Jinjin Chen

This study identifies dysregulated epithelial cell death signaling in inflammatory bowel disease, showing it persists during remission despite therapy.

hoodscanR identifies and analyzes cell neighborhoods in spatial transcriptomics data, revealing transcriptional differences in tumor cells across neighborhoods.

The paper introduces smartid, a method for accurately detecting markers in rare cell populations using a modified TF-IDF approach with Gaussian Mixture Model, improving cell type annotation in single-cell RNA-seq data.

mastR identifies markers from bulk RNA-seq data using a permutation test and signal-to-noise ratio approach, outperforming existing methods in benchmark tests.

This paper shows that temporarily blocking type I interferon during viral infection boosts CD8+ T cell memory and vaccine effectiveness by promoting TSCM cell formation.

This study shows that library size in spatial transcriptomics data confounds biological signals and recommends against normalizing it unless necessary.