Anshul Kundaje
@anshulkundaje.bsky.social
Genomics, Machine Learning, Statistics, Big Data and Football (Soccer, GGMU)
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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
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
Work led by @ievarau.bsky.social and @damlaob.bsky.social w/ @anshulkundaje.bsky.social @wywywa.bsky.social @flowerwhatelse.bsky.social labs & more
🚀 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/...
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/...
JASPAR 2026: expansion of transcription factor binding profiles and integration of deep learning models
Abstract. JASPAR (https://jaspar.elixir.no/) is an open-access database that has provided high-quality, manually curated, and non-redundant DNA binding pro
doi.org
December 2, 2025 at 7:53 AM
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
Work led by @ievarau.bsky.social and @damlaob.bsky.social w/ @anshulkundaje.bsky.social @wywywa.bsky.social @flowerwhatelse.bsky.social labs & more
Reposted by Anshul Kundaje
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!)
(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...
www.biorxiv.org
November 19, 2025 at 8:57 PM
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!)
(TLDR; low-affinity motifs matter as pioneers!)
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".
Thanks. Happy to help if you run into any issues. If the goal is differential signal prediction, would need a slightly different fine tuning set up for optimal performance
October 18, 2025 at 7:13 AM
Thanks. Happy to help if you run into any issues. If the goal is differential signal prediction, would need a slightly different fine tuning set up for optimal performance
Should have used this!
October 16, 2025 at 2:12 PM
Should have used this!
And just to be clear, I have no specific comments on the other primary models implemented in the CRESTED package including the ones they developed. They look good from the paper. I'm simply stating that the "Dilated CNN" implementation in the package is NOT ChromBPNet. 4/4
October 15, 2025 at 2:18 PM
And just to be clear, I have no specific comments on the other primary models implemented in the CRESTED package including the ones they developed. They look good from the paper. I'm simply stating that the "Dilated CNN" implementation in the package is NOT ChromBPNet. 4/4
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:
Came across this interesting paper www.nature.com/articles/s41... that compares their model to a "Dilated CNN" model from the CRESTED package that is supposed to "ChromBPNet inspired". Performance of the dilated CNN is miserable. This is categorically NOT a ChromBPNet model 3/3
IceQream: Quantitative chromosome accessibility analysis using physical TF models - Nature Communications
Cis regulatory elements endow genomes with sequence-encoded logic to drive cellular differentiation. Here, the authors introduce a biophysically principled sequence model that characterises complex TF...
www.nature.com
October 15, 2025 at 1:39 AM
Came across this interesting paper www.nature.com/articles/s41... that compares their model to a "Dilated CNN" model from the CRESTED package that is supposed to "ChromBPNet inspired". Performance of the dilated CNN is miserable. This is categorically NOT a ChromBPNet model 3/3
Please don't refer to models from other packages as ChromBPNet. There is much more to ChromBPNet than the architecture. The training procedure, bias correction & data sampling strategy has a huge impact on performance. 2/
October 15, 2025 at 1:39 AM
Please don't refer to models from other packages as ChromBPNet. There is much more to ChromBPNet than the architecture. The training procedure, bias correction & data sampling strategy has a huge impact on performance. 2/
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...
And I think this is just the tip of the iceberg. There will be many ways to push this further. Really huge breakthrough IMO from my first reading. Can't wait to use this & build on it. Huge congrats to the team! 3/3
September 22, 2025 at 8:34 AM
And I think this is just the tip of the iceberg. There will be many ways to push this further. Really huge breakthrough IMO from my first reading. Can't wait to use this & build on it. Huge congrats to the team! 3/3
Also an absolute showcase for what self supervised learning can do when done right. IMO, this is the first paper that really shows the power of self supervised genomic language models. 2/
September 22, 2025 at 8:34 AM
Also an absolute showcase for what self supervised learning can do when done right. IMO, this is the first paper that really shows the power of self supervised genomic language models. 2/
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)