iRBP-Motif-PSSM: Identification of RNA-Binding Proteins Based on Collaborative Learning. - Xin Gao; Donghua Wang; Jun Zhang 078; Qing Liao 001; Bin Liu 014 (IEEE Access, 2019)

NCBRPred: predicting nucleic acid binding residues in proteins based on multilabel learning. - Jun Zhang 078; Qingcai Chen; Bin Liu 014 (Briefings Bioinform., 2021)

SMI-BLAST: a novel supervised search framework based on PSI-BLAST for protein remote homology detection. - Xiaopeng Jin; Qing Liao 001; Hang Wei 005; Jun Zhang 078; Bin Liu 014 (Bioinform., 2021)

DeepDRBP-2L: A New Genome Annotation Predictor for Identifying DNA-Binding Proteins and RNA-Binding Proteins Using Convolutional Neural Network and Long Short-Term Memory. - Jun Zhang 078; Qingcai Chen; Bin Liu 014 (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

iDRNA-ITF: identifying DNA- and RNA-binding residues in proteins based on induction and transfer framework. - Ning Wang 054; Ke Yan 003; Jun Zhang 078; Bin Liu 014 (Briefings Bioinform., 2022)

PreRBP-TL: prediction of species-specific RNA-binding proteins based on transfer learning. - Jun Zhang 078; Ke Yan 003; Qingcai Chen; Bin Liu 014 (Bioinform., 2022)

iDRBP-ECHF: Identifying DNA- and RNA-binding proteins based on extensible cubic hybrid framework. - Jiawei Feng; Ning Wang 054; Jun Zhang 078; Bin Liu 014 (Comput. Biol. Medicine, 2022)

iEnhancer-ELM: Improve Enhancer Identification by Extracting Multi-scale Contextual Information based on Enhancer Language Models. - Jiahao Li; Zhourun Wu; Wenhao Lin; Jiawei Luo; Jun Zhang 078; Qingcai Chen; Junjie Chen 004 (CoRR, 2022)

IDRBP-PPCT: Identifying Nucleic Acid-Binding Proteins Based on Position-Specific Score Matrix and Position-Specific Frequency Matrix Cross Transformation. - Ning Wang 054; Jun Zhang 078; Bin Liu 014 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

iDRBP-EL: Identifying DNA- and RNA- Binding Proteins Based on Hierarchical Ensemble Learning. - Ning Wang 054; Jun Zhang 078; Bin Liu 014 (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

MIX-TPI: a flexible prediction framework for TCR-pMHC interactions based on multimodal representations. - Minghao Yang; Zhi-An Huang; Wei Zhou 001; Junkai Ji; Jun Zhang 078; Shan He 001; Zexuan Zhu (Bioinform., 2023)

PAIR: protein-aptamer interaction prediction based on language models and contrastive learning framework. - Jun Zhang 078; Zhiqiang Yan; Hao Zeng; Zexuan Zhu (BIBM, 2024)

TG-CDDPM: text-guided antimicrobial peptides generation based on conditional denoising diffusion probabilistic model. - Junhang Cao; Jun Zhang 078; Qiyuan Yu; Junkai Ji; Jianqiang Li; Shan He; Zexuan Zhu (Briefings Bioinform., 2024)

MDTL-ACP: Anticancer Peptides Prediction Based on Multi-Domain Transfer Learning. - Junhang Cao; Wei Zhou 001; Qiyuan Yu; Junkai Ji; Jun Zhang 078; Shan He 001; Zexuan Zhu (IEEE J. Biomed. Health Informatics, 2025)