How does aging reshape a tissue that must continually rebuild itself hundreds of times? Our latest: Using spatial transcriptomics, we find that ovarian aging disrupts the coordination of cells across space and time before reproductive cycles stop. #OvarianAging

Nature Aging@nataging.nature.com · 2mo ago

Online now! Spatial atlas of aging mouse ovary shows that reproductive decline reflects progressive loss of spatiotemporal coordination #OvarianAging #WomensHealth @hattaca.bsky.social @davidsebfischer.bsky.social @akochersberger.bsky.social @jennifergarrison.bsky.social doi.org/10.1038/s435...

Congratulations to our PhD student Chelsea Lai, who was awarded an NSF GRFP earlier this week!

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!

Çağrı Çevrim@cagricevrim.bsky.social · 10mo ago

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... 🧵

🚨 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...

biorxiv.org

✨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

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

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

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...

cell.com

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

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...

science.org

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...

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...

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... 🧵

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

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?

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...

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.

nature.com

A wonderful interview with our @yalecvrc.bsky.social colleague Martin Schwartz! Where science is like art: learning to define your taste in questions

Itai Yanai@itaiyanai.bsky.social · last yr.

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.

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...

Teaching machines the language of biology: Scaling large language models for next-generation single-cell analysis

research.google

As promised, a 'skeet' -orial on our paper published last week !

Cell - a Cell Press journal@cp-cell.bsky.social · last yr.

Now online! Engineering TCR-controlled fuzzy logic into CAR T cells enhances therapeutic specificity

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)

🚨 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!

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...

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 ...

cell.com

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:

Growth of the maternal intestine during reproduction @cellcellpress.bsky.social @irenemiguel-aliaga.bsky.social www.cell.com/cell/fulltex...

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

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...

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.

thelancet.com

@ImmunityCP preview: Restimulation by macrophages exhausts T cells www.cell.com/immunity/ful... on www.cell.com/immunity/ful...

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...

cell.com

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/...

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.

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/

ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants

Despite extensive mapping of cis-regulatory elements (cREs) across cellular contexts with chromatin accessibility assays, the sequence syntax and genetic variants that regulate transcription factor (T...

biorxiv.org

Anshul Kundaje@anshulkundaje.bsky.social · 2y ago

Aiming to release our long awaited ChromBPNet preprint by early next week as well. I'm recovering from back to back infections for the past 6 weeks. But we're almost there. We have some solid variant prediction benchmarks in there against large supervised models and lots more. Stay tuned.

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