Prediction of protein-protein interaction sites using an ensemble method. - Lei Deng 002; Jihong Guan; Qiwen Dong; Shuigeng Zhou (BMC Bioinform., 2009)

PredUs: a web server for predicting protein interfaces using structural neighbors. - Qiangfeng Cliff Zhang; Lei Deng 002; Markus Fisher; Jihong Guan; Barry Honig; Donald Petrey (Nucleic Acids Res., 2011)

A semi-supervised boosting SVM for predicting hot spots at protein-protein Interfaces. - Bin Xu; Xiaoming Wei; Lei Deng 002; Jihong Guan; Shuigeng Zhou (BMC Syst. Biol., 2012)

Boosting Prediction Performance of Protein-Protein Interaction Hot Spots by Using Structural Neighborhood Properties - (Extended Abstract). - Lei Deng 002; Jihong Guan; Xiaoming Wei; Yuan Yi; Shuigeng Zhou (RECOMB, 2013)

Boosting Prediction Performance of Protein-Protein Interaction Hot Spots by Using Structural Neighborhood Properties. - Lei Deng 002; Jihong Guan; Xiaoming Wei; Yuan Yi; Qiangfeng Cliff Zhang; Shuigeng Zhou (J. Comput. Biol., 2013)

PrePPI: a structure-informed database of protein-protein interactions. - Qiangfeng Cliff Zhang; Donald Petrey; José Ignacio Garzón; Lei Deng 002; Barry Honig (Nucleic Acids Res., 2013)

Structure-Based Prediction of Protein Phosphorylation Sites Using an Ensemble Approach. - Yong Gao; Weilin Hao; Zhigang Chen 001; Lei Deng 002 (ICIC (3), 2014)

A Multi-Instance Multi-Label Learning Approach for Protein Domain Annotation. - Yang Meng; Lei Deng 002; Zhigang Chen 001; Cheng Zhou; Diwei Liu; Chao Fan; Ting Yan (ICIC (3), 2014)

PredHS: a web server for predicting protein-protein interaction hot spots by using structural neighborhood properties. - Lei Deng 002; Qiangfeng Cliff Zhang; Zhigang Chen 001; Yang Meng; Jihong Guan; Shuigeng Zhou (Nucleic Acids Res., 2014)

An Integrated Framework for Functional Annotation of Protein Structural Domains. - Lei Deng 002; Zhigang Chen 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

PredRBR: Accurate Prediction of RNA-Binding Residues in proteins using Gradient Tree Boosting. - Diwei Liu; Yongjun Tang; Chao Fan; Zhigang Chen 001; Lei Deng 002 (BIBM, 2016)

PredRSA: a gradient boosted regression trees approach for predicting protein solvent accessibility. - Chao Fan; Diwei Liu; Rui Huang; Zhigang Chen 001; Lei Deng 002 (BMC Bioinform., 2016)

BiRWLGO: A global network-based strategy for lncRNA function annotation using bi-random walk. - Jingpu Zhang; Shuai Zou; Lei Deng 002 (BIBM, 2017)

A sparse autoencoder-based deep neural network for protein solvent accessibility and contact number prediction. - Lei Deng 002; Chao Fan; Zhiwen Zeng (BMC Bioinform., 2017)

A boosting approach for prediction of protein-RNA binding residues. - Yongjun Tang; Diwei Liu; Zixiang Wang; Ting Wen; Lei Deng 002 (BMC Bioinform., 2017)

Revealing Dynamic Communities in networks using genetic algorithm with Merging and Splitting Operators. - Weihua Zhan; Lei Deng 002; Jihong Guan; Jun Niu (CoRR, 2017)

Exploring Disease Similarity by Integrating Multiple Data Sources. - Lei Deng 002; Danyi Ye; Junmin Zhao; Jingpu Zhang (BIBM, 2018)

