Prediction of protein - peptide binding residues using classification algorithms. - Shima Shafiee; Abdolhossein Fathi; Fardin Abdali Mohammadi (BIBE, 2020)

Prediction of protein-peptide-binding amino acid residues regions using machine learning algorithms. - Shima Shafiee; Abdolhossein Fathi (CSICC, 2021)

SPPPred: Sequence-Based Protein-Peptide Binding Residue Prediction Using Genetic Programming and Ensemble Learning. - Shima Shafiee; Abdolhossein Fathi; Ghazaleh Taherzadeh (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Integrating Structural Information: Comparing Classification-Based and Segmentation-Based Predictors in Bioinformatics (Case Study: Protein-Peptide Region Residue-Level Interaction) Using Structural Information. - Shima Shafiee; Abdolhossein Fathi; Faezeh Safari (CSICC, 2025)

Protein-peptide interaction region residues prediction using a generative sampling technique and ensemble deep learning-based models. - Shima Shafiee; Abdolhossein Fathi; Ghazaleh Taherzadeh (Appl. Soft Comput., 2025)