We are so excited to see our work out in @nature.com! We present a multi-omic single-cell atlas of 12 organs in human fetal development, explore the enhancer landscape, use deep learning to infer rules of transcription factor activity, and interpret non-coding variants in complex traits: #GeneReg 🧬🖥️

John Greally@greally.bsky.social · 4mo ago

This @anshulkundaje.bsky.social, Kyle Fahr and William Greenleaf paper is finally out, we've been following it for a while in its preprint form, phenomenal work. www.nature.com/articles/s41...

Proud of JASPAR 2026 release with major expansion of PFM profiles and a new collection of deep learning models interpreted to extract learnt motifs! Work led by @ievarau.bsky.social and @damlaob.bsky.social w/ @anshulkundaje.bsky.social @wywywa.bsky.social @flowerwhatelse.bsky.social labs & more

Norwegian Centre for Molecular Biosciences and Medicine (NCMBM)@ncmbm.bsky.social · 8mo ago

🚀 JASPAR goes Deep Learning! A major milestone for regulatory genomics. Excited to share the newest JASPAR 2026 update, led by @amathelier.bsky.social from @ncmbm.bsky.social and supported by an international network of contributors across ten countries! 📄Publication: doi.org/10.1093/nar/...

We are pleased to announce a new preprint by @mlweilert.bsky.social: “Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs” (www.biorxiv.org/content/10.1...). See summary and longer recap below: (TLDR; low-affinity motifs matter as pioneers!)

Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs

Low-affinity transcription factor (TF) motifs are an important element of the cis-regulatory code, yet they are notoriously difficult to map and mechanistically incompletely understood, limiting our a...

biorxiv.org

🧬📢 Looking forward to our next speaker in our lineup for the #Embryo2026 meeting, Anshul Kundaje from Stanford University. He will speak on the topic of "Deep learning the regulatory syntax of fetal development and the genetic basis of developmental disorders".

Here's the link to the system, try it! qedscience.com @qedscience.bsky.social

q.e.d Science

Critical Thinking AI for constructive criticism and science evaluation

qedscience.com

BIG ANNOUNCEMENT📣: I haven’t been this excited to be part of something new in 15 years… Thrilled to reveal the passion project I’ve been working on for the past year and a half!🙀🥳 (thread 👇)

🧬Excited to be at #ASHG2025! My lab is presenting 5 studies this week. Join us for talks and posters on #SingleCell #CRISPR, #DeepLearning & more! Thread below with all presentation details 👇

NEW — I dug into the story of ICE abducting a 13-year-old boy in Massachusetts and moving him 500 miles across state lines without notifying his mother, local cop's complicity, and how the federal government's justification for such cruelty is already falling apart:

ICE took a 13-year-old they said had a gun. Local cops say he didn’t.

Now he's detained 500 miles away from his Massachusetts home.

thehandbasket.co

Friendly reminder that there is only one official release of ChromBPNet at our lab GitHub github.com/kundajelab/chr… There are other versions floating around eg. in the CRESTED package that are NOT anywhere close to the official implementation. 1/

Today I am so pleased to present our work on how chromatin remodelers affect mesoscale chromatin organization. www.science.org/doi/10.1126/...

ATP-dependent remodeling of chromatin condensates reveals distinct mesoscale outcomes

Adenosine triphosphate (ATP)–dependent chromatin remodeling enzymes mobilize nucleosomes, but how such mobilization affects chromatin condensation is unclear. We investigate effects of two major remod...

science.org

I'm very pleased to announce the official publication of our lab's paper "DNA mutagenesis driven by transcription factor competition with mismatch repair" in today's issue of Cell! www.cell.com/cell/abstrac...

DNA mutagenesis driven by transcription factor competition with mismatch repair

Competition between transcription factors and mismatch repair machinery drives localized hypermutation at regulatory elements, with implications for cancer and genome evolution.

cell.com

SCOOP — The White House instructed all federal agency leadership on Tuesday to send out a mandatory message to workers blaming the impending potential government shutdown on House Democrats, The Handbasket was first to learn. Absolutely no modifications to the email were permitted. My story:

Trump mandates all federal agencies send email blaming Dems for potential gov’t shutdown

Workers call the partisan email "a vile slap in the face."

thehandbasket.co

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...

New paper from my lab and @jshendure.bsky.social lab! Led by the brilliant @zukailiu.bsky.social and @cxqiu.bsky.social. We tackled how anterior and posterior progenitor cells cooperate to self-organize into an embryonic structure (termed AP-gastruloid). (1/n) www.biorxiv.org/content/10.1...

