ProtEC: A Transformer Based Deep Learning System for Accurate Annotation of Enzyme Commission Numbers. - Azwad Tamir; Milad Salem; Jiann-Shiun Yuan (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

ProtGO: A Transformer based Fusion Model for accurately predicting Gene Ontology (GO) Terms from full scale Protein Sequences. - Azwad Tamir; Jiann-Shiun Yuan (CoRR, 2024)

KITE-DDI: A Knowledge Graph Integrated Transformer Model for Accurately Predicting Drug-Drug Interaction Events From Drug SMILES and Biomedical Knowledge Graph. - Azwad Tamir; Jiann-Shiun Yuan (IEEE Access, 2025)