Brian Hie
@brianhie.bsky.social
AI for biology | Stanford and Arc Institute
Reposted by Brian Hie
Nature research paper: Semantic design of functional de novo genes from a genomic language model
go.nature.com/48uEnAn
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
November 25, 2025 at 8:58 AM
Nature research paper: Semantic design of functional de novo genes from a genomic language model
go.nature.com/48uEnAn
go.nature.com/48uEnAn
Reposted by Brian Hie
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
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.
www.science.org
November 5, 2025 at 9:57 PM
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
www.science.org/doi/10.1126/... #TBsky
Reposted by Brian Hie
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...
www.biorxiv.org
November 17, 2025 at 6:20 AM
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...
Reposted by Brian Hie
Published today in @nature.com, @adititm.bsky.social & researchers from the @brianhie.bsky.social lab report that the large-scale genomic model, Evo, is capable of using surrounding genomic context to produce novel, functional genes, enabling an an emergent approach they've termed 'semantic design'.
November 19, 2025 at 6:17 PM
Published today in @nature.com, @adititm.bsky.social & researchers from the @brianhie.bsky.social lab report that the large-scale genomic model, Evo, is capable of using surrounding genomic context to produce novel, functional genes, enabling an an emergent approach they've termed 'semantic design'.
Reposted by Brian Hie
What if we could autocomplete DNA based on function?
Today in @Nature, we share semantic design—a strategy for function-guided design with genomic language models that leverages genomic context to create de novo genes and systems with desired functions. 🧵
www.nature.com/articles/s41...
Today in @Nature, we share semantic design—a strategy for function-guided design with genomic language models that leverages genomic context to create de novo genes and systems with desired functions. 🧵
www.nature.com/articles/s41...
November 19, 2025 at 4:31 PM
What if we could autocomplete DNA based on function?
Today in @Nature, we share semantic design—a strategy for function-guided design with genomic language models that leverages genomic context to create de novo genes and systems with desired functions. 🧵
www.nature.com/articles/s41...
Today in @Nature, we share semantic design—a strategy for function-guided design with genomic language models that leverages genomic context to create de novo genes and systems with desired functions. 🧵
www.nature.com/articles/s41...
Today in @nature.com, in work led by @adititm.bsky.social, we report the ability to prompt Evo to generate functional de novo genes.
You shall know a gene by the company it keeps!
You shall know a gene by the company it keeps!
November 19, 2025 at 4:24 PM
Today in @nature.com, in work led by @adititm.bsky.social, we report the ability to prompt Evo to generate functional de novo genes.
You shall know a gene by the company it keeps!
You shall know a gene by the company it keeps!
Reposted by Brian Hie
Combine multimer structure prediction and an antibody language model to design de novo antibodies with nanomolar binding affinity.
@synbiogaolab.bsky.social @brianhie.bsky.social
www.biorxiv.org/content/10.1...
@synbiogaolab.bsky.social @brianhie.bsky.social
www.biorxiv.org/content/10.1...
September 25, 2025 at 8:02 PM
Combine multimer structure prediction and an antibody language model to design de novo antibodies with nanomolar binding affinity.
@synbiogaolab.bsky.social @brianhie.bsky.social
www.biorxiv.org/content/10.1...
@synbiogaolab.bsky.social @brianhie.bsky.social
www.biorxiv.org/content/10.1...
Reposted by Brian Hie
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.
September 24, 2025 at 4:32 PM
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.
Reposted by Brian Hie
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.
Reposted by Brian Hie
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...
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...
www.biorxiv.org
September 17, 2025 at 5:37 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Brian Hie
Genome language models can generate new, high-fitness bacteriophages!
@samuelhking.bsky.social @claudiadriscoll.bsky.social
@david-li.bsky.social @danguo.bsky.social @adititm.bsky.social Garyk Brixi @maxewilkinson.bsky.social @brianhie.bsky.social
www.biorxiv.org/content/10.1...
@samuelhking.bsky.social @claudiadriscoll.bsky.social
@david-li.bsky.social @danguo.bsky.social @adititm.bsky.social Garyk Brixi @maxewilkinson.bsky.social @brianhie.bsky.social
www.biorxiv.org/content/10.1...
September 17, 2025 at 9:15 PM
Genome language models can generate new, high-fitness bacteriophages!
