Garyk Brixi

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@garykbrixi

Building discovery engines for biology. @Stanford · @ArcInstitute

garykbrixi.com Joined November 2022

348 Following 1.7K Followers 230 Posts

Latest posts 5

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Garyk Brixi @garykbrixi Sep 22

Genomes are full of dark matter of unknown functions.

We present Minerva, a new method for discovery guided by genome language models. Minerva reveals the interactions hidden in non-coding DNA, pointing to hundreds of new putative RNAs and repetitive elements per bacterial genome. Minerva allows us to find and study elements invisible to traditional methods at orders of magnitude greater scale than before.

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Garyk Brixi @garykbrixi Oct 29

Language models can learn new tasks from just a few examples in their prompt, with no retraining. This is called in-context learning (ICL). Now genome language models can do it too.

With a handful of examples, Evo 2 ICL generates proteins, de novo antibodies, CRISPR-Cas9 loci, mitochondrial genomes and entire bacteriophages.

We can even use the synthetic sequences iteratively to construct a chain-of-thought (CoT) and achieve harder design goals.

New work with Yukun A. Hao, @BrianHie and team 🧵

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Garyk Brixi @garykbrixi Oct 22

Evo helps agents mine genomes

Congrats @pdhsu @gwanggyus @timjhudelmaier and team

Arc Institute Verified account @arcinstitute Oct 22

Much of the functional biology encoded in genomes remains hidden in noncoding DNA.

In a preprint out today, @pdhsu and team introduce COMPASS, a genomic language model-based approach to systematically map this underexplored sequence space.

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Garyk Brixi @garykbrixi Oct 13

You can now run Minerva in your browser.
Predict base-pairing, repeats, and other coevolution in seconds: huggingface.co/spaces/gbrixi/…

Garyk Brixi Verified account @garykbrixi Sep 22

Genomes are full of dark matter of unknown functions.

We present Minerva, a new method for discovery guided by genome language models. Minerva reveals the interactions hidden in non-coding DNA, pointing to hundreds of new putative RNAs and repetitive elements per bacterial genome. Minerva allows us to find and study elements invisible to traditional methods at orders of magnitude greater scale than before.

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Garyk Brixi @garykbrixi Aug 6

Generated genomes that work!

Next challenge for DNA design: moving further from natural distributions towards specific desired functions

Samuel King Verified account @samuelhking Aug 6

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

science.org/doi/10.1126/sc…

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