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Anshul Kundaje

@anshulkundaje.bsky.social
9.5K followers 4.5K following 966 posts

Genomics, Machine Learning, Statistics, Big Data and Football (Soccer, GGMU)

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Reposted by Anshul Kundaje
Selin Jessa @selinjessa.com · 14/04/2026
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 🧬🖥️
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Anthony Mathelier @amathelier.bsky.social · 02/12/2025
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
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Zeitlinger Lab @zeitlingerlab.bsky.social · 19/11/2025
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!)
biorxiv.org
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...
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Max Planck Institute for Molecular Genetics @molgen.mpg.de · 07/11/2025
🧬📢 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".
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Oded Rechavi @odedrechavi.bsky.social · 15/10/2025
Here's the link to the system, try it! qedscience.com @qedscience.bsky.social
qedscience.com
q.e.d Science
Critical Thinking AI for constructive criticism and science evaluation
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Oded Rechavi @odedrechavi.bsky.social · 15/10/2025
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 👇)
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Luca Pinello @lucapinello.bsky.social · 15/10/2025
🧬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 👇
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Marisa Kabas @marisakabas.bsky.social · 15/10/2025
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:
thehandbasket.co
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.
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Anshul Kundaje @anshulkundaje.bsky.social · 15/10/2025
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/
github.com
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Camille Moore @camille-moore.bsky.social · 02/10/2025
Today I am so pleased to present our work on how chromatin remodelers affect mesoscale chromatin organization. www.science.org/doi/10.1126/...
science.org
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...
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ralucagordan.bsky.social @ralucagordan.bsky.social · 03/10/2025
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...
cell.com
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.
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Marisa Kabas @marisakabas.bsky.social · 30/09/2025
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:
thehandbasket.co
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."
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Tong Wang @twangmdphd.bsky.social · 29/09/2025
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...
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Nobu Hamazaki @nobuhamazaki.bsky.social · 26/09/2025
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...
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Daniel Bolnick @danielbolnick.bsky.social · 26/09/2025
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.
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Eric Topol @erictopol.bsky.social · 24/09/2025
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...
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Anshul Kundaje @anshulkundaje.bsky.social · 22/09/2025
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/
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Yun S. Song @yun-s-song.bsky.social · 22/09/2025
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)
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Yuri Pritykin @yuripritykin.bsky.social · 19/09/2025
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 👇
doi.org
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...
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Anshul Kundaje @anshulkundaje.bsky.social · 19/09/2025
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/
t.co
https://www.nature.com/articles/d41586-025-02979-9
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David Ochoa @d0choa.bsky.social · 18/09/2025
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!
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Jesse Engreitz @jengreitz.bsky.social · 18/09/2025
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/
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Jesse Engreitz @jengreitz.bsky.social · 18/09/2025
1. Search for your favorite GWAS variant and find predicted target genes and cell types (e.g. e2g.stanford.edu/variant/10_7...): 2/
E2G Browser - rs1250566
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Jesse Engreitz @jengreitz.bsky.social · 18/09/2025
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/
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Open Targets @opentargets.org · 18/09/2025
@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.stanford.edu
E2G
E2G is a tool based on the Open Targets Platform for predicting enhancer-gene interactions.
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Open Targets @opentargets.org · 18/09/2025
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...
blog.opentargets.org
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...
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Anshul Kundaje @anshulkundaje.bsky.social · 17/09/2025
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
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Polly Fordyce @pollyfordyce.bsky.social · 17/09/2025
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...
chemh.stanford.edu
Faculty Recruitment
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Denny Carter @dennycarter.bsky.social · 17/09/2025
RFK Jr. is not well
The hearing has resumed.

Dr. Monarez catalogued a number of false statements that Kennedy made to her: “He said that C.D.C. employees were killing children and they don’t care. He said that C.D.C. employees were bought by the pharmaceutical industry. He said C.D.C. forced people to wear masks and social distance, like a dictatorship. And the one I think that hurt me the most was a particularly vivid phrase: He said during the Covid outbreak, C.D.C. told hospitals to turn away sick Covid patients until they had blue lips before allowing them to get treatment.”

