TF-finder: A software package for identifying transcription factors involved in biological processes using microarray data and existing knowledge base. - Xiaoqi Cui; Tong Wang; Huann-Sheng Chen; Victor Busov; Hairong Wei (BMC Bioinform., 2010)

TF-Cluster: A pipeline for identifying functionally coordinated transcription factors via network decomposition of the shared coexpression connectivity matrix (SCCM). - Jeff Nie; Ron M. Stewart; Hang Zhang; James A. Thomson; Fang Ruan; Xiaoqi Cui; Hairong Wei (BMC Syst. Biol., 2011)

Bottom-up GGM algorithm for constructing multilayered hierarchical gene regulatory networks that govern biological pathways or processes. - Sapna Kumari; Wenping Deng; Chathura Gunasekara; Vincent Chiang; Huann-Sheng Chen; Hao Ma; Xin Davis; Hairong Wei (BMC Bioinform., 2016)

The improved (2D)2PCA algorithm and its parallel implementation based on image block. - Haifeng Song 002; Guangsheng Chen; Hairong Wei; Weiwei Yan (Microprocess. Microsystems, 2016)

JRmGRN: joint reconstruction of multiple gene regulatory networks with common hub genes using data from multiple tissues or conditions. - Wenping Deng; Kui Zhang; Sanzhen Liu; Patrick X. Zhao; Shizhong Xu; Hairong Wei (Bioinform., 2018)

Construction of a hierarchical gene regulatory network centered around a transcription factor. - Hairong Wei (Briefings Bioinform., 2019)