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2020 – today
- 2021
[j24]Edison Ong
, Michael F. Cooke, Anthony Huffman, Zuoshuang Xiang, Mei U. Wong, Haihe Wang, Meenakshi Seetharaman, Ninotchka Valdez, Yongqun He:
Vaxign2: the second generation of the first Web-based vaccine design program using reverse vaccinology and machine learning. Nucleic Acids Res. 49(Webserver-Issue): 671-678 (2021)
2010 – 2019
- 2019
- [j23]Samantha Sayers, Li Li, Edison Ong, Shunzhou Deng, Guanghua Fu, Yu Lin, Brian Yang, Shelley Zhang, Zhenzong Fa, Bin Zhao, Zuoshuang Xiang, Yongqing Li, Xing-Ming Zhao, Michal Olszewski, Luonan Chen, Yongqun He:
Victors: a web-based knowledge base of virulence factors in human and animal pathogens. Nucleic Acids Res. 47(Database-Issue): D693-D700 (2019) - 2018
- [j22]Yongqun He, Zuoshuang Xiang, Jie Zheng, Yu Lin, James A. Overton, Edison Ong:
The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability. J. Biomed. Semant. 9(1): 3:1-3:10 (2018) - 2017
- [j21]Edison Ong, Zuoshuang Xiang, Bin Zhao, Yue Liu, Yu Lin, Jie Zheng, Chris Mungall, Mélanie Courtot, Alan Ruttenberg, Yongqun He:
Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration. Nucleic Acids Res. 45(Database-Issue): D347-D352 (2017) - 2016
- [j20]Abra Guo, Rebecca Racz, Junguk Hur, Yu Lin, Zuoshuang Xiang, Lili Zhao, Jordan Rinder, Guoqian Jiang, Qian Zhu, Yongqun He:
Ontology-based collection, representation and analysis of drug-associated neuropathy adverse events. J. Biomed. Semant. 7: 29 (2016) - [c11]Edison Ong, Zuoshuang Xiang, Jie Zheng, Barry Smith, Yongqun He:
Ontobull and BFOConvert: Web-based Programs to Support Automatic Ontology Conversion. ICBO/BioCreative 2016 - [c10]Arzucan Özgür, Junguk Hur, Zuoshuang Xiang, Edison Ong, Dragomir R. Radev, Yongqun He:
Ignet: A Centrality and INO-based Web System for Analyzing and Visualizing Literature-mined Networks. ICBO/BioCreative 2016 - 2015
- [j19]Junguk Hur, Arzucan Özgür, Zuoshuang Xiang, Yongqun He:
Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions. J. Biomed. Semant. 6: 2 (2015) - [j18]Zuoshuang Xiang, Jie Zheng, Yu Lin, Yongqun He:
Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns. J. Biomed. Semant. 6: 4 (2015) - [j17]Yu Lin, Zuoshuang Xiang, Yongqun He:
Ontology-based representation and analysis of host-Brucella interactions. J. Biomed. Semant. 6: 37 (2015) - 2014
- [j16]Jie Zheng, Zuoshuang Xiang, Christian J. Stoeckert Jr., Yongqun He:
Ontodog: a web-based ontology community view generation tool. Bioinform. 30(9): 1340-1342 (2014) - [j15]Yongqun He, Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Abra Guo, Shelley Zhang, Desikan Jagannathan, Luca Toldo, Cui Tao, Barry Smith:
OAE: The Ontology of Adverse Events. J. Biomed. Semant. 5: 29 (2014) - [j14]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, Kaoru Saijo, Hiroshi Masuya, Yukio Nakamura, Matthew H. Brush, Melissa A. Haendel, Jie Zheng, Christian J. Stoeckert Jr., Bjoern Peters, Christopher J. Mungall, Thomas E. Carey, David J. States, Brian D. Athey, Yongqun He:
CLO: The cell line ontology. J. Biomed. Semant. 5: 37 (2014) - [j13]Rebecca Racz, Xinna Li, Mukti Patel, Zuoshuang Xiang, Yongqun He:
DNAVaxDB: the first web-based DNA vaccine database and its data analysis. BMC Bioinform. 15(S-4): S2 (2014) - [j12]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, Priya Dungarani, Guerlain Ulysse, Kanika Kochhar, Boris Vidri, Kelsey Strait, George W. Jourdian, Zuoshuang Xiang:
Updates on the web-based VIOLIN vaccine database and analysis system. Nucleic Acids Res. 42(Database-Issue): 1124-1132 (2014) - [c9]Zuoshuang Xiang, Yu Lin, Yongqun He:
