James Fraser
@fraserlab.com
Professor and Chair @UCSF/@UCSF_BTS - dynamic structural biology and open science - (he/him) - fraserlab.com
Reposted by James Fraser
TTPD Episode 9 with @fraserlab.com: I Can Do It With a Broken Grant Cycle
(Sorry for the crappy audio in places!)
Topics: Government Shutdown/Reopening, Travels, Jane Richardson's impact (en.wikipedia.org/wiki/Jane_S....), Arena BioWorks closing, AI review tools
wankowiczlab.com/2025/11/24/T...
(Sorry for the crappy audio in places!)
Topics: Government Shutdown/Reopening, Travels, Jane Richardson's impact (en.wikipedia.org/wiki/Jane_S....), Arena BioWorks closing, AI review tools
wankowiczlab.com/2025/11/24/T...
November 24, 2025 at 3:22 PM
TTPD Episode 9 with @fraserlab.com: I Can Do It With a Broken Grant Cycle
(Sorry for the crappy audio in places!)
Topics: Government Shutdown/Reopening, Travels, Jane Richardson's impact (en.wikipedia.org/wiki/Jane_S....), Arena BioWorks closing, AI review tools
wankowiczlab.com/2025/11/24/T...
(Sorry for the crappy audio in places!)
Topics: Government Shutdown/Reopening, Travels, Jane Richardson's impact (en.wikipedia.org/wiki/Jane_S....), Arena BioWorks closing, AI review tools
wankowiczlab.com/2025/11/24/T...
Reposted by James Fraser
Can’t wait to be there repping @arpa-h.bsky.social and spreading the word about amazing work happening with @fraserlab.com, @qbi-ucsf.bsky.social, and others!
We look forward to welcoming Dr. @andykilianski.bsky.social, Program Manager at ARPA-H for a seminar hosted by James Fraser.
Learn about how ARPA-H is investing in bold, transformative research to shape the future of health in the United States: qbi.ucsf.edu/seminar-kili...
Learn about how ARPA-H is investing in bold, transformative research to shape the future of health in the United States: qbi.ucsf.edu/seminar-kili...
October 27, 2025 at 2:39 AM
Can’t wait to be there repping @arpa-h.bsky.social and spreading the word about amazing work happening with @fraserlab.com, @qbi-ucsf.bsky.social, and others!
Reposted by James Fraser
TTPD #8 with @fraserlab.com: Open access, Clear science, Full hearts, Can’t lose!
We chat about the Compact for Academic Excellence in Higher Education, HHMI open access, the government shutdown, the BEAR, the Nobel Prizes, and The Life of a Showgirl! wankowiczlab.com/2025/10/23/T...
We chat about the Compact for Academic Excellence in Higher Education, HHMI open access, the government shutdown, the BEAR, the Nobel Prizes, and The Life of a Showgirl! wankowiczlab.com/2025/10/23/T...
The Tortured Proteins Department, Episode 8
This is the official web page for the Stephanie Wankowicz Lab at Vanderbilt University.
wankowiczlab.com
October 23, 2025 at 3:39 PM
TTPD #8 with @fraserlab.com: Open access, Clear science, Full hearts, Can’t lose!
We chat about the Compact for Academic Excellence in Higher Education, HHMI open access, the government shutdown, the BEAR, the Nobel Prizes, and The Life of a Showgirl! wankowiczlab.com/2025/10/23/T...
We chat about the Compact for Academic Excellence in Higher Education, HHMI open access, the government shutdown, the BEAR, the Nobel Prizes, and The Life of a Showgirl! wankowiczlab.com/2025/10/23/T...
Reposted by James Fraser
Two main ways to encode structural heterogeneity beyond B-factors or TLS: multiconformer or multi-model (ensemble) models.
October 21, 2025 at 4:30 PM
Two main ways to encode structural heterogeneity beyond B-factors or TLS: multiconformer or multi-model (ensemble) models.
