Brian Naughton
@btnaughton.bsky.social
genetics/data/programming. ex-Hexagon, ex-Stanford ex-23andMe ex-TCD http://blog.booleanbiotech.com 🇮🇪
A treasure trove of biotech and early SV oral histories by Sally Hughes: digicoll.lib.berkeley.edu/search?p=%28...
Genentech (Boyer, Goeddel (recommended!)), VC (Byers, Rock, Valentine), Kaiser ("History of the Kaiser Permanente Medical Care Program"), Lilly, Paul Berg, Stan Cohen, lots more.
Genentech (Boyer, Goeddel (recommended!)), VC (Byers, Rock, Valentine), Kaiser ("History of the Kaiser Permanente Medical Care Program"), Lilly, Paul Berg, Stan Cohen, lots more.
( (creator:[Hughes, Sally Smith])) - Search Results - Digital Collections
Digital Collections Search Results.
digicoll.lib.berkeley.edu
October 30, 2025 at 12:54 AM
A treasure trove of biotech and early SV oral histories by Sally Hughes: digicoll.lib.berkeley.edu/search?p=%28...
Genentech (Boyer, Goeddel (recommended!)), VC (Byers, Rock, Valentine), Kaiser ("History of the Kaiser Permanente Medical Care Program"), Lilly, Paul Berg, Stan Cohen, lots more.
Genentech (Boyer, Goeddel (recommended!)), VC (Byers, Rock, Valentine), Kaiser ("History of the Kaiser Permanente Medical Care Program"), Lilly, Paul Berg, Stan Cohen, lots more.
I’ve been testing BoltzGen a bit recently and while I haven’t done any experimental testing yet, the quality of the software is very clear. It installs, runs, logs everything, has tons of options. Very excited to test out the designs irl!
Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!
October 27, 2025 at 1:57 PM
I’ve been testing BoltzGen a bit recently and while I haven’t done any experimental testing yet, the quality of the software is very clear. It installs, runs, logs everything, has tons of options. Very excited to test out the designs irl!
I decided to experiment with my own (small) protein design competition!
It's specifically to test how well VHH pipelines work for binder design, without the usual careful tuning.
You submit a modal script, I run it and test on benchbb.bio
blog.booleanbiotech.com/vhh-competit...
It's specifically to test how well VHH pipelines work for binder design, without the usual careful tuning.
You submit a modal script, I run it and test on benchbb.bio
blog.booleanbiotech.com/vhh-competit...
October 16, 2025 at 4:54 PM
I decided to experiment with my own (small) protein design competition!
It's specifically to test how well VHH pipelines work for binder design, without the usual careful tuning.
You submit a modal script, I run it and test on benchbb.bio
blog.booleanbiotech.com/vhh-competit...
It's specifically to test how well VHH pipelines work for binder design, without the usual careful tuning.
You submit a modal script, I run it and test on benchbb.bio
blog.booleanbiotech.com/vhh-competit...
Reposted by Brian Naughton
Pretty interesting that AFAICT the filtering was done after the fact (so, library 1 had no filtering). This could make it an excellent dataset for training/testing filters/rankers. Too bad it looks like the dataset is not public
September 29, 2025 at 7:40 PM
Pretty interesting that AFAICT the filtering was done after the fact (so, library 1 had no filtering). This could make it an excellent dataset for training/testing filters/rankers. Too bad it looks like the dataset is not public
Another promising VHH model just dropped today from Manifold Bio. This one builds on BindCraft and ColabDesign. MIT license!
www.biorxiv.org/content/10.1...
The success rates appear to be lower than other tools, but this is highly target-dependent.
www.biorxiv.org/content/10.1...
The success rates appear to be lower than other tools, but this is highly target-dependent.
September 29, 2025 at 7:03 PM
Another promising VHH model just dropped today from Manifold Bio. This one builds on BindCraft and ColabDesign. MIT license!
www.biorxiv.org/content/10.1...
