陳昱嘉 Yu-Chia Chen
@evodevo-tw.bsky.social
Development x Evolution x Gene Regulation
Curious biologist from Taiwan
PhD candidate in the Harris Lab
BBS program @HarvardMed
Basketball addict | he, him, his
Curious biologist from Taiwan
PhD candidate in the Harris Lab
BBS program @HarvardMed
Basketball addict | he, him, his
Reposted by 陳昱嘉 Yu-Chia Chen
👇👇👇 New preprint dropped! Where we dive deep into the factors that restrict pluripotent stem cells to make the RIGHT cell types in the RIGHT place in planarians. Many surprises in this very exciting story. @kuangtse.bsky.social
🎓 After 5 years, the heart of my thesis is finally live!
Pluripotent Stem Cell Plasticity is Sculpted by a Slit‑Independent Robo Pathway in a Regenerative Animal 🧬🧠
Read it here 👉https://www.biorxiv.org/content/10.1101/2025.04.14.648795v1
More details in the🧵👇
Pluripotent Stem Cell Plasticity is Sculpted by a Slit‑Independent Robo Pathway in a Regenerative Animal 🧬🧠
Read it here 👉https://www.biorxiv.org/content/10.1101/2025.04.14.648795v1
More details in the🧵👇
Pluripotent Stem Cell Plasticity is Sculpted by a Slit-Independent Robo Pathway in a Regenerative Animal
Whole-body regeneration requires adult stem cells with high plasticity to differentiate into missing cell types. Planarians possess a unique configuration of organs embedded in a vast pool of pluripot...
www.biorxiv.org
April 17, 2025 at 5:24 PM
👇👇👇 New preprint dropped! Where we dive deep into the factors that restrict pluripotent stem cells to make the RIGHT cell types in the RIGHT place in planarians. Many surprises in this very exciting story. @kuangtse.bsky.social
New preprint alert! 🚨 Check out this awesome highlight thread by @kuangtse.bsky.social -- How does a pluripotent stem cell differentiate into the correct cell type at the right location? 🧐
🎓 After 5 years, the heart of my thesis is finally live!
Pluripotent Stem Cell Plasticity is Sculpted by a Slit‑Independent Robo Pathway in a Regenerative Animal 🧬🧠
Read it here 👉https://www.biorxiv.org/content/10.1101/2025.04.14.648795v1
More details in the🧵👇
Pluripotent Stem Cell Plasticity is Sculpted by a Slit‑Independent Robo Pathway in a Regenerative Animal 🧬🧠
Read it here 👉https://www.biorxiv.org/content/10.1101/2025.04.14.648795v1
More details in the🧵👇
Pluripotent Stem Cell Plasticity is Sculpted by a Slit-Independent Robo Pathway in a Regenerative Animal
Whole-body regeneration requires adult stem cells with high plasticity to differentiate into missing cell types. Planarians possess a unique configuration of organs embedded in a vast pool of pluripot...
www.biorxiv.org
April 18, 2025 at 10:23 PM
New preprint alert! 🚨 Check out this awesome highlight thread by @kuangtse.bsky.social -- How does a pluripotent stem cell differentiate into the correct cell type at the right location? 🧐
Reposted by 陳昱嘉 Yu-Chia Chen
Full spectrum of ‘zebrabow’ embryos. Credit to @jhenninger.bsky.social. #ZebrafishZunday 🧪
December 15, 2024 at 1:25 PM
Full spectrum of ‘zebrabow’ embryos. Credit to @jhenninger.bsky.social. #ZebrafishZunday 🧪
Reposted by 陳昱嘉 Yu-Chia Chen
It’s time for another #FluorescenceFriday! 👩🎨🎨🔬🫀multi-color labeled zebrafish heart with mosaic expression of diverse myl7:color plasmids 🏳️🌈🌈
December 6, 2024 at 3:15 PM
It’s time for another #FluorescenceFriday! 👩🎨🎨🔬🫀multi-color labeled zebrafish heart with mosaic expression of diverse myl7:color plasmids 🏳️🌈🌈
Reposted by 陳昱嘉 Yu-Chia Chen
Nice paper from Jenn Prescher and colleagues on tags for bioluminescence imaging of RNAs. www.nature.com/articles/s41...
