Mapping gene ontology to proteins based on protein-protein interaction data. - Minghua Deng; Zhidong Tu; Fengzhu Sun; Ting Chen 006 (Bioinform., 2004)

An integrative approach for causal gene identification and gene regulatory pathway inference. - Zhidong Tu; Li Wang; Michelle N. Arbeitman; Ting Chen 006; Fengzhu Sun (ISMB (Supplement of Bioinformatics), 2006)

Dysfunctional gene/protein networks in hepatitis C virus-induced hepatocellular cirrhosis and carcinoma. - Tao Huang 004; Guohui Ding 001; Yixue Li; Lei Liu; Eugene Tan; Hongyue Dai; Qi Liu 024; Zhidong Tu; Lu Xie (BCB, 2010)

TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications information. - Qi Liu 024; Yejun Tan; Tao Huang 004; Guohui Ding 001; Zhidong Tu; Lei Liu; Yixue Li; Hongyue Dai; Lu Xie (BMC Bioinform., 2010)

Inferring Signaling and Gene Regulatory Network from Genetic and Genomic Information. - Zhidong Tu; Jun Zhu; Fengzhu Sun (Handbook of Statistical Bioinformatics, 2011)

The role of Hepatitis C Virus in the dynamic protein interaction networks of hepatocellular cirrhosis and carcinoma. - Tao Huang 004; Lei Liu; Qi Liu 024; Guohui Ding 001; Yejun Tan; Zhidong Tu; Yixue Li; Hongyue Dai; Lu Xie (Int. J. Comput. Biol. Drug Des., 2011)

MODMatcher: Multi-Omics Data Matcher for Integrative Genomic Analysis. - Seungyeul Yoo; Tao Huang; Joshua D. Campbell; Eunjee Lee; Zhidong Tu; Mark W. Geraci; Charles A. Powell; Eric E. Schadt; Avrum Spira; Jun Zhu (PLoS Comput. Biol., 2014)

Integrative random forest for gene regulatory network inference. - Francesca Petralia; Pei Wang 014; Jialiang Yang; Zhidong Tu (Bioinform., 2015)