XPredRBR: Accurate and Fast Prediction of RNA-Binding Residues in Proteins Using eXtreme Gradient Boosting. - Lei Deng 002; Zuojin Dong; Hui Liu 026 (ISBRA, 2018)

Ontological function annotation of long non-coding RNAs through hierarchical multi-label classification. - Jingpu Zhang; Zuping Zhang 001; Zixiang Wang; Yuting Liu; Lei Deng 002 (Bioinform., 2018)

PDRLGB: precise DNA-binding residue prediction using a light gradient boosting machine. - Lei Deng 002; Juan Pan; Xiaojie Xu; Wenyi Yang; Chuyao Liu; Hui Liu 026 (BMC Bioinform., 2018)

Probing the functions of long non-coding RNAs by exploiting the topology of global association and interaction network. - Lei Deng 002; Hongjie Wu; Chuyao Liu; Weihua Zhan; Jingpu Zhang (Comput. Biol. Chem., 2018)

A deep neural network approach using distributed representations of RNA sequence and structure for identifying binding site of RNA-binding proteins. - Lei Deng 002; Youzhi Liu; Yechuan Shi; Hui Liu 026 (BIBM, 2019)

DKCirc2GO: Predicting Gene Ontology of circRNAs Using Dual KATZ Approach. - Lei Deng 002; Xin Sun; Wei Lin; Jingpu Zhang (BIBM, 2019)

D2VCB: A Hybrid Deep Neural Network for the Prediction of in-vivo Protein-DNA Binding from Combined DNA Sequence. - Lei Deng 002; Hui Wu; Hui Liu 026 (BIBM, 2019)

MADOKA: an ultra-fast approach for large-scale protein structure similarity searching. - Lei Deng 002; Guolun Zhong; Chenzhe Liu; Judong Luo; Hui Liu 026 (BMC Bioinform., 2019)

MultiSourcDSim: an integrated approach for exploring disease similarity. - Lei Deng 002; Danyi Ye; Junmin Zhao; Jingpu Zhang (BMC Medical Informatics Decis. Mak., 2019)

Integrating Multiple Heterogeneous Networks for Novel LncRNA-Disease Association Inference. - Jingpu Zhang; Zuping Zhang 001; Zhigang Chen 001; Lei Deng 002 (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

KATZLGO: Large-Scale Prediction of LncRNA Functions by Using the KATZ Measure Based on Multiple Networks. - Zuping Zhang 001; Jingpu Zhang; Chao Fan; Yongjun Tang; Lei Deng 002 (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Predicting circRNA-disease associations using meta path-based representation learning on heterogenous network. - Lei Deng 002; Jing Yang; Hui Liu 026 (BIBM, 2020)

DeepARC: An Attention-based Hybrid Model for Predicting Transcription Factor Binding Sites from Positional Embedded DNA Sequence. - Jialong Chen; Lei Deng 002 (BIBM, 2020)

Predict the Protein-protein Interaction between Virus and Host through Hybrid Deep Neural Network. - Lei Deng 002; Jiaojiao Zhao; Jingpu Zhang (BIBM, 2020)

Machine learning-based methods and novel data models to predict adverse drug reaction. - Jinxian Wang; Yuanyuan Deng; Liang Shu; Lei Deng 002 (BIBM, 2020)

DeepciRGO: functional prediction of circular RNAs through hierarchical deep neural networks using heterogeneous network features. - Lei Deng 002; Wei Lin; Jiacheng Wang; Jingpu Zhang (BMC Bioinform., 2020)

Gammachirp filter banks applied in roust speaker recognition based on GMM-UBM classifier. - Lei Deng 002; Yong Gao (Int. Arab J. Inf. Technol., 2020)

Pathway-Guided Deep Neural Network toward Interpretable and Predictive Modeling of Drug Sensitivity. - Lei Deng 002; Yideng Cai; Wenhao Zhang; Wenyi Yang; Bo Gao; Hui Liu 026 (J. Chem. Inf. Model., 2020)

