Liye Zhang

This study benchmarks five CNA inference tools using single-cell multi-omics data, finding Numbat performs best overall while CopyKAT excels with expression matrix input.

The paper introduces a toolkit for aligning and analyzing U insertion/deletion RNA editing data from kinetoplastid mitochondrial genomes.

The paper introduces ISnorm, a normalization method for single-cell RNA sequencing data using internal spike-in-like genes, which improves downstream analysis by accounting for transcriptome heterogeneity.

The paper introduces epiConv, a method for integrating scATAC-seq datasets from multiple sources, improving batch correction and enabling co-assay alignment and biological condition integration.

CaDrA identifies functionally relevant subsets of binary genomic features associated with specific outcomes, showing sensitivity and specificity in cancer datasets.

The paper identifies KPAF4, a mitochondrial PABP in Trypanosoma brucei, which regulates mRNA editing and 3' modification by preventing premature A/U-tailing and ensuring transcript stability.