A modular platform for bioluminescent RNA tracking - Nature Communications
Studying RNA dynamics in vivo often relies on fluorogenic approaches, but these can be hampered by factors such as limited sensitivity and sample autofluorescence. Here, the authors describe an ultras...
www.nature.com
December 2, 2024 at 11:54 PM
Nice paper from Jenn Prescher and colleagues on tags for bioluminescence imaging of RNAs. www.nature.com/articles/s41...
Reposted by 陳昱嘉 Yu-Chia Chen
Identification and developmental profiling of microRNAs in the acoel worm Hofstenia miamia https://www.biorxiv.org/content/10.1101/2024.12.01.626237v1
Identification and developmental profiling of microRNAs in the acoel worm Hofstenia miamia https://www.biorxiv.org/content/10.1101/2024.12.01.626237v1
The acoel worm Hofstenia miamia (H. miamia) has recently emerged as a model organism for studying wh
www.biorxiv.org
December 2, 2024 at 4:35 PM
Identification and developmental profiling of microRNAs in the acoel worm Hofstenia miamia https://www.biorxiv.org/content/10.1101/2024.12.01.626237v1
Reposted by 陳昱嘉 Yu-Chia Chen
Thrilled to present our latest BioRXiv on brain/body interactions during defensive freezing behaviour! (www.biorxiv.org/content/10.1...). You might think that a frozen animal has, well, frozen muscle activity, right? Wrong! Underneath the still surface of a fly, something in the legs is beating… 🧵
December 2, 2024 at 9:57 AM
Thrilled to present our latest BioRXiv on brain/body interactions during defensive freezing behaviour! (www.biorxiv.org/content/10.1...). You might think that a frozen animal has, well, frozen muscle activity, right? Wrong! Underneath the still surface of a fly, something in the legs is beating… 🧵
Reposted by 陳昱嘉 Yu-Chia Chen
Welcome to the #devbiolwriteclub Bluesky Boot Camp! I’ll be posting here regularly with thoughts and exercises to help scientists become better writers. Let’s start by managing expectations: I will NOT help you write better. I WILL help you become a better writer. 🧵 1/10
December 2, 2024 at 3:07 PM
Welcome to the #devbiolwriteclub Bluesky Boot Camp! I’ll be posting here regularly with thoughts and exercises to help scientists become better writers. Let’s start by managing expectations: I will NOT help you write better. I WILL help you become a better writer. 🧵 1/10
Reposted by 陳昱嘉 Yu-Chia Chen
During thanksgiving, I sometimes wish that I was a slingjaw wrasse. They can extend their jaws 1/3 of their entire body length. Perfect for getting seconds without standing up. We printed one today from a specimen we collected in Okinawa
November 28, 2024 at 9:14 AM
During thanksgiving, I sometimes wish that I was a slingjaw wrasse. They can extend their jaws 1/3 of their entire body length. Perfect for getting seconds without standing up. We printed one today from a specimen we collected in Okinawa
Reposted by 陳昱嘉 Yu-Chia Chen
I’m delighted to share that I will be starting my lab @univmiami.bsky.social in Spring 2025! We will study cellular and developmental biology in non-bilaterian animals – cnidarians, ctenophores, placozoans, and sponges – to explore early animal evolution.
November 27, 2024 at 4:26 PM
I’m delighted to share that I will be starting my lab @univmiami.bsky.social in Spring 2025! We will study cellular and developmental biology in non-bilaterian animals – cnidarians, ctenophores, placozoans, and sponges – to explore early animal evolution.
