Honglue Shi

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.

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

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

The paper improves a virus-mediated genome editing method in plants by using multiple gRNAs and an enhanced TnpB variant for efficient multiplexed editing.

The paper identifies CRISPR-Cas12a variants with expanded PAM recognition, enabling targeting of ~25% of the human genome.

This study identifies a trade-off between PAM recognition breadth and CRISPR-Cas9 editing efficiency, proposing a two-step target capture mechanism to improve genome editing.

This paper engineers a plant virus to deliver a compact CRISPR-Cas system for transgene-free germline editing in Arabidopsis.

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.

The paper shows CRISPR-Cas12a bends DNA to destabilize base pairs during target recognition, similar to CRISPR-Cas9 but with different hybridization directionality.

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