Spatial joint profiling of DNA methylome and transcriptome in mammalian tissues biorxiv.org/content/10.110… #biorxiv_genomic

Delighted to share a new review paper from the lab. We discussed recent key findings in enhancer biology. Thanks Dan Larson and Tineke Lenstra for this opportunity!! sciencedirect.com/science/articl…

Very excited to share our new work on gastruloids by the incredible Cat Triandafillou! We mapped gene expression across 26 individual gastruloids at single-cell resolution and discovered some pretty amazing patterns about how these "mini-embryos" organize themselves.

A conserved coupling of transcriptional ON and OFF periods underlies bursting dynamics | Nature Structural & Molecular Biology nature.com/articles/s4159…

Analyzing human myocarditis at the tissue transcriptomics levels, with two different platforms, we found that the disease is characterize by widespread molecular perturbations independent of leukocyte-rich foci. Myocarditis is not so patchy after all! biorxiv.org/content/10.110…

🔬🧬 New in Nature Communications: Nanoscale 3D DNA tracing in non‑denatured cells maps the #3Dgenome at nm‑resolution and reveals Cohesin‑dependent dynamic loops! 🚀 #OpenAccess  nature.com/articles/s4146… EllenbergLab Jungmann Lab #Genomics #SuperResolution

How challenging is the prediction of transcriptional responses to CRISPR gene perturbations ? A simple model, just scaling RNA correlation vectors, results in accurate predictions for many perturbations. The model is intuitive & grounded in a simple approximation. 1/2

In our first review, scientists revisit how physical forces shape collective #AnimalBehavior, revealing how individual-environment coupling underlies group dynamics across taxa — from fish schools to ant rafts. 🐟 🐜 🔗 go.aps.org/4lUbDGv #CollectiveBehavior

A simple flow of gas over water may have helped kickstart life on early Earth. Research shows how evaporation and fluid flow in a narrow channel can drive isothermal DNA replication, offering a plausible, low-temp setting for early molecular evolution. elifesciences.org/articles/10015…

Molecular co-accessibility identifies coordinated regulation between distant cis-regulatory elements biorxiv.org/content/10.110… #biorxiv_genomic

Preload deficiency is a treatable cause of fatigue and exercise intolerance in SLE thelancet.com/journals/lanrh… This collaborative work from Hopkins Rheumatology and Johns Hopkins Cardiology brings hope to the many patients with Lupus who experience debilitating lack of stamina #cardiacimmunology

🚨New preprint from the lab🚨 🧬 What keeps certain chromatin domains anchored at the nuclear periphery? Our new genome-wide HiDRO screen uncovers a key role for RNA-binding protein hnRNPK. biorxiv.org/content/10.110…

Happy to share our work on how chromatin organization is established for the first time in early mouse embryos, in part via interplay with remarkable hypertranscription. Marvelous work by Guang Yu, Kai Xu, Weikun Xia and Ke Zhang! nature.com/articles/s4158…

🚨Preprint alert!🚨What happens to our blood vessels as we age? To begin answering this at the transcriptome level, we built the Human Aging Endothelial Cell Atlas (HAECA), profiling >375,000 endothelial cells from 12 tissues across adulthood. (1/9) biorxiv.org/content/10.110….

Glad to share our latest publication in Nature Genetics Nature Genetics: Tracing the evolution of single-cell 3D genomes in Kras-driven cancers. In this work, we generated the first single-cell 3D genome atlases of any cancer using any technique.

A brief summary/perspective on my recently published PhD work: Nucleosomes constrain 1D DNA diffusion by eukaryotic transcription factors nature.com/articles/s4159… Taekjip Ha

💡 Cancer cells don’t just mutate—they reorganize their DNA in 3D space. Our new study shows how the genome’s folding pattern shifts as tumors progress, cell by cell 🧩🧬. It’s the first 3D genome atlas of cancer progression. Thread 👇

A single E. coli cell, placed on a dish, will become 70 billion cells in just 12 hours. That’s exponential growth. But a new preprint shows that it's possible to engineer E. coli to grow linearly instead, where only one daughter cell continues dividing and the other stops.

17,186 genes were differentially expressed between biopsy-derived brain tissue from 275 living patients and 243 postmortem samples. This represents ~80% of all genes. This finding raises concerns for brain disease omics research, as most studies rely on postmortem tissue

Apoptotic vesicle release from a cell as it gives up the ghost under oxidative stress, as seen by MOSAIC lattice light sheet mode.