We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics. www.biorxiv.org/content/10.1... (1/n)

✨Exciting news: the main story of my PhD is out in Science! Together with Christine Moene @cmoene.bsky.social, we explored what happens when you scramble the genome—revealing how Sox2’s position shapes enhancer activation. 📖 Read the full story here: www.science.org/doi/10.1126/...

Congrats to my friends in the Boettiger lab for this really beautiful live imaging work. A big leap forward in understanding the dynamic side of genome organization. www.science.org/doi/10.1126/...

Functional maps of a genomic locus reveal confinement of an enhancer by its target gene by the @basvansteensellab.bsky.social www.science.org/doi/10.1126/...

New preprint from our lab! What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells? Find out here: www.biorxiv.org/content/10.1... 👇 1/

Excited to finally present the lab's latest work in defining candidate causal genetic variants that drive autoimmune diseases and their effects on primary human T cell expression and function! www.nature.com/articles/s41...

@riyavsinha.bsky.social @jengreitz.bsky.social sky.social @anshulkundaje.bsky.social y.social have made the ENCODE-rE2G data available to browse through the E2G portal, a custom-built extension of the Platform 👇 We plan to further integrate their data 👀 e2g.stanford.edu

Excited for a major milestone in our efforts to map enhancers and interpret variants in the human genome: The E2G Portal! e2g.stanford.edu This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues. Uses cases 👇 1/

Please apply to our tenure-track faculty position at @stanford-chemh.bsky.social! We are searching for a new colleague working at the interface between computation and molecular sciences. See post below and pls forward widely! chemh.stanford.edu/opportunitie...

www.cell.com/cell/abstrac... A host organelle (in sea slugs) integrates stolen chloroplasts for animal photosynthesis

Most neurodevelopmental disorders are caused by having 1 functional gene copy. Using SCN2A, we show that upregulating the functional copy rescues neuronal phenotypes. Amazing work with @neurobender.bsky.social led by Serena Tamura, Andrew Nelson, Perry Spratt & others. www.nature.com/articles/s41...

I am tremendously excited to share our work revealing the epigenomic landscape of single vascular cells. We discover that enhancers are not only cell type but vascular site specific and regulate the genetic drivers of disease risk. Let's dive in! 🧬👇 #epigenetics www.embopress.org/doi/full/10....

Hard to understate how wonderful it is to see our manuscript in print today @natcardiovascres.nature.com. We discover ADAR1 to control dsRNA sensor MDA5 in atherosclerosis, creating a new paradigm of endogenous dsRNA sensing as a causal mechanism of disease. Let's get into it 👇 #RNAsky rdcu.be/eGEyu

Doomscrolling pause to chat CRISPR libraries! Preprint describes our new, data-driven approach to combine on-target and off-target predictions much more intelligently for *selecting* guides, which we use to develop our newest Cas9 knockout library, Jacquere. Thread: www.biorxiv.org/content/10.1...

out today: my labmate Shubham developed a super clever new technique to profile TF-DNA interactions with unprecedented resolution of low-affinity binding sites, revealing patterns in how these sites are organized in the genome to modulate TF occupancy: www.nature.com/articles/s41...

Very proud of our paper on "scrambling-by-hopping" LADs, which was just published: www.nature.com/articles/s41.... Congrats to Lise Dauban and the rest of the team – this was a real tour-de-force!

1. 🚨New preprint: tinyurl.com/tenk10k-causal. We explored causal effects of gene expression in immune cell types on complex traits and diseases by combining single-cell expression quantitative trait loci (sc-eQTL) mapping in 5M+ cells from 1,925 donors in TenK10K study and GWAS. 🧵

New York Times story with profiles of researchers whose grants were terminated. [Gift Link] www.nytimes.com/2025/08/24/o...

@jengreitz.bsky.social l & my lab want to co-hire a computational biologist/biostatistician with project management expertise to help map the regulatory code of the human genome and discover genetic mechanisms of disease. Details below careersearch.stanford.edu/jobs/computa... Plz RT

2/ NIPBL is widely considered as the cohesin loader. We acutely lowered NIPBL expression in cells with a degron, down to ~5-10%. This caused major Hi-C defects, just as we would expect if cohesin had stopped loading. Yet to our surprise cohesin binding is only reduced 2-fold. 🤨

Our lab at Yale @yalemedicine.bsky.social seeks #postdocs with in vivo expertise to pioneer research at the intersection of tissue remodeling & aging. Work with us to uncover immunological & vascular drivers of ovarian aging, applying single-cell, spatial omics, and ML! jobrxiv.org/job/yale-uni...

Day 3 of our 31 Days of Action campaign seems like the perfect time to say THANK YOU to all 75k (!!!!) of our followers! What started as a single post has turned into a vibrant grassroots movement & community of science activists. Tell your friends! www.standupforscience.net/31-days-of-a...

From @aaas.org check-in with Sudip Parikh: a letter by 14 Republican senators urge the Office of Management and Budget to release NIH funding. If this includes your state (AL, ME, WV, SC, KY, KS, AR, PA, NC, IN, AK), Sudip recommends contacting & thanking them for being American science leaders.

This entire series of statements from Federal employees speaking out against Doge cuts is remarkable. Definitely worth a listen. Each statement is short and powerful, and the creators of the series did well to platform folks across multiple agencies. Our Federal workers are among the best of us.

