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...

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...

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...

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.

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 🧵

#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

Video is up! "Genome modeling and design across all domains of life with Evo 2" youtu.be/Rarn97Wpl1A With the author Garyk Brixi!

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...

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...

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.

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 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

#YearInReview An AI-based method to develop better antibody medicines faster: https://buff.ly/3P74SCo @brianhie.bsky.social

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

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

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

We have found and fixed a bug in the code for Evo model inference affecting package versions from Nov 15-Dec 16, 2024, which has been corrected in the latest release. If you installed the package during this timeframe, please upgrade to correct the issue.

Real genotype-to-phenotype is now much closer in this beautiful work on a genomic foundation model from @brianhie.bsky.social. www.science.org/doi/10.1126/...

The Evo model made the cover of Science this month 🧬🖥️🧪 Perspective: Learning the language of DNA www.science.org/doi/10.1126/... Research paper: Sequence modeling and design from molecular to genome scale with Evo www.science.org/doi/10.1126/... Code (Apache) github.com/evo-design/e...

Really cool model from Brian Hie and Patrick Hsu! www.science.org/doi/10.1126/...

Evo: A genomic language model of prokaryote genomes generates functional cas9 proteins and transposons. @brianhiestand.bsky.social www.science.org/doi/10.1126/...

New at Science Evo, a large language of life (LLLM) genomic foundation model, predicting & generating tasks from molecular to genomic scale science.org/doi/10.1126/...

Thrilled to see this published! Lots of progress since our preprint, including experimental validation of Evo-generated Cas9 and IS200/IS605 transposases. I am definitely a true believer when it comes to DNA language models, they have quickly become central to my discovery efforts. bit.ly/3OsmUPr

A weirdly effective way to make better antibodies even ones that have already been optimized: