Dong-Jun Yu

Publication Activity (10 Years)

Years Active: 2012-2024
Publications (10 Years): 68

Top Topics

Subcellular Localization

Top Venues

Briefings Bioinform.

J. Chem. Inf. Model.

IEEE ACM Trans. Comput. Biol. Bioinform.

Publications

Jia-Shun Wu, Yan Liu, Fang Ge, Dong-Jun Yu
Prediction of protein-ATP binding residues using multi-view feature learning via contextual-based co-attention network. Comput. Biol. Medicine 172 (2024)
Shuo Li, Yan Liu, Long-Chen Shen, He Yan, Jiangning Song, Dong-Jun Yu
GMFGRN: a matrix factorization and graph neural network approach for gene regulatory network inference. Briefings Bioinform. 25 (2) (2024)
He Yan, Yan Liu, Yanmeng Li, Qiaolin Ye, Dong-Jun Yu, Yong Qi
Robust GEPSVM classifier: An efficient iterative optimization framework. Inf. Sci. 657 (2024)
Zihao Yan, Fang Ge, Yan Liu, Yumeng Zhang, Fuyi Li, Jiangning Song, Dong-Jun Yu
TransEFVP: A Two-Stage Approach for the Prediction of Human Pathogenic Variants Based on Protein Sequence Embedding Fusion. J. Chem. Inf. Model. 64 (4) (2024)
Yi-Heng Zhu, Zi Liu, Yan Liu, Zhiwei Ji, Dong-Jun Yu
ULDNA: integrating unsupervised multi-source language models with LSTM-attention network for high-accuracy protein-DNA binding site prediction. Briefings Bioinform. 25 (2) (2024)
Zi Liu, Chengxin Zhang, Qidi Zhang, Yang Zhang, Dong-Jun Yu
TM-search: An Efficient and Effective Tool for Protein Structure Database Search. J. Chem. Inf. Model. 64 (3) (2024)
Ming Zhang, Chao Gong, Fang Ge, Dong-Jun Yu
FCMSTrans: Accurate Prediction of Disease-Associated nsSNPs by Utilizing Multiscale Convolution and Deep Feature Combination within a Transformer Framework. J. Chem. Inf. Model. 64 (4) (2024)
He Yan, Li Cheng, Qiaolin Ye, Dong-Jun Yu, Yong Qi
Robust generalized canonical correlation analysis. Appl. Intell. 53 (18) (2023)
Fang Ge, Muhammad Arif, Zihao Yan, Hanin H. Alahmadi, Apilak Worachartcheewan, Dong-Jun Yu, Watshara Shoombuatong
MMPatho: Leveraging Multilevel Consensus and Evolutionary Information for Enhanced Missense Mutation Pathogenic Prediction. J. Chem. Inf. Model. 63 (22) (2023)
Yan Liu, Guo Wei, Chen Li, Long-Chen Shen, Robin B. Gasser, Jiangning Song, Dijun Chen, Dong-Jun Yu
TripletCell: a deep metric learning framework for accurate annotation of cell types at the single-cell level. Briefings Bioinform. 24 (3) (2023)
Zi Liu, Yi-Heng Zhu, Long-Chen Shen, Xuan Xiao, Wangren Qiu, Dong-Jun Yu
Integrating unsupervised language model with multi-view multiple sequence alignments for high-accuracy inter-chain contact prediction. Comput. Biol. Medicine 166 (2023)
Fang Ge, Chen Li, Shahid Iqbal, Muhammad Arif, Fuyi Li, Maha A. Thafar, Zihao Yan, Apilak Worachartcheewan, Xiaofeng Xu, Jiangning Song, Dong-Jun Yu
VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants. Briefings Bioinform. 24 (1) (2023)
Ying Zhang, Fang Ge, Fuyi Li, Xibei Yang, Jiangning Song, Dong-Jun Yu
Prediction of Multiple Types of RNA Modifications via Biological Language Model. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (5) (2023)
Yan Liu, He Yan, Long-Chen Shen, Dong-Jun Yu
Learning Cell Annotation under Multiple Reference Datasets by Multisource Domain Adaptation. J. Chem. Inf. Model. 63 (1) (2023)
