Ginny Xiaohe Li

The paper identifies a novel transient SOX9+ pericentral hepatocyte population in acute liver injury that mediates early tissue repair and immune modulation.

FragPipe-Analyst provides an R shiny web server and R package for downstream analysis and visualization of quantitative proteomics data from FragPipe.

HLAProphet improves HLA protein quantification by using personalized allele information from DNA sequencing, increasing peptide identifications and aligning with RNA expression and loss of heterozygosity.

The paper introduces MSFragger-DIA, a tool for fast and sensitive peptide identification from DIA proteomics data, integrated into FragPipe, and demonstrates its performance across various sample types.

ParProx enables scalable multivariable regression analysis of ultrahigh-dimensional omics data using group lasso with biological priors, producing interpretable models.

The paper introduces a protein-centric method to aggregate exome variants for association analysis with clinical outcomes, identifying sequence units predictive of survival that conventional gene-level analysis misses.

PTMscape predicts post-translational modification sites across the proteome and identifies hotspots of modification crosstalk using a unified framework.