Dong-Jun Yu

104 papers Journal 100Unranked 4
YearRankTypeTitle / Venue / Authors
2026 J jnl
AeroCOPDNet: A deep learning framework for COPD detection from lung sounds.
Biomed. Signal Process. Control.
Md Emran Hasan, Yue-Fang Wu, Dong-Jun Yu
2026 J jnl
DeepDBPI: DNA-Binding Protein Identifier Using a Deep Learning Model with Transformed Denoised Features.
J. Chem. Inf. Model.
Kamran Arshad, Muhammad Arif, Dong-Jun Yu
2026 J jnl
SMENET: A Multi-View Semantic Model for Multi-Level Enzyme Function Prediction.
IEEE Trans. Comput. Biol. Bioinform.
Hanwen Zhou, Wei Zhang, Zhaohong Deng, Guanjin Wang, Zhisheng Wei, Lei Wang, Xiaoyong Pan, Hong-Bin Shen, Dong-Jun Yu, Jing Wu
2025 J jnl
CATransUnetLBP: Accurate Prediction of Protein-Ligand Binding Pockets Using a Hybrid Network.
IEEE Trans. Comput. Biol. Bioinform.
Cheng Cai, Zhaohong Deng, Andong Li, Yun Zuo, Haoran Chen, Zhisheng Wei, Lei Wang, Xiaoyong Pan, Hong-Bin Shen, Dong-Jun Yu
2025 J jnl
DMMAFS: Protein Function Prediction Based on Multi-Modal Multi-Attention Fusion Features.
IEEE Trans. Comput. Biol. Bioinform.
Liangwen He, Zhaohong Deng, Fuping Hu, Zhongyu Wang, Yun Zuo, Lin Zhu, Haoran Chen, Xiaoyong Pan, Zhisheng Wei, Lei Wang, Hong-Bin Shen, Dong-Jun Yu, Jing Wu
2025 J jnl
Dual-Branch Contrastive Network with Deep Separable Convolution for Enhanced 6mA Site Identification.
J. Chem. Inf. Model.
Youwei Sun, Zhifei Wang, Ying Zhang, Jiangning Song, Dong-Jun Yu
2025 J jnl
Identification of Protein-Nucleotide Binding Residues With Deep Multi-Task and Multi-Scale Learning.
IEEE J. Biomed. Health Informatics
Jiashun Wu, Fang Ge, Shanruo Xu, Yan Liu, Jiangning Song, Dong-Jun Yu
2025 J jnl
Identifying Protein-Nucleotide Binding Residues via Grouped Multi-task Learning and Pre-trained Protein Language Models.
J. Chem. Inf. Model.
Jiashun Wu, Yan Liu, Ying Zhang, Xiaoyu Wang, He Yan, Yiheng Zhu, Jiangning Song, Dong-Jun Yu
2025 J jnl
Integrating Graph Convolutional Networks for Missing Gene Expression Imputation.
IEEE Trans. Comput. Biol. Bioinform.
Ying Zhang, Hong-Jin Yu, Zihao Yan, Tong Pan, Yiwen Zhang, Yan Liu, Shanshan Li, Yuming Guo, Jiangning Song, Dong-Jun Yu
2025 J jnl
MKFGO: integrating multi-source knowledge fusion with pretrained language model for high-accuracy protein function prediction.
Briefings Bioinform.
Yi-Heng Zhu, Shuxin Zhu, Xuan Yu, He Yan, Yan Liu, Xiaojun Xie, Dong-Jun Yu, Rui Ye
2025 J jnl
MORE: a multi-omics data-driven hypergraph integration network for biomedical data classification and biomarker identification.
Briefings Bioinform.
Yuhan Wang, Zhikang Wang, Xuan Yu, Xiaoyu Wang, Jiangning Song, Dong-Jun Yu, Fang Ge
2025 J jnl
MUSIC-GCN: A Novel Multi-Tasking Pipeline for Analyzing Single-Cell Transcriptomic Data Using Residual Graph Convolution Network.
IEEE Trans. Comput. Biol. Bioinform.
Yan Liu, Guo Wei, Jia-Shun Wu, Chen Li, He Yan, Long-Chen Shen, Robin B. Gasser, Jiangning Song, Dijun Chen, Dong-Jun Yu
2025 J jnl
MutPNI: A Unified Model Architecture for Accurately Predicting the Effects of Mutations on Protein-Nucleic Acid Interactions.