Ying Zhang, Zhikang Wang, Yiwen Zhang, Shanshan Li, Yuming Guo, Jiangning Song, Dong-Jun Yu
Interpretable prediction models for widespread m6A RNA modification across cell lines and tissues. Bioinform. 39 (12) (2023)
Matee Ullah, Fazal Hadi, Jiangning Song, Dong-Jun Yu
PScL-2LSAESM: bioimage-based prediction of protein subcellular localization by integrating heterogeneous features with the two-level SAE-SM and mean ensemble method. Bioinform. 39 (1) (2023)
Qunzhuo Wu, Zhaohong Deng, Wei Zhang, Xiaoyong Pan, Kup-Sze Choi, Yun Zuo, Hong-Bin Shen, Dong-Jun Yu
MLNGCF: circRNA-disease associations prediction with multilayer attention neural graph-based collaborative filtering. Bioinform. 39 (8) (2023)
Yang Hua, Xiaoning Song, Zhen-Hua Feng, Xiaojun Wu, Josef Kittler, Dong-Jun Yu
CPInformer for Efficient and Robust Compound-Protein Interaction Prediction. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (1) (2023)
Jun Hu, Wen-Wu Zeng, Ning-Xin Jia, Muhammad Arif, Dong-Jun Yu, Gui-Jun Zhang
Improving DNA-Binding Protein Prediction Using Three-Part Sequence-Order Feature Extraction and a Deep Neural Network Algorithm. J. Chem. Inf. Model. 63 (3) (2023)
Matee Ullah, Fazal Hadi, Jiangning Song, Dong-Jun Yu
PScL-DDCFPred: an ensemble deep learning-based approach for characterizing multiclass subcellular localization of human proteins from bioimage data. Bioinform. 38 (16) (2022)
Yi-Heng Zhu, Chengxin Zhang, Yan Liu, Gilbert S. Omenn, Peter L. Freddolino, Dong-Jun Yu, Yang Zhang
TripletGO: Integrating Transcript Expression Profiles with Protein Homology Inferences for Gene Function Prediction. Genom. Proteom. Bioinform. 20 (5) (2022)
Fang Ge, Ying Zhang, Jian Xu, Muhammad Arif, Jiangning Song, Dong-Jun Yu
Prediction of disease-associated nsSNPs by integrating multi-scale ResNet models with deep feature fusion. Briefings Bioinform. 23 (1) (2022)
He Yan, Yong Qi, Qiaolin Ye, Dong-Jun Yu
Robust Least Squares Twin Support Vector Regression With Adaptive FOA and PSO for Short-Term Traffic Flow Prediction. IEEE Trans. Intell. Transp. Syst. 23 (9) (2022)
Guan-Yu Zhu, Yan Liu, Peng-Hao Wang, Xibei Yang, Dong-Jun Yu
Learning Protein Embedding to Improve Protein Fold Recognition Using Deep Metric Learning. J. Chem. Inf. Model. 62 (17) (2022)
Shahid Iqbal, Fang Ge, Fuyi Li, Tatsuya Akutsu, Yuanting Zheng, Robin B. Gasser, Dong-Jun Yu, Geoffrey I. Webb, Jiangning Song
PROST: AlphaFold2-aware Sequence-Based Predictor to Estimate Protein Stability Changes upon Missense Mutations. J. Chem. Inf. Model. 62 (17) (2022)
Qunzhuo Wu, Zhaohong Deng, Xiaoyong Pan, Hong-Bin Shen, Kup-Sze Choi, Shitong Wang, Jing Wu, Dong-Jun Yu
MDGF-MCEC: a multi-view dual attention embedding model with cooperative ensemble learning for CircRNA-disease association prediction. Briefings Bioinform. 23 (5) (2022)
Ke Han, Long-Chen Shen, Yi-Heng Zhu, Jian Xu, Jiangning Song, Dong-Jun Yu
MAResNet: predicting transcription factor binding sites by combining multi-scale bottom-up and top-down attention and residual network. Briefings Bioinform. 23 (1) (2022)
Liang Rao, Ning-Xin Jia, Jun Hu, Dong-Jun Yu, Gui-Jun Zhang
