Now out @natbiotech.nature.com ! Do lncRNAs commonly bind 1000s of genomic sites? Maybe they do, but the dozens of studies that report genomic binding maps of lncRNAs are deeply flawed, with probes binding suprious DNA sites rather than RNA-bound ones.

Why do guinea pigs have so many natural bypass arteries — and mice and humans almost none? We develop in vivo Perturb-seq for endothelial cells to ask how protective collateral arteries are built. Preprint with by Irene Fan, Ronghao Zhou, and Kristy Red-Horse: www.biorxiv.org/content/10.6...

Why can't we explain enhancer action despite 2 decades of chromosome conformation technologies? 😬 Our new study spearheaded by Leonid Mirny's group points to a flaw in our assumptions, and to a solution from physical principles By @timothyfoldes.bsky.social 💻& @karissalhansen.bsky.social 🧪 🧵👇

The American Heart Association just posted this and tbh, I LOLed.

Oh my. This is spectacular. sinceyouarrived.world/taken

Exciting study from Leonid Mirny and co: Cohesin bridging as a physical principle of enhancer-promoter communication www.biorxiv.org/content/10.6...

Excited to share a new preprint from the lab led by @lukekoblan.bsky.social and William Colgan in which we describe our efforts to define a quantitative cell fate map of mouse embryogenesis! www.biorxiv.org/content/10.6...

Although cohesin-sensitive, long-range enhancer activation is equivalent in nature to proximal activation. Cooperativity can arise from different levels of activation inputs operating on a non-linear response function. @eliasfriman.bsky.social @uoe-igc.bsky.social www.biorxiv.org/content/10.6...

New preprint @cxqiu.bsky.social @jshendure.bsky.social ! Can we learn regulatory grammars of human cell types — by training on mouse development and transferring across 241 mammalian genomes? Introducing STEAM & a whole-organism scATAC-seq atlas from E10 to birth. www.biorxiv.org/content/10.6...

Asked the AI to make a fun slide about potential de-skilling from AI use. Need to specify more clearly what I mean by "fun".

Other highlights: 🧬 ENCODE-rE2G scores now in L2G → 5% gain in selectivity 📊 710 new GWAS Catalog studies → 5,000+ new credible sets (incl. Rand et al., Nat Genet 2025) ⚡ ClickHouse migration complete → ~2x query speed ☁️ Platform data now on AWS Open Data Program

Hey this seems like some good news District Court strikes down RFK Jr vaccine policies as not based on science www.nytimes.com/2026/03/16/h...

>60% of all predicted transcriptional activation domains (TADs) overlap with strong degrons www.biorxiv.org/content/10.1... A major role for acidic residues in TADs is to prevent degrada- tion www.biorxiv.org/content/10.1...

What drives the science behind IGVF? In this IGVF Q&A, members share how the team is tackling long-standing genomics challenges and building a comprehensive catalog of variant effects to advance human health & research. Tune in: youtu.be/zPzGIjSQJ4U?...

🧬 @danielibrahim.bsky.social, moderated by @stefanschoenfelder.bsky.social, on enhancer-promoter specificity & how promoter-proximal regions act as molecular filters. Register: us02web.zoom.us/webinar/regi... March 5, 4PM UK. #Genomics #GeneRegulation

The impact is already hitting science agencies hard. The NIH—the world's largest public biomedical research funder—has had to rely on leftover stopgap funds. New grant awards have slowed to a trickle — exacerbating the effects of a record-long shutdown in October. (h/t @jeremymberg.bsky.social)

Congress rejected massive cuts to US science budgets for 2026, but much of the money still isn’t flowing to researchers. The culprit? The White House Office of Management and Budget (OMB) is quietly slow-walking the release of funds. 🧵👇

New paper alert 🚀 Our organism-wide single-cell ATAC-seq atlas of mammalian aging is now out in @science.org, led by our fantastic graduate student Ziyu Lu from @rockefeller.edu! www.science.org/doi/10.1126/...

We wrote a perspective "How to build the regulatory genome: a constructionist guide to the cis-regulatory code", out in Development yesterday. Title says it all. Find it here: journals.biologists.com/dev/article/...

Interested in transcriptional regulation, enhancers and 3D genome folding? In this new study we wondered about the role of cohesin loading at enhancers for long-range transcriptional control www.biorxiv.org/content/10.6... detailed 🧵👇

Practical utility of sequence-to-omics models for improving the reproducibility of genetic fine-mapping https://www.biorxiv.org/content/10.64898/2026.02.04.703796v1

Yesterday, five-year-old Liam and his dad Adrian were released from Dilley detention center. I picked them up last night and escorted them back to Minnesota this morning. Liam is now home. With his hat and his backpack.

We mapped the fitness landscape of the 10kb MYC locus using SpRY-Cas9 saturation mutagenesis. 67% of the essential bps are noncoding. So even for a protein coding gene locus, most genetic information may be encoded outside of coding regions.