Reposted by 陳昱嘉 Yu-Chia Chen
Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature Genetics
ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...
www.nature.com
November 27, 2024 at 4:13 AM
Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by 陳昱嘉 Yu-Chia Chen
(1) How can we build complex structures from a limited set of progenitors and cell types? In our new preprint, we describe patterns of cell fate decisions during early development and (in some cases) identify molecular correlates of different behaviors.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Unbiased profiling of multipotency landscapes reveals spatial modulators of clonal fate biases
Embryogenesis is commonly viewed through a tree model of cell differentiation, which does not adequately represent the spatiotemporal modulation of cell multipotency underlying morphogenesis. Here we ...
www.biorxiv.org
November 25, 2024 at 10:47 PM
(1) How can we build complex structures from a limited set of progenitors and cell types? In our new preprint, we describe patterns of cell fate decisions during early development and (in some cases) identify molecular correlates of different behaviors.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by 陳昱嘉 Yu-Chia Chen
(please amplify) 4% of scientists face an important barrier to an the ENTIRE FIELD of single-cell genomics and here is why
November 25, 2024 at 3:22 PM
(please amplify) 4% of scientists face an important barrier to an the ENTIRE FIELD of single-cell genomics and here is why
Reposted by 陳昱嘉 Yu-Chia Chen
#NewPI achievement unlocked: the first
#obrownlab publication is officially accepted (🍾) about #zebrafish #glia (green) and the vasculature (magenta). Thanks to our reviewers and congrats to all of the lab members! What a great 1st paper experience. Happy #fluorescencefriday ya'll!
#obrownlab publication is officially accepted (🍾) about #zebrafish #glia (green) and the vasculature (magenta). Thanks to our reviewers and congrats to all of the lab members! What a great 1st paper experience. Happy #fluorescencefriday ya'll!
November 22, 2024 at 8:12 PM
#NewPI achievement unlocked: the first
#obrownlab publication is officially accepted (🍾) about #zebrafish #glia (green) and the vasculature (magenta). Thanks to our reviewers and congrats to all of the lab members! What a great 1st paper experience. Happy #fluorescencefriday ya'll!
#obrownlab publication is officially accepted (🍾) about #zebrafish #glia (green) and the vasculature (magenta). Thanks to our reviewers and congrats to all of the lab members! What a great 1st paper experience. Happy #fluorescencefriday ya'll!
Reposted by 陳昱嘉 Yu-Chia Chen
Another go-to graph for "AHA!" moments: phylogenetic trees. This @embl.org hosted interactive tree viz tool is intuitive and so so so customizable.
November 24, 2024 at 10:55 AM
Another go-to graph for "AHA!" moments: phylogenetic trees. This @embl.org hosted interactive tree viz tool is intuitive and so so so customizable.
Reposted by 陳昱嘉 Yu-Chia Chen
"Dark TFs": new manuscript mapped 166 uncharacterized human transcription factors, finding half bind genomic "dark matter," often closed chromatin rich in transposable elements.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
November 19, 2024 at 11:41 PM
"Dark TFs": new manuscript mapped 166 uncharacterized human transcription factors, finding half bind genomic "dark matter," often closed chromatin rich in transposable elements.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by 陳昱嘉 Yu-Chia Chen
In this review @gracebower.bsky.social & I discuss recent evidence showing that, unlike canonical enhancers, long-range enhancers located hundreds of kb from their targets rely on additional mechanisms to ensure robust gene activation during mammal development. www.sciencedirect.com/science/arti...
November 22, 2024 at 8:20 PM
In this review @gracebower.bsky.social & I discuss recent evidence showing that, unlike canonical enhancers, long-range enhancers located hundreds of kb from their targets rely on additional mechanisms to ensure robust gene activation during mammal development. www.sciencedirect.com/science/arti...
Reposted by 陳昱嘉 Yu-Chia Chen
Calcein staining showing the skeleton on the aboral side of a juvenile sea star (Patiria miniata)
Everything looks better with a rainbow LUT 🌈😊
#microscopy #echinoderms #fluorescence
Everything looks better with a rainbow LUT 🌈😊
#microscopy #echinoderms #fluorescence
November 23, 2024 at 8:58 PM
Calcein staining showing the skeleton on the aboral side of a juvenile sea star (Patiria miniata)
Everything looks better with a rainbow LUT 🌈😊
#microscopy #echinoderms #fluorescence
Everything looks better with a rainbow LUT 🌈😊
#microscopy #echinoderms #fluorescence
Reposted by 陳昱嘉 Yu-Chia Chen
"A picture contains 1,000 projects."