Ontobat: An Ontology-based Semantic Web Approach for Linked Data Processing and Analysis. ICBO 2014: 93-95 - 2013
- [j11]Zuoshuang Xiang, Yongqun He:
Genome-wide prediction of vaccine targets for human herpes simplex viruses using Vaxign reverse vaccinology. BMC Bioinform. 14(S-4): S2 (2013) - [j10]Thomas E. Todd, Omar Tibi, Yu Lin, Samantha Sayers, Denise N. Bronner, Zuoshuang Xiang, Yongqun He:
Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates. BMC Bioinform. 14(S-6): S3 (2013) - [j9]Zuoshuang Xiang, Tingting Qin, Zhaohui S. Qin, Yongqun He:
A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks. BMC Syst. Biol. 7(S-3): S9 (2013) - [c8]Zuoshuang Xiang, Yongqun He:
HINO: BFO-aligned ontology representation of human molecular interactions and pathways. ICBO 2013: 122 - [i1]Yongqun He, Zuoshuang Xiang:
HINO: a BFO-aligned ontology representing human molecular interactions and pathways. CoRR abs/1311.3355 (2013) - 2012
- [j8]Junguk Hur, Arzucan Özgür, Zuoshuang Xiang, Yongqun He:
Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining. J. Biomed. Semant. 3: 18 (2012) - [c7]Zuoshuang Xiang, Yu Lin, Yongqun He:
Ontorat web server for automatic generation and annotations of new ontology terms. ICBO 2012 - [c6]Jie Zheng, Zuoshuang Xiang, Christian J. Stoeckert Jr., Yongqun He:
Ontodog: A Web-based Ontology Community View Generator. ICBO 2012 - 2011
- [j7]Yu Lin, Zuoshuang Xiang, Yongqun He:
Brucellosis Ontology (IDOBRU) as an extension of the Infectious Disease Ontology. J. Biomed. Semant. 2: 9 (2011) - [j6]Arzucan Özgür, Zuoshuang Xiang, Dragomir R. Radev, Yongqun He:
Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology. J. Biomed. Semant. 2(S-2): S8 (2011) - [j5]Brian Yang, Samantha Sayers, Zuoshuang Xiang, Yongqun He:
Protegen: a web-based protective antigen database and analysis system. Nucleic Acids Res. 39(Database-Issue): 1073-1078 (2011) - [c5]Yongqun He, Zuoshuang Xiang, Sirarat Sarntivijai, Luca Toldo, Werner Ceusters:
AEO: A Realism-Based Biomedical Ontology for the Representation of Adverse Events. ICBO 2011 - [c4]Yu Lin, Zuoshuang Xiang, Yongqun He:
Towards a Semantic Web Application: Ontology-Driven Ortholog Clustering Analysis. ICBO 2011 - [c3]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:
Cell Line Ontology: Redesigning the Cell Line Knowledgebase to Aid Integrative Translational Informatics. ICBO 2011 - [c2]Zuoshuang Xiang, Yu Lin, Yongqun He:
OntoFox and its Application in Development of Brucellosis Ontology. ICBO 2011 - [c1]Zuoshuang Xiang, Chris Mungall, Alan Ruttenberg, Yongqun He:
Ontobee: A Linked Data Server and Browser for Ontology Terms. ICBO 2011
2000 – 2009
- 2008
- [j4]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, Janet R. Gilsdorf, George W. Jourdian, Yongqun He:
VIOLIN: vaccine investigation and online information network. Nucleic Acids Res. 36(Database-Issue): 923-928 (2008) - 2007
- [j3]Zuoshuang Xiang, Zhaohui S. Qin, Yongqun He:
CRCView: a web server for analyzing and visualizing microarray gene expression data using model-based clustering. Bioinform. 23(14): 1843-1845 (2007) - [j2]Zuoshuang Xiang, Rebecca M. Minter, Xiaoming Bi, Peter J. Woolf, Yongqun He:
miniTUBA: medical inference by network integration of temporal data using Bayesian analysis. Bioinform. 23(18): 2423-2432 (2007) - 2006
- [j1]Zuoshuang Xiang, Wenjie Zheng, Yongqun He:
BBP: Brucella genome annotation with literature mining and curation. BMC Bioinform. 7: 347 (2006)
Coauthor Index
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