Great experience compiling years of collective screening experience to produce what we hope is a comprehensive protocol for others to accessibly scale up experiments! And some fun new data hidden in there :) @joshtycko.com www.nature.com/articles/s41...

High-throughput measurements of protein domain functions using magnetic separation - Nature Protocols

This Protocol presents a scalable magnetic separation-based method for screening large protein domain libraries in mammalian cells, providing a simple and quantitative alternative to fluorescence-acti...

nature.com

Does every enhancer work with every promoter? With @jengreitz.bsky.social and Will Greenleaf, we revisit this long-debated question and resolve an outstanding contradiction in the field. A tour 🧵👇 www.biorxiv.org/content/10.6...

Intrinsic promoter responsiveness dictates sensitivity to transcriptional activation by enhancers

Enhancers activate specific target promoters, but whether intrinsic enhancer-promoter compatibility contributes to this specificity is debated. Recent studies using different reporter assays have reac...

biorxiv.org

Personalized therapies hold tremendous promise but challenge traditional models of drug and biologic development. The @fda.gov outlines a path to market entry for products where a randomized trial is not feasible. Learn more: nej.md/4nUQdcl

After leukemia treatments failed, Alyssa Tapley, at age 13, was told she would die. Then, doctors tried an experimental gene-edited therapy. She became the first human to try the treatment made possible by U.S. federal funding. Now 16, she’s cancer-free and planning her future.

Very well done story on 60 Minutes about the harms of grant terminations and freezes at Harvard with Joan Brugge, Don Engbar, David Liu, and a very compelling young cancer patient, now cured with Liu's technology. Transcript and video here www.cbsnews.com/news/researc...

Battle between Trump and universities hurting scientific research in need of federal funding

Federal research funding to universities has fueled breakthroughs for years. The White House is pressuring universities to align with the president's political agenda, or risk losing their funding.

cbsnews.com

The Editor Got a Letter From ‘Dr. B.S.’ So Did a Lot of Other Editors. The rise of artificial intelligence has produced serial writers to science and medical journals, most likely using chatbots to boost the number of citations they’ve published #GiftLink www.nytimes.com/2025/11/04/s...

The Editor Got a Letter From ‘Dr. B.S.’ So Did a Lot of Other Editors.

nytimes.com

We then used sequence-to-activity deep learning models, to predict effects of non-coding edits on TF binding and chromatin accessibility. We first show that a ChromBPNet model can predict the same GATA site disruption mechanism exploited by the FDA-approved Casgevy medicine, specifically in T cells:

A highlight of my summer was this collab w/ @twangmdphd.bsky.social ! CRISPR base editors are driving several clinical trials, but it's hard to quantify off-target edits and their effects. Tong developed a sequencing assay to identify off-targets *in primary cells* 🧬🖥️🧪 #genomics #chromatin #CRISPR

Tong Wang@twangmdphd.bsky.social · 10mo ago

1/ Happy to share our preprint from the Greenleaf Lab: beCasKAS, our method to directly detect CRISPR base editor off-targets in primary cells. We additionally show how non-coding edits can be triaged for epigenetic dysregulation using deep learning. www.biorxiv.org/content/10.1...

Sensitive, direct detection of non-coding off-target base editor unwinding and editing in primary cells [new] Direct seq. quantifies off-target base editor & DNA unwinding.

Sensitive, direct detection of non-coding off-target base editor unwinding and editing in primary cells https://www.biorxiv.org/content/10.1101/2025.09.25.678665v1

1/ Happy to share our preprint from the Greenleaf Lab: beCasKAS, our method to directly detect CRISPR base editor off-targets in primary cells. We additionally show how non-coding edits can be triaged for epigenetic dysregulation using deep learning. www.biorxiv.org/content/10.1...

Delighted to share our latest work deciphering the landscape of chromatin accessibility and modeling the DNA sequence syntax rules underlying gene regulation during human fetal development! www.biorxiv.org/content/10.1... Read on for more: 🧵 1/16 #GeneReg 🧬🖥️

Dissecting regulatory syntax in human development with scalable multiomics and deep learning

Transcription factors (TFs) establish cell identity during development by binding regulatory DNA in a sequence-specific manner, often promoting local chromatin accessibility, and regulating gene expre...

biorxiv.org

www.biorxiv.org/content/10.1... Our study published today on #bioRxiv describe the identification of a deaminase that converts 5mC to T, enabling direct sequencing of the human methylome and genome. This achievement was made possible through a collaborative effort across all departments at #NEB.

(1st post @BlueSky) Preprint alert🚨a long thread. Cautions in the use of @nanopore sequencing to map DNA modifications: officially reported “accuracy” ≠ reliable mapping in real applications. We performed a critical assessment of nanopore sequencing (across different versions of models) for the 1/n

who knew it would be easier to get everyone to switch social media platforms than getting them to use hg38