Acrobeles roundworm head, photo by Kaiden Power @wormkaiden.bsky.social
How many open questions about ECM patterning can you find in these pictures?
Acrobeles roundworm head, photo by Kaiden Power @wormkaiden.bsky.social
How many open questions about ECM patterning can you find in these pictures?
November 22, 2024 at 2:27 PM
"A picture contains 1,000 projects."
Acrobeles roundworm head, photo by Kaiden Power @wormkaiden.bsky.social
How many open questions about ECM patterning can you find in these pictures?
Acrobeles roundworm head, photo by Kaiden Power @wormkaiden.bsky.social
How many open questions about ECM patterning can you find in these pictures?
Reposted by 陳昱嘉 Yu-Chia Chen
7 years ago, I met a junior fellow named Jason Buenrostro who blew me away with a vision of futuristic genomic technologies
Today, we (Ajay Labade, Caroline Comenho) are excited to share our first steps into that future: Expansion in situ genome sequencing
1/
Today, we (Ajay Labade, Caroline Comenho) are excited to share our first steps into that future: Expansion in situ genome sequencing
1/
November 11, 2024 at 7:33 PM
7 years ago, I met a junior fellow named Jason Buenrostro who blew me away with a vision of futuristic genomic technologies
Today, we (Ajay Labade, Caroline Comenho) are excited to share our first steps into that future: Expansion in situ genome sequencing
1/
Today, we (Ajay Labade, Caroline Comenho) are excited to share our first steps into that future: Expansion in situ genome sequencing
1/
Cell division is NOT a must for differentiation during early zebrafish embryogenesis.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Cell state transitions are decoupled from cell division during early embryo development - Nature Cell Biology
Kukreja et al. show that blocking cell division in zebrafish does not affect differentiation of major cell types during gastrulation and segmentation, but it does decelerate differentiation of particu...
www.nature.com
November 23, 2024 at 3:08 AM
Cell division is NOT a must for differentiation during early zebrafish embryogenesis.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by 陳昱嘉 Yu-Chia Chen
For not quite #FluorescenceFriday, here are pluteus larvae of sea urchin under polarized light 👾🚀
November 22, 2024 at 11:34 AM
For not quite #FluorescenceFriday, here are pluteus larvae of sea urchin under polarized light 👾🚀
Reposted by 陳昱嘉 Yu-Chia Chen
#FluorescentFriday
#Zebrafish
Visualization of neutrophil migration kinetics after tailfin wound at a whole animal scale.
We need more research done at a whole-animal scale... so much we don't ask because we're just looking at the small local wound under the 🔬
#Zebrafish
Visualization of neutrophil migration kinetics after tailfin wound at a whole animal scale.
We need more research done at a whole-animal scale... so much we don't ask because we're just looking at the small local wound under the 🔬
November 23, 2024 at 12:01 AM
#FluorescentFriday
#Zebrafish
Visualization of neutrophil migration kinetics after tailfin wound at a whole animal scale.
We need more research done at a whole-animal scale... so much we don't ask because we're just looking at the small local wound under the 🔬
#Zebrafish
Visualization of neutrophil migration kinetics after tailfin wound at a whole animal scale.
We need more research done at a whole-animal scale... so much we don't ask because we're just looking at the small local wound under the 🔬
Reposted by 陳昱嘉 Yu-Chia Chen
Excited to share work that @ceriweber.bsky.social started and drove in my lab. Tails!! We know a lot about limb bone growth, but vertebrae have completely different embryonic and evolutionary origins. What controls growth and proportion in the vertebral skeleton?
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Cellular and molecular mechanisms that shape the development and evolution of tail vertebral proportion in mice and jerboas
Despite the functional importance of the vertebral skeleton, little is known about how individual vertebrae elongate or achieve disproportionate lengths as in the giraffe neck. Rodent tails are an abu...
www.biorxiv.org
November 21, 2024 at 2:29 PM
Excited to share work that @ceriweber.bsky.social started and drove in my lab. Tails!! We know a lot about limb bone growth, but vertebrae have completely different embryonic and evolutionary origins. What controls growth and proportion in the vertebral skeleton?
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...