Yi-Chia Huang 黃怡嘉
@yichiahuang.bsky.social
Reposted by Yi-Chia Huang 黃怡嘉
🎵WHY DO ENHANCER!
SUDDENLY APPEAR!
EVERY TIME!
THEY ARE NEAR!?!
JUST LIKE ME!
THEY LONG TO BE!
CLOSE TO POLII! 🎵
www.nature.com/articles/s41...
SUDDENLY APPEAR!
EVERY TIME!
THEY ARE NEAR!?!
JUST LIKE ME!
THEY LONG TO BE!
CLOSE TO POLII! 🎵
www.nature.com/articles/s41...
Distal enhancers loop to proximal enhancers, not to promoters - Nature Reviews Molecular Cell Biology
This Comment posits that enhancers stimulate the transcription machinery only through short-range interactions and, therefore, that enhancer activity at a distance is mediated by chromatin loops betwe...
www.nature.com
September 9, 2025 at 5:42 PM
🎵WHY DO ENHANCER!
SUDDENLY APPEAR!
EVERY TIME!
THEY ARE NEAR!?!
JUST LIKE ME!
THEY LONG TO BE!
CLOSE TO POLII! 🎵
www.nature.com/articles/s41...
SUDDENLY APPEAR!
EVERY TIME!
THEY ARE NEAR!?!
JUST LIKE ME!
THEY LONG TO BE!
CLOSE TO POLII! 🎵
www.nature.com/articles/s41...
Reposted by Yi-Chia Huang 黃怡嘉
🎓 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 4:08 PM
🎓 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🧵👇
Reposted by Yi-Chia Huang 黃怡嘉
In this Review, Mätlik et al. discuss the influence of histone bivalency (activating H3K4me3 + repressive H3K27me3) on neuronal development and maturation. #openaccess
Learn more here:
➡️ tinyurl.com/gd352306
Learn more here:
➡️ tinyurl.com/gd352306
April 16, 2025 at 3:25 PM
In this Review, Mätlik et al. discuss the influence of histone bivalency (activating H3K4me3 + repressive H3K27me3) on neuronal development and maturation. #openaccess
Learn more here:
➡️ tinyurl.com/gd352306
Learn more here:
➡️ tinyurl.com/gd352306
Reposted by Yi-Chia Huang 黃怡嘉
👇👇👇 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
Reposted by Yi-Chia Huang 黃怡嘉
We made it to the cover! :)
April 17, 2025 at 4:48 PM
We made it to the cover! :)
Reposted by Yi-Chia Huang 黃怡嘉
Happy National Learn About Butterflies Day! 🦋 MBL Director Nipam Patel showed students from The Hockaday School and Wareham High School his collection this week!
📷: An emerald swallowtail butterfly. Credit: Nipam Patel
📷: Patel teaches Hockaday students. Credit: Alex Megerle
📷: An emerald swallowtail butterfly. Credit: Nipam Patel
📷: Patel teaches Hockaday students. Credit: Alex Megerle
March 14, 2025 at 8:31 PM
Happy National Learn About Butterflies Day! 🦋 MBL Director Nipam Patel showed students from The Hockaday School and Wareham High School his collection this week!
📷: An emerald swallowtail butterfly. Credit: Nipam Patel
📷: Patel teaches Hockaday students. Credit: Alex Megerle
📷: An emerald swallowtail butterfly. Credit: Nipam Patel
📷: Patel teaches Hockaday students. Credit: Alex Megerle
Reposted by Yi-Chia Huang 黃怡嘉
In honor of #WorldHearingDay, explore the focus of the Piotrowski Lab – understanding the development & regeneration of the #zebrafish lateral line & the potential applications for promoting mammalian hair cell #regeneration to restore #hearingloss or #deafness.
Piotrowski Lab
The primary focus of our lab is understanding the development and regeneration of the zebrafish lateral line and the potential applications for promoting…
www.stowers.org
March 3, 2025 at 10:06 PM
In honor of #WorldHearingDay, explore the focus of the Piotrowski Lab – understanding the development & regeneration of the #zebrafish lateral line & the potential applications for promoting mammalian hair cell #regeneration to restore #hearingloss or #deafness.
Reposted by Yi-Chia Huang 黃怡嘉
Perfect way to start the new lab and the new year! Excited to talk about octopus cells with everyone
January 11, 2025 at 10:11 PM
Perfect way to start the new lab and the new year! Excited to talk about octopus cells with everyone
Reposted by Yi-Chia Huang 黃怡嘉
Hello Bluesky friends! I am a #newPI starting at UC Irvine in April, interested in gene regulation and functional genomics in stem cell models of development (esp neural crest). We are hiring at all levels – please reach out/spread the word! sskimlab.org
Kim Lab at UC Irvine
Visit the post for more.
sskimlab.org
January 20, 2025 at 11:08 PM
Hello Bluesky friends! I am a #newPI starting at UC Irvine in April, interested in gene regulation and functional genomics in stem cell models of development (esp neural crest). We are hiring at all levels – please reach out/spread the word! sskimlab.org
Reposted by Yi-Chia Huang 黃怡嘉
Ok people. I’m drawing silhouettes this afternoon. If you have a paper coming up and you are in need of a #silhouette please let me know and I will have it ready today. As always I upload all my silhouettes to phylopic.org
I also have tutorials on how to put a silhouette in a plot in R.
