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 🧬🖥️

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

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!)

🧬📢 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

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:

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/...

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...

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:

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.

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/

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 👇

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!

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/

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

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...

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

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...

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...

Details here peercommunityin.org

Join @peercommunityin.bsky.social

100% agree. Especially with how much money is spent a year toward pub fees (10-30K+) that could go to other career opportunities. Plus, I can get high quality reviews from peers without a formal journal system. Sadly as a postdoc, I feel like my hands are tied, but I would love to help the cause.

Yes, @kseniakrasileva.bsky.social have moved to an increasingly open science model where we not only preprint early, sometimes far before journal submission, but even make datasets open before preprinting (wheat genome example: zenodo.org/records/1021...). We welcome feedback from our community.

I'm curious if other mid career PIs have considered completely abandoning the trad publication model. We've been making gradual moves towards that end goal. But it's been difficult to completely jump ship for one main reason for me at least. 1/

When the cell needs to respond to the environment: A chromatin-splicing love affair

I truly hope NIH completely eliminates publication fees from NIH grants next year. It will be the only way academics will even consider switching to a new model of publishing.

But how does this relate to human disease?? Through an awesome collaboration with the @anshulkundaje.bsky.social lab, we trained ChromBPNet models with scATACseq datasets for each cell type and vascular site, and predict human variant effect on a cell type/site basis @soumyakundu.bsky.social

It seems like federal district courts are in full revolt against SCOTUS. I've never seen such direct scathing criticism of SCOTUS like this from the bench over their shadow docket rulings quietly overturning precedent without explanation. From the Harvard decision today.

I suspected this during my first postdoc, when I was working with snATAC-seq data. Nice to see people doing the hard work! Multiple overlapping binding sites determine #transcription factor occupancy doi.org/10.1038/s415...

I'm curious if anyone has used any of GENBIO AIDO foundation models to do anything useful? They end up getting a lot of invited talks at several popular AI4bio meetings, have attended a few, but I am confused about what their models r actually delivering?

I wrote about gene-gene interactions (epistasis) and the implications for heritability, trait definitions, natural selection, and therapeutic interventions. Biology is clearly full of causal interactions, so why don't we see them in the data? A 🧵:

Very honored to receive the Royal Society Research Culture Award - this represents the work of a great team who've worked non-stop since we launched bioRxiv in 2013 royalsociety.org/news/2025/08... www.cshl.edu/inglis-and-s...

@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

If you like transcription regulation and its mechanisms, this WIP list is for you. I'm sure I've forgotten lots of people, so don't hesitate to let me know so I can add you to the list. go.bsky.app/8vTgeXB

Excited / nervous to share the “magnum opus” of my postdoc in Andreas Wagner’s lab! "De-novo promoters emerge more readily from random DNA than from genomic DNA" This project is the accumulation of 4 years of work, and lays the foundation for my future group. In short, we… (1/4)

scVerse conference is at Stanford this year! Encourage folks (especially Bay Area/West coast folks) to sign up and attend. Cool workshops/talks and other events + great community of developers for one of the most widely used open source software for single cell data analysis!

@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

FlyBase, a Drosophila database, will lose a third of its team in early October because the Harvard grant that covered the employees’ salaries was canceled. Scientists warn that losing FlyBase could devastate fly research. By @claudia-lopez.bsky.social www.thetransmitter.org/community/ha...