Anshul Kundaje
@anshulkundaje.bsky.social
Genomics, Machine Learning, Statistics, Big Data and Football (Soccer, GGMU)
Pinned
Anshul Kundaje
@anshulkundaje.bsky.social
· Aug 12
Job Alert: A stealth startup focused on non-cancer diagnostics is keen to hire a deep learning for genomics/bio engineer. I am an advisor for the startup & closely involved. Please see the job description below and get in touch if interested. Plz forward.
Reposted by Anshul Kundaje
🧬📢 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".
November 7, 2025 at 5:36 PM
🧬📢 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".
Reposted by Anshul Kundaje
q.e.d Science
Critical Thinking AI for constructive criticism and science evaluation
qedscience.com
October 15, 2025 at 12:22 PM
Reposted by Anshul Kundaje
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 👇)
October 15, 2025 at 12:22 PM
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 👇)
Reposted by Anshul Kundaje
🧬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 👇
October 15, 2025 at 1:41 PM
🧬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 👇
Reposted by Anshul Kundaje
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.
www.thehandbasket.co
October 15, 2025 at 1:44 PM
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/
There are other versions floating around eg. in the CRESTED package that are NOT anywhere close to the official implementation. 1/
https://github.com/kundajelab/chr…
October 15, 2025 at 1:39 AM
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/
There are other versions floating around eg. in the CRESTED package that are NOT anywhere close to the official implementation. 1/
Reposted by Anshul Kundaje
Today I am so pleased to present our work on how chromatin remodelers affect mesoscale chromatin organization.
www.science.org/doi/10.1126/...
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...
www.science.org
October 2, 2025 at 10:55 PM
Today I am so pleased to present our work on how chromatin remodelers affect mesoscale chromatin organization.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Anshul Kundaje
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.
www.cell.com
October 2, 2025 at 11:37 PM
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...
Reposted by Anshul Kundaje
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:
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."
www.thehandbasket.co
September 30, 2025 at 9:45 PM
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:
My story:
Reposted by Anshul Kundaje
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...
www.biorxiv.org/content/10.1...
September 29, 2025 at 6:28 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Anshul Kundaje
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...
September 26, 2025 at 6:06 PM
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...
Reposted by Anshul Kundaje
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.
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...
NSF Graduate Research Fellowship Program (GRFP)
www.nsf.gov
September 26, 2025 at 5:10 PM
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.
Reposted by Anshul Kundaje
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...
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...
September 24, 2025 at 10:38 PM
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...
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)
www.biorxiv.org/content/10.1...
(1/n)
September 22, 2025 at 8:34 AM
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/
Reposted by Anshul Kundaje
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)
www.biorxiv.org/content/10.1...
(1/n)
September 22, 2025 at 5:29 AM
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)
www.biorxiv.org/content/10.1...
(1/n)
Reposted by Anshul Kundaje
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
bioRxiv: doi.org/10.1101/2025...
🧵 Key findings below 👇
September 19, 2025 at 7:21 PM
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
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/
https://www.nature.com/articles/d41586-025-02979-9
t.co
September 19, 2025 at 7:01 PM
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/
Reposted by Anshul Kundaje
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!
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/
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/
September 18, 2025 at 5:06 PM
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!
Reposted by Anshul Kundaje
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/
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/
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...
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
September 18, 2025 at 4:14 PM
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/
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/
Reposted by Anshul Kundaje
1. Search for your favorite GWAS variant and find predicted target genes and cell types (e.g. e2g.stanford.edu/variant/10_7...):
2/
2/
September 18, 2025 at 4:14 PM
1. Search for your favorite GWAS variant and find predicted target genes and cell types (e.g. e2g.stanford.edu/variant/10_7...):
2/
2/
Reposted by Anshul Kundaje
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/
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/
September 18, 2025 at 4:14 PM
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/
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/
Reposted by Anshul Kundaje
@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
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
September 18, 2025 at 10:39 AM
@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
We plan to further integrate their data 👀
e2g.stanford.edu
Reposted by Anshul Kundaje
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...
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
September 18, 2025 at 10:39 AM
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...
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...
@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
September 17, 2025 at 6:29 PM
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
Reposted by Anshul Kundaje
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...
@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
September 17, 2025 at 5:54 PM
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...
@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...