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Edison Ong

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2020 – today

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2024
[j15]
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Isha Arora, Arkadij Kummer, Hao Zhou, Mihaela Gadjeva, Eric J. Ma, Gwo-Yu Chuang, Edison Ong:
mtx-COBRA: Subcellular localization prediction for bacterial proteins. Comput. Biol. Medicine 171: 108114 (2024)
2023
[c14]
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Anthony Huffman, Edison Ong, Timothy Brunson, Nasim Sanati, Jie Zheng, Anna Maria Masci, Guanming Wu, Yongqun He:
Ontology-based Representation and Analysis of Conditional Vaccine Immune Responses Using Omics Data. ICBO 2023: 1-12
2022
[j14]
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Anthony Huffman, Edison Ong, Junguk Hur, Adonis D'mello, Hervé Tettelin, Yongqun He:
COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning. Briefings Bioinform. 23(4) (2022)
[j13]
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Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A. Natale, John Beverley, Ling Zheng, Yehoshua Perl, Zhigang Wang, Yingtong Liu, Edison Ong, Yang Wang, Philip Huang, Long Tran, Jinyang Du, Zalan Shah, Easheta Shah, Roshan Desai, Hsin-Hui Huang, Yujia Tian, Eric Merrell, William D. Duncan, Sivaram Arabandi, Lynn M. Schriml, Jie Zheng, Anna Maria Masci, Liwei Wang, Hongfang Liu, Fatima Zohra Smaili, Robert Hoehndorf, Zoë May Pendlington, Paola Roncaglia, Xianwei Ye, Jiangan Xie, Yi-Wei Tang, Xiaolin Yang, Suyuan Peng, Luxia Zhang, Luonan Chen, Junguk Hur, Gilbert S. Omenn, Brian D. Athey, Barry Smith:
A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology. J. Biomed. Semant. 13(1): 25 (2022)
2021
[j12]
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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)
2020
[j11]
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  - journals/bioinformatics/OngWWSVH20
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Edison Ong, Haihe Wang, Mei U. Wong, Meenakshi Seetharaman, Ninotchka Valdez, Yongqun He:
Vaxign-ML: supervised machine learning reverse vaccinology model for improved prediction of bacterial protective antigens. Bioinform. 36(10): 3185-3191 (2020)
[c13]
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Yongqun He, Hong Yu, Edison Ong, Yang Wang, Yingtong Liu, Anthony Huffman, Hsin-Hui Huang, John Beverley, Asiyah Yu Lin, William D. Duncan, Sivaram Arabandi, Jiangan Xie, Junguk Hur, Xiaolin Yang, Luonan Chen, Gilbert S. Omenn, Brian D. Athey, Barry Smith:
CIDO: The Community-Based Coronavirus Infectious Disease Ontology. ICBO/ODLS 2020: 1-10
[p1]
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Robin Haw, Fred Loney, Edison Ong, Yongqun He, Guanming Wu:
Perform Pathway Enrichment Analysis Using ReactomeFIViz. Protein-Protein Interaction Networks 2020: 165-179

2010 – 2019

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2019
[j10]
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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, Sirarat Sarntivijai, Stephan C. Schürer, K. Sue O'Shea, Alexander D. Diehl:
OSCI: standardized stem cell ontology representation and use cases for stem cell investigation. BMC Bioinform. 20-S(5): 237-247 (2019)
[j9]
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Hong Yu, Solomiya Nysak, Noemi Garg, Edison Ong, Xianwei Ye, Xiangyan Zhang, Yongqun He:
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. BMC Bioinform. 20-S(7): 117-128 (2019)
[j8]
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Edison Ong, Peter Sun, Kimberly Berke, Jie Zheng, Guanming Wu, Yongqun He:
VIO: ontology classification and study of vaccine responses given various experimental and analytical conditions. BMC Bioinform. 20-S(21): 704 (2019)
[j7]
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  - journals/nar/SayersLODFLYZFZ19
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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)
[c12]
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Yongqun He, Edison Ong, Jennifer Schaub, Frederick Dowd, John F. O'Toole, Anastasios Siapos, Christian G. Reich, Sarah Seager, Ling Wang, Hong Yu, Jie Zheng, Christian J. Stoeckert Jr., Xiaolin Yang, Sheng Yang, Becky Steck, Christopher Park, Laura Barisoni, Matthias Kretzler, Jonathan Himmelfarb, Ravi Iyengar, Sean D. Mooney:
OPMI: the Ontology of Precision Medicine and Investigation and its Support for Clinical Data and Metadata Representation and Analysis. ICBO 2019: 1-10
[c11]
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Edison Ong, Yongqun He:
Ontolion: A Web-based Integrative Ontology Development Platform. ICBO 2019: 1
[c10]
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Ling Wan, Edison Ong, Yongqun He:
ICDO: Ontological Representation of the International Classification of Diseases (ICD) and its Application in English and Chinese Healthy Data Standardization. ICBO 2019: 1
2018
[j6]
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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)
[c9]
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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, Sean D. Mooney:
KTAO: A Kidney Tissue Atlas Ontology to Support Community-Based Kidney Knowledge Base Development and Data Integration. ICBO 2018
[c8]
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Edison Ong, Yongqun He, Jie Zheng:
eXtensible Ontology Development (XOD) using Web-based Ontoanimal Tools. ICBO 2018
2017
[j5]
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Edison Ong, Sirarat Sarntivijai, Simon Jupp, Helen E. Parkinson, Yongqun He:
Comparison, alignment, and synchronization of cell line information between CLO and EFO. BMC Bioinform. 18(S-17): 25-33 (2017)
[j4]
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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:
Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses. BMC Bioinform. 18(S-17): 43-53 (2017)
[j3]
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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)
[c7]
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Meiu Wong, Rebecca Racz, Edison Ong, Yongqun He:
Towards precision informatics of pharmacovigilance: OAE-CTCAE mapping and OAE-based representation and analysis of adverse events in patients treated with cancer drugs. AMIA 2017
[c6]
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Edison Ong, Yongqun He:
OLOBO: A New Ontology for Linking and Integrating Open Biological and Biomedical Ontologies. ICBO 2017
2016
[c5]
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Edison Ong, Yongqun He:
Application of Ontobedia on Cell Line Ontology Development. AMIA 2016
[c4]
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Edison Ong, Jiangan Xie, Zhaohui Ni, Qingping Liu, Yu Lin, Vasileios Stathias, Caty Chung, Stephan C. Schürer, Yongqun He:
The Cell Line Ontology Integration and Analysis of the Knowledge of LINCS Cell Lines. ICBO/BioCreative 2016
[c3]
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Edison Ong, Zuoshuang Xiang, Jie Zheng, Barry Smith, Yongqun He:
Ontobull and BFOConvert: Web-based Programs to Support Automatic Ontology Conversion. ICBO/BioCreative 2016
[c2]
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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
[j2]
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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:
A Scalable Method for Molecular Network Reconstruction Identifies Properties of Targets and Mutations in Acute Myeloid Leukemia. J. Comput. Biol. 22(4): 266-288 (2015)
[c1]
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Edison Ong, Yongqun He:
GOfox: Semantics-based simplified hierarchical classification and interactive visualization to support GO enrichment analysis. ICBO 2015
2014
[j1]
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Trish P. Tran, Edison Ong, Andrew P. Hodges, Giovanni Paternostro, Carlo Piermarocchi:
Prediction of kinase inhibitor response using activity profiling, in vitro screening, and elastic net regression. BMC Syst. Biol. 8: 74 (2014)

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