Chin Wee Tan

This study develops a subcutaneous tumor model that naturally forms tertiary lymphoid structures (TLS) and identifies CXCL9 as a key regulator of TLS formation and function.

bgnorm improves signal separation and marker positivity classification in multiplex spatial proteomics by addressing technical variation through background correction, normalization, and quality control.

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

IdentifiHR predicts homologous recombination deficiency in high-grade serous ovarian carcinoma using gene expression, achieving 85% accuracy in TCGA and 91% in an independent cohort.

The paper introduces SM3DD, a 3D spatial transcriptomics analysis method, and finds differences in transcript distances between normal and SARS-CoV-2 patient lung tissues.

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.

The paper identifies transcriptional modules and cytokine signaling pathways that drive functional heterogeneity in T follicular helper cells across different infections.

PRISM is a Python package for interactive analysis of multiplexed tissue microarrays, enabling translational and clinical research using spatial proteomic data from multiple platforms.

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.

vissE identifies and visualizes higher-order molecular phenotypes from functional enrichment analysis by summarizing redundancies into biological themes.

standR is a Bioconductor package that improves the analysis of Nanostring GeoMx DSP spatial transcriptomic data by addressing technical variability and enhancing statistical power.