Very excited to share our work on high-resolution single-cell Micro-C, which is on bioRxiv now. Here we reveal that cohesin-mediated loop extrusion participates in transcription with kilobase-resolution single-cell 3D structures. biorxiv.org/content/10.110…

Inheritable 'memory' genes drive #cancer drug tolerance, but their discovery in clinical samples is a major challenge. Our new theory, moving away from Luria-Delbruck, detects them from a *single* scRNA-seq dataset! With #ArchishmanRaju led by Suvranil tinyurl.com/4pef8scy

🧵5 Top Free Alternatives to BioRender for Scientific Illustrations! These five websites offer free scientific illustrations for biologists. Great for presentations, research papers and other research communication needs. Save and share the post!

New pre-print(s) from the Sternberg Lab in collaboration with Leifu Chang! We uncover an unprecedented molecular mechanism of CRISPR-Cas12f-like proteins, which drive RNA-guided transcription independently of canonical promoter motifs. Full story here: tinyurl.com/mr3fd493

Enhancers, how do they work (in vivo)? To find out, we mutagenized 7 human enhancers comprehensively in 12bp blocks and scored for activity in developing mouse embryos. rdcu.be/erD22 nature #mutagenesis #noncoding #enhancers

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

Our preprint describing the Range Extender element, which is required and sufficient for long-range enhancer activation at the Shh locus, is out in nature. nature.com/articles/s4158…

I'm super excited to share that I will be joining the Department of Biology at Stanford University as an Assistant Professor in October 2025! I’ll also be a member of the Stanford Stem Cell Institute Stanford Stem Cell. Incredibly grateful to be starting my dream job!🧠🧬🖥️

@nbcnews has published a powerful feature on the death of pioneering Chinese American neuroscientist Dr. Jane Wu, who died by suicide on July 10, 2024, after Northwestern University abruptly shut down her laboratory: nbcnews.com/news/asian-ame…

Nice blogpost on "PhD-level" AI agents which hits on a concern I've also felt: their current failure modes are the zero tolerance nightmare scenario for an academic researcher (inventing references, manufacturing data, "solving" bugs by removing functionality, etc).

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.

Today I learned you can just spray mRNA on plant leaves and they'll make proteins. New preprint just sprayed a bunch of green florescent protein mRNA on different plant leaves and found signal.

Prof. Nikolai Slavov When I moved from physics to biology, I was surprised by the reflexively congratulatory tone of Q&A sessions. This was a big change from (happened to a visiting speaker) “you’re completely wrong because your model violates detailed balance [a statistical mechanics principle].”

Our RAEFISH spatial transcriptomics technology is now published in Cell Cell! RAEFISH enables sequencing-free whole genome spatial transcriptomics at single molecule resolution. This work represents the first time that transcripts from more than 23,000 genes were

In addition to the science from Gerd's lab, he is also a first-rate mentor!

Been working on a really strange retron bacterial immune system, here's the preprint: biorxiv.org/content/10.110… Type VI retrons are unlike any other. Phage infection triggers reverse transcription of a DNA fragment that activates translation of a toxin to kill the infected cell.

Excited to share our new paper just published in Nature Genetics Nature Genetics! 🧬 “Genome-scale CRISPR screens identify PTGES3 as a direct modulator of androgen receptor function in advanced prostate cancer.” 👉 nature.com/articles/s4158…

A preprint‼️that's bound to ruffle some 🪶 "Widespread DNA off-targeting confounds studies of RNA chromatin occupancy" led by our Micah Goldrich and Louis Delhaye from Pieter Mestdagh. TL;DR we show that many of lncRNA chromatin occupancy maps are flawed🧵biorxiv.org/content/10.110…

This is how science should be: we were notified that we may have made an error; we invested time and money on investigating the error; we concluded that indeed there was an error; we let the world know. Respect for Neville and the team!