J. Chem. Inf. Model.
Zihao Yan, Fang Ge, Ying Zhang, He Yan, Yan Liu, Yi-Heng Zhu, Jiangning Song, Dong-Jun Yu
2025 J jnl
PScL-SDNNMAE: Protein Subcellular Localization Prediction Using Classical and Masked Autoencoder-Based Multi-View Features With Ensemble Feature Selection.
IEEE Trans. Comput. Biol. Bioinform.
Shenjian Gu, Matee Ullah, Jiangning Song, Dong-Jun Yu
2025 J jnl
Structure-Directed Pan-Specific T-Cell Receptor-Peptide-Major Histocompatibility Complex Interaction Prediction.
J. Chem. Inf. Model.
Letao Gao, Yumeng Zhang, Fang Ge, Shanshan Li, Yuming Guo, Jiangning Song, Dong-Jun Yu
2025 J jnl
Supervised contrastive learning enhances MHC-II peptide binding affinity prediction.
Expert Syst. Appl.
Long-Chen Shen, Yan Liu, Zi Liu, Yumeng Zhang, Zhikang Wang, Yuming Guo, Jamie Rossjohn, Jiangning Song, Dong-Jun Yu
2025 J jnl
TransABseq: A Two-Stage Approach for Predicting Antigen-Antibody Binding Affinity Changes upon Mutation Based on Protein Sequences.
J. Chem. Inf. Model.
Cui-Feng Li, Zihao Yan, Fang Ge, Xuan Yu, Jing Zhang, Ming Zhang, Dong-Jun Yu
2025 J jnl
Use of data Mining in Identifying the risk factors of optic neuropathy.
Comput. J.
Abdulkawi Yahya Radman Al-Shamiri, Dong-Jun Yu, Peipei Li, Balqis Yahya Ali Abdullah Al-Mahweeti
2025 J jnl
m2ST: dual multi-scale graph clustering for spatially resolved transcriptomics.
Bioinform.
Wei Zhang, Ziqi Zhang, Hailong Yang, Te Zhang, Shu Jiang, Ning Qiao, Zhaohong Deng, Xiaoyong Pan, Hong-Bin Shen, Dong-Jun Yu, Shitong Wang
2025 J jnl
scRCA: A Siamese network-based pipeline for annotating cell types using noisy single-cell RNA-seq reference data.
Comput. Biol. Medicine
Yan Liu, Chen Li, Long-Chen Shen, He Yan, Guo Wei, Robin B. Gasser, Xiaohua Hu, Jiangning Song, Dong-Jun Yu
2024 J jnl
APMG: 3D Molecule Generation Driven by Atomic Chemical Properties.
IEEE ACM Trans. Comput. Biol. Bioinform.
Yang Hua, Zhenhua Feng, Xiaoning Song, Hui Li, Tianyang Xu, Xiao-Jun Wu, Dong-Jun Yu
2024 J jnl
BLAM6A-Merge: Leveraging Attention Mechanisms and Feature Fusion Strategies to Improve the Identification of RNA N6-Methyladenosine Sites.
IEEE ACM Trans. Comput. Biol. Bioinform.
Yunpeng Xia, Ying Zhang, Dian Liu, Yi-Heng Zhu, Zhikang Wang, Jiangning Song, Dong-Jun Yu
2024 J jnl
FCMSTrans: Accurate Prediction of Disease-Associated nsSNPs by Utilizing Multiscale Convolution and Deep Feature Combination within a Transformer Framework.
J. Chem. Inf. Model.
Ming Zhang, Chao Gong, Fang Ge, Dong-Jun Yu
2024 J jnl
GMFGRN: a matrix factorization and graph neural network approach for gene regulatory network inference.
Briefings Bioinform.
Shuo Li, Yan Liu, Long-Chen Shen, He Yan, Jiangning Song, Dong-Jun Yu
2024 J jnl
GPTrans: A Biological Language Model-Based Approach for Predicting Disease-Associated Mutations in G Protein-Coupled Receptors.
J. Chem. Inf. Model.
Xiaohua Wang, Ming Zhang, Xibei Yang, Dong-Jun Yu, Fang Ge
2024 J jnl
Improving Antifreeze Proteins Prediction With Protein Language Models and Hybrid Feature Extraction Networks.