The GRFP announcement from NSF cuts out an entire cohort of 2nd year students from consideration, without warning. This is so deeply unfair that it warrants a formal protest from the scientific community. If someone wants to work with me to craft an open letter and solicit signatures, LMK.

Dan Garisto@dangaristo.bsky.social · 10mo ago

New: After a long wait, the GRFP solicitation is live! Deadlines have been extended to early November, so applicants have a bit over a month to submit. www.nsf.gov/funding/oppo...

The projected rise in global cancer deaths 1990 —5.9 million 2023—10.4 million 2050—18.8 million is yet another reason we need to get primary prevention into high gear, which is now possible but not getting done www.thelancet.com/journals/lan...

This is truly an incredible breakthrough IMO. Really exemplifies what you get when deep domain expertise (popgen/evolution/disease genetics in this case) fuses with cleverly crafted ML. What u get r sleek, well thought out architectures that absolutely destroy the behemoths. Wow!! 1/

Yun S. Song@yun-s-song.bsky.social · 11mo ago

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)

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)

Excited to share our new study: Single-cell multiomics reveals archetypal regulatory programs shared across CD4 and CD8 T cell subsets in viral infection bioRxiv: doi.org/10.1101/2025... 🧵 Key findings below 👇

Single-cell multiomics reveals archetypal regulatory programs shared across CD4 and CD8 T cell subsets in viral infection

T cells protect against pathogens and tumors and can differentiate into various functionally distinct subsets. While each subset exhibits a characteristic epigenomic and transcriptional profile, essen...

doi.org

bioRxiv Immunology@biorxiv-immuno.bsky.social · 11mo ago

Single-cell multiomics reveals archetypal regulatory programs shared across CD4 and CD8 T cell subsets in viral infection https://www.biorxiv.org/content/10.1101/2025.09.08.675014v1

An editorial was published in Nature recently claiming that glam journal publication of LLMs (like DeepSeek-R1 this case) marks a step towards greater transparency, accountability & credibility www.nature.com/articles/d41.... I have thoughts ... 1/

If you care about regulatory variants don’t miss the E2G extension of the @opentargets.org Platform. There are synergies that only a fully open science allows and this is a good one!

Jesse Engreitz@jengreitz.bsky.social · 11mo ago

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/

This extends code from the Open Targets Platform — huge thanks to @opentargets.org for this resource. I use it every day! A subset of the ENCODE-rE2G predictions are now available through the Open Targets Platform as well. Thanks @d0choa.bsky.social ! bsky.app/profile/open... 5/

Open Targets@opentargets.org · 11mo ago

The Open Targets Platform autumn release is out! 🍂 We have ingested the full dataset of over 13 million enhancer-gene regulatory interactions in the human genome across 1,458 DNase-seq experiments covering 369 cell types and tissues from the ENCODE-rE2G model blog.opentargets.org/open-targets...

1. Search for your favorite GWAS variant and find predicted target genes and cell types (e.g. e2g.stanford.edu/variant/10_7...): 2/

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/

@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

E2G

E2G is a tool based on the Open Targets Platform for predicting enhancer-gene interactions.

e2g.stanford.edu

The Open Targets Platform autumn release is out! 🍂 We have ingested the full dataset of over 13 million enhancer-gene regulatory interactions in the human genome across 1,458 DNase-seq experiments covering 369 cell types and tissues from the ENCODE-rE2G model blog.opentargets.org/open-targets...

Open Targets Platform 25.09 has been released!

The September 25 release includes enhancer-gene data predicted by ENCODE-rE2G, molQTL credible sets for targets, new options for the variant structural viewer, and a number of data updates from GWAS C...

blog.opentargets.org

New faculty position opening at @stanford-chemh.bsky.social . Especially interested in candidates with deep expertise and vision for the future of AI/ML/computational models of biomolecules. Please RT

Polly Fordyce@pollyfordyce.bsky.social · 11mo ago

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...

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...

Faculty Recruitment

chemh.stanford.edu

RFK Jr. is not well

Happy to share our new paper! We present high-resolution Micro-C maps across Drosophila embryogenesis, integrated with 149 ChIP-seq datasets. This systematic analysis enabled clustering of loops & boundaries into 4 distinct classes with distinct regulatory roles. www.cell.com/cell-genomic...

3D chromatin structures precede genome activation in Drosophila embryogenesis

Dolsten et al. map the 3D chromatin architecture across early Drosophila development using high-resolution Micro-C, and, by integrative analysis with 149 public ChIP-seq datasets, identify four classe...

cell.com