Hattie Chung
@hattaca.bsky.social
Assistant Professor @YaleMed | tissue biology, computation, systems biology |
www.hattiechunglab.bio
www.hattiechunglab.bio
Reposted by Hattie Chung
Lab’s 1st preprint!
Menstruation is understudied due to societal taboos + a biological challenge: mice (a key system for research + drug discovery) don’t menstruate.
@cagricevrim.bsky.social made menstruating mice + used them to discover early events in menstruation.
He is on the job market!
Menstruation is understudied due to societal taboos + a biological challenge: mice (a key system for research + drug discovery) don’t menstruate.
@cagricevrim.bsky.social made menstruating mice + used them to discover early events in menstruation.
He is on the job market!
I’m thrilled to share my postdoc work and the first paper from the McKinley Lab! 🎉
@karalmckinley.bsky.social
We built the first transgenic model of menstruation in mice.
We used it to uncover how the endometrium organizes and sheds during menstruation. 🧪
www.biorxiv.org/content/10.1...
🧵
@karalmckinley.bsky.social
We built the first transgenic model of menstruation in mice.
We used it to uncover how the endometrium organizes and sheds during menstruation. 🧪
www.biorxiv.org/content/10.1...
🧵
Induction of menstruation in mice reveals the regulation of menstrual shedding
During menstruation, an inner layer of the endometrium is selectively shed, while an outer, progenitor-containing layer is preserved to support repeated regeneration. Progress in understanding this co...
www.biorxiv.org
October 10, 2025 at 1:26 PM
Lab’s 1st preprint!
Menstruation is understudied due to societal taboos + a biological challenge: mice (a key system for research + drug discovery) don’t menstruate.
@cagricevrim.bsky.social made menstruating mice + used them to discover early events in menstruation.
He is on the job market!
Menstruation is understudied due to societal taboos + a biological challenge: mice (a key system for research + drug discovery) don’t menstruate.
@cagricevrim.bsky.social made menstruating mice + used them to discover early events in menstruation.
He is on the job market!
Reposted by Hattie Chung
🚨 New preprints from our lab!
First, we introduce Cryo-mtscATAC-seq, led by Maren (@ms-maren.bsky.social ), enabling high-throughput clonal tracing from frozen human samples by isolating nuclei with their mitochondria (“CryoCells”).
👉 www.biorxiv.org/content/10.1...
Cryo-mtscATAC-seq for single-cell mitochondrial DNA genotyping and clonal tracing in archived human tissues
High-throughput clonal tracing of primary human samples relies on naturally occurring barcodes, such as somatic mitochondrial DNA (mtDNA) mutations detected via single-cell ATAC-seq (mtscATAC-seq). Fr...
www.biorxiv.org
September 24, 2025 at 12:39 PM
🚨 New preprints from our lab!
First, we introduce Cryo-mtscATAC-seq, led by Maren (@ms-maren.bsky.social ), enabling high-throughput clonal tracing from frozen human samples by isolating nuclei with their mitochondria (“CryoCells”).
👉 www.biorxiv.org/content/10.1...
Reposted by Hattie Chung
✨If Monet studied mouse ovaries 🎨 Stromal cells 💜 Follicular cells 🔵 and Fatty Cells 🟡. Together, they reveal the cellular architecture and functional zones of the ovary 🔬 Image provided by @shmimberly.bsky.social 🧪 #FluorescenceFriday #ReproductiveBiology
August 22, 2025 at 4:35 PM
✨If Monet studied mouse ovaries 🎨 Stromal cells 💜 Follicular cells 🔵 and Fatty Cells 🟡. Together, they reveal the cellular architecture and functional zones of the ovary 🔬 Image provided by @shmimberly.bsky.social 🧪 #FluorescenceFriday #ReproductiveBiology
Reposted by Hattie Chung
New paper on the role of H3K4me3 at enhancers! We (led by Haoming Yu) used dCas9 epigenome editing to add H3K4me3 to intergenic enhancers. This was (1) sufficient to turn up transcription at open, active regions and (2) has no effect on target gene transcription. genesdev.cshlp.org/content/earl...
H3K4me3 amplifies transcription at intergenic active regulatory elements
A biweekly scientific journal publishing high-quality research in molecular biology and genetics, cancer biology, biochemistry, and related fields
genesdev.cshlp.org
August 20, 2025 at 1:29 AM
New paper on the role of H3K4me3 at enhancers! We (led by Haoming Yu) used dCas9 epigenome editing to add H3K4me3 to intergenic enhancers. This was (1) sufficient to turn up transcription at open, active regions and (2) has no effect on target gene transcription. genesdev.cshlp.org/content/earl...
