Xiao Yi

DPHL v2: An updated and comprehensive DIA pan-human assay library for quantifying more than 14,000 proteins.

DPHL v2 improves upon DPHL v1 by including semi-tryptic peptides and protein isoforms, increasing identified and dysregulated proteins in colorectal cancer analysis.

BatchServer: a web server for batch effect evaluation, visualization and correction

BatchServer provides a web platform for evaluating, visualizing, and correcting batch effects in omics data using autoComBat, PVCA, and UMAP.

Optimization of Spectral Library Size Improves DIA-MS Proteome Coverage

This paper presents a computational strategy to optimize spectral library size for DIA-MS data, improving peptide and protein identification rates in colorectal and carcinoma samples.

DPHL: A pan-human protein mass spectrometry library for robust biomarker discovery using Data-Independent Acquisition and Parallel Reaction Monitoring

The paper introduces DPHL, a pan-human protein mass spectrometry library built using DIA and PRM, and demonstrates its utility in identifying differentially expressed proteins in prostate cancer and DLBCL.

Phenotype Prediction using a Tensor Representation and Deep Learning from Data Independent Acquisition Mass Spectrometry

This paper develops a deep learning method using DIA tensor for phenotype prediction from mass spectrometry data, achieving high accuracy in cancer classification.

Identification of protein abundance changes in biopsy-level hepatocellular carcinoma tissues using PCT-SWATH

This study uses PCT-SWATH to analyze proteomic changes in HCC biopsy samples, identifying 23 upregulated pathways and 13 downregulated ones, with notable changes in virus-infection-related proteins in HBV+ patients.