IEEE ACM Trans. Comput. Biol. Bioinform.
Jiashun Wu, Yan Liu, Yiheng Zhu, Dong-Jun Yu
2024 J jnl
MINDG: a drug-target interaction prediction method based on an integrated learning algorithm.
Bioinform.
Hailong Yang, Yue Chen, Yun Zuo, Zhaohong Deng, Xiaoyong Pan, Hong-Bin Shen, Kup-Sze Choi, Dong-Jun Yu
2024 J jnl
MLSNet: a deep learning model for predicting transcription factor binding sites.
Briefings Bioinform.
Yuchuan Zhang, Zhikang Wang, Fang Ge, Xiaoyu Wang, Yiwen Zhang, Shanshan Li, Yuming Guo, Jiangning Song, Dong-Jun Yu
2024 J jnl
MetalTrans: A Biological Language Model-Based Approach for Predicting Disease-Associated Mutations in Protein Metal-Binding Sites.
J. Chem. Inf. Model.
Ming Zhang, Xiaohua Wang, Shanruo Xu, Fang Ge, Ian Costa Paixao, Jiangning Song, Dong-Jun Yu
2024 J jnl
Prediction of protein-ATP binding residues using multi-view feature learning via contextual-based co-attention network.
Comput. Biol. Medicine
Jia-Shun Wu, Yan Liu, Fang Ge, Dong-Jun Yu
2024 J jnl
Robust GEPSVM classifier: An efficient iterative optimization framework.
Inf. Sci.
He Yan, Yan Liu, Yanmeng Li, Qiaolin Ye, Dong-Jun Yu, Yong Qi
2024 J jnl
TM-search: An Efficient and Effective Tool for Protein Structure Database Search.
J. Chem. Inf. Model.
Zi Liu, Chengxin Zhang, Qidi Zhang, Yang Zhang, Dong-Jun Yu
2024 J jnl
TransC-ac4C: Identification of N4-Acetylcytidine (ac4C) Sites in mRNA Using Deep Learning.
IEEE ACM Trans. Comput. Biol. Bioinform.
Dian Liu, Zi Liu, Yunpeng Xia, Zhikang Wang, Jiangning Song, Dong-Jun Yu
2024 J jnl
TransEFVP: A Two-Stage Approach for the Prediction of Human Pathogenic Variants Based on Protein Sequence Embedding Fusion.
J. Chem. Inf. Model.
Zihao Yan, Fang Ge, Yan Liu, Yumeng Zhang, Fuyi Li, Jiangning Song, Dong-Jun Yu
2024 J jnl
ULDNA: integrating unsupervised multi-source language models with LSTM-attention network for high-accuracy protein-DNA binding site prediction.
Briefings Bioinform.
Yi-Heng Zhu, Zi Liu, Yan Liu, Zhiwei Ji, Dong-Jun Yu
2023 J jnl
CPInformer for Efficient and Robust Compound-Protein Interaction Prediction.
IEEE ACM Trans. Comput. Biol. Bioinform.
Yang Hua, Xiaoning Song, Zhenhua Feng, Xiaojun Wu, Josef Kittler, Dong-Jun Yu
2023 J jnl
Improving DNA-Binding Protein Prediction Using Three-Part Sequence-Order Feature Extraction and a Deep Neural Network Algorithm.
J. Chem. Inf. Model.
Jun Hu, Wenwu Zeng, Ning-Xin Jia, Muhammad Arif, Dong-Jun Yu, Gui-Jun Zhang
2023 J jnl
Integrating unsupervised language model with multi-view multiple sequence alignments for high-accuracy inter-chain contact prediction.
Comput. Biol. Medicine
Zi Liu, Yi-Heng Zhu, Long-Chen Shen, Xuan Xiao, Wangren Qiu, Dong-Jun Yu
2023 J jnl
Interpretable prediction models for widespread m6A RNA modification across cell lines and tissues.
Bioinform.
Ying Zhang, Zhikang Wang, Yiwen Zhang, Shanshan Li, Yuming Guo, Jiangning Song, Dong-Jun Yu
2023 J jnl
Learning Cell Annotation under Multiple Reference Datasets by Multisource Domain Adaptation.
J. Chem. Inf. Model.
Yan Liu, He Yan, Long-Chen Shen, Dong-Jun Yu
2023 J jnl
MLNGCF: circRNA-disease associations prediction with multilayer attention neural graph-based collaborative filtering.
