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!

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...

🚨 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...

✨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

I'm so sorry Anders 🤯

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...

A world of possibilities contained in the ovary :)

One of our favorite ovary images

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!

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...

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...

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

Thank you Jenn!!

Thank you Haiqi!

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

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.

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...

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...

Pluripotent stem cells that differentiate into vascularized cardiac and hepatic organoids. Wow! www.science.org/doi/10.1126/...

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...

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...

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...
🧵

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?

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.

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...

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.

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

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...

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

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)

Postdoctoral Associate at Hattie Chung Lab Post a job in 3min, or find thousands of job offers like this one at jobRxiv!

jobrxiv.org/job/yale-uni...

🚨 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!

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 ...

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...

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...