She said he was “very, very upset” and very animated in their meetings.
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Yuri Pritykin @yuripritykin.bsky.social · 16/09/2025
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...
cell.com
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...
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Ed Hollox @edhollox.bsky.social · 16/09/2025
Details here peercommunityin.org
peercommunityin.org
Peer Community In - free peer review & validation of preprints of articles
PCI is a non-profit open science organization of scientists to evaluate, recommend and publish research preprints in free open access
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Ed Hollox @edhollox.bsky.social · 16/09/2025
Join @peercommunityin.bsky.social
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Dani Stevens, Ph.D. @danimstevens.bsky.social · 16/09/2025
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.
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Dani Stevens, Ph.D. @danimstevens.bsky.social · 16/09/2025
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.
zenodo.org
Chromosome-level genome assembly of Triticum turgidum var 'Kronos'
This data is made available under the Toronto Agreement. All of the data listed here is available under the prepublication data sharing principle of the Toronto agreement (1). By using this data, you ...
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Anshul Kundaje @anshulkundaje.bsky.social · 16/09/2025
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/
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Cell Reports @cp-cellreports.bsky.social · 15/09/2025
When the cell needs to respond to the environment: A chromatin-splicing love affair
dlvr.it
When the cell needs to respond to the environment: A chromatin-splicing love affair
Alternative splicing allows rapid phenotypic adaptation, but the underlying mechanisms remain unclear. Moreau et al. highlight new findings on the critical role of chromatin modifications and 3D nuclear organization in regulating splicing dynamics. Understanding these chromatin-mediated processes provides insights into how organisms sustainably adapt to environmental challenges for rapid responses.
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Anshul Kundaje @anshulkundaje.bsky.social · 16/09/2025
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.
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Chad Weldy, MD, PhD @chadweldy.bsky.social · 10/09/2025
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
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Alejandra Caraballo @esqueer.net · 03/09/2025
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.
A screenshot of page 28 of a legal document discussing the difficulty lower courts face when interpreting unclear or rapidly evolving guidance from the Supreme Court.

The following phrases and sentences are highlighted in yellow:

* "That said, the Supreme Court’s recent emergency docket rulings regarding grant terminations have not been models of clarity, and have left many issues unresolved."
* "California was a four-paragraph per curiam decision issued in the context of a stay application."
* "The outcome, which no party had requested, was, thus, inconsistent with the views of eight justices"
* "the issues are complex and evolving."
* "this Court, not the district courts or courts of appeals, will often still be the ultimate decisionmaker as to the interim legal status of major new federal statutes and executive actions."
* "...it is unhelpful and unnecessary to criticize district courts for “defy[ing]” the Supreme Court when they are working to find the right answer in a rapidly evolving doctrinal landscape, where they must grapple with both existing precedent and interim guidance from the Supreme Court that appears to set that precedent aside without much explanation or consensus."
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Anthony Ramnauth @philoneurosci.bsky.social · 03/09/2025
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...
doi.org
Multiple overlapping binding sites determine transcription factor occupancy - Nature
A new method enables comprehensive screening and identification of low-affinity DNA binding sites for transcription factors, and reveals that nucleotides flanking high-affinity binding sites create ov...
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Anshul Kundaje @anshulkundaje.bsky.social · 02/09/2025
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?
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Sasha Gusev @sashagusevposts.bsky.social · 27/08/2025
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 🧵:
open.substack.com
Beneath the surface of the sum
When genetic interactions matter and when they don't
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Richard Sever @richardsever.bsky.social · 27/08/2025
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...
royalsociety.org
Invisibility cloak pioneer Sir John Pendry awarded Royal Society’s top prize | Royal Society
The Royal Society announces the medals and awards recipients 2025
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Demetre Daskalakis @drdemetre.bsky.social · 30/08/2025
podcasts.apple.com/us/podcast/t...
podcasts.apple.com
The C.D.C.’s Vaccine Chief on Why Quitting Was His Only Option
Podcast Episode · The Daily · 08/29/2025 · 29m
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Anshul Kundaje @anshulkundaje.bsky.social · 19/08/2025
@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
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Alexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 28/08/2025
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
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Timothy Fuqua @timothyfuqua.bsky.social · 28/08/2025
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)
biorxiv.org
De-novo promoters emerge more readily from random DNA than from genomic DNA
Promoters are DNA sequences that help to initiate transcription. Point mutations can create de-novo promoters, which can consequently transcribe inactive genes or create novel transcripts. We know lit...
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Anshul Kundaje @anshulkundaje.bsky.social · 26/08/2025
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!
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Anshul Kundaje @anshulkundaje.bsky.social · 19/08/2025
@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
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The Transmitter @thetransmitter.bsky.social · 13/08/2025
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...
thetransmitter.org
Harvard University lays off fly database team
The layoffs jeopardize this resource, which has served more than 4,000 labs for about three decades.
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