An improved ontological representation of dendritic cells as a paradigm for all cell types. - Anna Maria Masci; Cecilia N. Arighi; Alexander D. Diehl; Anne E. Lieberman; Chris Mungall; Richard H. Scheuermann; Barry Smith 001; Lindsay G. Cowell (BMC Bioinform., 2009)

owl_cpp, a C++ Library for Working with OWL Ontologies. - Mikhail K. Levin; Alan Ruttenberg; Anna Maria Masci; Lindsay G. Cowell (ICBO, 2011)

Connecting Ontologies for the Representation of Biological Pathways. - Anna Maria Masci; Mikhail K. Levin; Alan Ruttenberg; Lindsay G. Cowell (ICBO, 2011)

Bridging Multiple Ontologies: Representation of the Liver Immune Response. - Anna Maria Masci; Jeffrey Roach; Bernard de Bono; Pierre Grenon; Lindsay G. Cowell (ICBO, 2011)

Logical Development of the Cell Ontology. - Terrence F. Meehan; Anna Maria Masci; Amina Abdulla; Lindsay G. Cowell; Judith A. Blake; Christopher J. Mungall; Alexander D. Diehl (BMC Bioinform., 2011)

Hematopoietic cell types: Prototype for a revised cell ontology. - Alexander D. Diehl; Alison Deckhut Augustine; Judith A. Blake; Lindsay G. Cowell; Elizabeth S. Gold; Timothy A. Gondré-Lewis; Anna Maria Masci; Terrence F. Meehan; Penelope A. Morel; Anastasia Nijnik; Bjoern Peters; Bali Pulendran; et al. (J. Biomed. Informatics, 2011)

OBCS: The Ontology of Biological and Clinical Statistics. - Jie Zheng 001; Marcelline R. Harris; Anna Maria Masci; Yu Lin; Alfred O. Hero III; Barry Smith 001; Yongqun He (ICBO, 2014)

Protein Ontology: a controlled structured network of protein entities. - Darren A. Natale; Cecilia N. Arighi; Judith A. Blake; Carol J. Bult; Karen R. Christie; Julie Cowart; Peter D'Eustachio; Alexander D. Diehl; Harold J. Drabkin; Olivia Helfer; Hongzhan Huang; Anna Maria Masci; et al. (Nucleic Acids Res., 2014)

OBIB-a novel ontology for biobanking. - Mathias Brochhausen; Jie Zheng 001; David L. Birtwell; Heather Williams; Anna Maria Masci; Helena Judge Ellis; Christian J. Stoeckert Jr. (J. Biomed. Semant., 2016)

The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis. - Jie Zheng 001; Marcelline R. Harris; Anna Maria Masci; Yu Lin; Alfred O. Hero III; Barry Smith 001; Yongqun He (J. Biomed. Semant., 2016)

Standardization of the Histopathology Cancer Report: An Ontological Approach. - Anna Maria Masci; Shannon McCall; Alessandro Racioppi; Helena Judge Ellis; Jihad S. Obeid; Barry Smith 001; Christian J. Stoeckert Jr.; Jie Zheng 001 (ICBO, 2018)

Alignment of the Ontology of Host-Microbiome Interactions (OHMI) High Level Terms with Existing OBO Ontologies. - Yongqun He; Jie Zheng 001; Anna Maria Masci; Jihad S. Obeid (ICBO, 2019)

OHMI: the ontology of host-microbiome interactions. - Yongqun He; Haihe Wang; Jie Zheng 001; Daniel P. Beiting; Anna Maria Masci; Hong Yu 014; Kaiyong Liu; Jianmin Wu; Jeffrey L. Curtis; Barry Smith 001; Alexander V. Alekseyenko; Jihad S. Obeid (J. Biomed. Semant., 2019)

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)

Ontology-guided segmentation and object identification for developmental mouse lung immunofluorescent images. - Anna Maria Masci; Scott White; Ben Neely; Maryanne Ardini-Polaske; Carol B. Hill; Ravi S. Misra; Bruce J. Aronow; Nathan Gaddis; Lina Yang; Susan E. Wert; Scott M. Palmer; Cliburn Chan (BMC Bioinform., 2021)

Environmental Health Language Collaborative (EHLC): a Route to Environmental Health Science Data Harmonization. - Anna Maria Masci; Stephanie Holmgren; Charles Schmitt; Rima Habre; Anne E. Thessen; Rebecca Boyles; Carmen J. Marsit (ICBO, 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)

ON TO A Better Path to Choose Your Best Ontologies. - Asiyah Yu Lin; John Graybeal; Anna Maria Masci; Juliane Schneider; Ruth Duerr; Eric G. Stephan; Hande Küçük-McGinty (ICBO, 2024)

Compare the OBO Foundry Principles with the FAIR and TRUST Principles. - Anna Maria Masci; Daniela Rosu 002; Asiyah Yu Lin (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)