ATPdock: a template-based method for ATP-specific protein-ligand docking. Bioinform. 38 (2) (2022)
He Yan, Liyong Fu, Tian'an Zhang, Jun Hu, Qiaolin Ye, Yong Qi, Dong-Jun Yu
Robust distance metric optimization driven GEPSVM classifier for pattern classification. Pattern Recognit. 129 (2022)
Yi-Heng Zhu, Chengxin Zhang, Dong-Jun Yu, Yang Zhang
Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction. PLoS Comput. Biol. 18 (12) (2022)
He Yan, Liyong Fu, Yong Qi, Li Cheng, Qiaolin Ye, Dong-Jun Yu
Learning a robust classifier for short-term traffic state prediction. Knowl. Based Syst. 242 (2022)
Jun Hu, Yan-Song Bai, Lin-Lin Zheng, Ning-Xin Jia, Dong-Jun Yu, Gui-Jun Zhang
Protein-DNA Binding Residue Prediction via Bagging Strategy and Sequence-Based Cube-Format Feature. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (6) (2022)
Lu-Xing Zhang, He Yan, Yan Liu, Jian Xu, Jiangning Song, Dong-Jun Yu
Enhancing Characteristic Gene Selection and Tumor Classification by the Robust Laplacian Supervised Discriminative Sparse PCA. J. Chem. Inf. Model. 62 (7) (2022)
He Yan, Liyong Fu, Yong Qi, Dong-Jun Yu, Qiaolin Ye
Robust ensemble method for short-term traffic flow prediction. Future Gener. Comput. Syst. 133 (2022)
Muhammad Arif, Muhammad Kabir, Saeed Ahmed, Abid Khan, Fang Ge, Adel Khelifi, Dong-Jun Yu
DeepCPPred: A Deep Learning Framework for the Discrimination of Cell-Penetrating Peptides and Their Uptake Efficiencies. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (5) (2022)
Yi-Heng Zhu, Jun Hu, Fang Ge, Fuyi Li, Jiangning Song, Yang Zhang, Dong-Jun Yu
Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features. Briefings Bioinform. 22 (3) (2021)
Ying Zhang, Yan Liu, Jian Xu, Xiaoyu Wang, Xinxin Peng, Jiangning Song, Dong-Jun Yu
Leveraging the attention mechanism to improve the identification of DNA N6-methyladenine sites. Briefings Bioinform. 22 (6) (2021)
Matee Ullah, Ke Han, Fazal Hadi, Jian Xu, Jiangning Song, Dong-Jun Yu
PScL-HDeep: image-based prediction of protein subcellular location in human tissue using ensemble learning of handcrafted and deep learned features with two-layer feature selection. Briefings Bioinform. 22 (6) (2021)
Jing Xu, Fuyi Li, André Leier, Dongxu Xiang, Hsin-Hui Shen, Tatiana T. Marquez-Lago, Jian Li, Dong-Jun Yu, Jiangning Song
Comprehensive assessment of machine learning-based methods for predicting antimicrobial peptides. Briefings Bioinform. 22 (5) (2021)
Yan Liu, Yi-Heng Zhu, Xiaoning Song, Jiangning Song, Dong-Jun Yu
Why can deep convolutional neural networks improve protein fold recognition? A visual explanation by interpretation. Briefings Bioinform. 22 (5) (2021)
Jun Hu, Liang Rao, Yi-Heng Zhu, Gui-Jun Zhang, Dong-Jun Yu
TargetDBP+: Enhancing the Performance of Identifying DNA-Binding Proteins via Weighted Convolutional Features. J. Chem. Inf. Model. 61 (1) (2021)
Yang Li, Chengxin Zhang, Eric W. Bell, Wei Zheng, Xiaogen Zhou, Dong-Jun Yu, Yang Zhang
Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks. PLoS Comput. Biol. 17 (3) (2021)
Xiaoning Song, Yao Chen, Zhen-Hua Feng, Guosheng Hu, Dong-Jun Yu, Xiaojun Wu
SP-GAN: Self-Growing and Pruning Generative Adversarial Networks. IEEE Trans. Neural Networks Learn. Syst. 32 (6) (2021)