Our lab at Yale @yalemedicine.bsky.social seeks #postdocs with in vivo expertise to pioneer research at the intersection of tissue remodeling & aging. Work with us to uncover immunological & vascular drivers of ovarian aging, applying single-cell, spatial omics, and ML! jobrxiv.org/job/yale-uni...
Postdoctoral Fellow, Hattie Chung Lab (Yale School of Medicine)
Post a job in 3min, or find thousands of job offers like this one at jobRxiv!
jobrxiv.org
August 8, 2025 at 6:06 PM
Our lab at Yale @yalemedicine.bsky.social seeks #postdocs with in vivo expertise to pioneer research at the intersection of tissue remodeling & aging. Work with us to uncover immunological & vascular drivers of ovarian aging, applying single-cell, spatial omics, and ML! jobrxiv.org/job/yale-uni...
Reposted by Hattie Chung
Really excited to share our new @cellpress.bsky.social Cell paper with @fertiglab.bsky.social and colleagues. 1/n
www.cell.com/cell/fulltex...
@jktgfoundation.bsky.social @itcrtraining.bsky.social @smbmathbiology.bsky.social #mathbio #mathonco @mathonco.bsky.social @deniswirtz.bsky.social
www.cell.com/cell/fulltex...
@jktgfoundation.bsky.social @itcrtraining.bsky.social @smbmathbiology.bsky.social #mathbio #mathonco @mathonco.bsky.social @deniswirtz.bsky.social
Human interpretable grammar encodes multicellular systems biology models to democratize virtual cell laboratories
We developed a plain text modeling language—a cell behavior hypothesis grammar—to
easily build virtual cell models and connect them to data, helping scientists to unlock
the hidden dynamics of tissues...
www.cell.com
July 28, 2025 at 2:20 PM
Really excited to share our new @cellpress.bsky.social Cell paper with @fertiglab.bsky.social and colleagues. 1/n
www.cell.com/cell/fulltex...
@jktgfoundation.bsky.social @itcrtraining.bsky.social @smbmathbiology.bsky.social #mathbio #mathonco @mathonco.bsky.social @deniswirtz.bsky.social
www.cell.com/cell/fulltex...
@jktgfoundation.bsky.social @itcrtraining.bsky.social @smbmathbiology.bsky.social #mathbio #mathonco @mathonco.bsky.social @deniswirtz.bsky.social
Excited to share that we've received an NIH R35 MIRA! This grant will support our work building tools to study how cell states change over space and time in disease. Grateful to our community, and especially the wonderful team I get to work with.
@yalecvrc.bsky.social
@yalecvrc.bsky.social
July 31, 2025 at 8:39 PM
Excited to share that we've received an NIH R35 MIRA! This grant will support our work building tools to study how cell states change over space and time in disease. Grateful to our community, and especially the wonderful team I get to work with.
@yalecvrc.bsky.social
@yalecvrc.bsky.social
Reposted by Hattie Chung
In a study of professors, women got 378 new work requests over 4 weeks vs 118 for men. Women spent more time on service, advising & teaching; men on research. Orgs should track who is taking extra duties & ensure they are rewarded and distributed fairly. www.forbes.com/sites/kimels...
Being Too Helpful At Work Can Hurt Your Career—Here’s How To Say No
Women are more likely to take on behind-the-scenes duties at work—extra tasks like onboarding or event planning—and it's hurting their careers. Here's how to say no.
www.forbes.com
July 7, 2025 at 8:03 PM
In a study of professors, women got 378 new work requests over 4 weeks vs 118 for men. Women spent more time on service, advising & teaching; men on research. Orgs should track who is taking extra duties & ensure they are rewarded and distributed fairly. www.forbes.com/sites/kimels...
Reposted by Hattie Chung
Pluripotent stem cells that differentiate into vascularized cardiac and hepatic organoids. Wow! www.science.org/doi/10.1126/...
Gastruloids enable modeling of the earliest stages of human cardiac and hepatic vascularization
Although model organisms have provided insight into the earliest stages of cardiac and hepatic vascularization, we know very little about this process in humans because of ethical restrictions and the...
www.science.org
June 6, 2025 at 2:25 AM
Pluripotent stem cells that differentiate into vascularized cardiac and hepatic organoids. Wow! www.science.org/doi/10.1126/...
