DNF: A differential network flow method to identify rewiring drivers for gene regulatory networks. - Jiang Xie 003; Fuzhang Yang; Jiao Wang; Mathew Karikomi; Yiting Yin; Jiamin Sun; Tieqiao Wen; Qing Nie (Neurocomputing, 2020)

DURIAN: an integrative deconvolution and imputation method for robust signaling analysis of single-cell transcriptomics data. - Mathew Karikomi; Peijie Zhou; Qing Nie (Briefings Bioinform., 2022)