Long-Chen Shen, Yan Liu, Jiangning Song, Dong-Jun Yu
SAResNet: self-attention residual network for predicting DNA-protein binding. Briefings Bioinform. 22 (5) (2021)
Yan Liu, Ke Han, Yi-Heng Zhu, Ying Zhang, Long-Chen Shen, Jiangning Song, Dong-Jun Yu
Improving protein fold recognition using triplet network and ensemble deep learning. Briefings Bioinform. 22 (6) (2021)
Yanchao Li, Yongli Wang, Dong-Jun Yu, Ning Ye, Peng Hu, Ruxin Zhao
ASCENT: Active Supervision for Semi-Supervised Learning. IEEE Trans. Knowl. Data Eng. 32 (5) (2020)
Muhammad Arif, Saeed Ahmad, Farman Ali, Ge Fang, Min Li, Dong-Jun Yu
TargetCPP: accurate prediction of cell-penetrating peptides from optimized multi-scale features using gradient boost decision tree. J. Comput. Aided Mol. Des. 34 (8) (2020)
Jun Hu, Xiaogen Zhou, Yi-Heng Zhu, Dong-Jun Yu, Gui-Jun Zhang
TargetDBP: Accurate DNA-Binding Protein Prediction Via Sequence-Based Multi-View Feature Learning. IEEE ACM Trans. Comput. Biol. Bioinform. 17 (4) (2020)
Ming-Cai Chen, Yang Li, Yi-Heng Zhu, Fang Ge, Dong-Jun Yu
SSCpred: Single-Sequence-Based Protein Contact Prediction Using Deep Fully Convolutional Network. J. Chem. Inf. Model. 60 (6) (2020)
He Yan, Qiaolin Ye, Dong-Jun Yu
Efficient and robust TWSVM classification via a minimum L1-norm distance metric criterion. Mach. Learn. 108 (6) (2019)
Xiaoning Song, Guosheng Hu, Jian-Hao Luo, Zhen-Hua Feng, Dong-Jun Yu, Xiao-Jun Wu
Fast SRC using quadratic optimisation in downsized coefficient solution subspace. Signal Process. 161 (2019)
Yi-Heng Zhu, Jun Hu, Xiaoning Song, Dong-Jun Yu
DNAPred: Accurate Identification of DNA-Binding Sites from Protein Sequence by Ensembled Hyperplane-Distance-Based Support Vector Machines. J. Chem. Inf. Model. 59 (6) (2019)
Yang Li, Jun Hu, Chengxin Zhang, Dong-Jun Yu, Yang Zhang
ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks. Bioinform. 35 (22) (2019)
Jingzheng Li, Xibei Yang, Xiaoning Song, Jinhai Li, Pingxin Wang, Dong-Jun Yu
Neighborhood attribute reduction: a multi-criterion approach. Int. J. Mach. Learn. Cybern. 10 (4) (2019)
Xiao-Rong Bao, Yi-Heng Zhu, Dong-Jun Yu
DeepTF: Accurate Prediction of Transcription Factor Binding Sites by Combining Multi-scale Convolution and Long Short-Term Memory Neural Network. IScIDE (2) (2019)
He Yan, Qiaolin Ye, Tian'an Zhang, Dong-Jun Yu, Yiqing Xu
L1-Norm GEPSVM Classifier Based on an Effective Iterative Algorithm for Classification. Neural Process. Lett. 48 (1) (2018)
Jun Hu, Zi Liu, Dong-Jun Yu, Yang Zhang
LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening. Bioinform. 34 (13) (2018)
Chun-Qiu Xia, Ke Han, Yong Qi, Yang Zhang, Dong-Jun Yu
A Self-Training Subspace Clustering Algorithm under Low-Rank Representation for Cancer Classification on Gene Expression Data. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (4) (2018)
Jun Hu, Yang Li, Yang Zhang, Dong-Jun Yu
ATPbind: Accurate Protein-ATP Binding Site Prediction by Combining Sequence-Profiling and Structure-Based Comparisons. J. Chem. Inf. Model. 58 (2) (2018)
He Yan, Qiaolin Ye, Tian'an Zhang, Dong-Jun Yu, Xia Yuan, Yiqing Xu, Liyong Fu
