Hattie Chung
@hattaca.bsky.social
📤 1508
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Assistant Professor @YaleMed | tissue biology, computation, systems biology | www.hattiechunglab.bio
reposted by
Hattie Chung
Kara McKinley
about 1 month ago
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!
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Hattie Chung
Leif S. Ludwig
about 2 months ago
🚨 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...
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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...
https://www.biorxiv.org/content/10.1101/2025.09.17.675534v1.full
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Hattie Chung
Society for Developmental Biology
3 months ago
✨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
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Hattie Chung
Bluma Lesch
3 months ago
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...
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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
https://genesdev.cshlp.org/content/early/2025/08/18/gad.352841.125
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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...
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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!
https://jobrxiv.org/job/yale-university-27778-postdoctoral-fellow-hattie-chung-lab-yale-school-of-medicine/
3 months ago
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Hattie Chung
Paul Macklin
4 months ago
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
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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...
https://www.cell.com/cell/fulltext/S0092-8674(25)00750-0
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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
4 months ago
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Hattie Chung
Amy Diehl, Ph.D.
5 months ago
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...
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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.
https://www.forbes.com/sites/kimelsesser/2025/07/07/being-too-helpful-at-work-can-hurt-your-career-heres-how-to-say-no/
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Rita Strack
6 months ago
Pluripotent stem cells that differentiate into vascularized cardiac and hepatic organoids. Wow!
www.science.org/doi/10.1126/...
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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...
https://www.science.org/doi/10.1126/science.adu9375
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Hattie Chung
Eric Topol
6 months ago
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...
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Hattie Chung
Eric Topol
6 months ago
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...
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Hattie Chung
Lars Velten
6 months ago
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...
🧵
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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...
https://doi.org/10.1038/s41586-025-09041-8
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reposted by
Hattie Chung
Caroline Bartman
6 months ago
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?
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Hattie Chung
Eric Topol
6 months ago
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...
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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.
https://www.nature.com/articles/s41551-025-01387-8
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A wonderful interview with our
@yalecvrc.bsky.social
colleague Martin Schwartz! Where science is like art: learning to define your taste in questions
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7 months ago
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Hattie Chung
Itai Yanai
7 months ago
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.
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David van Dijk
7 months ago
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...
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Teaching machines the language of biology: Scaling large language models for next-generation single-cell analysis
https://research.google/blog/teaching-machines-the-language-of-biology-scaling-large-language-models-for-next-generation-single-cell-analysis/
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Hattie Chung
Paul Francois
7 months ago
As promised, a 'skeet' -orial on our paper published last week !
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Hattie Chung
Albert Vilella, PhD.
7 months ago
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)
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🚨 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!
8 months ago
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Hattie Chung
Leo Schärfen
8 months ago
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...
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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 ...
https://www.cell.com/molecular-cell/fulltext/S1097-2765(25)00187-X
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reposted by
Hattie Chung
Marc Veldhoen
about 1 year ago
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:
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reposted by
Hattie Chung
Waggoner Lab
8 months ago
Growth of the maternal intestine during reproduction
@cellcellpress.bsky.social
@irenemiguel-aliaga.bsky.social
www.cell.com/cell/fulltex...
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Hattie Chung
Max Wilkinson
9 months ago
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 🐯
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Hattie Chung
Carolyn Bertozzi
9 months ago
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...
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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...
https://www.biorxiv.org/content/10.1101/2025.02.12.637979v1
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Hattie Chung
Yale Cardiovascular Research Center
10 months ago
Fantastic Cardiology Grand Rounds on advances in polygenic risk scores from field leader Pradeep Natarajan
@pnatarajanmd.bsky.social
, introduced by our own Hattie Chung
@hattaca.bsky.social
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reposted by
Hattie Chung
Eric Topol
10 months ago
New: The largest medical A.I. randomized controlled trial yet performed, enrolling >100,000 women undergoing mammography screening The use of AI led to 29% higher detection of cancer, no increase of false positives, and reduced workload compared with radiologists w/o AI
thelancet.com/journals/lan...
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Screening performance and characteristics of breast cancer detected in the Mammography Screening with Artificial Intelligence trial (MASAI): a randomised, controlled, parallel-group, non-inferiority, ...
