Ping Li, Yuqing Qian, Junhai Xu, Yijie Ding*, Fei Guo*, Prediction of ncRNA-Disease Association Based on Correntropy Induced Loss Matrix Factorization Model, IEEE Transactions on Computational Biology and Bioinformatics, 2025, 22(4): 1861-1874.
Yuqing Qian, Xin Zhang, Yizheng Wang, Quan Zou, Chen Cao*, Yijie Ding*, Xiaoyi Guo*, DTI-RME: a robust and multi-kernel ensemble approach for drug-target interaction prediction, BMC Biology, 2025, 23, 225.
Qian Liao, Yu Zhang, Ying Chu, Yi Ding, Zhen Liu, Xianyi Zhao, Yizheng Wang, Jie Wan, Yijie Ding*, Prayag Tiwari*, Quan Zou*, Ke Han*, Application of Artificial Intelligence In Drug-target Interactions Prediction: A Review, npj Biomedical Innovations, 2025, DOI: 10.1038/s44385-024-00003-9.
Xiaoyi Guo, Yijie Ding*, Quan Zou*, Kernelized Fuzzy System for Predicting Therapeutic Peptides via Deep Stacked Encoder, IEEE Transactions on Computational Biology and Bioinformatics, 2025, 22(4): 1494-1504.
Zhichao Xiao, Yan Li, Yijie Ding*, Liang Yu*, EPIPDLF: a pre-trained deep learning framework for predicting enhancer-promoter interactions, Bioinformatics, 2025, btae716.
Hao Xie, Leyao Wang, Yuqing Qian, Yijie Ding*, Fei Guo*, Methyl-GP: accurate generic DNA methylation prediction based on a language model and representation learning, Nucleic Acids Research, 2025, 53(6): gkaf223.
Yuqing Qian, Yizheng Wang, Junkai Liu, Quan Zou, Yijie Ding*, Xiaoyi Guo*, Weiping Ding*, A survey on multi-view fusion for predicting links in biomedical bipartite networks: Methods and applications, Information Fusion: 2025, 117(7270): 102894.
Chen Cao, Mengting Shao, Jianhua Wang, Zhenghui Li, Haoran Chen, Tianyi You, Mulin Jun Li, Yijie Ding*, Quan Zou*, webTWAS 2.0: update platform for identifying complex disease susceptibility genes through transcriptome-wide association study, Nucleic Acids Research: 2024, 112: 102563.
Yizheng Wang, Yixiao Zhai, Yijie Ding*, Quan Zou*, SBSM-Pro: support bio-sequence machine for proteins, Science China Information Sciences: 2024, 67(11): 1-16.
Zhichao Xiao, Yijie Ding*, Liang Yu*, Multiple kernel-based fuzzy system for identifying enhancers, Expert Systems with Applications: 2024, 264: 125981.
Leyao Wang; Yuqing Qian; Hao Xie; Yijie Ding*; Fei Guo*, Structured Sparse Regularization-based Deep Fuzzy Networks for RNA N6-Methyladenosine Sites Prediction, IEEE Transactions on Fuzzy Systems: 2024, DOI: 10.1109/TFUZZ.2024.3428402.
Junkai Liua; Fuyuan Hu; Quan Zou; Prayag Tiwari; Hongjie Wu*; Yijie Ding*, Drug Repositioning by Multi-Aspect Heterogeneous Graph Contrastive Learning and Positive-Fusion Negative Sampling, Information Fusion: 2024, DOI: 10.1016/j.inffus.2024.102563.
Yijie Ding; Prayag Tiwari; Fei Guo; Quan Zou*, Weiping Ding*, Fuzzy Neural Tangent Kernel Model for Identifying DNA N4-methylcytosine Sites, IEEE Transactions on Fuzzy Systems: 2024, DOI: 10.1109/TFUZZ.2024.3425616.
Yuqing Qian; Quan Zou; Mengyuan Zhao; Yi Liu; Fei Guo*; Yijie Ding*, scRNMF: an imputation method for single-cell RNA-seq data by robust and non-negative matrix factorization, PLoS Computational Biology: 2024, DOI: 10.1371/journal.pcbi.xxx.
Chengwei Ai; Hongpeng Yang; Xiaoyi Liu; Ruihan Dong; Yijie Ding*; Fei Guo*, MTMol-GPT: De novo multi-target molecular generation with transformer-based generative adversarial imitation learning, PLoS Computational Biology: 2024, DOI: 10.1371/journal.pcbi.1012229.
