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Scribe, Intellia Cut Jobs, Pivot Their Pipelines.
Hum Gene Ther
January 2025
Genetic Engineering & Biotechnology News, Mary Ann Liebert, Inc., Publishers, New Rochelle, New York, USA.
Mechanism-guided engineering of a minimal biological particle for genome editing.
Proc Natl Acad Sci U S A
January 2025
Innovative Genomics Institute, University of California, Berkeley, CA 94720.
The widespread application of genome editing to treat and cure disease requires the delivery of genome editors into the nucleus of target cells. Enveloped delivery vehicles (EDVs) are engineered virally derived particles capable of packaging and delivering CRISPR-Cas9 ribonucleoproteins (RNPs). However, the presence of lentiviral genome encapsulation and replication proteins in EDVs has obscured the underlying delivery mechanism and precluded particle optimization.
View Article and Find Full Text PDFFunctional protein mining with conformal guarantees.
Nat Commun
January 2025
Innovative Genomics Institute; University of California, Berkeley, CA, USA.
Molecular structure prediction and homology detection offer promising paths to discovering protein function and evolutionary relationships. However, current approaches lack statistical reliability assurances, limiting their practical utility for selecting proteins for further experimental and in-silico characterization. To address this challenge, we introduce a statistically principled approach to protein search leveraging principles from conformal prediction, offering a framework that ensures statistical guarantees with user-specified risk and provides calibrated probabilities (rather than raw ML scores) for any protein search model.
View Article and Find Full Text PDFRNA language models predict mutations that improve RNA function.
Nat Commun
December 2024
Innovative Genomics Institute, University of California, Berkeley, CA, USA.
Structured RNA lies at the heart of many central biological processes, from gene expression to catalysis. RNA structure prediction is not yet possible due to a lack of high-quality reference data associated with organismal phenotypes that could inform RNA function. We present GARNET (Gtdb Acquired RNa with Environmental Temperatures), a new database for RNA structural and functional analysis anchored to the Genome Taxonomy Database (GTDB).
View Article and Find Full Text PDFPackaged delivery of CRISPR-Cas9 ribonucleoproteins accelerates genome editing.
bioRxiv
October 2024
Department of Chemistry, University of California, Berkeley, California 94720, USA.
Effective genome editing requires a sufficient dose of CRISPR-Cas9 ribonucleoproteins (RNPs) to enter the target cell while minimizing immune responses, off-target editing and cytotoxicity. Clinical use of Cas9 RNPs currently entails electroporation into cells , but no systematic comparison of this method to packaged RNP delivery has been made. Here we compared two delivery strategies, electroporation and enveloped delivery vehicles (EDVs), to investigate the Cas9 dosage requirements for genome editing.
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