100,000 Participants scanned ✅ We are delighted to have completed the world's largest whole body imaging project, scanning the brains, hearts, abdomens, blood vessels, bones and joints of 100,000 volunteers.

Update on funding curves and late non-competitive renewals. First, funding curves for new and competitive renewals. 1/n

Friends, the incredible Raven the Science Maven is looking to make videos to help the public understand the value of our federal science organizations. Here’s the amazing one she made about NASA. Any idea who might be able to help her on videos about the FDA and CDC?

The human transcription factor occupancy landscape viewed using high-resolution in situ base-conversion strand-specific single-molecule chromatin accessibility mapping https://www.biorxiv.org/content/10.1101/2025.06.27.662080v1

With this budget, ICE alone would have nearly as large a detention operation as all 50 states' prison systems combined. Bigger budget than the Marine Corps. Police-state levels of spending

“I personally was pretty surprised, actually, at how efficient the government was,” Sahil Lavingia told NPR's Juana Summers.

So important! Please contact your Republican senators, especially Sen. Susan Collins (R-ME), Sen. Shelley Moore Capito (R-WV), Sen. Bill Cassidy (R-LA), Sen. Katie Britt (R-AL), and Sen. Dave McCormick (R-PA). 🙏 amplify!

To sum up: 1. Enhancer poising explains how >20 independent rare variants in the ZRS cause polydactyly; 2. ZIC3 mediates anterior poising – without ZIC3 binding mice are resistant to GOF mutations; 3. Enhancer poising enables pathogenic gene activation by noncoding variants at other loci. 13/n

New video! I look at how obscure research can lead to amazing discoveries, in light of how a US district court ruled that some NIH grant terminations are ‘void and illegal.’ Features a clip from Reed Jobs, venture fund founder and son of Apple founder Steve Jobs. @statnews.com youtu.be/oIPYHfROxng

Textbooks: “Enhancers are just a bunch of TFBSs” But how do they REALLY work? New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social A 🧵 (1/n) Free access link: rdcu.be/erD22

I'm sorry but the largest protest of my lifetime is not the 7th or 8th biggest news story in the country behind "what does Gen Z want from Instagram?" This shit is humiliating. Rearrange your layout to meet this moment. Omitting the thing happening in every American city is malpractice.

Excited to share my first PhD paper in the @sbmontgom.bsky.social lab with @tamigj.bsky.social (www.biorxiv.org/content/10.1...)! Standard QTL methods treat each gene independently. But what if a single variant regulates multiple nearby genes at once - what we call “allelic proxitropy”? 🧵 ⬇️

“We urge you as NIH Director to restore grants delayed or terminated for political reasons so that life-saving science can continue.” Over one hundred NIH employees publish a letter of dissent to Trump administration attacks on medical research, the “Bethesda Declaration.” 🧪

“Health concerns are a universal human concern,” @jeremymberg.bsky.social told CNN. “The NIH system… has been unbelievably productive in terms of generating progress on specific diseases.” www.cnn.com/2025/06/09/h... #BethesdaDeclaration #StandUpForScience

This morning, courageous NIH workers shared a document they are calling the “Bethesda Declaration” with Dr. Bhattacharya, urging him to reverse some of the actions that are badly misaligned with progress toward the NIH mission. 1/3

"Sources said the administration is specifically considering a full termination of federal grant funding for the University of California and California State University systems." Pure vandalism. This could never happen in a country with functioning checks and balances.

The university of California is a powerhouse of innovation, healthcare, and social mobility for California and the US.

must be incredibly frustrating and disheartening to have federal funding that was promised to you for important work suddenly and arbitrarily ripped away

I don't think anyone outside of universities, pharma and biotech, independent research institutions have any idea of what is happening right now. If you haven't sounded the alarm among your friends, family and colleagues, now is the time to do it.

There are 2 previous historical cases of countries destroying their science and universities, crippling them for decades: Lysenkoism in the USSR and Nazi Germany. The Trump administration will be the 3rd. It's not just budgets but research, institutions, expertise, and training the next generation.

thanks to Musk we are on the path to 25 million excess deaths abroad because of US aid cut off. 25 million. 4 holocausts plus. unbelievably horrific...and mostly greeted with a shrug.

The war on science in the US is already having an effect on private sector research like AlphaFold. Bears repeating but the private sector builds on top of things created by academic research for the public good. This hurts everyone.

🚨Our new paper is online🚨 We use zero-distance⚡photo-crosslinking⚡to reveal direct protein-DNA interactions in living cells, enabling quantitative analysis of the DNA-interacting proteome on a timescale of minutes. #DNA #Chromatin #Proteomics www.cell.com/cell/fulltex...

They're terminating OPT. Today the nominee to head USCIS stated directly: he will end Optional Practical Training, the single largest channel for high-skill immigrants to work in the US. 6 weeks ago I warned about this & summarized the research on impacts of this drastic action—> @piie.com

Looking forward to discussing all things #genetic #variation next week at the Mutational Scanning Symposium! Come say Hi 👋 at Poster 11 for @ensembl.bsky.social Variant Effect Predictor updates and how to integrate your latest research outputs as a plugin 🤓 See you in Barcelona ☀️ #VariantEffect25