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Savage Lab

@savagecatsonly.bsky.social
400 followers 215 following 35 posts

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

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Reposted by Savage Lab
UC Berkeley MCB @berkeleymcb.bsky.social · 17/09/2026
Exciting research from the labs of MCB’s David Savage @savagecatsonly.bsky.social and Christina Listgarten, featuring MCB postdoc Maria Lukarska @marialukarska.bsky.social! 🧬🔬
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Reposted by Savage Lab
Zehan Zhou @zehanzhou.bsky.social · 05/08/2026
We are PUBLISHED!!! Our mechanistic work on how CRISPR-Cas ancestors unwind DNA and how this can be used to engineer hypercompact plant editors can now be found on Mol Cell- if you are interested in what defines a good genome editor, this read is for you 😎 🔗 www.sciencedirect.com/science/arti...
sciencedirect.com
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Reposted by Savage Lab
marialukarska.bsky.social @marialukarska.bsky.social · 30/07/2026
Our ProteinGuide paper is finally out! Thanks to all the co-authors @junhaobearxiong.bsky.social, @ishangaur.bsky.social, @hnisonoff.bsky.social, @loltrogge.bsky.social, @jlistgarten.bsky.social, @savagecatsonly.bsky.social! @innovativegenomics.bsky.social www.nature.com/articles/s41...
nature.com
Property guidance for protein sequence generative models with ProteinGuide - Nature Biotechnology
On-the-fly conditioning of pretrained protein generative models guides protein generation toward specific properties.
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Reposted by Savage Lab
Nature Biotechnology @natbiotech.nature.com · 29/07/2026
Property guidance for protein sequence generative models with ProteinGuide - @jlistgarten.bsky.social @savagecatsonly.bsky.social www.nature.com/articles/s41...
nature.com
Property guidance for protein sequence generative models with ProteinGuide - Nature Biotechnology
On-the-fly conditioning of pretrained protein generative models guides protein generation toward specific properties.
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Savage Lab @savagecatsonly.bsky.social · 25/07/2026
Check out our new preprint on base editors and the thread below!
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Reposted by Savage Lab
marialukarska.bsky.social @marialukarska.bsky.social · 24/07/2026
I’m happy to share our pre-print exploring the activity and specificity trade-offs in adenine base editors. Thanks to my amazing co-authors Luke Oltrogge, @hnisonoff.bsky.social, and all the other contributors @jlistgarten.bsky.social @savagecatsonly.bsky.social @innovativegenomics.bsky.social 🧵1/7
biorxiv.org
Activity and specificity trade-offs in adenine base editors
Adenine base editors (ABEs) are CRISPR effectors that introduce A-T to G-C transitions in the genome using a nucleotide deaminase fused to a Cas protein. ABEs have been evolved to have very high editi...
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Reposted by Savage Lab
Innovative Genomics Institute @innovativegenomics.bsky.social · 08/04/2026
New preprint from Dave Savage (Savage Lab) and Yun S. Song: Deep models of protein evolution in time generate realistic evolutionary trajectories and functional proteins. Read here: ow.ly/iJk950YCF8q #AI #AIresearch
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Savage Lab @savagecatsonly.bsky.social · 31/03/2026
Can CRISPR edits enable precise tuning of plant gene expression? We think: yes. In our newest manuscript, we measured the effects of >30,000 CRISPR-like promoter mutations in sorghum protoplasts.
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Reposted by Savage Lab
Nature Biotechnology @natbiotech.nature.com · 27/03/2026
Mapping cis-regulatory mutations at scale in sorghum enables modulation of gene expression - @savagecatsonly.bsky.social go.nature.com/3O7mDEN
go.nature.com
Mapping cis-regulatory mutations at scale in sorghum enables modulation of gene expression - Nature Biotechnology
Variant mapping of sorghum promoters identifies CRISPR-accessible mutations that upregulate gene expression.
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Reposted by Savage Lab
Nature Biotechnology @natbiotech.nature.com · 11/03/2026
Engineered TnpB genome editors for plants and human cells identified by ribonucleoprotein mutational scanning - @savagecatsonly.bsky.social go.nature.com/4loaOGn
go.nature.com
Engineered TnpB genome editors for plants and human cells identified by ribonucleoprotein mutational scanning - Nature Biotechnology
TnpB endonucleases are engineered for improved genome editing.
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Reposted by Savage Lab
Zehan Zhou @zehanzhou.bsky.social · 15/01/2026
How do the ancestors of CRISPR-Cas unwind DNA and how can this lead to better genome editing? With our collaboration between @doudna-lab.bsky.social x @jacobsenucla.bsky.social x Zev Bryant's lab x @savagecatsonly.bsky.social we've uncovered the secrets behind TnpB's dynamics!
biorxiv.org
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Savage Lab @savagecatsonly.bsky.social · 22/12/2025
New from Ugrappa Nagalakshmi and Jorge Rodriguez 🌱✂️– Gene editing in plants just got a lot easier! Using engineered TnpB, they demonstrate high-efficiency, heritable, transgene-free editing in plants. (1/7)
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Savage Lab @savagecatsonly.bsky.social · 05/08/2025
Congrats to our savage lab undergrads on their research and presentations in our inaugural undergrad research symposium 🎉🥳
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Reposted by Savage Lab
Doudna Lab @doudna-lab.bsky.social · 29/07/2025
‼️ New pre-print from co-leads @owentuck.bsky.social and Jason Hu! Check out this fascinating example of how coevolution enables defense system innovation.
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Savage Lab @savagecatsonly.bsky.social · 01/06/2025
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! ⬇️
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Reposted by Savage Lab
brittneywthornton.bsky.social @brittneywthornton.bsky.social · 04/03/2025
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).
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Reposted by Savage Lab
Ben Adler @benadler.bsky.social · 26/02/2025
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...
nature.com
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.
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Savage Lab @savagecatsonly.bsky.social · 26/02/2025
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)
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Reposted by Savage Lab
Innovative Genomics Institute @innovativegenomics.bsky.social · 07/02/2025
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
Photo of Noam Prywes standing in from of bamboo plants
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Savage Lab @savagecatsonly.bsky.social · 24/01/2025
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...
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Reposted by Savage Lab
Innovative Genomics Institute @innovativegenomics.bsky.social · 22/01/2025
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
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