HNet-DNN: Inferring New Drug-Disease Associations with Deep Neural Network Based on Heterogeneous Network Features. - Hui Liu 026; Wenhao Zhang; Yinglong Song; Lei Deng 002; Shuigeng Zhou (J. Chem. Inf. Model., 2020)

DrugCombDB: a comprehensive database of drug combinations toward the discovery of combinatorial therapy. - Hui Liu 026; Wenhao Zhang; Bo Zou; Jinxian Wang; Yuanyuan Deng; Lei Deng 002 (Nucleic Acids Res., 2020)

A multi-task graph convolutional network modeling of drug-drug interactions and synergistic efficacy. - Yuanyuan Deng; Song Yu; Lei Deng 002; Hui Liu 026; Xuejun Liu; Yi Luo (BIBM, 2021)

GCNSDA: Predicting snoRNA-disease associations via graph convolutional network. - Dayun Liu; Yi Luo; Jingjing Zheng; Hanlin Xu; Jiaxuan Zhang; Lei Deng 002 (BIBM, 2021)

iPiDA-GBNN: Identification of Piwi-interacting RNA-disease associations based on gradient boosting neural network. - Yurong Qian; Qihua He; Lei Deng 002 (BIBM, 2021)

CMIVGSD: circRNA-miRNA Interaction Prediction Based on Variational Graph Auto-Encoder and Singular Value Decomposition. - Yurong Qian; Jingjing Zheng; Zhe Zhang; Ying Jiang; Jiaxuan Zhang; Lei Deng 002 (BIBM, 2021)

Accurately Predicting circRNA-disease Associations Using Variational Graph Auto-encoders and LightGBM. - Siyuan Shen; Yurong Qian; Jingjing Zheng; Junyi Liu; Lei Deng 002 (BIBM, 2021)

LGCMDS: Predicting miRNA-Drug Sensitivity based on Light Graph Convolution Network. - Song Yu; Hanlin Xu; Yizhan Li; Dayun Liu; Lei Deng 002 (BIBM, 2021)

Nabe: an energetic database of amino acid mutations in protein-nucleic acid binding interfaces. - Junyi Liu; Siyu Liu; Chenzhe Liu; Yaping Zhang; Yuliang Pan; Zixiang Wang; Jiacheng Wang; Ting Wen; Lei Deng 002 (Database J. Biol. Databases Curation, 2021)

SMALF: miRNA-disease associations prediction based on stacked autoencoder and XGBoost. - Dayun Liu; Yibiao Huang; Wenjuan Nie; Jiaxuan Zhang; Lei Deng 002 (BMC Bioinform., 2021)

CRPGCN: predicting circRNA-disease associations using graph convolutional network based on heterogeneous network. - Zhihao Ma; Zhufang Kuang; Lei Deng 002 (BMC Bioinform., 2021)

MSCFS: inferring circRNA functional similarity based on multiple data sources. - Liang Shu; Cheng Zhou; Xinxu Yuan; Jingpu Zhang; Lei Deng 002 (BMC Bioinform., 2021)

LDAH2V: Exploring Meta-Paths Across Multiple Networks for lncRNA-Disease Association Prediction. - Lei Deng 002; Wenkai Li; Jingpu Zhang (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

DeepFusionGO: Protein function prediction by fusing heterogeneous features through deep learning. - Zhijian Huang; Rongtao Zheng; Lei Deng 002 (BIBM, 2022)

inACP: An integrated approach to the prediction of anticancer peptides. - Guolun Zhong; Lei Deng 002 (BIBM, 2022)

Contrastive learning-based computational histopathology predict differential expression of cancer driver genes. - Haojie Huang; Gongming Zhou; Xuejun Liu; Lei Deng 002; Chen Wu; Dachuan Zhang; Hui Liu 026 (Briefings Bioinform., 2022)

Attention-wise masked graph contrastive learning for predicting molecular property. - Hui Liu 026; Yibiao Huang; Xuejun Liu; Lei Deng 002 (Briefings Bioinform., 2022)

