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Brian Hie

@brianhie.bsky.social

AI for biology | Stanford and Arc Institute

9 Posts2709 Follower119 Folgt
Martin Steinegger 🇺🇦@martinsteinegger.bsky.social · 7mo ago

Milot’s venture into establishing his own lab is incredibly excitinge. I highly recommend to join Milot on his mission to advance molecular biology through open-source bioinformatics.

Milot Mirdita@milot.bsky.social · 7mo ago

My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring! mirdita.org

Nature@nature.com · 8mo ago

Nature research paper: Semantic design of functional de novo genes from a genomic language model go.nature.com/48uEnAn

Semantic design of functional de novo genes from a genomic language model - Nature

By learning a semantics of gene function based on genomic context, the genomic language model Evo autocompletes DNA prompts to generate novel genes encoding protein and RNA molecules with defined activities, whose sequences generalize beyond those found in nature.

go.nature.com

Bryan Bryson@thebrysonlab.bsky.social · 9mo ago

Excited to share our newest manuscript on antigen discovery and vaccine design for tuberculosis lead by Owen Leddy (everyone hiring new faculty in a few years, remember this name!) www.science.org/doi/10.1126/... #TBsky

Immunopeptidomics can inform the design of mRNA vaccines for the delivery of Mycobacterium tuberculosis MHC class II antigens

MHC class II immunopeptidomics in human phagocytes infected with Mycobacterium tuberculosis enables vaccine immunogen design and optimization.

science.org

Bryan Bryson@thebrysonlab.bsky.social · 9mo ago

Excited to share our lab's newest preprint (strap in if you're excited about metabolism, species differences, or Mtb gene expression): www.biorxiv.org/content/10.1...

Systems analysis reveals alternate metabolic states adopted by Mycobacterium tuberculosis across species

Mycobacterium tuberculosis (Mtb) persists within macrophages, yet how different host species shape bacterial state remains poorly understood. Here, we directly compared the intracellular transcriptome...

biorxiv.org

Xiaojing Gao@synbiogaolab.bsky.social · 11mo ago

Having often dealt with the frustration of binder-limited projects, we sought a more accessible source for nanobodies than yeast display or llama. Here we introduce Germinal, computationally designing antibody-like binders with such a hit rate that only tens need to be screened for each target.

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Adrian Woolfson@adrianwoolfson.bsky.social · 11mo ago

A landmark paper from Brian Hie’s group at the Arc Institute. The de novo design of the synthetic genome of an entirely novel biological entity www.biorxiv.org/content/10.1...

Generative design of novel bacteriophages with genome language models

Many important biological functions arise not from single genes, but from complex interactions encoded by entire genomes. Genome language models have emerged as a promising strategy for designing biol...

biorxiv.org

Paul Hoskisson 🧫 🦠🐸@paulhoskisson.bsky.social · 11mo ago

This is super cool from @brianhie.bsky.social et al- Generative design of novel bacteriophages with genome language models www.biorxiv.org/content/10.1...

Generative design of novel bacteriophages with genome language models

Many important biological functions arise not from single genes, but from complex interactions encoded by entire genomes. Genome language models have emerged as a promising strategy for designing biol...

biorxiv.org

Samuel King@samuelhking.bsky.social · 11mo ago

Many of the most complex and useful functions in biology emerge at the scale of whole genomes. Today, we share our preprint “Generative design of novel bacteriophages with genome language models”, where we validate the first, functional AI-generated genomes 🧵

Brian Hie@brianhie.bsky.social · last yr.

We trained a genomic language model on all observed evolution, which we are calling Evo 2. The model achieves an unprecedented breadth in capabilities, enabling prediction and design tasks from molecular to genome scale and across all three domains of life.

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Di Jiang@dijiang319.bsky.social · 2y ago

New @biorxiv-synthbio.bsky.social on #Evo 👀⤵️🧵 introducing Evo 1.5 for semantic mining + SynGenome - an AI-generated genomics database #AI #synbio #LLM🧬 @adititm.bsky.social @brianhie.bsky.social et al. @arcinstitute.org

Aditi Merchant@adititm.bsky.social · 2y ago

Excited to have the first project of my PhD out!! By leveraging genomic language model Evo’s ability to learn relationships across genes (i.e., "know a gene by the company it keeps"), we show that we can use prompt-engineering to generate highly divergent proteins with retained functionality. 🧵1/N

Aditi Merchant@adititm.bsky.social · 2y ago

Excited to have the first project of my PhD out!! By leveraging genomic language model Evo’s ability to learn relationships across genes (i.e., "know a gene by the company it keeps"), we show that we can use prompt-engineering to generate highly divergent proteins with retained functionality. 🧵1/N

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