Does the noncoding genome actually carry more genetic information than coding seqs? Motivated by this question we mutated every bp in the 10kb MYC locus. Results are even more exciting: Decoding the MYC locus reveals a druggable ultraconserved RNA element www.biorxiv.org/content/10.6...

Today in @nature.com, we describe how discarded reads in biobank-scale WGS can help resolve the genetic predictors and consequences of Epstein-Barr Virus (EBV) infection. Wonderful working with @ryandhindsa.bsky.social @sherrynyeo.bsky.social @erinmayc.bsky.social www.nature.com/articles/s41...

AlphaGenome is out in @nature.com today along with model weights! 🧬 📄 Paper: www.nature.com/articles/s41... 💻 Weights: github.com/google-deepm... Getting here wasn’t a straight path. We discussed the story behind the model, paper & API in the following roundtable: youtu.be/V8lhUqKqzUc

An NIH source tells me that after this story was published, agency leadership held an emergency meeting about Council approval and is looking for ways to speed up the pipeline. "Better late than never?" the source says.

ICE has detained at least 3,800 kids under the second Trump administration — more than 500 of whom were under 5 years old. Children shouldn't be locked up by our government.

"Senate Democrats will not provide the votes to proceed to the appropriations bill if the DHS funding bill is included,” Schumer said Saturday evening. talkingpointsmemo.com/news/democra...

Nature research paper: Construction of complex and diverse DNA sequences using DNA three-way junctions go.nature.com/4qu2ExZ

New preprint on technologies to scale up CRISPR screens. We use them to map 665,856 pairwise genetic perturbations and outline a path to comprehensive interaction mapping in human cells. We also introduce an approach for cloning lentiviral libraries with billions of elements.

Excited to share our latest work in @ajhgnews.bsky.social 🧬📄 We mapped the regulatory landscape of human liver at single-nucleus resolution using snMultiome, connecting genetic variants to the cell-type mechanisms underlying cardiometabolic disease. www.sciencedirect.com/science/arti...

The conference (agreement between House and Senate) appropriations bill that includes HHS and NIH was released this morning. www.appropriations.senate.gov/news/majorit... 1/5

How can we identify circRNAs that might be functional? Together with @jengreitz.bsky.social, Howard Chang, and team, we found that answering this question is much more challenging than previously thought! academic.oup.com/nar/article/... See thread below:

The @zeitlingerlab.bsky.social is pleased to announce @sergio-gma91.bsky.social’s preprint “High-resolution binding data of TFIID and cofactors show promoter-specific differences in vivo” (www.biorxiv.org/content/10.6...). TLDR; TFIID behaves differently depending on promoter type. More below:

Thinking about using Cas13 to screen for functional circRNAs? Think again! Thread coming soon

How well does TWAS estimate a gene’s direction of effect on a trait? We think of this as an important stress-test for the accuracy of TWAS. In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time! doi.org/10.64898/202... 1/n

Together with @ronghuizhu.bsky.social, we are thrilled to present our new perturb-seq study of 22M primary CD4+ T cells, across donors and timepoints – the result of a decade-long collaboration between the Marson @marsonlab.bsky.social and Pritchard @jkpritch.bsky.social labs 🧵 tinyurl.com/gwt2025

Join @stirlingchurchman.bsky.social, @moffittlab.bsky.social, @saramostafavi.bsky.social, me and all speakers for the 2026 CSHL meeting Systems Biology: Global Regulation of Gene Expression, March 11-14. Abstract deadline January 9! More infos and registration at meetings.cshl.edu/meetings.asp...

A free, open-access library of high-quality organism illustrations for science communication

Do transcriptional activators work on any promoter? Our data says no. 🙅‍♂️ Despite driving ~2/3 of mammalian genes, CpG island (CGI) promoters have remained a puzzle. We identified >50 activators that are exclusively compatible with this promoter class. 🧬

Genome-scale perturb-seq in primary human CD4+ T cells maps context-specific regulators of T cell programs and human immune traits https://www.biorxiv.org/content/10.64898/2025.12.23.696273v1

We’re excited to share our new Nature Genetics paper examining the genetic architecture of aortic valve function and aortic stenosis. We used deep learning of cardiac MRI and MTAG to study disease biology long before clinical diagnosis. nature.com/articles/s41... 1/10

A reminder to use the right P2A sequence to produce separate proteins - the images are from a GPCR-P2A-mCherry construct using a P2A variant without (upper row) and with (lower row) a preceding GSG linker.

GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult. Our latest work on causal models for this is out yesterday: www.nature.com/articles/s41... A short🧵:

The new Enabling Discovery through GEnomics (EDGE) Program page is posted. Please contact us at [email protected] if you have questions. www.nsf.gov/funding/oppo...

The Court wrote a roadmap for illegal gerrymanders: Just wait to pass them until the “eve” of the election, and no one can stop you.

Oh hey, looks like I can upload longer videos here now! Here’s my most recent one covering the latest findings on ecDNA retention mechanisms from the Chang & Mischel labs.