O-GlcNAcPRED-II: an integrated classification algorithm for identifying O-GlcNAcylation sites based on fuzzy undersampling and a K-means PCA oversampling technique. - Cangzhi Jia; Yun Zuo 001; Quan Zou 001 (Bioinform., 2018)

A Deep Neural Network for Antimicrobial Peptide Recognition. - Jianyuan Lin; Xiangxiang Zeng; Yun Zuo 001; Ying Ju; Xiangrong Liu (BIBM, 2019)

Pm6 A: an Integrated Classification Algorithm for 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Identifying m6 A Sites. - Yun Zuo 001; Xiangrong Liu; Xiangxiang Zeng (BIBM, 2021)

CarSite-II: an integrated classification algorithm for identifying carbonylated sites based on K-means similarity-based undersampling and synthetic minority oversampling techniques. - Yun Zuo 001; Jianyuan Lin; Xiangxiang Zeng; Quan Zou 001; Xiangrong Liu (BMC Bioinform., 2021)

MLysPRED: graph-based multi-view clustering and multi-dimensional normal distribution resampling techniques to predict multiple lysine sites. - Yun Zuo 001; Yue Hong; Xiangxiang Zeng; Qiang Zhang 026; Xiangrong Liu (Briefings Bioinform., 2022)

MLNGCF: circRNA-disease associations prediction with multilayer attention neural graph-based collaborative filtering. - Qunzhuo Wu; Zhaohong Deng; Wei Zhang 221; Xiaoyong Pan; Kup-Sze Choi; Yun Zuo 001; Hong-Bin Shen; Dong-Jun Yu (Bioinform., 2023)

MlyPredCSED: based on extreme point deviation compensated clustering combined with cross-scale convolutional neural networks to predict multiple lysine sites in human. - Yun Zuo 001; Xingze Fang; Jiankang Chen; Jiayi Ji; Yuwen Li; Zeyu Wu; Xiangrong Liu; Xiangxiang Zeng; Zhaohong Deng; Hongwei Yin; Anjing Zhao (Briefings Bioinform., 2024)

MSlocPRED: deep transfer learning-based identification of multi-label mRNA subcellular localization. - Yun Zuo 001; Bangyi Zhang; Wenying He; Yue Bi; Xiangrong Liu; Xiangxiang Zeng; Zhaohong Deng (Briefings Bioinform., 2024)

MuSE: A deep learning model based on multi-feature fusion for super-enhancer prediction. - Wenying He; Haolu Zhou; Yun Zuo 001; Yude Bai; Fei Guo 001 (Comput. Biol. Chem., 2024)

ILYCROsite: Identification of lysine crotonylation sites based on FCM-GRNN undersampling technique. - Yun Zuo 001; Minquan Wan; Yang Shen; Xinheng Wang; Wenying He; Yue Bi; Xiangrong Liu; Zhaohong Deng (Comput. Biol. Chem., 2024)

NBCR-ac4C: A Deep Learning Framework Based on Multivariate BERT for Human mRNA N4-Acetylcytidine Sites Prediction. - Wenying He; Yu Han; Yun Zuo 001; Yude Bai; Fei Guo 001 (J. Chem. Inf. Model., 2024)

Glypred: Lysine Glycation Site Prediction via CCU-LightGBM-BiLSTM Framework with Multi-Head Attention Mechanism. - Yun Zuo 001; Bangyi Zhang; Yinkang Dong; Wenying He; Yue Bi; Xiangrong Liu; Xiangxiang Zeng; Zhaohong Deng (J. Chem. Inf. Model., 2024)

PreMLS: The undersampling technique based on ClusterCentroids to predict multiple lysine sites. - Yun Zuo 001; Xingze Fang; Jiayong Wan; Wenying He; Xiangrong Liu; Xiangxiang Zeng; Zhaohong Deng (PLoS Comput. Biol., 2024)

DCFICSH: A Dual-Channel Fusion Model Combining Multi-Modal Data for Identifying Cell-Specific Silencers and Their Strength in the Human Genome. - Jingdong Yuan; Qinqin Zhu; Haolu Zhou; Yu Han; Yun Zuo 001; Yude Bai; Wenying He (ICIC (19), 2025)

PreAIS: Prediction of A-to-I editing sites based on DNN-CNN deep learning models. - Xingze Fang; Yun Zuo 001; Youxu Tan; Xiangrong Liu; Xiangxiang Zeng; Zhaohong Deng (Comput. Biol. Chem., 2025)

Explainable RNA-Small Molecule Binding Affinity Prediction Based on Multiview Enhancement Learning. - Zeyu Wu; Zhaohong Deng; Qunzhuo Wu; Yun Zuo 001; Xiaoyong Pan; Hongbin Shen; Xingze Fang; Yuxi Ge; Shudong Hu (J. Chem. Inf. Model., 2025)

HMBVIP: A Novel Hierarchical Multi-Bio-View Intelligent Prediction Networks for Drug-Target Interaction Prediction. - Hailong Yang 001; Qiao Ning; Ze Song; Yue Chen; Guanjin Wang; Zhaohong Deng; Yun Zuo 001; Yuxi Ge; Shudong Hu (J. Chem. Inf. Model., 2025)

Diff-SE: A Diffusion-Augmented Contrastive Learning Framework for Super-Enhancer Prediction. - Haolu Zhou; Yu Han; Yude Bai; Yun Zuo 001; Wenying He; Fei Guo 001 (J. Chem. Inf. Model., 2025)