Reposted by Hattie Chung
Microvascular obstruction is known to be a #LongCovid feature. Now a potential mechanism found for the obstruction induced by death of endothelial cells->sticky red blood cells. Which wouldn't respond to blood thinners or anti-platelet Rx
www.nature.com/articles/d41...
www.nature.com/articles/s41...
www.nature.com/articles/d41...
www.nature.com/articles/s41...
June 4, 2025 at 7:38 PM
Microvascular obstruction is known to be a #LongCovid feature. Now a potential mechanism found for the obstruction induced by death of endothelial cells->sticky red blood cells. Which wouldn't respond to blood thinners or anti-platelet Rx
www.nature.com/articles/d41...
www.nature.com/articles/s41...
www.nature.com/articles/d41...
www.nature.com/articles/s41...
Reposted by Hattie Chung
Our ability to accurately determine an individual's risk for heart and vascular disease is getting transformed
—New A.I. transformer model
www.thelancet.com/journals/lan...
—Meta-prediction
www.nature.com/articles/s41...
—New A.I. transformer model
www.thelancet.com/journals/lan...
—Meta-prediction
www.nature.com/articles/s41...
June 2, 2025 at 8:21 PM
Our ability to accurately determine an individual's risk for heart and vascular disease is getting transformed
—New A.I. transformer model
www.thelancet.com/journals/lan...
—Meta-prediction
www.nature.com/articles/s41...
—New A.I. transformer model
www.thelancet.com/journals/lan...
—Meta-prediction
www.nature.com/articles/s41...
Reposted by Hattie Chung
Out @nature.com: Clonal tracing with somatic epimutations
🧬 Single cell methylome encodes cell state & clonal identity
🔨 EPI-Clone reads out both (+mutations, +RNA) at scale
🩸 Clonal expansions of HSCs are universal from age 50, not driven by CH mutations
doi.org/10.1038/s415...
🧵
🧬 Single cell methylome encodes cell state & clonal identity
🔨 EPI-Clone reads out both (+mutations, +RNA) at scale
🩸 Clonal expansions of HSCs are universal from age 50, not driven by CH mutations
doi.org/10.1038/s415...
🧵
Clonal tracing with somatic epimutations reveals dynamics of blood ageing - Nature
The discovery that DNA methylation of different CpG sites can serve as digital barcodes of clonal identity led to the development of EPI-Clone, an algorithm that enables single-cell lineage tracing th...
doi.org
May 21, 2025 at 3:44 PM
Out @nature.com: Clonal tracing with somatic epimutations
🧬 Single cell methylome encodes cell state & clonal identity
🔨 EPI-Clone reads out both (+mutations, +RNA) at scale
🩸 Clonal expansions of HSCs are universal from age 50, not driven by CH mutations
doi.org/10.1038/s415...
🧵
🧬 Single cell methylome encodes cell state & clonal identity
🔨 EPI-Clone reads out both (+mutations, +RNA) at scale
🩸 Clonal expansions of HSCs are universal from age 50, not driven by CH mutations
doi.org/10.1038/s415...
🧵
Reposted by Hattie Chung
title of assistant professor's talk: amino acid metabolism of effector T cells in LCMV infection
title of senior full professor's talk: Why do cells eat?
title of senior full professor's talk: Why do cells eat?
May 20, 2025 at 4:19 PM
title of assistant professor's talk: amino acid metabolism of effector T cells in LCMV infection
title of senior full professor's talk: Why do cells eat?
title of senior full professor's talk: Why do cells eat?
Reposted by Hattie Chung
Cells as living drugs is a big part of future medical approaches.
There's been so much about engineering T cells (CAR-T) for treatment of cancer and autoimmune diseases. But engineering macrophages (CAR-M) is next up for blocking inflammation.
www.nature.com/articles/s41...
There's been so much about engineering T cells (CAR-T) for treatment of cancer and autoimmune diseases. But engineering macrophages (CAR-M) is next up for blocking inflammation.
www.nature.com/articles/s41...
Targeting inflammation with chimeric antigen receptor macrophages using a signal switch - Nature Biomedical Engineering
Anti-TNF CAR macrophages show anti-inflammatory efficacy in both acute and chronic inflammatory disease mouse models.
www.nature.com
May 10, 2025 at 7:39 PM
Cells as living drugs is a big part of future medical approaches.
There's been so much about engineering T cells (CAR-T) for treatment of cancer and autoimmune diseases. But engineering macrophages (CAR-M) is next up for blocking inflammation.
www.nature.com/articles/s41...
