BBP: Brucella genome annotation with literature mining and curation. - Zuoshuang Xiang; Wenjie Zheng; Yongqun He (BMC Bioinform., 2006)

miniTUBA: medical inference by network integration of temporal data using Bayesian analysis. - Zuoshuang Xiang; Rebecca M. Minter; Xiaoming Bi; Peter J. Woolf; Yongqun He (Bioinform., 2007)

CRCView: a web server for analyzing and visualizing microarray gene expression data using model-based clustering. - Zuoshuang Xiang; Zhaohui S. Qin; Yongqun He (Bioinform., 2007)

VIOLIN: vaccine investigation and online information network. - Zuoshuang Xiang; Thomas E. Todd; Kim P. Ku; Bethany L. Kovacic; Charles B. Larson; Fang Chen; Andrew P. Hodges; Yuying Tian; Elizabeth A. Olenzek; Boyang Zhao; Lesley A. Colby; Howard G. Rush; et al. (Nucleic Acids Res., 2008)

AEO: A Realism-Based Biomedical Ontology for the Representation of Adverse Events. - Yongqun He; Zuoshuang Xiang; Sirarat Sarntivijai; Luca Toldo; Werner Ceusters (ICBO, 2011)

Towards a Semantic Web Application: Ontology-Driven Ortholog Clustering Analysis. - Yu Lin; Zuoshuang Xiang; Yongqun He (ICBO, 2011)

Cell Line Ontology: Redesigning the Cell Line Knowledgebase to Aid Integrative Translational Informatics. - Sirarat Sarntivijai; Zuoshuang Xiang; Terrence F. Meehan; Alexander D. Diehl; Uma Vempati; Stephan C. Schürer; Chao Pang; James Malone; Helen E. Parkinson; Brian D. Athey; Yongqun He (ICBO, 2011)

OntoFox and its Application in Development of Brucellosis Ontology. - Zuoshuang Xiang; Yu Lin; Yongqun He (ICBO, 2011)

Ontobee: A Linked Data Server and Browser for Ontology Terms. - Zuoshuang Xiang; Chris Mungall; Alan Ruttenberg; Yongqun He (ICBO, 2011)

Brucellosis Ontology (IDOBRU) as an extension of the Infectious Disease Ontology. - Yu Lin; Zuoshuang Xiang; Yongqun He (J. Biomed. Semant., 2011)

Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology. - Arzucan Özgür; Zuoshuang Xiang; Dragomir R. Radev; Yongqun He (J. Biomed. Semant., 2011)

Protegen: a web-based protective antigen database and analysis system. - Brian Yang; Samantha Sayers; Zuoshuang Xiang; Yongqun He (Nucleic Acids Res., 2011)

Ontorat web server for automatic generation and annotations of new ontology terms. - Zuoshuang Xiang; Yu Lin; Yongqun He (ICBO, 2012)

Ontodog: A Web-based Ontology Community View Generator. - Jie Zheng 001; Zuoshuang Xiang; Christian J. Stoeckert Jr.; Yongqun He (ICBO, 2012)

Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining. - Junguk Hur; Arzucan Özgür; Zuoshuang Xiang; Yongqun He (J. Biomed. Semant., 2012)

HINO: BFO-aligned ontology representation of human molecular interactions and pathways. - Zuoshuang Xiang; Yongqun He (ICBO, 2013)

Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates. - Thomas E. Todd; Omar Tibi; Yu Lin; Samantha Sayers; Denise N. Bronner; Zuoshuang Xiang; Yongqun He (BMC Bioinform., 2013)

Genome-wide prediction of vaccine targets for human herpes simplex viruses using Vaxign reverse vaccinology. - Zuoshuang Xiang; Yongqun He (BMC Bioinform., 2013)

A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks. - Zuoshuang Xiang; Tingting Qin; Zhaohui S. Qin; Yongqun He (BMC Syst. Biol., 2013)

HINO: a BFO-aligned ontology representing human molecular interactions and pathways. - Yongqun He; Zuoshuang Xiang (CoRR, 2013)