@samuelhking.bsky.social @claudiadriscoll.bsky.social
@david-li.bsky.social @danguo.bsky.social @adititm.bsky.social Garyk Brixi @maxewilkinson.bsky.social @brianhie.bsky.social
www.biorxiv.org/content/10.1...
@samuelhking.bsky.social @claudiadriscoll.bsky.social
@david-li.bsky.social @danguo.bsky.social @adititm.bsky.social Garyk Brixi @maxewilkinson.bsky.social @brianhie.bsky.social
www.biorxiv.org/content/10.1...
Reposted by Brian Hie
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 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...
www.biorxiv.org
September 17, 2025 at 6:16 PM
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 www.biorxiv.org/content/10.1...
Reposted by Brian Hie
In a new preprint from @brianhie.bsky.social's lab, the team reports the first generative design of viable bacteriophage genomes.
Leveraging Evo 1 & Evo 2, they generated whole genome sequences, resulting in 16 viable phages with distinct genomic architectures.
Leveraging Evo 1 & Evo 2, they generated whole genome sequences, resulting in 16 viable phages with distinct genomic architectures.
September 17, 2025 at 3:12 PM
In a new preprint from @brianhie.bsky.social's lab, the team reports the first generative design of viable bacteriophage genomes.
Leveraging Evo 1 & Evo 2, they generated whole genome sequences, resulting in 16 viable phages with distinct genomic architectures.
Leveraging Evo 1 & Evo 2, they generated whole genome sequences, resulting in 16 viable phages with distinct genomic architectures.
Reposted by Brian Hie
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 🧵
Today, we share our preprint “Generative design of novel bacteriophages with genome language models”, where we validate the first, functional AI-generated genomes 🧵
September 17, 2025 at 3:03 PM
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 🧵
Today, we share our preprint “Generative design of novel bacteriophages with genome language models”, where we validate the first, functional AI-generated genomes 🧵
Reposted by Brian Hie
#AI is transforming #biology, enabling rapid innovation — but with progress comes risk.
A new National Academies report examines how AI-driven biological tools could impact #biosecurity, from potential misuse to their role in risk mitigation.
Read: buff.ly/2unawE4
A new National Academies report examines how AI-driven biological tools could impact #biosecurity, from potential misuse to their role in risk mitigation.
Read: buff.ly/2unawE4
March 14, 2025 at 4:01 PM
#AI is transforming #biology, enabling rapid innovation — but with progress comes risk.
A new National Academies report examines how AI-driven biological tools could impact #biosecurity, from potential misuse to their role in risk mitigation.
Read: buff.ly/2unawE4
A new National Academies report examines how AI-driven biological tools could impact #biosecurity, from potential misuse to their role in risk mitigation.
Read: buff.ly/2unawE4
Reposted by Brian Hie
Video is up!
"Genome modeling and design across all domains of life with Evo 2" youtu.be/Rarn97Wpl1A
With the author Garyk Brixi!
"Genome modeling and design across all domains of life with Evo 2" youtu.be/Rarn97Wpl1A
With the author Garyk Brixi!
Genome modeling and design across all domains of life with Evo 2 | Garyk Brixi
YouTube video by Valence Labs
youtu.be
March 13, 2025 at 11:55 PM
Video is up!
"Genome modeling and design across all domains of life with Evo 2" youtu.be/Rarn97Wpl1A
With the author Garyk Brixi!
"Genome modeling and design across all domains of life with Evo 2" youtu.be/Rarn97Wpl1A
With the author Garyk Brixi!
Reposted by Brian Hie
Evo2: a fully open genome language model that can predict the functional effects of variation and generate large genomic segments
@garykbrixi.bsky.social @matthewdurrant.com @michaelpoli.bsky.social @genophoria.bsky.social @pdhsu.bsky.social @brianhie.bsky.social
www.biorxiv.org/content/10.1...
@garykbrixi.bsky.social @matthewdurrant.com @michaelpoli.bsky.social @genophoria.bsky.social @pdhsu.bsky.social @brianhie.bsky.social
www.biorxiv.org/content/10.1...
February 27, 2025 at 10:11 PM
Evo2: a fully open genome language model that can predict the functional effects of variation and generate large genomic segments
@garykbrixi.bsky.social @matthewdurrant.com @michaelpoli.bsky.social @genophoria.bsky.social @pdhsu.bsky.social @brianhie.bsky.social
www.biorxiv.org/content/10.1...
