1/14 On behalf of the amazing team in Jonathan Weissman's Lab, we’re excited to share PEtracer (biorxiv.org/content/10.110…) a prime editing-based evolving lineage recorder compatible with both scRNA-seq and high-resolution imaging readouts in intact tissue. By applying PEtracer in a syngeneic mouse

New from the Rouhanifard Lab! What if we could sort single cells based on whether a specific gene was actively being transcribed—and then ask what drives that burst? Introducing: NuclampFISH

STAMP brings us non-destructive single-cell profiling without the sequencing omic.ly/stamp-brings-u…

I am thrilled to share with the world a new preprint, spearheaded by the truly amazing Jose Reyes in partnership with Lowe Lab. Focused on the benign to malignant transition in PDAC, uncovering roles of plasticity, tissue remodeling and P53 -> biorxiv.org/content/10.110…

We turn 25 today! July 7th marks the 25th anniversary of the human genome going online and the start of the UCSC Genome Browser. Then vs. now, we have 165k monthly visitors, and our codebase is over three million lines of code. See our news for more: bit.ly/genomeBrowser2…

New research out in Science Magazine provides a lineage-resolved analysis of embryonic gene expression evolution in C. elegans & C. briggsae ft. Christopher Large, Rupa Khanal, John Murray (Penn Genetics) & Junhyong Kim (Penn Biology) science.org/doi/10.1126/sc…

Uncle Iroh and Zuko

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.

[0/8] Super stoked to share our work with Arjun Raj on tissue organization in the gastruloid. We use lineage tracing and spatial transcriptomics to show that diversity among stem cell clones promotes, rather than hinders, gastruloid development: biorxiv.org/content/10.110…

Wow!!! Big advance for women with pathogenic mitochondrial DNA variants in NEJM! nejm.org/doi/full/10.10… nejm.org/doi/full/10.10…

I am a strong believer that depth of data can be just as powerful as scale of data. Deep analysis of small groups of humans, and even individuals, can lead to novel biological insights and principles. Today I am the guinea pig. In my own blood, Caleb Lareau finds strong evidence

For innate immune cells, the lack of diverse receptor rearrangements has prevented the study of clonal evolution of the innate immune system in human tissues and tumors. With @satpathology and @caleblareau, I’m delighted to share my PhD work that tackles this challenge:

Thanks to Riya Sinha in my lab, IGV Team browser will natively support dynseq (dynamic sequence tracks) in an upcoming release. These tracks are very useful to directly visualize base-resolution scores (e.g. contribution scores from ML models, conservation etc). 1/

(1/n) Excited to share our new preprint! We uncover that RNA actively promotes nucleation and function of pathogenic condensates, amplifying locus-specific oncogenic transcription and promoting tumorigenesis. #epigenetics #condensates #cancer #RNA biorxiv.org/content/10.110…

The luscious brushwork in the paintings of Eric Bowman (born 1960)

Our paper is now out in final form at Nature Genetics! For those who missed the preprint, we used large-scale Perturb-seq targeting transcription factors to push primary fibroblasts into diverse transcriptional states, including those observed in cell atlas studies.

I'm excited to share our new preprint on LagTag, a method that recovers both past and present chromatin states from the same mammalian cells. biorxiv.org/content/10.110…

Now online in Cancer Discovery: Systematic Evaluation of GAPs and GEFs Identifies a Targetable Dependency for Hematopoietic Malignancies - by Pu Zhang, Zhendong (Tom) Cao, Anthony Daniyan, Abdel-Wahab Lab, Junwei Shi, and colleagues doi.org/10.1158/2159-8… Penn Medicine - Abramson Cancer Center Memorial Sloan Kettering Cancer Center

Excited to share our CITE-seq atlas of the aging human immune system across tissues. Great collaboration with Donna Farber, Yosef Lab, Teichlab, Jo Jones Cambridge University and partnership with CZI Science! nature.com/articles/s4159…

Blocking Nav1.8 can effectively treat acute pain... But what about our patients with chronic pain? Excited to share our recently published perspective on the challenges of targeting Nav channels to treat chronic pain nature.com/articles/s4158…