Bioinform.
Qunzhuo Wu, Zhaohong Deng, Wei Zhang, Xiaoyong Pan, Kup-Sze Choi, Yun Zuo, Hong-Bin Shen, Dong-Jun Yu
2023 J jnl
MMPatho: Leveraging Multilevel Consensus and Evolutionary Information for Enhanced Missense Mutation Pathogenic Prediction.
J. Chem. Inf. Model.
Fang Ge, Muhammad Arif, Zihao Yan, Hanin H. Alahmadi, Apilak Worachartcheewan, Dong-Jun Yu, Watshara Shoombuatong
2023 J jnl
PScL-2LSAESM: bioimage-based prediction of protein subcellular localization by integrating heterogeneous features with the two-level SAE-SM and mean ensemble method.
Bioinform.
Matee Ullah, Fazal Hadi, Jiangning Song, Dong-Jun Yu
2023 J jnl
Prediction of Multiple Types of RNA Modifications via Biological Language Model.
IEEE ACM Trans. Comput. Biol. Bioinform.
Ying Zhang, Fang Ge, Fuyi Li, Xibei Yang, Jiangning Song, Dong-Jun Yu
2023 J jnl
Robust generalized canonical correlation analysis.
Appl. Intell.
He Yan, Li Cheng, Qiaolin Ye, Dong-Jun Yu, Yong Qi
2023 J jnl
TripletCell: a deep metric learning framework for accurate annotation of cell types at the single-cell level.
Briefings Bioinform.
Yan Liu, Guo Wei, Chen Li, Long-Chen Shen, Robin B. Gasser, Jiangning Song, Dijun Chen, Dong-Jun Yu
2023 J jnl
VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants.
Briefings Bioinform.
Fang Ge, Chen Li, Shahid Iqbal, Muhammad Arif, Fuyi Li, Maha A. Thafar, Zihao Yan, Apilak Worachartcheewan, Xiaofeng Xu, Jiangning Song, Dong-Jun Yu
2022 J jnl
ATPdock: a template-based method for ATP-specific protein-ligand docking.
Bioinform.
Liang Rao, Ning-Xin Jia, Jun Hu, Dong-Jun Yu, Gui-Jun Zhang
2022 J jnl
DeepCPPred: A Deep Learning Framework for the Discrimination of Cell-Penetrating Peptides and Their Uptake Efficiencies.
IEEE ACM Trans. Comput. Biol. Bioinform.
Muhammad Arif, Muhammad Kabir, Saeed Ahmed, Abid Khan, Fang Ge, Adel Khelifi, Dong-Jun Yu
2022 J jnl
Enhancing Characteristic Gene Selection and Tumor Classification by the Robust Laplacian Supervised Discriminative Sparse PCA.
J. Chem. Inf. Model.
Lu-Xing Zhang, He Yan, Yan Liu, Jian Xu, Jiangning Song, Dong-Jun Yu
2022 J jnl
Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction.
PLoS Comput. Biol.
Yi-Heng Zhu, Chengxin Zhang, Dong-Jun Yu, Yang Zhang
2022 J jnl
Learning Protein Embedding to Improve Protein Fold Recognition Using Deep Metric Learning.
J. Chem. Inf. Model.
Guan-Yu Zhu, Yan Liu, Peng-Hao Wang, Xibei Yang, Dong-Jun Yu
2022 J jnl
Learning a robust classifier for short-term traffic state prediction.
Knowl. Based Syst.
He Yan, Liyong Fu, Yong Qi, Li Cheng, Qiaolin Ye, Dong-Jun Yu
2022 J jnl
MAResNet: predicting transcription factor binding sites by combining multi-scale bottom-up and top-down attention and residual network.
Briefings Bioinform.
Ke Han, Long-Chen Shen, Yi-Heng Zhu, Jian Xu, Jiangning Song, Dong-Jun Yu
2022 J jnl
MDGF-MCEC: a multi-view dual attention embedding model with cooperative ensemble learning for CircRNA-disease association prediction.
Briefings Bioinform.
Qunzhuo Wu, Zhaohong Deng, Xiaoyong Pan, Hong-Bin Shen, Kup-Sze Choi, Shitong Wang, Jing Wu, Dong-Jun Yu
2022 J jnl
PROST: AlphaFold2-aware Sequence-Based Predictor to Estimate Protein Stability Changes upon Missense Mutations.