TSNAPred: predicting type-specific nucleic acid binding residues via an ensemble approach. - Wenjuan Nie; Lei Deng 002 (Briefings Bioinform., 2022)

DeepDDS: deep graph neural network with attention mechanism to predict synergistic drug combinations. - Jinxian Wang; Xuejun Liu; Siyuan Shen; Lei Deng 002; Hui Liu 026 (Briefings Bioinform., 2022)

Computational anti-COVID-19 drug design: progress and challenges. - Jinxian Wang; Ying Zhang; Wenjuan Nie; Yi Luo; Lei Deng 002 (Briefings Bioinform., 2022)

Graph2MDA: a multi-modal variational graph embedding model for predicting microbe-drug associations. - Lei Deng 002; Yibiao Huang; Xuejun Liu; Hui Liu 026 (Bioinform., 2022)

MSPCD: predicting circRNA-disease associations via integrating multi-source data and hierarchical neural network. - Lei Deng 002; Dayun Liu; Yizhan Li; Runqi Wang; Junyi Liu; Jiaxuan Zhang; Hui Liu 026 (BMC Bioinform., 2022)

Predicting circRNA-drug sensitivity associations via graph attention auto-encoder. - Lei Deng 002; Zixuan Liu; Yurong Qian; Jingpu Zhang (BMC Bioinform., 2022)

Dual-Channel Heterogeneous Graph Neural Network for Predicting microRNA-Mediated Drug Sensitivity. - Lei Deng 002; Ziyu Fan; Xiaojun Xiao; Hui Liu 026; Jiaxuan Zhang (J. Chem. Inf. Model., 2022)

Graph Neural Network with Self-Supervised Learning for Noncoding RNA-Drug Resistance Association Prediction. - Jingjing Zheng; Yurong Qian; Jie He; Zerui Kang; Lei Deng 002 (J. Chem. Inf. Model., 2022)

MSCNE: Predict miRNA-Disease Associations Using Neural Network Based on Multi-Source Biological Information. - Genwei Han; Zhufang Kuang; Lei Deng 002 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

MGATMDA: Predicting Microbe-Disease Associations via Multi-Component Graph Attention Network. - Dayun Liu; Junyi Liu; Yi Luo; Qihua He; Lei Deng 002 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Enhancing Protein Solubility Prediction through Pre-trained Language Models and Graph Convolutional Neural Networks. - Jie Chen; Yurong Qian; Zhijian Huang; Xiaojun Xiao; Lei Deng 002 (BIBM, 2023)

TGC-ARG: Predicting Antibiotic Resistance through Transformer-based Modeling and Contrastive Learning. - Yihan Dong; Xiaowen Hu; Zhijian Huang; Lei Deng 002 (BIBM, 2023)

CLPiDA: A Contrastive Learning Approach for Predicting Potential PiRNA-Disease Associations. - Xiaowen Hu; Yuanpeng Zhang; Jiaxuan Zhang; Lei Deng 002 (BIBM, 2023)

Predicting Associations between circRNAs and Drug Sensitivity using Heterogeneous Graphs and Graph Attention Networks. - Xiaojun Xiao; Yurong Qian; Zhijian Huang; Rongtao Zheng; Lei Deng 002 (BIBM, 2023)

PTDA-SWGCL: Predicting tRNA-Disease Associations using Supplementarily Weighted Graph Contrastive Learning. - Yuanpeng Zhang; Yurong Qian; Xiaojun Xiao; Xiaowen Hu; Zhijian Huang; Lei Deng 002 (BIBM, 2023)

DeepCoVDR: deep transfer learning with graph transformer and cross-attention for predicting COVID-19 drug response. - Zhijian Huang; Pan Zhang; Lei Deng 002 (Bioinform., 2023)

GCNPCA: miRNA-Disease Associations Prediction Algorithm Based on Graph Convolutional Neural Networks. - Jiwen Liu; Zhufang Kuang; Lei Deng 002 (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

