Kunxian Shu

This study constructs a mitochondrial functional activity-associated programmed cell death index (MPCDI) using scRNA-seq and RNA-seq data to classify HCC patients and identify prognostic genes.

The paper reanalyzes human tissue proteomics data using pangenome references to identify novel peptides and variants, demonstrating the effectiveness of proteogenomics approaches with pangenome data.

The paper identifies two novel biomarker genes, NES and ESAM, in NSCLC through multi-omics analysis and validates their association with gene expression and DNA methylation changes.

The paper analyzes intron losses and gains across 104 nematode genomes, showing nematodes are not an outlier in intron evolution but follow typical eukaryotic patterns.

Phoenix Enhancer improves proteomics data analysis by clustering spectra to identify potential mis-identifications and enhance peptide spectrum match confidence.