Savage Lab
@savagecatsonly.bsky.social
Compartmentalizing your metabolism, and y’know, CRISPR stuff. Account managed by grad students and postdocs 🤙
@ucberkeleyofficial.bsky.social @innovativegenomics.bsky.social @hhmi.bsky.social
savagelab.org
@ucberkeleyofficial.bsky.social @innovativegenomics.bsky.social @hhmi.bsky.social
savagelab.org
Pinned
Guide your favorite protein generative model with experimental data? Meet ProteinGuide - a method to condition pre-trained models on properties without retraining. We validated it both in silico by guiding ProteinMPNN and ESM3 on 3 tasks and in vitro by engineering base editors.
We love generating data! But what should we do with it? We collaborated w/ the Listgarten lab on ProteinGuide - a new method for using experimental data to guide protein generative models. Congrats to @junhaobearxiong.bsky.social, @hnisonoff.bsky.social, @marialukarska.bsky.social, Ishan, & Luke! ⬇️
Congrats to our savage lab undergrads on their research and presentations in our inaugural undergrad research symposium 🎉🥳
August 5, 2025 at 8:56 PM
Congrats to our savage lab undergrads on their research and presentations in our inaugural undergrad research symposium 🎉🥳
Reposted by Savage Lab
‼️ New pre-print from co-leads @owentuck.bsky.social and Jason Hu! Check out this fascinating example of how coevolution enables defense system innovation.
Excited to finally share this work!
We noticed a pair of genes - a nuclease and a protease - shuffles between antiviral systems. We show how proteolysis activates the nuclease, triggering defense in known and unknown immune contexts.
tinyurl.com/2uwwy4ty
We noticed a pair of genes - a nuclease and a protease - shuffles between antiviral systems. We show how proteolysis activates the nuclease, triggering defense in known and unknown immune contexts.
tinyurl.com/2uwwy4ty
Recurrent acquisition of nuclease-protease pairs in antiviral immunity
Antiviral immune systems diversify by integrating new genes into existing pathways, creating new mechanisms of viral resistance. We identified genes encoding a predicted nuclease paired with a trypsin...
tinyurl.com
July 29, 2025 at 9:18 PM
‼️ New pre-print from co-leads @owentuck.bsky.social and Jason Hu! Check out this fascinating example of how coevolution enables defense system innovation.
We love generating data! But what should we do with it? We collaborated w/ the Listgarten lab on ProteinGuide - a new method for using experimental data to guide protein generative models. Congrats to @junhaobearxiong.bsky.social, @hnisonoff.bsky.social, @marialukarska.bsky.social, Ishan, & Luke! ⬇️
Guide your favorite protein generative model with experimental data? Meet ProteinGuide - a method to condition pre-trained models on properties without retraining. We validated it both in silico by guiding ProteinMPNN and ESM3 on 3 tasks and in vitro by engineering base editors.
June 1, 2025 at 10:41 AM
We love generating data! But what should we do with it? We collaborated w/ the Listgarten lab on ProteinGuide - a new method for using experimental data to guide protein generative models. Congrats to @junhaobearxiong.bsky.social, @hnisonoff.bsky.social, @marialukarska.bsky.social, Ishan, & Luke! ⬇️
Reposted by Savage Lab
Excited to share our new preprint on mutational scanning of the TnpB RNP! We identify several highly activating, single-position mutations in TnpB’s protein and reRNA. These datasets enabled us to engineer enhanced TnpB protein variants (>50x plant editing levels compared to WT).
What's better than 1 deep mutational scanning (DMS) library? 2! In a new pre-print @brittneywthornton.bsky.social and @rfw.bsky.social et al. map the mutational landscape of ISDra2 TnpB protein and reRNA and leverage these datasets to engineer highly active variants (1/9)
March 4, 2025 at 3:12 AM
Excited to share our new preprint on mutational scanning of the TnpB RNP! We identify several highly activating, single-position mutations in TnpB’s protein and reRNA. These datasets enabled us to engineer enhanced TnpB protein variants (>50x plant editing levels compared to WT).
Reposted by Savage Lab
It is finally out!
