Prediction of kinase inhibitor response using activity profiling, in vitro screening, and elastic net regression. - Trish P. Tran; Edison Ong; Andrew P. Hodges; Giovanni Paternostro; Carlo Piermarocchi (BMC Syst. Biol., 2014)

GOfox: Semantics-based simplified hierarchical classification and interactive visualization to support GO enrichment analysis. - Edison Ong; Yongqun He (ICBO, 2015)

A Scalable Method for Molecular Network Reconstruction Identifies Properties of Targets and Mutations in Acute Myeloid Leukemia. - Edison Ong; Anthony Szedlak; Yunyi Kang; Peyton Smith; Nicholas Smith; Madison McBride; Darren Finlay; Kristiina Vuori; James Mason; Edward D. Ball; Carlo Piermarocchi; Giovanni Paternostro (J. Comput. Biol., 2015)

Application of Ontobedia on Cell Line Ontology Development. - Edison Ong; Yongqun He (AMIA, 2016)

The Cell Line Ontology Integration and Analysis of the Knowledge of LINCS Cell Lines. - Edison Ong; Jiangan Xie; Zhaohui Ni; Qingping Liu; Yu Lin; Vasileios Stathias; Caty Chung; Stephan C. Schürer; Yongqun He (ICBO/BioCreative, 2016)

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)

Towards precision informatics of pharmacovigilance: OAE-CTCAE mapping and OAE-based representation and analysis of adverse events in patients treated with cancer drugs. - Meiu Wong; Rebecca Racz; Edison Ong; Yongqun He (AMIA, 2017)

OLOBO: A New Ontology for Linking and Integrating Open Biological and Biomedical Ontologies. - Edison Ong; Yongqun He (ICBO, 2017)

Comparison, alignment, and synchronization of cell line information between CLO and EFO. - Edison Ong; Sirarat Sarntivijai; Simon Jupp; Helen E. Parkinson; Yongqun He (BMC Bioinform., 2017)

Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses. - Edison Ong; Jiangan Xie; Zhaohui Ni; Qingping Liu; Sirarat Sarntivijai; Yu Lin; Daniel J. Cooper; Raymond Terryn; Vasileios Stathias; Caty Chung; Stephan C. Schürer; Yongqun He (BMC Bioinform., 2017)

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)

KTAO: A Kidney Tissue Atlas Ontology to Support Community-Based Kidney Knowledge Base Development and Data Integration. - Yongqun He; Becky Steck; Edison Ong; Laura Mariani; Chrysta Lienczewski; Ulysses J. Balis; Matthias Kretzler; Jonathan Himmelfarb; John F. Bertram; Evren U. Azeloglu; Ravi Iyengar; Deborah Hoshizaki; et al. (ICBO, 2018)

eXtensible Ontology Development (XOD) using Web-based Ontoanimal Tools. - Edison Ong; Yongqun He; Jie Zheng 001 (ICBO, 2018)

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)

OPMI: the Ontology of Precision Medicine and Investigation and its Support for Clinical Data and Metadata Representation and Analysis. - Yongqun He; Edison Ong; Jennifer Schaub; Frederick Dowd; John F. O'Toole; Anastasios Siapos; Christian G. Reich; Sarah Seager; Ling Wang 001; Hong Yu 014; Jie Zheng 001; Christian J. Stoeckert Jr.; et al. (ICBO, 2019)

Ontolion: A Web-based Integrative Ontology Development Platform. - Edison Ong; Yongqun He (ICBO, 2019)

ICDO: Ontological Representation of the International Classification of Diseases (ICD) and its Application in English and Chinese Healthy Data Standardization. - Ling Wan; Edison Ong; Yongqun He (ICBO, 2019)

OSCI: standardized stem cell ontology representation and use cases for stem cell investigation. - Yongqun He; William D. Duncan; Daniel J. Cooper; Jens Hansen; Ravi Iyengar; Edison Ong; Kendal Walker; Omar Tibi; Sam Smith; Lucas M. Serra; Jie Zheng 001; Sirarat Sarntivijai; et al. (BMC Bioinform., 2019)

VIO: ontology classification and study of vaccine responses given various experimental and analytical conditions. - Edison Ong; Peter Sun; Kimberly Berke; Jie Zheng 001; Guanming Wu; Yongqun He (BMC Bioinform., 2019)

ODAE: Ontology-based systematic representation and analysis of drug adverse events and its usage in study of adverse events given different patient age and disease conditions. - Hong Yu 014; Solomiya Nysak; Noemi Garg; Edison Ong; Xianwei Ye; Xiangyan Zhang; Yongqun He (BMC Bioinform., 2019)

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)

CIDO: The Community-Based Coronavirus Infectious Disease Ontology. - Yongqun He; Hong Yu 014; Edison Ong; Yang Wang; Yingtong Liu; Anthony Huffman; Hsin-Hui Huang; John Beverley; Asiyah Yu Lin; William D. Duncan; Sivaram Arabandi; Jiangan Xie; et al. (ICBO/ODLS, 2020)

Vaxign-ML: supervised machine learning reverse vaccinology model for improved prediction of bacterial protective antigens. - Edison Ong; Haihe Wang; Mei U. Wong; Meenakshi Seetharaman; Ninotchka Valdez; Yongqun He (Bioinform., 2020)

Perform Pathway Enrichment Analysis Using ReactomeFIViz. - Robin Haw; Fred Loney 001; Edison Ong; Yongqun He; Guanming Wu (Protein-Protein Interaction Networks, 2020)

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)

COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning. - Anthony Huffman; Edison Ong; Junguk Hur; Adonis D'mello; Hervé Tettelin; Yongqun He (Briefings Bioinform., 2022)

A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology. - Yongqun He; Hong Yu 014; Anthony Huffman; Asiyah Yu Lin; Darren A. Natale; John Beverley; Ling Zheng; Yehoshua Perl; Zhigang Wang; Yingtong Liu; Edison Ong; Yang Wang; et al. (J. Biomed. Semant., 2022)

Ontology-based Representation and Analysis of Conditional Vaccine Immune Responses Using Omics Data. - Anthony Huffman; Edison Ong; Timothy Brunson; Nasim Sanati; Jie Zheng 001; Anna Maria Masci; Guanming Wu; Yongqun He (ICBO, 2023)

mtx-COBRA: Subcellular localization prediction for bacterial proteins. - Isha Arora; Arkadij Kummer; Hao Zhou; Mihaela Gadjeva; Eric J. Ma; Gwo-Yu Chuang; Edison Ong (Comput. Biol. Medicine, 2024)