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)

OGG-CoV: Ontology Representation and Analysis of Genes and Genomes of Coronaviruses (short paper). - Anthony Huffman; Yongqun He (ICBO/ODLS, 2020)

CIDO ontology updates and secondary analysis of host responses to COVID-19 infection based on ImmPort reports and literature. - Anthony Huffman; Anna Maria Masci; Jie Zheng 001; Nasim Sanati; Timothy Brunson; Guanming Wu; Yongqun He (J. Biomed. Semant., 2021)

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)

Grounding Realizable Entities. - Michael Rabenberg; Carter Benson; Federico Donato; Yongqun He; Anthony Huffman; Shane Babcock; John Beverley (ICBO, 2024)

Ontological representation, modeling, and analysis of parasite vaccines. - Anthony Huffman; Xumeng Zhang; Meghana Lanka; Jie Zheng 001; Anna Maria Masci; Yongqun He (J. Biomed. Semant., 2024)

Empowering standardization of cancer vaccines through ontology: enhanced modeling and data analysis. - Jie Zheng 001; Xingxian Li; Anna Maria Masci; Hayleigh Kahn; Anthony Huffman; Eliyas Asfaw; Yuanyi Pan; Jinjing Guo; Virginia He; Justin Song; Andrey I. Seleznev; Asiyah Yu Lin; et al. (J. Biomed. Semant., 2024)

A fourfold pathogen reference ontology suite. - John Beverley; Shane Babcock; Carter Benson; Giacomo De Colle; Sydney Cohen; Alexander D. Diehl; Ram A. N. R. Challa; Ray Mavrovich; Joshua Billig; Anthony Huffman; Yongqun He (J. Biomed. Semant., 2025)