@garykbrixi.bsky.social @matthewdurrant.com @michaelpoli.bsky.social @genophoria.bsky.social @pdhsu.bsky.social @brianhie.bsky.social
www.biorxiv.org/content/10.1...
Reposted by Brian Hie
All-atom fixed backbone protein sequence design with FAMPNN
@richardshuai.bsky.social Talal Widatalla @possuhuanglab.bsky.social @brianhie.bsky.social
www.biorxiv.org/content/10.1...
@richardshuai.bsky.social Talal Widatalla @possuhuanglab.bsky.social @brianhie.bsky.social
www.biorxiv.org/content/10.1...
February 21, 2025 at 10:37 PM
All-atom fixed backbone protein sequence design with FAMPNN
@richardshuai.bsky.social Talal Widatalla @possuhuanglab.bsky.social @brianhie.bsky.social
www.biorxiv.org/content/10.1...
@richardshuai.bsky.social Talal Widatalla @possuhuanglab.bsky.social @brianhie.bsky.social
www.biorxiv.org/content/10.1...
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.
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.
February 19, 2025 at 4:42 PM
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.
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.
Reposted by Brian Hie
Brian Hie harnessed the powerful parallels between DNA and human language to create an AI tool that interprets genomes. Read his conversation with Ingrid Wickelgren: www.quantamagazine.org/the-poetry-f...
The Poetry Fan Who Taught an LLM to Read and Write DNA | Quanta Magazine
By treating DNA as a language, Brian Hie’s “ChatGPT for genomes” could pick up patterns that humans can’t see, accelerating biological design.
www.quantamagazine.org
February 5, 2025 at 4:00 PM
Brian Hie harnessed the powerful parallels between DNA and human language to create an AI tool that interprets genomes. Read his conversation with Ingrid Wickelgren: www.quantamagazine.org/the-poetry-f...
Reposted by Brian Hie
The 2024 Good Tech Awards, spotlighted by @kevinroose.com for #AI/Science
nytimes.com/2024/12/30/t...
congrats!
@arcinstitute.org @brianhie.bsky.social @patrickhsuu.bsky.social @jameszou.bsky.social and the others for well deserved recognition
nytimes.com/2024/12/30/t...
congrats!
@arcinstitute.org @brianhie.bsky.social @patrickhsuu.bsky.social @jameszou.bsky.social and the others for well deserved recognition
January 1, 2025 at 5:55 PM
The 2024 Good Tech Awards, spotlighted by @kevinroose.com for #AI/Science
nytimes.com/2024/12/30/t...
congrats!
@arcinstitute.org @brianhie.bsky.social @patrickhsuu.bsky.social @jameszou.bsky.social and the others for well deserved recognition
nytimes.com/2024/12/30/t...
congrats!
@arcinstitute.org @brianhie.bsky.social @patrickhsuu.bsky.social @jameszou.bsky.social and the others for well deserved recognition
Reposted by Brian Hie
#YearInReview An AI-based method to develop better antibody medicines faster: https://buff.ly/3P74SCo
@brianhie.bsky.social
@brianhie.bsky.social
December 24, 2024 at 6:00 PM
#YearInReview An AI-based method to develop better antibody medicines faster: https://buff.ly/3P74SCo
@brianhie.bsky.social
@brianhie.bsky.social
Reposted by Brian Hie
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
December 22, 2024 at 7:23 PM
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
Reposted by Brian Hie
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
December 19, 2024 at 6:54 PM
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
Reposted by Brian Hie
A protein's position in the genome in relation to other genes is informative about function, so a genomic language model can be prompted to generate
- toxin/antitoxin pairs
- anti-CRISPR proteins
+ a database of 120B synthetic base pairs
www.biorxiv.org/content/10.1...
@brianhie.bsky.social
- toxin/antitoxin pairs
- anti-CRISPR proteins
+ a database of 120B synthetic base pairs
www.biorxiv.org/content/10.1...
@brianhie.bsky.social
December 18, 2024 at 10:14 PM
A protein's position in the genome in relation to other genes is informative about function, so a genomic language model can be prompted to generate
- toxin/antitoxin pairs
- anti-CRISPR proteins
+ a database of 120B synthetic base pairs
www.biorxiv.org/content/10.1...
@brianhie.bsky.social
- toxin/antitoxin pairs
- anti-CRISPR proteins
+ a database of 120B synthetic base pairs
www.biorxiv.org/content/10.1...
@brianhie.bsky.social