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Reposted by Anshul Kundaje

Camille Moore @camille-moore.bsky.social · 5d

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...

www.science.org

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Reposted by Anshul Kundaje

ralucagordan.bsky.social @ralucagordan.bsky.social · 5d

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

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Reposted by Anshul Kundaje

Marisa Kabas @marisakabas.bsky.social · 7d

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."

www.thehandbasket.co

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Reposted by Anshul Kundaje

Tong Wang @twangmdphd.bsky.social · 8d

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 · 11d

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 · 11d

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 · 11d

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

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Eric Topol @erictopol.bsky.social · 13d

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 · 16d

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

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Anshul Kundaje @anshulkundaje.bsky.social · 16d

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/

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Anshul Kundaje @anshulkundaje.bsky.social · 16d

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 · 16d

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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Reposted by Anshul Kundaje

Yun S. Song @yun-s-song.bsky.social · 16d

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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Reposted by Anshul Kundaje

Yuri Pritykin @yuripritykin.bsky.social · 18d

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 👇

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Anshul Kundaje @anshulkundaje.bsky.social · 18d

But lets be clear that glam journal publishing is a branding & marketing exercise. It is not in any way a step towards greater transparency, accountability & credibility. 12/12

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Anshul Kundaje @anshulkundaje.bsky.social · 18d

... to not support the gate keeping system followed by glam journal publishing. But I also get that for them it is a very cheap (only 13K for gold open access) but effective branding tool. So I definitely do not blame them for taking advantage of it. 11/

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Anshul Kundaje @anshulkundaje.bsky.social · 18d

So yes I would encourage them to release their models open weights, open source, with fabulous documentation & respond to community review. But also ... 10/

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Anshul Kundaje @anshulkundaje.bsky.social · 18d

I would go further & claim that companies are especially are not bound by any of the constraints that masochistic academics impose on themselves by tying their futures to exploitative & wasteful gate keeping publishing systems. 9/

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Anshul Kundaje @anshulkundaje.bsky.social · 18d

So kudos to Deepseek for being super transparent with their tech, models, documentation. But publishing this work in Nature or any other glam journal is entirely a branding and marketing exercise. Lets not pretend otherwise. 8/

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Anshul Kundaje @anshulkundaje.bsky.social · 18d

Occasionally they do live upto the hype. But most of the time that's not the case. The whole gate keeping exercise of glam journals is based on vibes about what is "hot" at the moment. 7/

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Anshul Kundaje @anshulkundaje.bsky.social · 18d

Lastly, I don't know how anyone can claim that publishing a paper in Nature is a way to dial back hype. It is literally a branding exercise. Papers published in glam journals are the most overhyped of all scientific literature. 6/

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Anshul Kundaje @anshulkundaje.bsky.social · 18d

Secondly, there are plenty of studies published in journals including Nature that are full of flaws. So I don't understand how anyone can claim that journal peer review is reliable quality control. 5/

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Anshul Kundaje @anshulkundaje.bsky.social · 18d

Firstly, open source, open weights models can be and are openly vetted, critiqued and developed on by many more than 3 anointed peer reviewers. That is true peer review by a massive community of folks with wide ranging expertise. 4/

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Anshul Kundaje @anshulkundaje.bsky.social · 18d

Peer review by 3 random reviewers and gate keeping by an editorial team from a glam journal is utterly unnecessary. And the point being made here that this form of journal peer review adds some form of verification is utterly misleading. 3/

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Anshul Kundaje @anshulkundaje.bsky.social · 18d

This commentary is skipping the key point that this LLM (DeepSeek-R1) is open source, open weights with transparent documentation and methods (released Jan 2025). That is a key difference relative to other closed source, closed weights LLMs (ChatGPT, Claude, Gemini etc). 2/

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Anshul Kundaje @anshulkundaje.bsky.social · 18d

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

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Reposted by Anshul Kundaje

David Ochoa @d0choa.bsky.social · 19d

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 · 19d

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 👇

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