Xiaoyu Song

Cell-type-aware TWAS from bulk-trained expression models and GWAS summary statistics reproduces individual-level MiXcan results (r > 0.99) and finds 32 genome-wide significant breast cancer genes.

This study performs a cell-type-aware transcriptome-wide association study (TWAS) of mammographic density phenotypes, identifying novel genes and prioritizing known GWAS loci through cell-type-specific gene expression analysis.

sCCIgen generates synthetic spatial transcriptomics data with known cell-cell interaction features to evaluate analytical tools.

The paper introduces conditional differential gene expression analysis to distinguish direct from mediated gene effects in RNA sequencing data, finding most differentially expressed genes are not directly causal.

This study examines the association between vitamin D-related gene variants and prostate cancer risk in Black men, finding no significant associations after adjustment but some suggestive results.

QuadST identifies interaction-changed genes in spatially resolved transcriptomics by analyzing distance-expression associations in cell-type pairs.

MiXcan performs cell-type-specific transcriptome-wide association studies, identifying more breast cancer susceptibility genes than conventional methods by considering cell-type heterogeneity.

iProMix decomposes bulk proteomic data to identify ACE2-protein associations in epithelial cells, revealing sex-specific interferon pathways linked to ACE2 abundance in lung adenocarcinoma tissues.

ProTrack provides an interactive web tool for exploring CPTAC proteogenomic data across multiple cancer types, enabling users to query and visualize multi-omics profiles without coding.

The paper introduces iProFun, a multi-omics tool to identify DNA copy number and methylation effects on proteogenomic traits in ovarian cancer, finding 500 and 122 genes with cis-associations.

This paper introduces a quantile regression method to identify eQTLs associated with gene expression distribution, finding new eQTLs with tissue-specific effects and enrichment in GWAS SNPs.