The success rates appear to be lower than other tools, but this is highly target-dependent.
www.biorxiv.org/content/10.1...
The success rates appear to be lower than other tools, but this is highly target-dependent.
New blogpost on the latest in AI antibody design.
Including some code to easily run Germinal and IgGM on modal!
blog.booleanbiotech.com/ai-antibody-...
Including some code to easily run Germinal and IgGM on modal!
blog.booleanbiotech.com/ai-antibody-...
Boolean Biotech
blog.booleanbiotech.com
September 28, 2025 at 2:25 PM
New blogpost on the latest in AI antibody design.
Including some code to easily run Germinal and IgGM on modal!
blog.booleanbiotech.com/ai-antibody-...
Including some code to easily run Germinal and IgGM on modal!
blog.booleanbiotech.com/ai-antibody-...
It has been interesting to use gitingest to paste entire codebases for new tools into Gemini and ask for severe bugs (logic, incorrect variables...).
I think it found at least one this morning. I have to double-check before filing but it's a real bug from what I can tell...
I think it found at least one this morning. I have to double-check before filing but it's a real bug from what I can tell...
September 25, 2025 at 4:34 PM
It has been interesting to use gitingest to paste entire codebases for new tools into Gemini and ask for severe bugs (logic, incorrect variables...).
I think it found at least one this morning. I have to double-check before filing but it's a real bug from what I can tell...
I think it found at least one this morning. I have to double-check before filing but it's a real bug from what I can tell...
Reposted by Brian Naughton
In another preprint from the @brianhie.bsky.social Lab and @synbiogaolab.bsky.social, they introduce Germinal, a generative AI system for de novo antibody design.
Germinal produces functional nanobodies in just dozens of tests, making custom antibody design more accessible than ever before.
Germinal produces functional nanobodies in just dozens of tests, making custom antibody design more accessible than ever before.
September 24, 2025 at 3:07 PM
In another preprint from the @brianhie.bsky.social Lab and @synbiogaolab.bsky.social, they introduce Germinal, a generative AI system for de novo antibody design.
Germinal produces functional nanobodies in just dozens of tests, making custom antibody design more accessible than ever before.
Germinal produces functional nanobodies in just dozens of tests, making custom antibody design more accessible than ever before.
A REALLY nice use of nanobanana (Gemini) is cleaning up blurry old images. Of course it depends what you ask for, but it is amazing at keeping the text and content the same.
September 19, 2025 at 1:53 PM
A REALLY nice use of nanobanana (Gemini) is cleaning up blurry old images. Of course it depends what you ask for, but it is amazing at keeping the text and content the same.
We decided to try to 3d print custom chess pieces.
The workflow of asking gemini to iterate on a design image, then uploading that image to adam.new worked amazingly well. 5 minutes work!
Left is the gemini image and right is the mesh.
The workflow of asking gemini to iterate on a design image, then uploading that image to adam.new worked amazingly well. 5 minutes work!
Left is the gemini image and right is the mesh.
September 13, 2025 at 10:14 PM
We decided to try to 3d print custom chess pieces.
The workflow of asking gemini to iterate on a design image, then uploading that image to adam.new worked amazingly well. 5 minutes work!
Left is the gemini image and right is the mesh.
The workflow of asking gemini to iterate on a design image, then uploading that image to adam.new worked amazingly well. 5 minutes work!
Left is the gemini image and right is the mesh.
I was reminded about Blackett's War by a mention on the @patio11 podcast. Terrific book about operations research / probability theory applied to real world problems.
Lots of anecdotes like this...
Lots of anecdotes like this...
September 6, 2025 at 3:05 PM
I was reminded about Blackett's War by a mention on the @patio11 podcast. Terrific book about operations research / probability theory applied to real world problems.
Lots of anecdotes like this...
Lots of anecdotes like this...