Least squares twin bounded support vector machines based on L1-norm distance metric for classification. Pattern Recognit. 74 (2018)
He Yan, Qiaolin Ye, Tian'an Zhang, Dong-Jun Yu
Efficient and Robust TWSVM Classifier Based on L1-Norm Distance Metric for Pattern Classification. ACPR (2017)
Jun Hu, Zi Liu, Dong-Jun Yu
Enhancing Protein-ATP and Protein-ADP Binding Sites Prediction Using Supervised Instance-Transfer Learning. ACPR (2017)
Jun Hu, Yang Li, Ming Zhang, Xibei Yang, Hong-Bin Shen, Dong-Jun Yu
Predicting Protein-DNA Binding Residues by Weightedly Combining Sequence-Based Features and Boosting Multiple SVMs. IEEE ACM Trans. Comput. Biol. Bioinform. 14 (6) (2017)
Jun Hu, Yang Li, Wuxia Yan, Jing-Yu Yang, Hong-Bin Shen, Dong-Jun Yu
KNN-based dynamic query-driven sample rescaling strategy for class imbalance learning. Neurocomputing 191 (2016)
Hengrong Ju, Xibei Yang, Hualong Yu, Tongjun Li, Dong-Jun Yu, Jingyu Yang
Cost-sensitive rough set approach. Inf. Sci. (2016)
Zhisen Wei, Ke Han, Jing-Yu Yang, Hong-Bin Shen, Dong-Jun Yu
Protein-protein interaction sites prediction by ensembling SVM and sample-weighted random forests. Neurocomputing 193 (2016)
Suping Xu, Xibei Yang, Hualong Yu, Dong-Jun Yu, Jingyu Yang, Eric C. C. Tsang
Multi-label learning with label-specific feature reduction. Knowl. Based Syst. 104 (2016)
Jun Hu, Yang Li, Jing-Yu Yang, Hong-Bin Shen, Dong-Jun Yu
GPCR-drug interactions prediction using random forest with drug-association-matrix-based post-processing procedure. Comput. Biol. Chem. 60 (2016)
Zhisen Wei, Jing-Yu Yang, Dong-Jun Yu
Predicting Protein-Protein Interactions with Weighted PSSM Histogram and Random Forests. IScIDE (2) (2015)
Dong-Jun Yu, Yang Li, Jun Hu, Xibei Yang, Jing-Yu Yang, Hong-Bin Shen
Disulfide Connectivity Prediction Based on Modelled Protein 3D Structural Information and Random Forest Regression. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (3) (2015)
Xibei Yang, Yong Qi, Dong-Jun Yu, Hualong Yu, Jingyu Yang
α-Dominance relation and rough sets in interval-valued information systems. Inf. Sci. 294 (2015)
Dong-Jun Yu, Jun Hu, Hui Yan, Xibei Yang, Jing-Yu Yang, Hong-Bin Shen
Enhancing protein-vitamin binding residues prediction by multiple heterogeneous subspace SVMs ensemble. BMC Bioinform. 15 (2014)
Dong-Jun Yu, Jun Hu, Jing Yang, Hong-Bin Shen, Jinhui Tang, Jing-Yu Yang
Designing Template-Free Predictor for Targeting Protein-Ligand Binding Sites with Classifier Ensemble and Spatial Clustering. IEEE ACM Trans. Comput. Biol. Bioinform. 10 (4) (2013)
Dong-Jun Yu, Jun Hu, Yan Huang, Hong-Bin Shen, Yong Qi, Zhenmin Tang, Jing-Yu Yang
TargetATPsite: A template-free method for ATP-binding sites prediction with residue evolution image sparse representation and classifier ensemble. J. Comput. Chem. 34 (11) (2013)
Dong-Jun Yu, Jun Hu, Zhenmin Tang, Hong-Bin Shen, Jian Yang, Jing-Yu Yang
Improving protein-ATP binding residues prediction by boosting SVMs with random under-sampling. Neurocomputing 104 (2013)
Ya-Nan Zhang, Dong-Jun Yu, Shu-Sen Li, Yong-Xian Fan, Yan Huang, Hong-Bin Shen
Predicting protein-ATP binding sites from primary sequence through fusing bi-profile sampling of multi-view features. BMC Bioinform. 13 (2012)