Han Xu

Acquired resistance to the PRMT5 inhibitor confers collateral sensitivity to MEK inhibition in MTAP-null non-small cell lung cancer

The paper identifies collateral sensitivity to MEK inhibition in MTAP-null NSCLC cells that develop resistance to PRMT5 inhibitors.

NF2 loss malignantly transforms human pancreatic acinar cells and enhances cell fitness under environmental stress

This study identifies NF2 as a critical tumor suppressor in PDAC, showing its role in promoting invasive behavior, enhancing cell fitness under stress, and contributing to drug resistance.

Mechanistic Insights into Proteomic Mutation-Phenotype Linkages from Tiling Mutagenesis Screens

The paper introduces ProTiler-Mut, a framework for analyzing tiling mutagenesis screens to uncover mutation-phenotype linkages, revealing new insights into functional mutation categories and protein interactions.

Guide-specific loss of efficiency and off-target reduction with Cas9 variants

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.

Systematic decomposition of sequence determinants governing CRISPR/Cas9 specificity

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.

GuidePro: A multi-source ensemble predictor for prioritizing sgRNAs in CRISPR/Cas9 protein knockouts

GuidePro integrates multiple predictive methods to prioritize sgRNAs for CRISPR/Cas9 protein knockouts, showing consistent performance across datasets.

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

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.

Computational correction of copy-number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells

The paper develops CERES, a computational method to correct copy-number effects in CRISPR-Cas9 essentiality screens, improving specificity in cancer cell line studies.

Integrative analysis and refined design of CRISPR knockout screens

The paper introduces MAGeCK-NEST, a method to improve CRISPR screen analysis by integrating PPI data and refining sgRNA design, leading to better hit calling and library design.