Yuqing Qian; Ziyu Zheng; Prayag Tiwari; Yijie Ding*; Quan Zou, Multiple Kronecker RLS fusion-based link propagation for drug-side effect prediction, Transactions on Machine Learning Research: 2024, online.
Xiaoyi Guo; Ziyu Zheng; Kang Hao Cheong; Quan Zou; Prayag Tiwari*; Yijie Ding*, Sequence homology score-based deep fuzzy network for identifying therapeutic peptides, Neural Networks: 2024, DOI: 10.1016/j.neunet.2024.106458.
Hongjie Wu; Junkai Liu; Runhua Zhang; Yaoyao Lu; Guozeng Cui; Yijie Ding*, A review of deep learning methods for ligand based drug virtual screening, Fundamental Research: 2024, DOI: 10.1016/j.fmre.2024.02.011.
Mingshuai Chen; Quan Zou; Ren Qi*; Yijie Ding*, PseU-KeMRF: A novel method for identifying RNA pseudouridine sites, IEEE/ACM Transactions on Computational Biology and Bioinformatics: 2024, DOI: 10.1109/TCBB.2024.3389094.
Mingshuai Chen; Mingai Sun; Xi Su; Prayag Tiwari*; Yijie Ding*, Fuzzy kernel evidence random forest for identifying pseudouridine sites, Briefings in Bioinformatics: 2024, DOI: 10.1093/bib/bbae169.
Mingliang Dou; Jijun Tang; Prayag Tiwari*; Yijie Ding*; Fei Guo*, Drug-drug interaction relation extraction based on deep learning: A review, ACM Computing Surveys: 2024, DOI: 10.1145/3645089.
Hao Xie; Yijie Ding*; Yuqing Qian; Prayag Tiwari; Fei Guo, Structured Sparse Regularization based Random Vector Functional Link Networks for DNA N4-methylcytosine sites prediction, Expert Systems With Applications: 2023, DOI: 10.1016/j.eswa.2023.121157.
Xiaoyi Liu; Hongpeng Yang; Chengwei Ai; Yijie Ding*; Fei Guo*; Jijun Tang, MVML-MPI: Multi-View Multi-Label Learning for Metabolic Pathway Inference, Briefings in Bioinformatics: 2023, DOI: 10.1093/bib/bbad393.
Hongjie Wu; Junkai Liu; Tengsheng Jiang; Quan Zou; Shujie Qi; Zhiming Cui; Prayag Tiwari*; Yijie Ding*, AttentionMGT-DTA: A multi-modal drug-target affinity prediction using graph transformer and attention mechanism, Neural Networks: 2023, DOI: 10.1016/j.neunet.2023.11.018.
Yijie Ding; Fei Guo; Prayag Tiwari; Quan Zou, Identification of drug-side effect association via multi-view semi-supervised sparse model, IEEE Transactions on Artificial Intelligence: 2023, DOI: 10.1109/TAI.2023.3314405.
Rui Fan; Yijie Ding*; Quan Zou*; Lei Yuan*, Multi-view local hyperplane nearest neighbor model based on independence criterion for identifying vesicular transport proteins, International Journal of Biological Macromolecules: 2023, DOI: 10.1016/j.ijbiomac.2023.125774.
Yijie Ding; Prayag Tiwari; Fei Guo; Quan Zou, Multi-Correntropy Fusion based Fuzzy System for Predicting DNA N4-methylcytosine Sites, Information Fusion: 2023, DOI: 10.1016/j.inffus.2023.101911.
Chengwei Ai; Hongpeng Yang; Yijie Ding*; Jijun Tang; Fei Guo*, Low Rank Matrix Factorization Algorithm Based on Multi-Graph Regularization for Detecting Drug-Disease Association, IEEE/ACM Transactions on Computational Biology and Bioinformatics: 2023, DOI: 10.1109/TCBB.2023.3274587.
Leyao Wang; Prayag Tiwari*; Yijie Ding*; Fei Guo*, Weighted Fuzzy System for Identifying DNA N4-methylcytosine Sites with Kernel Entropy Component Analysis, IEEE Transactions on Artificial Intelligence: 2023, DOI: 10.1109/TAI.2023.3266191.