J. Chem. Inf. Model.
Shahid Iqbal, Fang Ge, Fuyi Li, Tatsuya Akutsu, Yuanting Zheng, Robin B. Gasser, Dong-Jun Yu, Geoffrey I. Webb, Jiangning Song
2022 J jnl
PScL-DDCFPred: an ensemble deep learning-based approach for characterizing multiclass subcellular localization of human proteins from bioimage data.
Bioinform.
Matee Ullah, Fazal Hadi, Jiangning Song, Dong-Jun Yu
2022 J jnl
Prediction of disease-associated nsSNPs by integrating multi-scale ResNet models with deep feature fusion.
Briefings Bioinform.
Fang Ge, Ying Zhang, Jian Xu, Muhammad Arif, Jiangning Song, Dong-Jun Yu
2022 J jnl
Protein-DNA Binding Residue Prediction via Bagging Strategy and Sequence-Based Cube-Format Feature.
IEEE ACM Trans. Comput. Biol. Bioinform.
Jun Hu, Yan-Song Bai, Lin-Lin Zheng, Ning-Xin Jia, Dong-Jun Yu, Gui-Jun Zhang
2022 J jnl
Robust Least Squares Twin Support Vector Regression With Adaptive FOA and PSO for Short-Term Traffic Flow Prediction.
IEEE Trans. Intell. Transp. Syst.
He Yan, Yong Qi, Qiaolin Ye, Dong-Jun Yu
2022 J jnl
Robust distance metric optimization driven GEPSVM classifier for pattern classification.
Pattern Recognit.
He Yan, Liyong Fu, Tian'an Zhang, Jun Hu, Qiaolin Ye, Yong Qi, Dong-Jun Yu
2022 J jnl
Robust ensemble method for short-term traffic flow prediction.
Future Gener. Comput. Syst.
He Yan, Liyong Fu, Yong Qi, Dong-Jun Yu, Qiaolin Ye
2022 J jnl
TripletGO: Integrating Transcript Expression Profiles with Protein Homology Inferences for Gene Function Prediction.
Genom. Proteom. Bioinform.
Yi-Heng Zhu, Chengxin Zhang, Yan Liu, Gilbert S. Omenn, P. L. Freddolino, Dong-Jun Yu, Yang Zhang
2021 J jnl
Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features.
Briefings Bioinform.
Yi-Heng Zhu, Jun Hu, Fang Ge, Fuyi Li, Jiangning Song, Yang Zhang, Dong-Jun Yu
2021 J jnl
Comprehensive assessment of machine learning-based methods for predicting antimicrobial peptides.
Briefings Bioinform.
Jing Xu, Fuyi Li, André Leier, Dongxu Xiang, Hsin-Hui Shen, Tatiana T. Marquez-Lago, Jian Li, Dong-Jun Yu, Jiangning Song
2021 J jnl
Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks.
PLoS Comput. Biol.
Yang Li, Chengxin Zhang, Eric W. Bell, Wei Zheng, Xiaogen Zhou, Dong-Jun Yu, Yang Zhang
2021 J jnl
Improving protein fold recognition using triplet network and ensemble deep learning.
Briefings Bioinform.
Yan Liu, Ke Han, Yi-Heng Zhu, Ying Zhang, Long-Chen Shen, Jiangning Song, Dong-Jun Yu
2021 J jnl
Leveraging the attention mechanism to improve the identification of DNA N6-methyladenine sites.
Briefings Bioinform.
Ying Zhang, Yan Liu, Jian Xu, Xiaoyu Wang, Xinxin Peng, Jiangning Song, Dong-Jun Yu
2021 J jnl
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.
Matee Ullah, Ke Han, Fazal Hadi, Jian Xu, Jiangning Song, Dong-Jun Yu
2021 J jnl
SAResNet: self-attention residual network for predicting DNA-protein binding.
Briefings Bioinform.
Long-Chen Shen, Yan Liu, Jiangning Song, Dong-Jun Yu
2021 J jnl
SP-GAN: Self-Growing and Pruning Generative Adversarial Networks.
IEEE Trans. Neural Networks Learn. Syst.
Xiaoning Song, Yao Chen, Zhenhua Feng, Guosheng Hu, Dong-Jun Yu, Xiaojun Wu
2021 J jnl
TargetDBP+: Enhancing the Performance of Identifying DNA-Binding Proteins via Weighted Convolutional Features.
