learn from assemblies of #gastruloids @ spatio-temporal coordination of the modules in AP organization. Putting modules together, extremely informative
Reposted by Luca Braccioli Lab @ UU
Fantastic work from @bulutkarslioglu.bsky.social group. we r happy to contribute on the role of hypoxia in proper gastrulation ex utero as originally noted in Aguilera-Castrejon et al. Nature 2021 for robust gastrulation. Now this is shown to be important for taking gastruloids to the next level.
⚠️ I am really excited to share the work of Anastasios Balaskas, an excellent PhD candidate in the lab, with the wider world. Tasos made a significant advance: generating a stem cell-based embryo model that contains both posterior and anterior neural tissues of the late-stage gastrulating embryo.
June 23, 2025 at 6:34 PM
Fantastic work from @bulutkarslioglu.bsky.social group. we r happy to contribute on the role of hypoxia in proper gastrulation ex utero as originally noted in Aguilera-Castrejon et al. Nature 2021 for robust gastrulation. Now this is shown to be important for taking gastruloids to the next level.
Reposted by Luca Braccioli Lab @ UU
⚠️ I am really excited to share the work of Anastasios Balaskas, an excellent PhD candidate in the lab, with the wider world. Tasos made a significant advance: generating a stem cell-based embryo model that contains both posterior and anterior neural tissues of the late-stage gastrulating embryo.
June 23, 2025 at 7:51 AM
⚠️ I am really excited to share the work of Anastasios Balaskas, an excellent PhD candidate in the lab, with the wider world. Tasos made a significant advance: generating a stem cell-based embryo model that contains both posterior and anterior neural tissues of the late-stage gastrulating embryo.
Reposted by Luca Braccioli Lab @ UU
📢 Fresh off the press and featuring new exciting experiments! 🧪
We show how glycolytic activity instructs germ layer proportions through regulation of Nodal and Wnt signaling - happy to finally share this 😊
doi.org/10.1016/j.st...
B2B with @jesseveenvliet.bsky.social lab: doi.org/10.1016/j.st... 🤩
We show how glycolytic activity instructs germ layer proportions through regulation of Nodal and Wnt signaling - happy to finally share this 😊
doi.org/10.1016/j.st...
B2B with @jesseveenvliet.bsky.social lab: doi.org/10.1016/j.st... 🤩
April 16, 2025 at 5:40 PM
📢 Fresh off the press and featuring new exciting experiments! 🧪
We show how glycolytic activity instructs germ layer proportions through regulation of Nodal and Wnt signaling - happy to finally share this 😊
doi.org/10.1016/j.st...
B2B with @jesseveenvliet.bsky.social lab: doi.org/10.1016/j.st... 🤩
We show how glycolytic activity instructs germ layer proportions through regulation of Nodal and Wnt signaling - happy to finally share this 😊
doi.org/10.1016/j.st...
B2B with @jesseveenvliet.bsky.social lab: doi.org/10.1016/j.st... 🤩
Reposted by Luca Braccioli Lab @ UU
🚨Just one week left to apply! Join our team @imbavienna.bsky.social!
Thrilled to announce that I am looking for a Research Technician/Assistant to join my lab @imbavienna.bsky.social. Please consider applying if you’re enthusiastic about #devbio #stemcells #teamwork and excited to help shaping a new lab!
Thankful for any retweet! 🫶
imba.onlyfy.jobs/job/l6u2m980
Thankful for any retweet! 🫶
imba.onlyfy.jobs/job/l6u2m980
April 14, 2025 at 3:28 PM
🚨Just one week left to apply! Join our team @imbavienna.bsky.social!
Reposted by Luca Braccioli Lab @ UU
Thank you! A special thanks to the organizers for putting this fantastic meeting together @moritzbauer.bsky.social @bracciolilab.bsky.social Hendrik Marks, Susana Chuva de Sousa, Lopes and Niels Geijsen. And to Wilke Meijer and Suzan Stello for working together on this exciting project!!
Well done @virginiar-andra.bsky.social from our lab for being awarded the Best Poster Prize at the International Dutch Embryo Model Meeting today for our work on “Spatiotemporally resolved omics reveals dynamic antagonistic gradients” in embryo segmentation. Congratulations!
📢 Save the date! We are excited to announce the International Dutch Embryo Model Meeting 2025 in Nijmegen (NL) on Thursday 27 March and Friday 28 March! Registration is open now. More information: ru.nl/en/about-us/...
Big thanks to Hendrik Marks for taking the lead this time!
Big thanks to Hendrik Marks for taking the lead this time!
March 29, 2025 at 12:03 AM
Thank you! A special thanks to the organizers for putting this fantastic meeting together @moritzbauer.bsky.social @bracciolilab.bsky.social Hendrik Marks, Susana Chuva de Sousa, Lopes and Niels Geijsen. And to Wilke Meijer and Suzan Stello for working together on this exciting project!!
Reposted by Luca Braccioli Lab @ UU
Well done @virginiar-andra.bsky.social from our lab for being awarded the Best Poster Prize at the International Dutch Embryo Model Meeting today for our work on “Spatiotemporally resolved omics reveals dynamic antagonistic gradients” in embryo segmentation. Congratulations!
📢 Save the date! We are excited to announce the International Dutch Embryo Model Meeting 2025 in Nijmegen (NL) on Thursday 27 March and Friday 28 March! Registration is open now. More information: ru.nl/en/about-us/...
Big thanks to Hendrik Marks for taking the lead this time!
Big thanks to Hendrik Marks for taking the lead this time!
March 28, 2025 at 9:50 PM
Well done @virginiar-andra.bsky.social from our lab for being awarded the Best Poster Prize at the International Dutch Embryo Model Meeting today for our work on “Spatiotemporally resolved omics reveals dynamic antagonistic gradients” in embryo segmentation. Congratulations!
Reposted by Luca Braccioli Lab @ UU
Very happy to share that our paper on stem cell culture conditions is now out! doi.org/10.1371/jour... We found that modulating mESC culture conditions influences gastruloid elongation and lineage specification, and helps with making the protocol more reproducible in our hands! more below 🧵⬇️ [1/7]
Stem cell culture conditions affect in vitro differentiation potential and mouse gastruloid formation
Aggregating low numbers of mouse embryonic stem cells (mESCs) and inducing Wnt signalling generates ‘gastruloids’, self-organising complex structures that display an anteroposterior organisation of ce...
doi.org
March 28, 2025 at 3:20 PM
Very happy to share that our paper on stem cell culture conditions is now out! doi.org/10.1371/jour... We found that modulating mESC culture conditions influences gastruloid elongation and lineage specification, and helps with making the protocol more reproducible in our hands! more below 🧵⬇️ [1/7]
Reposted by Luca Braccioli Lab @ UU
And to finish a hat-trick of #gastruloid papers @bracciolilab.bsky.social on the influence of epigenetics on lineage decisions shorturl.at/aA6yy
Identifying cross-lineage dependencies of cell-type-specific regulators in mouse gastruloids
Correct gene expression levels are crucial for normal development. Advances in genomics enable the inference of gene regulatory programs active during…
shorturl.at
March 27, 2025 at 10:55 PM
And to finish a hat-trick of #gastruloid papers @bracciolilab.bsky.social on the influence of epigenetics on lineage decisions shorturl.at/aA6yy