Yizheng Wang; Xin Zhang; Ying Ju; Qing Liu; Quan Zou; Yazhou Zhang; Yijie Ding*; Ying Zhang*, Identification of human microRNA-disease association via low-rank approximation-based link propagation and multiple kernel learning, Frontiers of Computer Science: 2023, DOI: 10.1007/s11704-023-2490-5.
Leyao Wang; Yijie Ding*; Prayag Tiwari*; Wenhuan Lu; Junhai Xu; Khan Muhammad; Victor Hugo C. de Albuquerquee; Fei Guo*, A deep multiple kernel learning-based higher-order fuzzy inference system for identifying DNA N4-methylcytosine sites, Information Sciences: 2023, DOI: 10.1016/j.ins.2023.01.149.
Xiaoyi Guo; Prayag Tiwari*; Quan Zou*; Yijie Ding*, Subspace projection-based weighted echo state networks for predicting therapeutic peptides, Knowledge-Based Systems: 2023, DOI: 10.1016/j.knosys.2023.110307.
Ke Han; Jianchun Wang; Yu Wang; Lei Zhang; Mengyao Yu; Fang Xie; Dequan Zheng; Yaoqun Xu; Yijie Ding*; Jie Wan*, A review of methods for predicting DNA N6-methyladenine sites, Briefings in Bioinformatics: 2023, DOI: 10.1093/bib/bbac514.
Ping Li; Prayag Tiwari*; Junhai Xu; Yuqing Qian; Chengwei Ai; Yijie Ding*; Fei Guo*, Sparse Regularized Joint Projection Model for Identifying Associations of Non-coding RNAs and Human Diseases, Knowledge-Based Systems: 2022, DOI: 10.1016/j.knosys.2022.110044.
Xiaoyi Guo; Yuqing Qian; Prayag Tiwari*; Quan Zou*; Yijie Ding*, Kernel Risk Sensitive Loss-based Echo State Networks for Predicting Therapeutic Peptides with Sparse Learning, 2022 IEEE International Conference on Bioinformatics and Biomedicine, (IEEE BIBM): 2022, DOI: 10.1109/BIBM55620.2022.9994902. (CCF B conference)
Yuqing Qian; Yijie Ding*; Quan Zou*; Fei Guo*, Identification of Drug-Side Effect Association via Restricted Boltzmann Machines with Penalized Term, Briefings in Bioinformatics: 2022, DOI: 10.1093/bib/bbac458.
Yijie Ding; Prayag Tiwari; Fei Guo; Quan Zou, Shared subspace-based radial basis function neural network for identifying ncRNAs subcellular localization, Neural Networks: 2022, DOI: 10.1016/j.neunet.2022.09.026.
Yuqing Qian; Yijie Ding*; Quan Zou*; Fei Guo*, Multi-view Kernel Sparse Representation for Identification of Membrane Protein Types, IEEE/ACM Transactions on Computational Biology and Bioinformatics: 2022, DOI: 10.1109/TCBB.2022.3191325.
Shixuan Guan; Quan Zou; Hongjie Wu*; Yijie Ding*, Protein-DNA Binding Residues Prediction Using a Deep Learning Model with Hierarchical Feature Extraction, IEEE/ACM Transactions on Computational Biology and Bioinformatics: 2022, DOI: 10.1109/TCBB.2022.3190933.
Shixuan Guan#; Yuqing Qian#; Tengsheng Jiang; Min Jiang; Yijie Ding*; Hongjie Wu*, MV-H-RKM: A Multiple View-based Hypergraph Regularized Restricted Kernel Machine for Predicting DNA-binding Proteins, IEEE/ACM Transactions on Computational Biology and Bioinformatics: 2022, DOI: 10.1109/TCBB.2022.3183191.
Mengwei Sun; Prayag Tiwari*; Yuqing Qian; Yijie Ding*; Quan Zou*, MLapSVM-LBS: Predicting DNA-Binding Proteins via a Multiple Laplacian Regularized Support Vector Machine with Local Behavior Similarity, Knowledge-Based Systems: 2022, DOI: 10.1016/j.knosys.2022.109174.
Chengwei Ai; Prayag Tiwari*; Hongpeng Yang; Yijie Ding*; Jijun Tang; Fei Guo*, Identification of DNA N4-methylcytosine sites via multi-view kernel sparse representation model, IEEE Transactions on Artificial Intelligence: 2022, DOI: 10.1109/TAI.2022.3187060.
