Xi Chen

GIP identifies disease-associated signaling pathways by integrating gene networks and was applied to breast cancer data, revealing biologically meaningful pathway modules linked to antiestrogen resistance.

pathwayPCA is an R package that performs integrative pathway analysis with modern PCA methods and gene selection, enabling multi-omics data analysis and sample-specific pathway activity estimation.

MSIGNET identifies significant gene subnetworks using Metropolis sampling, showing better performance than existing tools on simulated data and providing biologically meaningful results in Parkinson's and ovarian cancer studies.