Peter H. Yoon

Prokaryotic homologs of the major vault protein form engineerable vault nanocapsules

The paper identifies prokaryotic homologs of the major vault protein that assemble into vault nanocapsules, revealing structural and size variability.

Competition among viral elements for VIPR RNA-directed genome silencing

The paper shows that VIPR systems in E. coli mediate competition between phages and their satellite counterparts, with satellites using decoy RNAs to counteract repression.

Autonomous AI agents discover reverse transcriptases with tandem repeat arrays

The paper uses large language models to discover a novel family of reverse transcriptases with tandem repeat arrays from metagenomic data.

tRNA-derived second messengers confer bacterial immunity

The paper identifies a bacterial immune pathway where tRNA cleavage generates second messengers that trigger cell death via RNA-guided nuclease activity.

Stepwise DNA unwinding gates TnpB genome-editing activity

Ymu1 TnpB unwinds DNA via a long-lived partially unwound intermediate before a rarely stable open state; the WFR triple variant stabilizes both, boosting plant editing.

Structure and evolution-guided design of minimal RNA-guided nucleases

The paper designs active RNA-guided nucleases using AI and structure-guided methods, validated by cryo-EM and functional testing across species.

A Noncontiguous Code for RNA-Guided DNA Recognition Preceded CRISPR

The paper identifies VIPR systems, which use noncontiguous RNA codes for DNA recognition, suggesting an ancient origin of adaptive immunity through viral interactions.

Triplex formation drives noncontiguous VIPR RNA-guided DNA recognition

The paper reveals the structural mechanism of VIPR RNA-guided DNA recognition through triplex formation, showing how noncontiguous RNA sequences direct DNA targeting.

Recurrent acquisition of nuclease-protease pairs in antiviral immunity

The paper identifies recurrent acquisition of nuclease-protease pairs in bacterial antiviral immunity and shows their proteolytic activation mechanism across different immune systems.

A miniature CRISPR-Cas10 enzyme confers immunity by an inverse signaling pathway

The paper shows that the CRISPR-related enzyme mCpol produces cyclic oligonucleotides to prevent cell death and counteract viral immune evasion.

Functional protein mining with conformal guarantees

This paper introduces a method for functional protein mining with statistical guarantees, improving reliability in homology detection and functional annotation.

RNA language models predict mutations that improve RNA function

The paper develops an RNA language model to predict mutations that enhance RNA thermostability using a new database of RNA sequences linked to environmental temperatures.

Rapid DNA unwinding accelerates genome editing by engineered CRISPR-Cas9

The paper shows that engineered GeoCas9 variants enhance genome editing by accelerating DNA unwinding, revealing a new role for the WED domain in this process.

Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes

The paper traces the evolutionary origin of eukaryotic RNA-guided endonucleases, showing they evolved from a specific clade of bacterial IS607 TnpB enzymes.