Leyao Wang; Yijie Ding*; Junhai Xu; Wenhuan Lu; Jijun Tang; Fei Guo*, Identification of DNA N4-Methylcytosine Sites via Fuzzy Model on Self Representation, Applied Soft Computing: 2022, DOI: 10.1016/j.asoc.2022.108840.
Chengwei Ai; Hongpeng Yang; Yijie Ding*; Jijun Tang; Fei Guo*, A multi-layer multi-kernel neural network for determining associations between non-coding RNAs and diseases, Neurocomputing: 2022, DOI: 10.1016/j.neucom.2022.04.068.
Yijie Ding; Prayag Tiwari; Quan Zou; Fei Guo; Hari Mohan Pandey, C-loss based Higher-order Fuzzy Inference Systems for Identifying DNA N4-methylcytosine Sites, IEEE Transactions on Fuzzy Systems: 2022, DOI: 10.1109/TFUZZ.2022.3159103.
Yijie Ding; Jijun Tang; Fei Guo*; Quan Zou*, Identification of drug-target interactions via multiple kernel-based triple collaborative matrix factorization, Briefings in Bioinformatics: 2022, DOI: 10.1093/bib/bbab582.
Yijie Ding; Wenying He; Jijun Tang; Quan Zou*; Fei Guo*, Laplacian Regularized Sparse Representation based Classifier for Identifying DNA N4-methylcytosine Sites via L2,1/2-matrix Norm, IEEE/ACM Transactions on Computational Biology and Bioinformatics: 2021, DOI: 10.1109/TCBB.2021.3133309.
Mengwei Sun; Yuqing Qian; Yijie Ding*; Jijun Tang; Quan Zou*, Membrane Protein Identification via Multi-view Graph Regularized k-Local Hyperplane Distance Nearest Neighbor Model, 2021 IEEE International Conference on Bioinformatics and Biomedicine, (IEEE BIBM): 2021, DOI: 10.1109/BIBM52615.2021.9669833. (CCF B conference)
Hongpeng Yang; Yijie Ding*; Jijun Tang; Fei Guo*, Inferring human microbe-drug associations via multiple kernel fusion on graph neural network, Knowledge-Based Systems: 2021, DOI: 10.1016/j.knosys.2021.107888.
Chao Yang; Yijie Ding*; Qiaozhen Meng; Jijun Tang; Fei Guo*,Granular multiple kernel learning for identifying RNA-binding protein residues via integrating sequence and structure information, Neural Computing and Applications: 2021, DOI: 10.1007/s00521-020-05573-4.
Haohao Zhou; Hao Wang; Jijun Tang; Yijie Ding*; Fei Guo*, Identify ncRNA subcellular localization via graph regularized k-local hyperplane distance nearest neighbor model on multi-kernel learning, IEEE/ACM Transactions on Computational Biology and Bioinformatics: 2021, DOI: 10.1109/TCBB.2021.3107621.
Hongpeng Yang; Yijie Ding*; Jijun Tang; Fei Guo*, Identifying potential association on gene-disease network via dual hypergraph regularized least squares, BMC Genomics: 2021, DOI: 10.1186/s12864-021-07864-z.
Yijie Ding; Chao Yang; Jijun Tang; Fei Guo*, Identification of protein-nucleotide binding residues via graph regularized k-local hyperplane distance nearest neighbor model, Applied Intelligence: 2021, DOI: 10.1007/s10489-021-02737-0.
Hongpeng Yang; Yijie Ding*; Jijun Tang; Fei Guo*, Drug-disease associations prediction via Multiple Kernel-based Dual Graph Regularized Least Squares, Applied Soft Computing: 2021, 112(2):107811, DOI: 10.1016/j.asoc.2021.107811.
Yijie Ding; Jijun Tang; Fei Guo*, Identification of Drug-Target Interactions via Multi-view Graph Regularized Link Propagation Model, Neurocomputing: 2021, DOI: 10.1016/j.neucom.2021.05.100.
Yuqing Qian; Limin Jiang; Yijie Ding*; Jijun Tang; Fei Guo*, A sequence-based multiple kernel model for identifying DNA-binding proteins, BMC Bioinformatics: 2021, DOI: 10.1186/s12859-020-03875-x.