HGNNLDA: Predicting lncRNA-Drug Sensitivity Associations via a Dual Channel Hypergraph Neural Network. - Dayun Liu; Xianghui Li; Liangliang Zhang; Xiaowen Hu; Jiaxuan Zhang; Zhirong Liu; Lei Deng 002 (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

NGCICM: A Novel Deep Learning-Based Method for Predicting circRNA-miRNA Interactions. - Zhihao Ma; Zhufang Kuang; Lei Deng 002 (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Prediction of circRNA-MiRNA Association Using Singular Value Decomposition and Graph Neural Networks. - Yurong Qian; Jingjing Zheng; Ying Jiang; Shaoqiu Li; Lei Deng 002 (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

ABLNCPP: Attention Mechanism-Based Bidirectional Long Short-Term Memory for Noncoding RNA Coding Potential Prediction. - Lei Deng 002; Ying Jiang; Xiaowen Hu; Rongtao Zheng; Zhijian Huang; Jingpu Zhang (J. Chem. Inf. Model., 2023)

Large-scale predicting protein functions through heterogeneous feature fusion. - Rongtao Zheng; Zhijian Huang; Lei Deng 002 (Briefings Bioinform., 2023)

A comprehensive review and evaluation of graph neural networks for non-coding RNA and complex disease associations. - Xiaowen Hu; Dayun Liu; Jiaxuan Zhang; Yanhao Fan; Tianxiang Ouyang; Yue Luo; Yuanpeng Zhang; Lei Deng 002 (Briefings Bioinform., 2023)

HGCLMDA: Predicting mRNA-Drug Sensitivity Associations via Hypergraph Contrastive Learning. - Xiaowen Hu; Yihan Dong; Jiaxuan Zhang; Lei Deng 002 (J. Chem. Inf. Model., 2023)

MFF-LncLoc: Subcellular Localization Prediction of lncRNAs Based on Multi-Feature Fusion Using Transformers. - Ziyu Fan; Ying Jiang; Shuning Yang; Lei Deng 002 (BIBM, 2024)

LSNSCDA: Unraveling CircRNA-Drug Sensitivity via Local Smoothing Graph Neural Network and Credible Negative Samples. - Ziyu Fan; Yuanpeng Zhang; Yahan Li; Zeyu Zhong; Lei Deng 002 (BIBM, 2024)

Hierarchical Molecular Structure Network with Co-attention Mechanism for Drug-Drug Interaction Prediction. - Yue Luo; Lei Deng 002 (BIBM, 2024)

Enhancing miRNA-Disease Prediction with Attention-Based Multi-View Contrastive Learning. - Tianxiang Ouyang; Zhijian Huang; Lei Deng 002 (BIBM, 2024)

DTA-Net: Dual-Task Attention Network for Medical Image Segmentation and Classification. - Haifeng Qi; Siyuan Shen; Zhijian Huang; Lei Deng 002 (BIBM, 2024)

Imputation of incomplete medical data using missing neighborhood perturbation denoising autoencoder. - Huamei Qi; Wenhui Yang; Sen Fu; Lei Deng 002 (BIBM, 2024)

A Self-Attention Synthesizing Model with Privacy-Preserving(ACCT-GAN) for Medical Tabular Data. - Huamei Qi; Wenqin Zou; Sen Fu; Lei Deng 002 (BIBM, 2024)

ADiffGDA: Exploring Gene-Drug Associations via Adaptive Graph Diffusion Networks. - Che Zhang; Yanhao Fan; Xiaowen Hu; Yurong Qian; Lei Deng 002 (BIBM, 2024)

HGTRDA: Enhancing Prediction of ncRNA-Mediated Drug Resistance with Hypergraph Transformer. - Che Zhang; Ruohui He; Yanhao Fan; Xiaowen Hu; Yurong Qian; Lei Deng 002 (BIBM, 2024)

