Brian Naughton
genetics/data/programming. ex-Hexagon, ex-Stanford ex-23andMe ex-TCD http://blog.booleanbiotech.com 🇮🇪
- Great piece on antibody developability in the AI era by Adil Yusuf ayusuf.substack.com/p/developabi...
- github.com/adaptyvbio/p... Very cool Claude skills for protein design from x.com/CotetTudor and Adaptyv. Their standard pipeline should enable anyone (+Claude) to easily design binders at close to state of the art! I'm happy to see it uses my biomodals repo in parts github.com/hgbrian/biom...
- Very cool Claude skills for protein design from x.com/CotetTudor and Adaptyv. Their standard pipeline should enable anyone (+Claude) to easily design binders at close to state of the art! I'm also happy to see it uses my biomodals repo in parts github.com/hgbrian/biom...
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- Blogpost: I took an oral probiotic for a month and did microbiome sequencing at @Plasmidsaurus. blog.booleanbiotech.com/oral-microbi...
- Releasing alignism, a small tool that I have found useful for doing multiple sequence alignment in browser. hgbrian.github.io/alignism/ - The hard work was done by the awesome biowasm team! - Does tree building too - V fast compared to e.g., muscle on EBI - Not tested that much!
- I semi-vibe coded a frontend for all the protein folding tools I've been running. It runs on modal and has 5 different open-source algorithms: Chai1, Boltz2, AF2, Protenix(-mini). Not 100% polished but hopefully of use to some use to people in the field! github.com/hgbrian/fold...
- I wrote up a short blogpost on using Claude Code / Opus 4.5 for computational biology blog.booleanbiotech.com/claude-code-...
- 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.
- 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...
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- 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.
- 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-...
- 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...
- Reposted by Brian NaughtonIn 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.
- 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.
- 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...
- Reposted by Brian NaughtonRecently 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
- Reposted by Brian NaughtonNow 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 🧵
- 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
- 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...
- Great article on cancer vaccines by @mackenziejem.bsky.social 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...
- 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_...
- BindEnergyCraft claims to improve BindCraft performance using an energy-based objective. "Code will be released soon."
- Clever mosquito detector, draws a circle around the mosquito so you can squash it. $200 bzigo.com
- 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?
- The inverse vaccine / tolerization stuff is amazing. Similar to peanut tolerization but for any autoimmune disease? www.theguardian.com/wellness/202...
- 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!
- TIL you can add .txt to a biorxiv fulltext link and get plain text. Handy for pasting into LLMs, e.g., the new BindCraft revision www.biorxiv.org/content/10.1...
- There are now a trio of great pieces covering the rapid rise of Chinese biotech: - atelfo.github.io/2024/12/20/w... - centuryofbio.com/p/commoditiz... - www.asimov.press/p/china-trials
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- sciencemachine.ai looks really interesting (default example analysis below) I am not sure how uploading to the browser can work for real sequencing data though. Maybe they will take a bucket url or something.
- I did not know @plasmidsaurus.bsky.social is doing eukaryote nanopore sequencing now. The price is good, especially $50 extra for extraction. Unfortunately you cannot yet send any tissue, only certain blood and cell culture.
- Since BoltzDesign1 just got published, people might also be interested in github.com/escalante-bi... by @nboyd.bsky.social It has a nicely flexible system for including custom losses. It's also surprisingly little code on top of Boltz (and the Jaxified Joltz).
- Reposted by Brian NaughtonSuper excited to share that our paper on a multi-modal cell-free RNA foundation model is out! A fantastic collaboration with @genophoria.bsky.social, @fhormozd.bsky.social and the @exai.bio team!
- Joining forces with the legendary @babak-a.bsky.social, @fhormozd.bsky.social, and @mkarimzadeh.bsky.social to bring you Exai-1; a multi-modal cell-free RNA foundation model for blood surveillance and liquid biopsy applications. Kudos to the broader @exai.bio team! www.biorxiv.org/content/10.1...
- Checking into options for home lab testing. A lot of places are now offering the Tasso device or similar for home collection: - mylabsdirect.com/product/comp... - rythmhealth.com - siphoxhealth.com - www.functionhealth.com - www.walkinlab.com
- interesting report on synbio in china by Zach Sun sepiabio.substack.com/p/observatio...
- new blogpost on protein binder design blog.booleanbiotech.com/protein-bind...
