ProtFold-DFG: protein fold recognition by combining Directed Fusion Graph and PageRank algorithm. - Jiangyi Shao; Bin Liu (Briefings Bioinform., 2021)

FoldRec-C2C: protein fold recognition by combining cluster-to-cluster model and protein similarity network. - Jiangyi Shao; Ke Yan 003; Bin Liu 014 (Briefings Bioinform., 2021)

TALE-cmap: Protein function prediction based on a TALE-based architecture and the structure information from contact map. - Xiao-Yao Qiu; Hao Wu 066; Jiangyi Shao (Comput. Biol. Medicine, 2022)

ProtRe-CN: Protein Remote Homology Detection by Combining Classification Methods and Network Methods via Learning to Rank. - Jiangyi Shao; Junjie Chen 004; Bin Liu 014 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Corrigendum to "TALE-cmap: Protein function prediction based on a TALE-based architecture and the structure information from contact map" [Comput. Biol. Med. 149 (2022) 105938]. - Xiao-Yao Qiu; Hao Wu 066; Jiangyi Shao (Comput. Biol. Medicine, 2023)

PreHom-PCLM: protein remote homology detection by combing motifs and protein cubic language model. - Jiangyi Shao; Qi Zhang; Ke Yan 003; Bin Liu 014 (Briefings Bioinform., 2023)

TPpred-SC: multi-functional therapeutic peptide prediction based on multi-label supervised contrastive learning. - Ke Yan 003; Hongwu Lv; Jiangyi Shao; Shutao Chen; Bin Liu 014 (Sci. China Inf. Sci., 2024)

DeepGO-ESM: Improving the Protein Function Prediction of DeepGraphGO via the Evolutionary Scale Modeling Framework. - Jianxiang Zhao; Jiangyi Shao (ICIC (26), 2025)

ProFun-SOM: Protein Function Prediction for Specific Ontology Based on Multiple Sequence Alignment Reconstruction. - Jiangyi Shao; Junjie Chen 004; Bin Liu 014 (IEEE Trans. Neural Networks Learn. Syst., 2025)