Brian Hie

AI for biology
@Stanford and @arcinstitute

[Brian Hie @BrianHie]

In new work, we lay out a vision for a high-level programming language for generative biology, called Proto.

Proto composes generative and predictive models spanning DNA, RNA, proteins, ligands, and their interactions, which we use to design complex biological functions. 1/n

[Brian Hie @BrianHie]

@samuelhking @anshulkundaje @ScienceMagazine Thanks Anshul!

[Brian Hie @BrianHie]

Our paper reporting the generative design of complete bacteriophage genomes is now published @ScienceMagazine. Check out this thread by @samuelhking for more details, including the new data included in the published version.

https://t.co/fhUQJWmsNX

[Samuel King @samuelhking]

Today in @ScienceMagazine, we report the first functional AI-generated genomes. 🧵

https://t.co/HCwWfenIc0

[Brian Hie @BrianHie]

@BoWang87 @ScienceMagazine @samuelhking Thanks Bo!

[The New York Times @nytimes]

Breaking News: Scientists have used A.I. to create new viruses for the first time, raising hopes for medical advances while also raising the possibility that the technology could someday be used to invent dangerous pathogens. https://t.co/MJG4mp0TTb

[Christina Agapakis @thisischristina]

Wrote one of my favorite blog posts on this when it was a preprint last year -- vibe coding the genome! https://t.co/K2K3nacwYY

[Eric Topol @EricTopol]

This is a big deal, folks. Very good explainer @NYTScience
https://t.co/6xMkzEGjeY

[Eric Topol @EricTopol]

A frontrunner of generative AI in biology was design of novel proteins, not found in nature. This has moved on now to designing viral genomes, the 1st reported today @ScienceMagazine. This has great potential to synthesize phage to counter antimicrobial resistance but also concern regarding biosecurity.
https://t.co/LbyXtjAWm8
https://t.co/jTN0KjfYSk

[Arc Institute @arcinstitute]

One of our most popular preprints of 2025 is now published in @ScienceMagazine. Congrats to @BrianHie, @samuelhking, and team on establishing a framework for generating and evaluating AI-generated genomes.

- Access the paper: https://t.co/p5qMhTroK2

[Brian Hie @BrianHie]

This was a very fun project to work on -- to me, it felt both futuristic and primitive at the same time. While these are the first whole genomes generated by AI, there is a clear path toward the responsible design of more complex biological systems.

https://t.co/KVDDa3JFlr

[Brian Hie @BrianHie]

ΦX174 was also the first whole-genome synthesized by Venter et al. in 2003. While our work is a milestone in genome design, it is also clearly just the beginning.

What will happen when generative genomics becomes as ubiquitous as Sanger sequencing or Gibson assembly? 5/n

[Samuel King @samuelhking]

This was a super fun conversation, thanks so much for having me @dancinflo !

[Bowen Jing @bjing2016]

It’s getting hard to keep track of all the new open-source cofolding models coming out. To help everyone stay up to date, I'm excited to share https://t.co/Gc9PaF6GoY, a PDB-synced leaderboard of open models, updated weekly. All predictions are available to view & download! (1/4)

[Arc Institute @arcinstitute]

The Proto team from @BrianHie's lab will be at the re:AGENT hackathon, a two-day weekend (8/15–8/16) in San Francisco for people interested in building AI scientists, datasets, or pipelines for biological design.

Apply by Thursday, July 30th, 12 PM PT at https://t.co/H2ddXzQBLP

[Ben Viggiano @bviggiano_13]

Super excited to announce that the Proto team from the @arcinstitute is co-hosting a hackathon with @gxl_ai, @AnthropicAI, @biohub, @benchflow_ai, and https://t.co/CcriiIUjr4! Applications close July 30th. We hope to see you there! https://t.co/spekhkniUP

[Brian Hie @BrianHie]

Come build cool stuff with Proto alongside agents from @gxl_ai and @claudeai from @AnthropicAI!

https://t.co/l18byQXwk2

[Akira Nishii @akiranishii3]

At @gxl_ai, we're excited to announce re:AGENT a two-day build weekend (8/15–8/16, SF) for people building tools for scientific agents. We have three tracks: build an AI scientist, create a large-scale scientific dataset or meta-analysis, or design a new biological system.

Apply by 7/30 at https://t.co/WICEnm3jAd

Thanks to our partners at @arcinstitute, @AnthropicAI, @benchflow_ai, https://t.co/zbgXtxMplG, and @biohub!

[Stanford HAI @StanfordHAI]

"In a short period of time, our team has built the largest fully open language model ever trained, the first AI-generated genomic database, and the first AI-generated viable genomes." Stanford HAI Faculty Affiliate @BrianHie on Evo 2, developed with support from a Stanford HAI Hoffman-Yee Research Grant: https://t.co/5OFFOAsqTs

[Aditi Merchant @aditimerch]

Happening today! Tune in to learn more about Proto and how to use it for your own biological design goals 🧬

[Machine Learning for Protein Engineering Seminar @ml4proteins]

We’re excited to host @aditimerch on Tuesday, July 21, for a presentation on her recent work, “A High-Level Programming Language for Generative Biology with Proto.” The talk will take place from 6:00–7:00 p.m. ET / 3:00–4:00 p.m. PT

[Rishabh (in SF) @rishabh16_]

We’re super excited to host @aditimerch this coming Tuesday, 21st July. As Agents4Science become more prevalent, molecular design frameworks like Proto, from @BrianHie’s group, are of great interest. See you there!

And in related news, I recently joined the organising team of @ml4proteins. Looking forward to hosting more awesome researchers in the future with the team 🎉

[John Pluvinage @jvpluv]

Together with @BrianHie's lab, we are looking for a lab manager to join the team @arcinstitute. If you love to organize, optimize, and accelerate scientific discovery, please consider applying! https://t.co/CgAQl3g74Z

[Brian Hie @BrianHie]

Job posting is here: https://t.co/qYzmxRIw33

[Brian Hie @BrianHie]

We are recruiting a lab manager @arcinstitute, alongside @jvpluv's lab, to support our work on ensuring that AI for biology benefits humanity.

This role will spearhead operations across diverse, very exciting projects in the works. Please consider joining us!