Yuqing Qian; Hao Meng; Weizhong Lu; Zhijun Liao*; Yijie Ding*; Hongjie Wu*. Identification of DNA-binding proteins via Hypergraph based Laplacian Support Vector Machine, Current Bioinformatics: 2021, DOI: 10.2174/1574893616666210806091922.
Yan Zheng; Hao Wang; Yijie Ding*; Fei Guo*,CEPZ: A Novel Predictor for Identification of DNase I Hypersensitive Sites, IEEE/ACM Transactions on Computational Biology and Bioinformatics:2021, DOI: 10.1109/TCBB.2021.3053661.
Yinuo Lyu; Zhen Zhang; Jiawei Li; Wenying He; Yijie Ding*; Fei Guo*,iEnhancer-KL: a novel two-layer predictor for identifying enhancer by position specific of nucleotide composition, IEEE/ACM Transactions on Computational Biology and Bioinformatics: 2021, DOI: 10.1109/TCBB.2021.3053608.
Hao Wang; Jijun Tang; Yijie Ding*; Fei Guo*, Exploring associations of non-coding RNAs in human diseases via three-matrix factorization with hypergraph-regular terms on center kernel alignment, Briefings in Bioinformatics, 2021, DOI: 10.1093/bib/bbaa409.
Yijie Ding; Jijun Tang; Fei Guo*. Human protein subcellular localization identification via fuzzy model on Kernelized Neighborhood Representation, Applied Soft Computing 2020, doi: 10.1016/j.asoc.2020.106596.
Yijie Ding, Jijun Tang, Fei Guo*, Identification of Drug-Target Interactions via Dual Laplacian Regularized Least Squares with Multiple Kernel Fusion, Knowledge-Based Systems, 2020,204,106254.
Hao Wang; Yijie Ding*; Jijun Tang; Fei Guo*, Identification of membrane protein types via multivariate information fusion with Hilbert-Schmidt Independence Criterion, Neurocomputing, 2020,383: 257-269.
Yijie Ding; Limin Jiang; Jijun Tang; Fei Guo*, Identification of human microRNA-disease association via hypergraph embedded bipartite local model, Computational Biology and Chemistry, 2020, DOI: 10.1016/j.compbiolchem.2020.107369.
Yi Zou; Hongjie Wu; Xiaoyi Guo; Li Peng; Yijie Ding*; Jijun Tang; Fei Guo*, MK-FSVM-SVDD: A Multiple Kernel-based Fuzzy SVM Model for Predicting DNA-binding Proteins via Support Vector Data Description, Current Bioinformatics, 2020, DOI: 10.2174/1574893615999200607173829.
Yijie Ding; Jijun Tang; Fei Guo*. Identification of drug-target interactions via fuzzy bipartite local model. Neural Computing and Applications: 2019, DOI: 10.1007/s00521-019-04569-z.
Yijie Ding; Jijun Tang; Fei Guo*. Protein Crystallization Identification via Fuzzy Model on Linear Neighborhood Representation. IEEE/ACM Transactions on Computational Biology and Bioinformatics: 2019, DOI: 10.1109/TCBB.2019.2954826.
Yijie Ding; Jijun Tang; Fei Guo*. The Computational Models of Drug-target Interaction Prediction. Protein and Peptide Letters: 2019, DOI: 10.2174/0929866526666190410124110.
Yijie Ding; Jijun Tang; Fei Guo*. Identification of Drug-side Effect Association via Semi-supervised Model and Multiple Kernel Learning. IEEE Journal of Biomedical and Health Informatics: 2019, 23(6), 2619-2632.
Yijie Ding; Jijun Tang; Fei Guo*. Identification of drug-side effect association via multiple information integration with centered kernel alignment. Neurocomputing: 2019 ,325 ,211-224.
Yijie Ding; Jijun Tang; Fei Guo*. Identification of drug-target interactions via multiple information integration. Information Sciences: 2017 ,418 ,546-560.
Yijie Ding; Jijun Tang; Fei Guo*. Identification of Protein-Ligand Binding Sites by Sequence Information and Ensemble Classifier. Journal of chemical information and modeling: 2017 ,57 (12) ,3149-3161.
Yijie Ding; Jijun Tang; Fei Guo*. Predicting protein-protein interactions via multivariate mutual information of protein sequences. BMC bioinformatics: 2016 ,17 (1) ,398.
Full publications: Researchgate
Last Update: 2025/9/9