LOCSVMPSI: a web server for subcellular localization of eukaryotic proteins using SVM and profile of PSI-BLAST. - Dan Xie 001; Ao Li 001; Minghui Wang; Zhewen Fan; Huanqing Feng (Nucleic Acids Res., 2005)

Gene Ontology analysis in multiple gene clusters under multiple hypothesis testing framework. - Sheng Zhong 003; Dan Xie 001 (Artif. Intell. Medicine, 2007)

TagSmart: analysis and visualization for yeast mutant fitness data measured by tag microarrays. - Chulyun Kim; Sangkyum Kim; Russell Dorer; Dan Xie 001; Jiawei Han 001; Sheng Zhong 003 (BMC Bioinform., 2007)

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 001; Wing Hung Wong; Huck H. Ng; Sheng Zhong 003 (PLoS Comput. Biol., 2009)

Modeling Co-Expression across Species for Complex Traits: Insights to the Difference of Human and Mouse Embryonic Stem Cells. - Jun Cai; Dan Xie 001; 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 001; Xiaoyi Cao; Sheng Zhong 003 (Bioinform., 2011)

Towards an Evolutionary Model of Transcription Networks. - Dan Xie 001; Chieh-Chun Chen; Xin He; Xiaoyi Cao; Sheng Zhong 003 (PLoS Comput. Biol., 2011)

Understanding Variation in Transcription Factor Binding by Modeling Transcription Factor Genome-Epigenome Interactions. - Chieh-Chun Chen; Shu Xiao; Dan Xie 001; Xiaoyi Cao; Chun-Xiao Song; Ting Wang; Chuan He; Sheng Zhong 003 (PLoS Comput. Biol., 2013)

Comparative analysis of regulatory information and circuits across distant species Open. - Alan P. Boyle; Carlos L. Araya; Cathleen Brdlik; Philip Cayting; Chao Cheng; Yong Cheng; Kathryn Gardner; LaDeana W. Hillier; Judith Janette; Lixia Jiang; Dionna Kasper; Trupti Kawli; et al. (Nat., 2014)