There's been so much about engineering T cells (CAR-T) for treatment of cancer and autoimmune diseases. But engineering macrophages (CAR-M) is next up for blocking inflammation.
www.nature.com/articles/s41...
A wonderful interview with our @yalecvrc.bsky.social colleague Martin Schwartz! Where science is like art: learning to define your taste in questions
In today's episode of the Night Science Podcast we talk with Martin Schwartz from Yale about the importance of stupidity in science: while learning science makes you feel smart, true scientific discovery often involves feeling stupid, because it means venturing into the unknown.
April 21, 2025 at 11:42 PM
A wonderful interview with our @yalecvrc.bsky.social colleague Martin Schwartz! Where science is like art: learning to define your taste in questions
Reposted by Hattie Chung
In today's episode of the Night Science Podcast we talk with Martin Schwartz from Yale about the importance of stupidity in science: while learning science makes you feel smart, true scientific discovery often involves feeling stupid, because it means venturing into the unknown.
April 21, 2025 at 11:31 AM
In today's episode of the Night Science Podcast we talk with Martin Schwartz from Yale about the importance of stupidity in science: while learning science makes you feel smart, true scientific discovery often involves feeling stupid, because it means venturing into the unknown.
Reposted by Hattie Chung
What if LLMs could “read” & “write” biology? 🤔
Introducing C2S‑Scale—a Yale and Google collab: we scaled LLMs (up to 27B!) to analyze & generate single‑cell data 🧬 ➡️ 📝
🔗 Blog: research.google/blog/teachin...
🔗 Preprint: biorxiv.org/content/10.1...
Introducing C2S‑Scale—a Yale and Google collab: we scaled LLMs (up to 27B!) to analyze & generate single‑cell data 🧬 ➡️ 📝
🔗 Blog: research.google/blog/teachin...
🔗 Preprint: biorxiv.org/content/10.1...
Teaching machines the language of biology: Scaling large language models for next-generation single-cell analysis
research.google
April 18, 2025 at 2:14 PM
What if LLMs could “read” & “write” biology? 🤔
Introducing C2S‑Scale—a Yale and Google collab: we scaled LLMs (up to 27B!) to analyze & generate single‑cell data 🧬 ➡️ 📝
🔗 Blog: research.google/blog/teachin...
🔗 Preprint: biorxiv.org/content/10.1...
Introducing C2S‑Scale—a Yale and Google collab: we scaled LLMs (up to 27B!) to analyze & generate single‑cell data 🧬 ➡️ 📝
🔗 Blog: research.google/blog/teachin...
🔗 Preprint: biorxiv.org/content/10.1...
Reposted by Hattie Chung
As promised, a 'skeet' -orial on our paper published last week !
Now online! Engineering TCR-controlled fuzzy logic into CAR T cells enhances therapeutic specificity
Engineering TCR-controlled fuzzy logic into CAR T cells enhances therapeutic specificity
Robot-assisted analysis and theoretical modeling of TCR/CAR crosstalk enable the design of adoptive T cell therapies that maximize anti-tumor activity and minimize toxicity in healthy tissues.
dlvr.it
April 14, 2025 at 1:05 PM
As promised, a 'skeet' -orial on our paper published last week !
Reposted by Hattie Chung
Ranking of Variant Effect Predictor (VEP) in-silico tools from a recently published review, based on Relative performance with rate on MAVE data)
1. CPT-1 (Broad Institute)
2. AlphaMissense (Google DeepMind and cols.)
3. ESCOTT (Sorbonne/INSERM France)
1. CPT-1 (Broad Institute)
2. AlphaMissense (Google DeepMind and cols.)
3. ESCOTT (Sorbonne/INSERM France)
April 16, 2025 at 9:41 AM
Ranking of Variant Effect Predictor (VEP) in-silico tools from a recently published review, based on Relative performance with rate on MAVE data)
1. CPT-1 (Broad Institute)
2. AlphaMissense (Google DeepMind and cols.)
3. ESCOTT (Sorbonne/INSERM France)
1. CPT-1 (Broad Institute)
2. AlphaMissense (Google DeepMind and cols.)
3. ESCOTT (Sorbonne/INSERM France)
🚨 Job alert! 🚨
The Chung Lab @ Yale seeks a motivated, creative postdoc to examine tissue remodeling in health and disease. We study ovarian aging and cardiovascular disease in human samples and animal models. Passionate about single-cell, spatial genomics, machine learning & therapeutics? Join us!