SGCLDGA: unveiling drug-gene associations through simple graph contrastive learning. - Yanhao Fan; Che Zhang; Xiaowen Hu; Zhijian Huang; Jiameng Xue; Lei Deng 002 (Briefings Bioinform., 2024)

IGCNSDA: unraveling disease-associated snoRNAs with an interpretable graph convolutional network. - Xiaowen Hu; Pan Zhang; Dayun Liu; Jiaxuan Zhang; Yuanpeng Zhang; Yihan Dong; Yanhao Fan; Lei Deng 002 (Briefings Bioinform., 2024)

DeepHeteroCDA: circRNA-drug sensitivity associations prediction via multi-scale heterogeneous network and graph attention mechanism. - Zhijian Huang; Kai Chen; Xiaojun Xiao; Ziyu Fan; Yuanpeng Zhang; Lei Deng 002 (Briefings Bioinform., 2024)

MvMRL: a multi-view molecular representation learning method for molecular property prediction. - Ru Zhang; Yanmei Lin; Yijia Wu; Lei Deng 002; Hao Zhang; Mingzhi Liao; Yuzhong Peng (Briefings Bioinform., 2024)

MolMVC: Enhancing molecular representations for drug-related tasks through multi-view contrastive learning. - Zhijian Huang; Ziyu Fan; Siyuan Shen; Min Wu; Lei Deng 002 (Bioinform., 2024)

Exploring ncRNA-Drug Sensitivity Associations via Graph Contrastive Learning. - Xiaowen Hu; Ying Jiang; Lei Deng 002 (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)

AntiViralDL: Computational Antiviral Drug Repurposing Using Graph Neural Network and Self-Supervised Learning. - Pan Zhang; Xiaowen Hu; Guangdi Li; Lei Deng 002 (IEEE J. Biomed. Health Informatics, 2024)

MSF-PFP: A Novel Multisource Feature Fusion Model for Protein Function Prediction. - Xinhui Li; Yurong Qian; Yue Hu; Jiaying Chen; Haitao Yue; Lei Deng 002 (J. Chem. Inf. Model., 2024)

Tab-Cox: An Interpretable Deep Survival Analysis Model for Patients With Nasopharyngeal Carcinoma Based on TabNet. - Huamei Qi; Yuxuan Hu; Ruohao Fan; Lei Deng 002 (IEEE J. Biomed. Health Informatics, 2024)

DeepFusionCDR: Employing Multi-Omics Integration and Molecule-Specific Transformers for Enhanced Prediction of Cancer Drug Responses. - Xiaowen Hu; Pan Zhang; Jiaxuan Zhang; Lei Deng 002 (IEEE J. Biomed. Health Informatics, 2024)

Unraveling Disease-Associated PIWI-Interacting RNAs with a Contrastive Learning Methods. - Xiaowen Hu; Hao Sun; Linchao Shan; Chenxi Ma; Hanming Quan; Yuanpeng Zhang; Jiaxuan Zhang; Ziyu Fan; Yongjun Tang; Lei Deng 002 (J. Chem. Inf. Model., 2025)

Enhancing Predictions of Drug Solubility Through Multidimensional Structural Characterization Exploitation. - Ziyu Fan; Linying Chen; Xinyi Wu; Zhijian Huang; Lei Deng 002 (IEEE J. Biomed. Health Informatics, 2025)

AGCLNDA: Enhancing the Prediction of ncRNA-Drug Resistance Association Using Adaptive Graph Contrastive Learning. - Yanhao Fan; Che Zhang; Xiaowen Hu; Zhijian Huang; Lei Deng 002 (IEEE J. Biomed. Health Informatics, 2025)

GEP-DNN4Mol: automatic chemical molecular design based on deep neural networks and gene expression programming. - Wen Zheng; Zhongji Li; Yuanyuan Chen; Wenjia Liao; Lei Deng 002; Hao Zhang; Yanmei Lin; Yuzhong Peng (Health Inf. Sci. Syst., 2025)