Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations. - Fatima Zohra Smaili; Xin Gao 001; Robert Hoehndorf (Bioinform., 2018)

OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction. - Fatima Zohra Smaili; Xin Gao 001; Robert Hoehndorf (Bioinform., 2019)

Formal axioms in biomedical ontologies improve analysis and interpretation of associated data. - Fatima Zohra Smaili; Xin Gao 001; Robert Hoehndorf (Bioinform., 2020)

Machine Learning Models for Biomedical Ontology Integration and Analysis. - Fatima Zohra Smaili (2020)

Semantic similarity and machine learning with ontologies. - Maxat Kulmanov; Fatima Zohra Smaili; Xin Gao 001; Robert Hoehndorf (Briefings Bioinform., 2021)

QAUST: Protein Function Prediction Using Structure Similarity, Protein Interaction, and Functional Motifs. - Fatima Zohra Smaili; Shuye Tian; Ambrish Roy; Meshari Alazmi; Stefan T. Arold; Srayanta Mukherjee; P. Scott Hefty; Wei Chen 029; Xin Gao 001 (Genom. Proteom. Bioinform., 2021)

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)