Muntathar Al-Shimary, @doudna-lab.bsky.social , @cresslab.bsky.social and I present a gene knockdown tool that works in diverse bacteriophages: CRISPRi through antisense RNA Targeting (CRISPRi-ART)!
Check it out @naturemicrobiol.bsky.social
www.nature.com/articles/s41...
Muntathar Al-Shimary, @doudna-lab.bsky.social , @cresslab.bsky.social and I present a gene knockdown tool that works in diverse bacteriophages: CRISPRi through antisense RNA Targeting (CRISPRi-ART)!
Check it out @naturemicrobiol.bsky.social
www.nature.com/articles/s41...
CRISPRi-ART enables functional genomics of diverse bacteriophages using RNA-binding dCas13d - Nature Microbiology
Leveraging RNA-targeting dCas13d enables selective interference with phage protein translation and facilitates measurement of phage gene fitness at a transcriptome-wide scale.
www.nature.com
February 26, 2025 at 4:43 PM
It is finally out!
Muntathar Al-Shimary, @doudna-lab.bsky.social , @cresslab.bsky.social and I present a gene knockdown tool that works in diverse bacteriophages: CRISPRi through antisense RNA Targeting (CRISPRi-ART)!
Check it out @naturemicrobiol.bsky.social
www.nature.com/articles/s41...
Muntathar Al-Shimary, @doudna-lab.bsky.social , @cresslab.bsky.social and I present a gene knockdown tool that works in diverse bacteriophages: CRISPRi through antisense RNA Targeting (CRISPRi-ART)!
Check it out @naturemicrobiol.bsky.social
www.nature.com/articles/s41...
What's better than 1 deep mutational scanning (DMS) library? 2! In a new pre-print @brittneywthornton.bsky.social and @rfw.bsky.social et al. map the mutational landscape of ISDra2 TnpB protein and reRNA and leverage these datasets to engineer highly active variants (1/9)
February 26, 2025 at 6:44 PM
What's better than 1 deep mutational scanning (DMS) library? 2! In a new pre-print @brittneywthornton.bsky.social and @rfw.bsky.social et al. map the mutational landscape of ISDra2 TnpB protein and reRNA and leverage these datasets to engineer highly active variants (1/9)
Reposted by Savage Lab
New research from IGI Investigator Dave Savage @savagecatsonly.bsky.social and first author Noam Prywes @prywes.bsky.social (pictured) details the landscape of possible Rubisco variants, suggesting ways to make the world's most abundant enzyme better at its job. 🌱🧪🧬
Read more: ow.ly/t2JO50ULh10
Read more: ow.ly/t2JO50ULh10
February 7, 2025 at 12:38 AM
New research from IGI Investigator Dave Savage @savagecatsonly.bsky.social and first author Noam Prywes @prywes.bsky.social (pictured) details the landscape of possible Rubisco variants, suggesting ways to make the world's most abundant enzyme better at its job. 🌱🧪🧬
Read more: ow.ly/t2JO50ULh10
Read more: ow.ly/t2JO50ULh10
What limits rubisco function? Is it the chemical mechanism? Evolution? In this paper, @prywes.bsky.social et. al explore this question by assaying >99% of single amino acid mutants in Form II rubisco (1/7) doi.org/10.1038/s415...
January 24, 2025 at 8:27 PM
What limits rubisco function? Is it the chemical mechanism? Evolution? In this paper, @prywes.bsky.social et. al explore this question by assaying >99% of single amino acid mutants in Form II rubisco (1/7) doi.org/10.1038/s415...
Reposted by Savage Lab
New research from IGI Investigator Dave Savage and first author Noam Prywes details the landscape of possible Rubisco variants, suggesting ways to make the world's most abundant enzyme better at its job. 🌱
Read more: ow.ly/t2JO50ULh10
Read more: ow.ly/t2JO50ULh10
January 22, 2025 at 6:08 PM
New research from IGI Investigator Dave Savage and first author Noam Prywes details the landscape of possible Rubisco variants, suggesting ways to make the world's most abundant enzyme better at its job. 🌱
Read more: ow.ly/t2JO50ULh10
Read more: ow.ly/t2JO50ULh10