WDNE: an integrative graphical model for inferring differential networks from multi-platform gene expression data with missing values. - Le Ou-Yang; Dehan Cai; Xiao-Fei Zhang; Hong Yan 001 (Briefings Bioinform., 2021)

Reconstructing viral haplotypes using long reads. - Dehan Cai; Yanni Sun (Bioinform., 2022)

HaploDMF: viral haplotype reconstruction from long reads via deep matrix factorization. - Dehan Cai; Jiayu Shang; Yanni Sun (Bioinform., 2022)

AccuVIR: an ACCUrate VIRal genome assembly tool for third-generation sequencing data. - Runzhou Yu; Dehan Cai; Yanni Sun (Bioinform., 2023)

Towards more accurate microbial source tracking via non-negative matrix factorization (NMF). - Ziyi Huang; Dehan Cai; Yanni Sun (Bioinform., 2024)