The Chung Lab @ Yale seeks a motivated, creative postdoc to examine tissue remodeling in health and disease. We study ovarian aging and cardiovascular disease in human samples and animal models. Passionate about single-cell, spatial genomics, machine learning & therapeutics? Join us!
April 2, 2025 at 1:27 PM
🚨 Job alert! 🚨
The Chung Lab @ Yale seeks a motivated, creative postdoc to examine tissue remodeling in health and disease. We study ovarian aging and cardiovascular disease in human samples and animal models. Passionate about single-cell, spatial genomics, machine learning & therapeutics? Join us!
The Chung Lab @ Yale seeks a motivated, creative postdoc to examine tissue remodeling in health and disease. We study ovarian aging and cardiovascular disease in human samples and animal models. Passionate about single-cell, spatial genomics, machine learning & therapeutics? Join us!
Reposted by Hattie Chung
Here is our paper showing in vivo folding of nascent RNA right after synthesis, published now in @cp-molcell.bsky.social!
With @karlaneugebauer.bsky.social, @isaac-vock.bsky.social, @mattdsimon.bsky.social
www.cell.com/molecular-ce...
With @karlaneugebauer.bsky.social, @isaac-vock.bsky.social, @mattdsimon.bsky.social
www.cell.com/molecular-ce...
Rapid folding of nascent RNA regulates eukaryotic RNA biogenesis
Schärfen et al. develop a method to measure the structure of nascent RNAs during their
synthesis by RNA polymerases. Base pairing occurs rapidly in cells, revealing the
strong regulatory potential of ...
www.cell.com
March 26, 2025 at 1:39 PM
Here is our paper showing in vivo folding of nascent RNA right after synthesis, published now in @cp-molcell.bsky.social!
With @karlaneugebauer.bsky.social, @isaac-vock.bsky.social, @mattdsimon.bsky.social
www.cell.com/molecular-ce...
With @karlaneugebauer.bsky.social, @isaac-vock.bsky.social, @mattdsimon.bsky.social
www.cell.com/molecular-ce...
Reposted by Hattie Chung
Myocarditis is a focus of many concerns. It is not a side effect of a particular vaccine but of the immune response following vaccination or infection! The latter, infection, is a much more serious event.
A systemic review of over 400 million people; 1947 to 2021:
A systemic review of over 400 million people; 1947 to 2021:
November 17, 2024 at 12:36 PM
Myocarditis is a focus of many concerns. It is not a side effect of a particular vaccine but of the immune response following vaccination or infection! The latter, infection, is a much more serious event.
A systemic review of over 400 million people; 1947 to 2021:
A systemic review of over 400 million people; 1947 to 2021:
Reposted by Hattie Chung
Growth of the maternal intestine during reproduction @cellcellpress.bsky.social @irenemiguel-aliaga.bsky.social
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
March 19, 2025 at 5:47 PM
Growth of the maternal intestine during reproduction @cellcellpress.bsky.social @irenemiguel-aliaga.bsky.social
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
Reposted by Hattie Chung
we recently found some really neat RNA-guided DNA-cutting systems in phages. Despite remarkable similarities to CRISPR systems, including encoding guide RNAs in arrays, they appear entirely evolutionarily distinct (but definitely related to snoRNAs 🤓)
We decided to call them TIGR-Tas systems 🐯
We decided to call them TIGR-Tas systems 🐯
March 1, 2025 at 12:18 AM
we recently found some really neat RNA-guided DNA-cutting systems in phages. Despite remarkable similarities to CRISPR systems, including encoding guide RNAs in arrays, they appear entirely evolutionarily distinct (but definitely related to snoRNAs 🤓)
We decided to call them TIGR-Tas systems 🐯
We decided to call them TIGR-Tas systems 🐯
Reposted by Hattie Chung
Excited to share this new work led by postdoc Brendan Floyd, deep mapping of cell-surface protein interactomes of T and B cells reveals maverick mitochondrial proteins and immune modulatory complexes.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Mapping the nanoscale organization of the human cell surface proteome reveals new functional associations and surface antigen clusters
The cell surface is a dynamic interface that controls cell-cell communication and signal transduction relevant to organ development, homeostasis and repair, immune reactivity, and pathologies driven b...
www.biorxiv.org
February 18, 2025 at 7:27 PM
Excited to share this new work led by postdoc Brendan Floyd, deep mapping of cell-surface protein interactomes of T and B cells reveals maverick mitochondrial proteins and immune modulatory complexes.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...