I also have tutorials on how to put a silhouette in a plot in R.
PhyloPic
PhyloPic is an open database of free silhouette images of animals, plants, and other life forms, available for reuse under Creative Commons licenses. Download silhouettes for use in educational materi...
phylopic.org
December 26, 2024 at 6:47 PM
Ok people. I’m drawing silhouettes this afternoon. If you have a paper coming up and you are in need of a #silhouette please let me know and I will have it ready today. As always I upload all my silhouettes to phylopic.org
I also have tutorials on how to put a silhouette in a plot in R.
I also have tutorials on how to put a silhouette in a plot in R.
Reposted by Yi-Chia Huang 黃怡嘉
To mark the 40th year since the homeobox discovery, we've commissioned a series of articles from leaders in the field demonstrating the impact of the discovery on different disciplines. Check out the full collection: https://journals.biologists.com/dev/collection/10249/40-years-of-the-homeobox
December 30, 2024 at 9:51 AM
To mark the 40th year since the homeobox discovery, we've commissioned a series of articles from leaders in the field demonstrating the impact of the discovery on different disciplines. Check out the full collection: https://journals.biologists.com/dev/collection/10249/40-years-of-the-homeobox
Reposted by Yi-Chia Huang 黃怡嘉
How to do differential expression with scRNAseq data? State of the art is "pseudo-bulk" analysis with RNA-seq methods like edgeR or DESeq2, where "cell type" is encoded as discrete categories. Biologically, discrete categories are not always the most appropriate concept.(1/3)
doi.org/10.1038/s415...
doi.org/10.1038/s415...
Analysis of multi-condition single-cell data with latent embedding multivariate regression - Nature Genetics
Latent embedding multivariate regression models multi-condition single-cell RNA-seq using a continuous latent space, enabling data integration, per-cell gene expression prediction and clustering-free ...
doi.org
January 3, 2025 at 7:18 PM
How to do differential expression with scRNAseq data? State of the art is "pseudo-bulk" analysis with RNA-seq methods like edgeR or DESeq2, where "cell type" is encoded as discrete categories. Biologically, discrete categories are not always the most appropriate concept.(1/3)
doi.org/10.1038/s415...
doi.org/10.1038/s415...
Reposted by Yi-Chia Huang 黃怡嘉
Change is rarely easy, but the right changes are worth it.
As the year comes to a close, we’re showcasing some research and publishing highlights from the year with the hashtag #12DaysOfeLife
Follow along over the next 12 days or check out our blog now!
https://buff.ly/3Dhn21z
As the year comes to a close, we’re showcasing some research and publishing highlights from the year with the hashtag #12DaysOfeLife
Follow along over the next 12 days or check out our blog now!
https://buff.ly/3Dhn21z
A look back at 2024
We take a look back at some of the key milestones and announcements of 2024.
buff.ly
December 19, 2024 at 1:15 PM
Change is rarely easy, but the right changes are worth it.
As the year comes to a close, we’re showcasing some research and publishing highlights from the year with the hashtag #12DaysOfeLife
Follow along over the next 12 days or check out our blog now!
https://buff.ly/3Dhn21z
As the year comes to a close, we’re showcasing some research and publishing highlights from the year with the hashtag #12DaysOfeLife
Follow along over the next 12 days or check out our blog now!
https://buff.ly/3Dhn21z
Reposted by Yi-Chia Huang 黃怡嘉
Our latest: how to generate the notochord
"Timely TGFβ signalling inhibition induces notochord"
A thread:
www.nature.com/articles/s41...
"Timely TGFβ signalling inhibition induces notochord"
A thread:
www.nature.com/articles/s41...
Timely TGFβ signalling inhibition induces notochord - Nature
Through analysis of developing chick embryos and in vitro differentiation of embryonic stem cells, a study develops a method to generate a model of the human trunk with a notochord.
www.nature.com
December 19, 2024 at 8:52 AM
Our latest: how to generate the notochord
"Timely TGFβ signalling inhibition induces notochord"
A thread:
www.nature.com/articles/s41...
"Timely TGFβ signalling inhibition induces notochord"
A thread:
www.nature.com/articles/s41...
Reposted by Yi-Chia Huang 黃怡嘉
My first post on bluesky!!