The findings suggest that AI contributes to the early detection of clinically relevant breast cancer and reduces screen-reading workload without increasing false positives.
https://thelancet.com/journals/landig/article/PIIS2589-7500(24)00267-X/fulltext
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Hattie Chung
Wendy Bickmore
11 months ago
Our new paper showing how loss of the nuclear pore protein TPR leads to activation of an inflammatory gene expression programme in senescence is now published in eLife:
bit.ly/4h1VcFi
@wbickmor.bsky.social
@uoe-igc.bsky.social
@elife.bsky.social
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Hattie Chung
Fabian Theis
10 months ago
Excited to see Moscot (moscot-tools.org) published in @Nature! We scaled Optimal Transport (OT) in single-cell genomics & added multimodality together with spatiotemporal trajectory inference, finding exciting new biology in the pancreas! 🚀 Read at
www.nature.com/articles/s41...
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Mapping cells through time and space with moscot - Nature
Moscot is an optimal transport approach that overcomes current limitations of similar methods to enable multimodal, scalable and consistent single-cell analyses of datasets across spatial and temporal...
https://www.nature.com/articles/s41586-024-08453-2
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Hattie Chung
Waggoner Lab
10 months ago
@ImmunityCP preview: Restimulation by macrophages exhausts T cells
www.cell.com/immunity/ful...
on
www.cell.com/immunity/ful...
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Restimulation by macrophages exhausts T cells
Inhibiting T cell exhaustion is an attractive cancer immunotherapy strategy. In this issue of Immunity, Waibl Polania et al. examine the microenvironmental signals regulating terminal T cell exhaustio...
https://www.cell.com/immunity/fulltext/S1074-7613(24)00574-0
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Hattie Chung
Anshul Kundaje
11 months ago
Very excited to announce that the single cell/nuc. RNA/ATAC/multi-ome resource from ENCODE4 is now officially public. This includes raw data, processed data, annotations and pseudobulk products. Covers many human & mouse tissues. 1/
www.encodeproject.org/single-cell/...
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Single cell – ENCODEHomo sapiens clickable body map
https://www.encodeproject.org/single-cell/?type=Experiment&assay_slims=Single+cell&status=released
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Hattie Chung
Arjun Raj
11 months ago
Reposting my offer for 1-1 mentoring for anyone… email me and we'll find a time! Especially happy to talk with those from diverse backgrounds and non-traditional career trajectories.
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Hattie Chung
Anshul Kundaje
11 months ago
Our ChromBPNet preprint out!
www.biorxiv.org/content/10.1...
Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/
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Hattie Chung
NU Duncan Lab
11 months ago
Registration is now open for the 2025 Reproductive Aging Conference! May 4-7, 2025 in San Jose, California This is the only international meeting dedicated solely to mechanisms of reproductive aging. Register today:
www.reproductiveagingconference.com
@jennifergarrison.bsky.social
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Excited to share our lab's first preprint: we used spatial transcriptomics to dissect how aging disrupts the cycling ovary! 🧵 This was an incredible team effort w/
@jennifergarrison.bsky.social
#TammyLan
@davidsebfischer.bsky.social
#AlisonKochersberger
#RuthRaichur
#SophiaSzady
11 months ago
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Hattie Chung
Hani Goodarzi
12 months ago
@thejohnnyyu.bsky.social
,
@therealnima.bsky.social
, Kevan Shokat, and I are excited to announce a historic achievement by our team at
@vevotherapeutics.bsky.social
:
tinyurl.com/4rrvap3t
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Vevo Therapeutics to Release World's Largest Atlas of Single-Cell Transcriptomic Data, Tahoe-100M, to Map How Drugs Impact Patient Cells and Accelerate Discovery of New Drugs
/PRNewswire/ -- Vevo Therapeutics, a biotechnology company using its Mosaic technology and next generation AI to uncover better drugs for more patients,...
https://www.prnewswire.com/news-releases/vevo-therapeutics-to-release-worlds-largest-atlas-of-single-cell-transcriptomic-data-tahoe-100m-to-map-how-drugs-impact-patient-cells-and-accelerate-discovery-of-new-drugs-302323245.html?tc=eml_cleartime
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Incredibly excited to see this brilliant work from
@gheimberg.bsky.social
#AvivRegev
out this week. Years in the making, Graham thought of this before foundation models became cool :) a model for searching & finding the closest cell state, and experimentally validated !
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12 months ago
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