Ontobat: An Ontology-based Semantic Web Approach for Linked Data Processing and Analysis. - Zuoshuang Xiang; Yu Lin; Yongqun He (ICBO, 2014)

Ontodog: a web-based ontology community view generation tool. - Jie Zheng 001; Zuoshuang Xiang; Christian J. Stoeckert Jr.; Yongqun He (Bioinform., 2014)

OAE: The Ontology of Adverse Events. - Yongqun He; Sirarat Sarntivijai; Yu Lin; Zuoshuang Xiang; Abra Guo; Shelley Zhang 002; Desikan Jagannathan; Luca Toldo; Cui Tao; Barry Smith 001 (J. Biomed. Semant., 2014)

CLO: The cell line ontology. - Sirarat Sarntivijai; Yu Lin; Zuoshuang Xiang; Terrence F. Meehan; Alexander D. Diehl; Uma D. Vempati; Stephan C. Schürer; Chao Pang; James Malone; Helen E. Parkinson; Yue Liu; Terue Takatsuki; et al. (J. Biomed. Semant., 2014)

DNAVaxDB: the first web-based DNA vaccine database and its data analysis. - Rebecca Racz; Xinna Li; Mukti Patel; Zuoshuang Xiang; Yongqun He (BMC Bioinform., 2014)

Updates on the web-based VIOLIN vaccine database and analysis system. - Yongqun He; Rebecca Racz; Samantha Sayers; Yu Lin; Thomas E. Todd; Junguk Hur; Xinna Li; Mukti Patel; Boyang Zhao; Monica Chung; Joseph Ostrow; Andrew Sylora; et al. (Nucleic Acids Res., 2014)

Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions. - Junguk Hur; Arzucan Özgür; Zuoshuang Xiang; Yongqun He (J. Biomed. Semant., 2015)

Ontology-based representation and analysis of host-Brucella interactions. - Yu Lin; Zuoshuang Xiang; Yongqun He (J. Biomed. Semant., 2015)

Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns. - Zuoshuang Xiang; Jie Zheng 001; Yu Lin; Yongqun He (J. Biomed. Semant., 2015)

Ontobull and BFOConvert: Web-based Programs to Support Automatic Ontology Conversion. - Edison Ong; Zuoshuang Xiang; Jie Zheng 001; Barry Smith 001; Yongqun He (ICBO/BioCreative, 2016)

Ignet: A Centrality and INO-based Web System for Analyzing and Visualizing Literature-mined Networks. - Arzucan Özgür; Junguk Hur; Zuoshuang Xiang; Edison Ong; Dragomir R. Radev; Yongqun He (ICBO/BioCreative, 2016)

Ontology-based collection, representation and analysis of drug-associated neuropathy adverse events. - Abra Guo; Rebecca Racz; Junguk Hur; Yu Lin; Zuoshuang Xiang; Lili Zhao; Jordan Rinder; Guoqian Jiang; Qian Zhu 003; Yongqun He (J. Biomed. Semant., 2016)

Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration. - Edison Ong; Zuoshuang Xiang; Bin Zhao; Yue Liu; Yu Lin; Jie Zheng 001; Chris Mungall; Mélanie Courtot; Alan Ruttenberg; Yongqun He (Nucleic Acids Res., 2017)

The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability. - Yongqun He; Zuoshuang Xiang; Jie Zheng 001; Yu Lin; James A. Overton; Edison Ong (J. Biomed. Semant., 2018)

Victors: a web-based knowledge base of virulence factors in human and animal pathogens. - Samantha Sayers; Li Li; Edison Ong; Shunzhou Deng; Guanghua Fu; Yu Lin; Brian Yang; Shelley Zhang 002; Zhenzong Fa; Bin Zhao; Zuoshuang Xiang; Yongqing Li; et al. (Nucleic Acids Res., 2019)

Vaxign2: the second generation of the first Web-based vaccine design program using reverse vaccinology and machine learning. - Edison Ong; Michael F. Cooke; Anthony Huffman; Zuoshuang Xiang; Mei U. Wong; Haihe Wang; Meenakshi Seetharaman; Ninotchka Valdez; Yongqun He (Nucleic Acids Res., 2021)