J. Chem. Inf. Model.
Jun Hu, Liang Rao, Yi-Heng Zhu, Gui-Jun Zhang, Dong-Jun Yu
2021 J jnl
Why can deep convolutional neural networks improve protein fold recognition? A visual explanation by interpretation.
Briefings Bioinform.
Yan Liu, Yi-Heng Zhu, Xiaoning Song, Jiangning Song, Dong-Jun Yu
2020 J jnl
ASCENT: Active Supervision for Semi-Supervised Learning.
IEEE Trans. Knowl. Data Eng.
Yanchao Li, Yongli Wang, Dong-Jun Yu, Ning Ye, Peng Hu, Ruxin Zhao
2020 J jnl
SSCpred: Single-Sequence-Based Protein Contact Prediction Using Deep Fully Convolutional Network.
J. Chem. Inf. Model.
Ming-Cai Chen, Yang Li, Yi-Heng Zhu, Fang Ge, Dong-Jun Yu
2020 J jnl
TargetCPP: accurate prediction of cell-penetrating peptides from optimized multi-scale features using gradient boost decision tree.
J. Comput. Aided Mol. Des.
Muhammad Arif, Saeed Ahmad, Farman Ali, Ge Fang, Min Li, Dong-Jun Yu
2020 J jnl
TargetDBP: Accurate DNA-Binding Protein Prediction Via Sequence-Based Multi-View Feature Learning.
IEEE ACM Trans. Comput. Biol. Bioinform.
Jun Hu, Xiaogen Zhou, Yi-Heng Zhu, Dong-Jun Yu, Gui-Jun Zhang
2019 J jnl
DNAPred: Accurate Identification of DNA-Binding Sites from Protein Sequence by Ensembled Hyperplane-Distance-Based Support Vector Machines.
J. Chem. Inf. Model.
Yi-Heng Zhu, Jun Hu, Xiaoning Song, Dong-Jun Yu
2019 — conf
DeepTF: Accurate Prediction of Transcription Factor Binding Sites by Combining Multi-scale Convolution and Long Short-Term Memory Neural Network.
IScIDE (2)
Xiao-Rong Bao, Yi-Heng Zhu, Dong-Jun Yu
2019 J jnl
Efficient and robust TWSVM classification via a minimum L1-norm distance metric criterion.
Mach. Learn.
He Yan, Qiaolin Ye, Dong-Jun Yu
2019 J jnl
Fast SRC using quadratic optimisation in downsized coefficient solution subspace.
Signal Process.
Xiaoning Song, Guosheng Hu, Jian-Hao Luo, Zhenhua Feng, Dong-Jun Yu, Xiao-Jun Wu
2019 J jnl
Neighborhood attribute reduction: a multi-criterion approach.
Int. J. Mach. Learn. Cybern.
Jingzheng Li, Xibei Yang, Xiaoning Song, Jinhai Li, Pingxin Wang, Dong-Jun Yu
2019 J jnl
ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks.
Bioinform.
Yang Li, Jun Hu, Chengxin Zhang, Dong-Jun Yu, Yang Zhang
2018 J jnl
A Self-Training Subspace Clustering Algorithm under Low-Rank Representation for Cancer Classification on Gene Expression Data.
IEEE ACM Trans. Comput. Biol. Bioinform.
Chun-Qiu Xia, Ke Han, Yong Qi, Yang Zhang, Dong-Jun Yu
2018 J jnl
ATPbind: Accurate Protein-ATP Binding Site Prediction by Combining Sequence-Profiling and Structure-Based Comparisons.
J. Chem. Inf. Model.
Jun Hu, Yang Li, Yang Zhang, Dong-Jun Yu
2018 J jnl
L1-Norm GEPSVM Classifier Based on an Effective Iterative Algorithm for Classification.
Neural Process. Lett.
He Yan, Qiaolin Ye, Tian'an Zhang, Dong-Jun Yu, Yiqing Xu
2018 J jnl
LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening.
Bioinform.
Jun Hu, Zi Liu, Dong-Jun Yu, Yang Zhang
2018 J jnl
Least squares twin bounded support vector machines based on L1-norm distance metric for classification.
Pattern Recognit.
