MGCPI: A Multi-granularity Neural Network for Predicting Compound-Protein Interactions. - Peixuan Lin; Likun Jiang; Fatma S. Ahmed; Xinru Ruan; Xiangrong Liu; Juan Liu 003 (ICIC (3), 2023)

NABP-BERT: NANOBODY®-antigen binding prediction based on bidirectional encoder representations from transformers (BERT) architecture. - Fatma S. Ahmed; Saleh K. H. Aly; Xiangrong Liu (Briefings Bioinform., 2024)

EPI-Trans: an effective transformer-based deep learning model for enhancer promoter interaction prediction. - Fatma S. Ahmed; Saleh K. H. Aly; Xiangrong Liu (BMC Bioinform., 2024)

NABP-LSTM-Att: Nanobody-Antigen binding prediction using bidirectional LSTM and soft attention mechanism. - Fatma S. Ahmed; Saleh K. H. Aly; Mohamed A. M. El-Tabakh; Xiangrong Liu (Comput. Biol. Chem., 2025)