The paper evaluates efficiency and off-target effects of high-fidelity Cas9 variants with different sgRNAs and develops a computational framework to predict their performance.

Nucleic Acids Research · Aug 14, 2023Peer-reviewedSystems Biology

Systematic decomposition of sequence determinants governing CRISPR/Cas9 specificity

Rongjie Fu, Wei He, Jinzhuang Dou, Oscar David Villarreal, Ella Bedford, Helen H. Wang, Connie Hou, Liang Zhang, Yalong Wang, Dacheng Ma, Yiwen Chen, Xue Gao, Martin Depken, Han Xu

This study systematically identifies sequence determinants of CRISPR/Cas9 specificity by analyzing off-target effects of 1,902 gRNAs on 13,314 targets, revealing three key factors and developing a predictive tool.

Nature Communications · Jan 25, 2022Peer-reviewedSystems Biology

De novo Identification of Essential Protein Domains from CRISPR/Cas9 Tiling-sgRNA Knockout Screens

Wei He, Liang Zhang, Oscar David Villarreal, Rongjie Fu, Ella Bedford, Jingzhuang Dou, Anish Y. Patel, Mark T. Bedford, Xiaobing Shi, Taiping Chen, Blaine Bartholomew, Han Xu

The paper introduces ProTiler, a method to identify essential protein domains from CRISPR/Cas9 tiling-sgRNA screens, finding 175 CKHS regions with high overlap to annotated domains and novel unannotated domains.

Nature Communications · Oct 4, 2019Peer-reviewedBioinformatics