He Yan, Qiaolin Ye, Tian'an Zhang, Dong-Jun Yu, Xia Yuan, Yiqing Xu, Liyong Fu
2017 — conf
Efficient and Robust TWSVM Classifier Based on L1-Norm Distance Metric for Pattern Classification.
ACPR
He Yan, Qiaolin Ye, Tian'an Zhang, Dong-Jun Yu
2017 — conf
Enhancing Protein-ATP and Protein-ADP Binding Sites Prediction Using Supervised Instance-Transfer Learning.
ACPR
Jun Hu, Zi Liu, Dong-Jun Yu
2017 J jnl
Predicting Protein-DNA Binding Residues by Weightedly Combining Sequence-Based Features and Boosting Multiple SVMs.
IEEE ACM Trans. Comput. Biol. Bioinform.
Jun Hu, Yang Li, Ming Zhang, Xibei Yang, Hong-Bin Shen, Dong-Jun Yu
2016 J jnl
Cost-sensitive rough set approach.
Inf. Sci.
Hengrong Ju, Xibei Yang, Hualong Yu, Tongjun Li, Dong-Jun Yu, Jingyu Yang
2016 J jnl
GPCR-drug interactions prediction using random forest with drug-association-matrix-based post-processing procedure.
Comput. Biol. Chem.
Jun Hu, Yang Li, Jing-Yu Yang, Hong-Bin Shen, Dong-Jun Yu
2016 J jnl
KNN-based dynamic query-driven sample rescaling strategy for class imbalance learning.
Neurocomputing
Jun Hu, Yang Li, Wuxia Yan, Jing-Yu Yang, Hong-Bin Shen, Dong-Jun Yu
2016 J jnl
Multi-label learning with label-specific feature reduction.
Knowl. Based Syst.
Suping Xu, Xibei Yang, Hualong Yu, Dong-Jun Yu, Jingyu Yang, Eric C. C. Tsang
2016 J jnl
Protein-protein interaction sites prediction by ensembling SVM and sample-weighted random forests.
Neurocomputing
Zhisen Wei, Ke Han, Jing-Yu Yang, Hong-Bin Shen, Dong-Jun Yu
2015 J jnl
Disulfide Connectivity Prediction Based on Modelled Protein 3D Structural Information and Random Forest Regression.
IEEE ACM Trans. Comput. Biol. Bioinform.
Dong-Jun Yu, Yang Li, Jun Hu, Xibei Yang, Jing-Yu Yang, Hong-Bin Shen
2015 — conf
Predicting Protein-Protein Interactions with Weighted PSSM Histogram and Random Forests.
IScIDE (2)
Zhisen Wei, Jing-Yu Yang, Dong-Jun Yu
2015 J jnl
α-Dominance relation and rough sets in interval-valued information systems.
Inf. Sci.
Xibei Yang, Yong Qi, Dong-Jun Yu, Hualong Yu, Jingyu Yang
2014 J jnl
Enhancing protein-vitamin binding residues prediction by multiple heterogeneous subspace SVMs ensemble.
BMC Bioinform.
Dong-Jun Yu, Jun Hu, Hui Yan, Xibei Yang, Jing-Yu Yang, Hong-Bin Shen
2013 J jnl
Designing Template-Free Predictor for Targeting Protein-Ligand Binding Sites with Classifier Ensemble and Spatial Clustering.
IEEE ACM Trans. Comput. Biol. Bioinform.
Dong-Jun Yu, Jun Hu, Jing Yang, Hong-Bin Shen, Jinhui Tang, Jing-Yu Yang
2013 J jnl
Improving protein-ATP binding residues prediction by boosting SVMs with random under-sampling.
Neurocomputing
Dong-Jun Yu, Jun Hu, Zhenmin Tang, Hong-Bin Shen, Jian Yang, Jing-Yu Yang
2013 J jnl
TargetATPsite: A template-free method for ATP-binding sites prediction with residue evolution image sparse representation and classifier ensemble.
J. Comput. Chem.
Dong-Jun Yu, Jun Hu, Yan Huang, Hong-Bin Shen, Yong Qi, Zhenmin Tang, Jing-Yu Yang
2012 J jnl
Predicting protein-ATP binding sites from primary sequence through fusing bi-profile sampling of multi-view features.
BMC Bioinform.
Ya-Nan Zhang, Dong-Jun Yu, Shu-Sen Li, Yong-Xian Fan, Yan Huang, Hong-Bin Shen