Yanxiang Deng

DNA methylation goes spatial! Introducing Spatial-DMT: a technology that co-profiles DNA methylation and transcriptome in the same tissue section. A fantastic collaboration with @zhouwanding lab. Kudos to Chin Nien Lee @ChinNLee2021 and Hongxiang Fu! biorxiv.org/content/10.110…

Congratulations to my Master's student, Lysia, on receiving the Outstanding Research Graduate Award!

🚨 Don’t forget to register for #Neuroepi25! ⏳ The deadline is fast approaching - Thursday 7th August 2025. This is your last chance to join; don't miss out on a fantastic meeting! Click here to register➡️ bit.ly/45dN5Ck #FusionNeuro #FusionAgingResearch…

Spatial profiling of chromatin accessibility in formalin-fixed paraffin-embedded tissues ft. Pengfei Guo, @LiranMao, @ChinNLee2021, Xiaowei Xu, @DengYanxiang (@PennPathLabMed), Yufan Chen, Angelysia Cardilla, Dengge Jin & Yucong Hua (@PennEngineers) nature.com/articles/s4146…

🚨 We’re hiring! The Qian Lab (@CHOP_Research & @PennMedicine ) is recruiting Postdocs and Research Technicians to study human brain development & neurodevelopmental disorders. 📍Philadelphia, Pennsylvania | 🧠 organoids, spatial omics, cerebral cortex

This paper, recently published in @NatureComms by @DengYanxiang details a method which unlocked the potential of an extensive collection of archived FFPE samples for studying gene regulation and disease mechanisms with spatial context. Read it now🔬: nature.com/articles/s4146…

We're still hiring! Please help share and reach out if you have any questions.

New paper: we developed Methylation Screening Array (MSA)–a scalable tool to dissect DNA methylation in large cohorts. By profiling 5mC & 5hmC, we uncover trait- and cell-type-specific cytosine mod signatures across tissue, aging. doi.org/10.1016/j.xgen… #Epigenetics #EWAS #5hmC

Our spatial FFPE-ATAC-seq is now published in @NatureComms! With extensive optimizations, it performs well across diverse tissues, unlocking the vast FFPE archive for spatial epigenomics. Big congrats to Pengfei Guo @pengfeo, Yufan Chen, and the team! nature.com/articles/s4146…

WE ARE HIRING: Postdoc Positions! Join us at UPenn in vibrant Philly, cutting-edge science, great city, amazing team. Please share and let's get in touch!

Excited to share our lab’s first review about which cell types in the body can be the target to combat aging! We summarized ~100 single-cell studies of aging tissues, identifying aging-associated cell types strongly depleted or expanded across the body: shorturl.at/Oi3W8

BREATHTAKING DISCOVERIES that change the world! Another first ⁦@Penn⁩ and CHOP⁦⁦⁦@ChildrensPhila⁩ nytimes.com/2025/05/15/hea… via @NYTimes

Excited to share our new @ScienceMagazine paper! Led by postdocs Ruchao Peng and Xin Xu, we used cryo-EM/ET to reveal the influenza ribonucleoprotein complex structure and its strand-sliding mechanism for RNA synthesis, paving the way for new antivirals. science.org/doi/10.1126/sc…

Excited to see nuclei.io pathologist-AI collaboration framework featured on the @natBME April 2025 cover! This is my 2nd cover article after @NatureMedicine! Letting AI to assist, not replace medical practice, will make the clinical decision-making faster, safer,…

Job alert! We are looking for postdoc interested in quantitative methods to understand metabolic programming in cancer and immune cells! Also recruiting technician to help manage lab instruments and projects. DM or email me or forward to anyone you think that might be interested!

Delighted to share a step-by-step protocol for spatially resolved epigenome-transcriptome co-sequencing to map tissue development, aging & disease. Fully committed to open science!! ⁦@sennetresearch⁩ ⁦@_hubmap⁩ ⁦@NIH_CommonFund⁩ @NCIHTAN nature.com/articles/s4159…

Perturb-tracing integrates CRISPR screening with barcode readout and chromatin tracing for loss-of-function screens, facilitating the study of chromatin folding regulators. @SStevenWang @YaleMed @Yale @YaleGenetics @YaleCellBio nature.com/articles/s4159…

Interested in single cell genomics but need help getting started? Check out the full agenda for our Single Cell Genomics Day on Friday 4/25. All talks will be live-streamed (no registration required) at satijalab.org/scgd25

Super excited to launch nimbusimage.com, our cloud-based image analysis platform! nimbusimage.com Docs here: docs.nimbusimage.com Free tier available!

Introducing RAEFISH, our lab's new flagship image-based spatial transcriptomics technology that simultaneously enables single-molecule spatial resolution and whole-genome level coverage of long and short, endogenous and engineered RNA species in cell cultures and intact tissues.