John Paul Shen

This study identifies KDM5D on the Y chromosome as a suppressor of CD8+ T cell antitumor immunity in males, linking it to TCR and cholesterol-exhaustion programs.

This study evaluates KRAS inhibitors in appendiceal adenocarcinoma models and patients, showing efficacy in reducing tumor growth and suggesting potential resistance mechanisms.

This study shows BET + MAPK inhibitors improve efficacy against BRAFV600E CRC by inducing epigenetic reprogramming and cellular plasticity through enhancer dynamics disruption.

DKOsim generates synthetic double knockout CRISPR data to simulate genetic interactions and optimize library design for growth-based screens.

The paper identifies adaptive plasticity tumor (APT) cells that reduce response to MAPK inhibitors in colorectal cancer by increasing stemness and ASCL2 expression, and shows that targeting APT cells improves therapy efficacy.

The paper develops CliPP to estimate subclonal mutation load (sML) and shows it predicts survival and immunotherapy response in cancers with low to moderate TMB.

DeMixSC improves deconvolution accuracy by using single-cell RNA-seq and a benchmark dataset to account for technological discrepancies in complex tissue samples.

The paper quantifies tumor-specific total mRNA expression from bulk data and shows its association with clinical outcomes across 15 cancer types.

The paper examines the expression of ACE2 and TMPRSS2 in single-cell RNA sequencing datasets from different parts of the gastrointestinal tract to assess SARS-CoV-2 entry potential in enterocytes.