Reposted by Brian Naughton
Recently tested some de-novo minibinders against two targets (thanks Adaptyv!) designed using our open-source design library, `mosaic`; our best method got hit rates of 7/10 and 8/10 and affinities as low as single-digit nanomolar. Wrote up some thoughts here: blog.escalante.bio/minibinder-d...
September 2, 2025 at 2:39 PM
Recently tested some de-novo minibinders against two targets (thanks Adaptyv!) designed using our open-source design library, `mosaic`; our best method got hit rates of 7/10 and 8/10 and affinities as low as single-digit nanomolar. Wrote up some thoughts here: blog.escalante.bio/minibinder-d...
Ibex from Prescient Design arxiv.org/abs/2507.09054 github.com/prescient-de...
- antibody folding with performance like Boltz/Chai but up to 100X faster
- does not fold the complex, just the antibody
- predicts holo and apo forms
- sadly, model weights are not freely available
- antibody folding with performance like Boltz/Chai but up to 100X faster
- does not fold the complex, just the antibody
- predicts holo and apo forms
- sadly, model weights are not freely available
August 13, 2025 at 4:31 PM
Ibex from Prescient Design arxiv.org/abs/2507.09054 github.com/prescient-de...
- antibody folding with performance like Boltz/Chai but up to 100X faster
- does not fold the complex, just the antibody
- predicts holo and apo forms
- sadly, model weights are not freely available
- antibody folding with performance like Boltz/Chai but up to 100X faster
- does not fold the complex, just the antibody
- predicts holo and apo forms
- sadly, model weights are not freely available
Reposted by Brian Naughton
Now that OpenCRISPR is in nature and rekindled the 'what's-a-novel-sequence' debate, I'm happy to share an app to check this, which I built for fun some time ago.
fuerstlab.shinyapps.io/SeqNovelty/
quick 🧵
fuerstlab.shinyapps.io/SeqNovelty/
quick 🧵
August 1, 2025 at 11:50 AM
Now that OpenCRISPR is in nature and rekindled the 'what's-a-novel-sequence' debate, I'm happy to share an app to check this, which I built for fun some time ago.
fuerstlab.shinyapps.io/SeqNovelty/
quick 🧵
fuerstlab.shinyapps.io/SeqNovelty/
quick 🧵
After many months heads down, we at Decade are growing! We are hiring a protein biochemist to help us radically improve cancer treatment.
If you like being early and making an impact, we are interested to hear from you! Details here: decade.bio/careers
If you like being early and making an impact, we are interested to hear from you! Details here: decade.bio/careers
decade.bio
July 25, 2025 at 8:23 PM
After many months heads down, we at Decade are growing! We are hiring a protein biochemist to help us radically improve cancer treatment.
If you like being early and making an impact, we are interested to hear from you! Details here: decade.bio/careers
If you like being early and making an impact, we are interested to hear from you! Details here: decade.bio/careers
Asking Claude to research binder designs metrics and it gave me my own blogpost back!
Time to start writing for the AIs? marginalrevolution.com/marginalrevo...
Time to start writing for the AIs? marginalrevolution.com/marginalrevo...
July 19, 2025 at 2:13 PM
Asking Claude to research binder designs metrics and it gave me my own blogpost back!
Time to start writing for the AIs? marginalrevolution.com/marginalrevo...
Time to start writing for the AIs? marginalrevolution.com/marginalrevo...
Great article on cancer vaccines by @mackenziejem.bsky.social
www.mackenziemorehead.com/the-failures...
www.mackenziemorehead.com/the-failures...
The Failures and Futures of Cancer Vaccines
The cancer vaccine field has yet to become a systematic science despite decades of work and a steadily rising number of clinical trials since the first clinical PoC a decade ago.
A core problem faci...
www.mackenziemorehead.com
June 26, 2025 at 5:41 PM
Great article on cancer vaccines by @mackenziejem.bsky.social
www.mackenziemorehead.com/the-failures...
www.mackenziemorehead.com/the-failures...
Vibe coded a run progress simulator with Gemini Canvas.
