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Reposted by James Fraser

Diffuse Project @diffuseproject.bsky.social · 1d

The Diffuse Project is looking for an amazing Project Manager to help us achieve our goal of unlocking protein dynamics! Are you a scientist who naturally loves organization, coordination, problem solving and working with a diverse team of scientists & engineers?

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Reposted by James Fraser

Prachee Avasthi @pracheeac.bsky.social · 4d

New Blog Post:
Scholarly Communication Is a Research Problem. This Means You.

pracheeac.substack.com/p/scholarly-...

Scholarly Communication Is a Research Problem. This Means You.

Scholarly Communication Is a Research Problem.

pracheeac.substack.com

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Reposted by James Fraser

Tina Perica @glukozica.bsky.social · 10d

First work on kinases from my lab! Working on this project, I often remembered the late Cyrus Chothia who said that if the data doesn’t fit a beautiful model, maybe it’s not the model, maybe you just need more data. :)

bioRxiv Biochemistry @biorxiv-biochem.bsky.social · 11d

Mechanism of MEK1 phosphorylation by the N-terminal acidic motif mediated asymmetric BRAF dimer https://www.biorxiv.org/content/10.1101/2025.09.26.678760v1

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Reposted by James Fraser

Stephanie Wankowicz @stephanieaw.bsky.social · 11d

TTPD #7 with @fraserlab.com.

We chatted about the recent meetings, news, preprint engagement notifications, and the point of rotations.
wankowiczlab.com/2025/09/27/T...
Spotify: open.spotify.com/episode/0JCB...

The Tortured Proteins Department, Episode 7

This is the official web page for the Stephanie Wankowicz Lab at Vanderbilt University.

wankowiczlab.com

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James Fraser @fraserlab.com · 12d

@richardsever.bsky.social !

Reposted by James Fraser

Oli Clarke @olibclarke.bsky.social · 12d

Also want to highlight that Takanori Nakane made some very helpful and constructive comments about our preprint, which we plan to address in a revised version: disq.us/p/33zqohj

disq.us

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Reposted by James Fraser

Michael Eisen @mbeisen.bsky.social · 13d

Technically correct, but proper way to say that is that AAAS and Cell Press publishing policies are incompatible with the open research sharing policies of HHMI.

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Reposted by James Fraser

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 13d

You are of course correct. Will be interesting to see whether the journals, authors or HHMI adapt

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James Fraser @fraserlab.com · 13d

So not fully compatible with the new HHMI policy on preprints

James Fraser @fraserlab.com · 13d

My read is that the initially submitted version is the only thing that can be posted as a preprint. But… that this version can be posted as a preprint anytime (even if it is no longer the private “current” version after the manuscript has evolved during peer review)

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James Fraser @fraserlab.com · 14d

Still technically not allowed by @nature.com family journals though right?

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Reposted by James Fraser

Jase Gehring @skyjase.bsky.social · 16d

fun way to combine open discussion with formal communication - post your review on social media!

James Fraser @fraserlab.com · 16d

My colleague Joe Bondy-Denomy and I wrote a brief comment on the @brianhie.bsky.social @arcinstitute.org preprint on bacteriophage generation: prereview.org/reviews/1717...

tldr: would be nice to have baselines of successful assembly+resistance from lightweight models to test importance of genAI!

PREreview of “Generative design of novel bacteriophages with genome language models”

Authored by James Fraser and Joseph Bondy-Denomy

prereview.org

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James Fraser @fraserlab.com · 16d

And now that we know posting a @prereview.bsky.social and a @disqusofficial.bsky.social comment on @biorxivpreprint.bsky.social doesn't notify the authors automatically - we emailed the corresponding author too!

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James Fraser @fraserlab.com · 16d

My colleague Joe Bondy-Denomy and I wrote a brief comment on the @brianhie.bsky.social @arcinstitute.org preprint on bacteriophage generation: prereview.org/reviews/1717...

tldr: would be nice to have baselines of successful assembly+resistance from lightweight models to test importance of genAI!

PREreview of “Generative design of novel bacteriophages with genome language models”

Authored by James Fraser and Joseph Bondy-Denomy

prereview.org

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Reposted by James Fraser

Stephanie Wankowicz @stephanieaw.bsky.social · 27d

Structural bioinformatics is incredibly powerful on its own or when paired with theory or experiment. One of the PDB's superpowers isn’t from one structure, but comparing many to uncover folds, binding sites, and subtle conformational shifts. chemrxiv.org/engage/chemr...

10 Rules for a Structural Bioinformatic Analysis

The Protein Data Bank (PDB) is one of the richest open‑source repositories in biology, housing over 277,000 macromolecular structural models alongside much of the experimental data that underpins thes...

chemrxiv.org

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Reposted by James Fraser

Prachee Avasthi @pracheeac.bsky.social · 23d

The last day for public comment on this topic is Monday, Sept 15. It’s time to unleash science.
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Gift link to op-ed: www.wsj.com/opinion/acad...

NIH Request for Information: grants.nih.gov/grants/guide...

Opinion | Academic Publishing Has Become a Racket

Scientists write and review papers without getting paid, and their institutions have to pay for access.

www.wsj.com

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Reposted by James Fraser

Prachee Avasthi @pracheeac.bsky.social · 23d

Right now is the best chance the scientific community has ever had to end the artificial scarcity of academic journals.
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James Fraser @fraserlab.com · 25d

🙌🙌🙌
the biorxiv id (not sure what you call it technically ) is assigned before screening - so should be possible!

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James Fraser @fraserlab.com · 25d

Do they similarly say they may not publish papers in the future in journals. Email addresses aren’t behind paywall generally… doesn’t really hold water

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