Excited to see my PhD work featured on the cover of NCB @naturecellbiology.bsky.social December issue! This image shows a gorgeous #zebrafish embryo undergoing cell division (the green cells with condensed chromatin)—a fundamental process we study in development.
🧵1/2
Excited to see my PhD work featured on the cover of NCB @naturecellbiology.bsky.social December issue! This image shows a gorgeous #zebrafish embryo undergoing cell division (the green cells with condensed chromatin)—a fundamental process we study in development.
🧵1/2
December 12, 2024 at 4:22 PM
My first post on bluesky!!
Excited to see my PhD work featured on the cover of NCB @naturecellbiology.bsky.social December issue! This image shows a gorgeous #zebrafish embryo undergoing cell division (the green cells with condensed chromatin)—a fundamental process we study in development.
🧵1/2
Excited to see my PhD work featured on the cover of NCB @naturecellbiology.bsky.social December issue! This image shows a gorgeous #zebrafish embryo undergoing cell division (the green cells with condensed chromatin)—a fundamental process we study in development.
🧵1/2
Reposted by Yi-Chia Huang 黃怡嘉
In one year, I genetically engineered the boring Arabidopsis into a beautiful ornamental flower 🧬🌹
Here is how and why I gave this model organism a visual upgrade 🧵(1/7)
Here is how and why I gave this model organism a visual upgrade 🧵(1/7)
December 12, 2024 at 11:24 AM
In one year, I genetically engineered the boring Arabidopsis into a beautiful ornamental flower 🧬🌹
Here is how and why I gave this model organism a visual upgrade 🧵(1/7)
Here is how and why I gave this model organism a visual upgrade 🧵(1/7)
Reposted by Yi-Chia Huang 黃怡嘉
Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨
We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research!
Read more: bmcgenomics.biomedcentral.com/articles/10....
1/8
High content of nuclei-free low-quality cells in reference single-cell atlases: a call for more stringent quality control using nuclear fraction - BMC Genomics
The advent of droplet-based single-cell RNA-sequencing (scRNA-seq) has dramatically increased data throughput, enabling the release of a diverse array of tissue cell atlases to the public. However, we...
bmcgenomics.biomedcentral.com
December 3, 2024 at 8:38 AM
Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨
We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research!
Read more: bmcgenomics.biomedcentral.com/articles/10....
1/8
Reposted by Yi-Chia Huang 黃怡嘉
We are interested in all aspects globally connecting the neural crest to evolution, biomedicine and specific sub-field of developmental biology. In this study we show the role of motor circuits in shaping neural crest-derived sympathetic nervous system: www.nature.com/articles/s41...
Motor innervation directs the correct development of the mouse sympathetic nervous system - Nature Communications
How tissues interact to help each other grow is a major question for biologists. Here, the authors show that motor innervation controls positioning of sympathetic progenitor cells to ensure correct sh...
www.nature.com
December 1, 2024 at 4:24 PM
We are interested in all aspects globally connecting the neural crest to evolution, biomedicine and specific sub-field of developmental biology. In this study we show the role of motor circuits in shaping neural crest-derived sympathetic nervous system: www.nature.com/articles/s41...
Reposted by Yi-Chia Huang 黃怡嘉
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 Yi-Chia Huang 黃怡嘉
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 Yi-Chia Huang 黃怡嘉
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 Yi-Chia Huang 黃怡嘉
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...
Reposted by Yi-Chia Huang 黃怡嘉
"It's a worm's world" a lovely article by Maddy Frank about our lab's work!
biology.wustl.edu/news/its-wor...
biology.wustl.edu/news/its-wor...
It's a worm's world: regeneration and regrowth in the Özpolat Lab
Inside a corner lab in the basement of Busch, thousands of worms lay in wait. The windowless room stays at a cool 18 degrees Celsius. Small plastic containers (think the ones you might have put some c...
biology.wustl.edu
November 21, 2024 at 8:15 PM
"It's a worm's world" a lovely article by Maddy Frank about our lab's work!
biology.wustl.edu/news/its-wor...
biology.wustl.edu/news/its-wor...
Reposted by Yi-Chia Huang 黃怡嘉
REX - a mammalian "range extender" element that can turn short-distance enhancers into long-distance enhancers.
New preprint from a collaboration led by Grace Bower and Evgeny Kvon.
doi.org/10.1101/2024...
New preprint from a collaboration led by Grace Bower and Evgeny Kvon.
doi.org/10.1101/2024...
May 27, 2024 at 4:26 PM
REX - a mammalian "range extender" element that can turn short-distance enhancers into long-distance enhancers.
New preprint from a collaboration led by Grace Bower and Evgeny Kvon.
doi.org/10.1101/2024...
New preprint from a collaboration led by Grace Bower and Evgeny Kvon.
doi.org/10.1101/2024...
Reposted by Yi-Chia Huang 黃怡嘉
