ChipInfo: software for extracting gene annotation and gene ontology information for microarray analysis. - Sheng Zhong 003; Cheng Li 016; Wing Hung Wong (Nucleic Acids Res., 2003)

Towards Ubiquitous Bio-Information Computing: Data Protocols, Middleware, and Web Services for Heterogeneous Biological Information Integration and Retrieval. - Pengyu Hong; Sheng Zhong 003; Wing Hung Wong (BIBE, 2004)

Comparative Analysis of Gene Sets in the Gene Ontology Space under the Multiple Hypothesis Testing Framework. - Sheng Zhong 003; Lu Tian; Cheng Li 016; Kai-Florian Storch; Wing Hung Wong (CSB, 2004)

In silico prediction of transcription factors that interact with the E2F family of transcription factors. - Sheng Zhong 003; Qing Zhou; Paloma Giangrande; Joseph R. Nevins; Wing Hung Wong (ICARCV, 2004)

Ubic2 - Towards Ubiquitous Bio-Information Computing: Data Protocols, Middleware, and Web Services for Heterogeneous Biological Information Integration and Retrieval. - Pengyu Hong; Sheng Zhong 003; Wing Hung Wong (Int. J. Softw. Eng. Knowl. Eng., 2005)

Dissecting Early Differentially Expressed Genes in a Mixture of Differentiating Embryonic Stem Cells. - Feng Hong; Fang Fang; Xuming He 002; Xiaoyi Cao; Hiram Chipperfield; Dan Xie; Wing Hung Wong; Huck H. Ng; Sheng Zhong 003 (PLoS Comput. Biol., 2009)

Network-based comparison of temporal gene expression patterns. - Wei Huang; Xiaoyi Cao; Sheng Zhong 003 (Bioinform., 2010)

Modeling Co-Expression across Species for Complex Traits: Insights to the Difference of Human and Mouse Embryonic Stem Cells. - Jun Cai; Dan Xie; Zhewen Fan; Hiram Chipperfield; John Marden; Wing H. Wong; Sheng Zhong 003 (PLoS Comput. Biol., 2010)

Mapping personal functional data to personal genomes. - Marcelo Rivas-Astroza; Dan Xie; Xiaoyi Cao; Sheng Zhong 003 (Bioinform., 2011)

Towards an Evolutionary Model of Transcription Networks. - Dan Xie; Chieh-Chun Chen; Xin He; Xiaoyi Cao; Sheng Zhong 003 (PLoS Comput. Biol., 2011)

Enabling interspecies epigenomic comparison with CEpBrowser. - Xiaoyi Cao; Sheng Zhong 003 (Bioinform., 2013)

Understanding Variation in Transcription Factor Binding by Modeling Transcription Factor Genome-Epigenome Interactions. - Chieh-Chun Chen; Shu Xiao; Dan Xie; Xiaoyi Cao; Chun-Xiao Song; Ting Wang; Chuan He; Sheng Zhong 003 (PLoS Comput. Biol., 2013)

GeNemo: a search engine for web-based functional genomic data. - Yongqing Zhang; Xiaoyi Cao; Sheng Zhong 003 (Nucleic Acids Res., 2016)

GITAR: An Open Source Tool for Analysis and Visualization of Hi-C Data. - Riccardo Calandrelli; Qiuyang Wu; Jihong Guan; Sheng Zhong 003 (Genom. Proteom. Bioinform., 2018)

A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome. - Jia Lu; Xiaoyi Cao; Sheng Zhong 003 (PLoS Comput. Biol., 2018)

EpiAlignment: alignment with both DNA sequence and epigenomic data. - Jia Lu; Xiaoyi Cao; Sheng Zhong 003 (Nucleic Acids Res., 2019)