A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge. - Jiang Du 003; Joel S. Rozowsky; Jan O. Korbel; Zhengdong D. Zhang; Thomas E. Royce; Martin H. Schultz; Michael Snyder 001; Mark Gerstein (Bioinform., 2006)

Modeling ChIP Sequencing In Silico with Applications. - Zhengdong D. Zhang; Joel S. Rozowsky; Michael Snyder 001; Joseph T. Chang; Mark Gerstein (PLoS Comput. Biol., 2008)

Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants. - Jiang Du 003; Robert D. Bjornson; Zhengdong D. Zhang; Yong Kong; Michael Snyder 001; Mark B. Gerstein (PLoS Comput. Biol., 2009)

Detection of copy number variation from array intensity and sequencing read depth using a stepwise Bayesian model. - Zhengdong D. Zhang; Mark B. Gerstein (BMC Bioinform., 2010)

ACT: aggregation and correlation toolbox for analyses of genome tracks. - Justin Jee; Joel S. Rozowsky; Kevin Y. Yip; Lucas Lochovsky; Robert D. Bjornson; Guoneng Zhong; Zhengdong D. Zhang; Yutao Fu; Jie Wang; Zhiping Weng; Mark Gerstein (Bioinform., 2011)

SubNet: a Java application for subnetwork extraction. - Christophe Lemetre; Quanwei Zhang; Zhengdong D. Zhang (Bioinform., 2013)

SubNet: a Java application for subnetwork extraction. - Quanwei Zhang; Zhengdong D. Zhang (Bioinform., 2013)

Prioritization of Schizophrenia Risk Genes by a Network-Regularized Logistic Regression Method. - Wen Zhang; Jhin-Rong Lin; Rubén Nogales-Cadenas; Quanwei Zhang; Ying Cai; Zhengdong D. Zhang (IWBBIO, 2016)

PGA: post-GWAS analysis for disease gene identification. - Jhih-rong Lin; Daniel Jaroslawicz; Ying Cai; Quanwei Zhang; Zhen Wang; Zhengdong D. Zhang (Bioinform., 2018)

HEDD: Human Enhancer Disease Database. - Zhen Wang; Quanwei Zhang; Wen Zhang; Jhih-rong Lin; Ying Cai; Joydeep Mitra; Zhengdong D. Zhang (Nucleic Acids Res., 2018)