Reposted by James Fraser
I spend a lot of time talking to potential grantees about our open science policy. Some field notes here:
open.substack.com/pub/seemay/p...
open.substack.com/pub/seemay/p...
Why careerism can be bad for science training
Some field notes from scholarly publishing discussions with scientists
open.substack.com
October 21, 2025 at 3:52 PM
I spend a lot of time talking to potential grantees about our open science policy. Some field notes here:
open.substack.com/pub/seemay/p...
open.substack.com/pub/seemay/p...
Reposted by James Fraser
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?
October 7, 2025 at 2:11 AM
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?
Reposted by James Fraser
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.
pracheeac.substack.com/p/scholarly-...
Scholarly Communication Is a Research Problem. This Means You.
Scholarly Communication Is a Research Problem.
pracheeac.substack.com
October 4, 2025 at 4:11 PM
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.
pracheeac.substack.com/p/scholarly-...
Reposted by James Fraser
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. :)
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
September 28, 2025 at 10:33 AM
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. :)
Reposted by James Fraser
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...
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
September 27, 2025 at 8:00 PM
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...
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...
Reposted by James Fraser
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
September 26, 2025 at 2:41 AM
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
Reposted by James Fraser
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.
September 25, 2025 at 6:21 PM
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.
Reposted by James Fraser
You are of course correct. Will be interesting to see whether the journals, authors or HHMI adapt
September 25, 2025 at 6:41 PM
You are of course correct. Will be interesting to see whether the journals, authors or HHMI adapt
Reposted by James Fraser
fun way to combine open discussion with formal communication - post your review on social media!
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!
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
September 22, 2025 at 6:32 PM
fun way to combine open discussion with formal communication - post your review on social media!
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!
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
September 22, 2025 at 3:56 PM
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!
tldr: would be nice to have baselines of successful assembly+resistance from lightweight models to test importance of genAI!
Reposted by James Fraser
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
September 11, 2025 at 2:28 PM
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...
Reposted by James Fraser
The last day for public comment on this topic is Monday, Sept 15. It’s time to unleash science.
3/3
Gift link to op-ed: www.wsj.com/opinion/acad...
NIH Request for Information: grants.nih.gov/grants/guide...
3/3
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
September 14, 2025 at 11:04 PM
The last day for public comment on this topic is Monday, Sept 15. It’s time to unleash science.
3/3
Gift link to op-ed: www.wsj.com/opinion/acad...
NIH Request for Information: grants.nih.gov/grants/guide...
3/3
Gift link to op-ed: www.wsj.com/opinion/acad...
NIH Request for Information: grants.nih.gov/grants/guide...
Reposted by James Fraser
Right now is the best chance the scientific community has ever had to end the artificial scarcity of academic journals.
1/
1/
September 14, 2025 at 11:04 PM
Right now is the best chance the scientific community has ever had to end the artificial scarcity of academic journals.
1/
1/
If the authors are aware the review occurred!
Community Reviews are science in real time!
Check out this new and recent example of open feedback in action: Hale et al.’s preprint got reviewed by a community-organized group through PREreview and then the authors replied to it.
📄 doi.org/10.1101/2025...
#OpenScience #Preprints #CommunityReview
Check out this new and recent example of open feedback in action: Hale et al.’s preprint got reviewed by a community-organized group through PREreview and then the authors replied to it.
📄 doi.org/10.1101/2025...
#OpenScience #Preprints #CommunityReview
September 11, 2025 at 8:14 PM
If the authors are aware the review occurred!
Reposted by James Fraser
Community Reviews are science in real time!
Check out this new and recent example of open feedback in action: Hale et al.’s preprint got reviewed by a community-organized group through PREreview and then the authors replied to it.
📄 doi.org/10.1101/2025...
#OpenScience #Preprints #CommunityReview
Check out this new and recent example of open feedback in action: Hale et al.’s preprint got reviewed by a community-organized group through PREreview and then the authors replied to it.