It worked great, until the context rot doom loop set in, and now it's difficult to fix the remaining minor bugs.
Still very impressive!
hgbrian.github.io/run_progress...
It worked great, until the context rot doom loop set in, and now it's difficult to fix the remaining minor bugs.
Still very impressive!
hgbrian.github.io/run_progress...
June 23, 2025 at 2:56 PM
Vibe coded a run progress simulator with Gemini Canvas.
It worked great, until the context rot doom loop set in, and now it's difficult to fix the remaining minor bugs.
Still very impressive!
hgbrian.github.io/run_progress...
It worked great, until the context rot doom loop set in, and now it's difficult to fix the remaining minor bugs.
Still very impressive!
hgbrian.github.io/run_progress...
I spent way too long on this but I made a small benchmark for OCR of biological sequences.
It's pretty incredible how poorly everything I tried works. Maybe by posting a benchmark it will lead to finding something out there that works!
github.com/hgbrian/bio_...
It's pretty incredible how poorly everything I tried works. Maybe by posting a benchmark it will lead to finding something out there that works!
github.com/hgbrian/bio_...
May 30, 2025 at 10:55 PM
I spent way too long on this but I made a small benchmark for OCR of biological sequences.
It's pretty incredible how poorly everything I tried works. Maybe by posting a benchmark it will lead to finding something out there that works!
github.com/hgbrian/bio_...
It's pretty incredible how poorly everything I tried works. Maybe by posting a benchmark it will lead to finding something out there that works!
github.com/hgbrian/bio_...
BindEnergyCraft claims to improve BindCraft performance using an energy-based objective.
"Code will be released soon."
"Code will be released soon."
May 30, 2025 at 7:43 PM
BindEnergyCraft claims to improve BindCraft performance using an energy-based objective.
"Code will be released soon."
"Code will be released soon."
I have been copying some amino acid sequences out of PDFs and so far nothing (Gemini, Claude, ChatGPT) works at >99% accuracy. I have to manually inspect everything!
Even when you can highlight the text in the PDF, it is very often wrong! Anyone know anything that works?
Even when you can highlight the text in the PDF, it is very often wrong! Anyone know anything that works?
May 20, 2025 at 11:42 PM
I have been copying some amino acid sequences out of PDFs and so far nothing (Gemini, Claude, ChatGPT) works at >99% accuracy. I have to manually inspect everything!
Even when you can highlight the text in the PDF, it is very often wrong! Anyone know anything that works?
Even when you can highlight the text in the PDF, it is very often wrong! Anyone know anything that works?
The inverse vaccine / tolerization stuff is amazing. Similar to peanut tolerization but for any autoimmune disease?
www.theguardian.com/wellness/202...
www.theguardian.com/wellness/202...
‘Inverse vaccines’: the promise of a ‘holy grail’ treatment for autoimmune diseases
Some researchers say a new approach, which suppresses a particular part of the immune system rather than amplifying it, could be available in the next five years
www.theguardian.com
May 16, 2025 at 10:37 PM
The inverse vaccine / tolerization stuff is amazing. Similar to peanut tolerization but for any autoimmune disease?
www.theguardian.com/wellness/202...
www.theguardian.com/wellness/202...
new blogpost: AI and protein patents blog.booleanbiotech.com/ai-protein-p...
Boolean Biotech
blog.booleanbiotech.com
May 5, 2025 at 3:14 PM
new blogpost: AI and protein patents blog.booleanbiotech.com/ai-protein-p...
We have gotten some really good responses to science questions from platform.futurehouse.org already. Both from "Crow" (short answers) and "Falcon" (deep research).
It looks like this is state of the art right now!
It looks like this is state of the art right now!
May 2, 2025 at 10:03 PM
We have gotten some really good responses to science questions from platform.futurehouse.org already. Both from "Crow" (short answers) and "Falcon" (deep research).
It looks like this is state of the art right now!
It looks like this is state of the art right now!