📄 doi.org/10.1101/2025...
#OpenScience #Preprints #CommunityReview
September 11, 2025 at 6:35 PM
Community Reviews are science in real time!
Check out this new and recent example of open feedback in action: Hale et al.’s preprint got reviewed by a community-organized group through PREreview and then the authors replied to it.
📄 doi.org/10.1101/2025...
#OpenScience #Preprints #CommunityReview
Check out this new and recent example of open feedback in action: Hale et al.’s preprint got reviewed by a community-organized group through PREreview and then the authors replied to it.
📄 doi.org/10.1101/2025...
#OpenScience #Preprints #CommunityReview
Reposted by James Fraser
This! Many people have expert opinions about their specific interest in a paper just from reading it that would be helpful. It needn’t be comprehensive to be exceptionally helpful, especially since people’s expertise can rarely cover the joint expertise of increasingly collaborative work anyway
September 8, 2025 at 11:47 PM
This! Many people have expert opinions about their specific interest in a paper just from reading it that would be helpful. It needn’t be comprehensive to be exceptionally helpful, especially since people’s expertise can rarely cover the joint expertise of increasingly collaborative work anyway
Reposted by James Fraser
I love writing spontaneous and unsolicited reviews. I would be thrilled folks did it to me too! I think it gets the heart of what we do science for - giving and getting feedback to get closer to the ‘truth’! Otherwise why post a preprint if you don’t want people to read and respond?
Why hasn't Preprint Peer Review caught on more?
I discovered a small, but simple reason - authors are missing out on the JOY of getting feedback because they aren't notified when feedback occurs.
more in thread below!
I discovered a small, but simple reason - authors are missing out on the JOY of getting feedback because they aren't notified when feedback occurs.
more in thread below!
September 8, 2025 at 9:12 PM
I love writing spontaneous and unsolicited reviews. I would be thrilled folks did it to me too! I think it gets the heart of what we do science for - giving and getting feedback to get closer to the ‘truth’! Otherwise why post a preprint if you don’t want people to read and respond?
Reposted by James Fraser
Great point. Make it opt out, not opt in, for authors to see feedback.
We need to grow a culture of rapid and constructive feedback to replace ‘peer review’… which is outdated, was not designed and is not fit for purpose.
How can we do that if public reviews are not even seen by the authors?
We need to grow a culture of rapid and constructive feedback to replace ‘peer review’… which is outdated, was not designed and is not fit for purpose.
How can we do that if public reviews are not even seen by the authors?
September 8, 2025 at 8:07 PM
Great point. Make it opt out, not opt in, for authors to see feedback.
We need to grow a culture of rapid and constructive feedback to replace ‘peer review’… which is outdated, was not designed and is not fit for purpose.
How can we do that if public reviews are not even seen by the authors?
We need to grow a culture of rapid and constructive feedback to replace ‘peer review’… which is outdated, was not designed and is not fit for purpose.
How can we do that if public reviews are not even seen by the authors?
Reposted by James Fraser
I was discouraged from giving biorxiv reviews when I realized they are buried as soon as a new version is posted.
September 8, 2025 at 8:06 PM
I was discouraged from giving biorxiv reviews when I realized they are buried as soon as a new version is posted.
Reposted by James Fraser
Why hasn't Preprint Peer Review caught on more?
I discovered a small, but simple reason - authors are missing out on the JOY of getting feedback because they aren't notified when feedback occurs.
more in thread below!
I discovered a small, but simple reason - authors are missing out on the JOY of getting feedback because they aren't notified when feedback occurs.
more in thread below!
September 8, 2025 at 7:55 PM
Reposted by James Fraser
This has happened to me as well bsky.app/profile/esch...
Thanks, I had no idea this existed. We do plan to revise and improve the preprint, schedules permitting. Will consider these comments!
September 8, 2025 at 7:53 PM
This has happened to me as well bsky.app/profile/esch...