Lei Deng

According to our database, Lei Deng authored at least 75 papers between 2011 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

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

IEEE J. Biomed. Health Informatics, October, 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

IEEE J. Biomed. Health Informatics, August, 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

J. Chem. Inf. Model., March, 2024

AntiViralDL: Computational Antiviral Drug Repurposing Using Graph Neural Network and Self-Supervised Learning.

Pan Zhang, Xiaowen Hu, Guangdi Li, Lei Deng

IEEE J. Biomed. Health Informatics, January, 2024

Exploring ncRNA-Drug Sensitivity Associations via Graph Contrastive Learning.

Xiaowen Hu, Ying Jiang, Lei Deng

IEEE ACM Trans. Comput. Biol. Bioinform., 2024

MvMRL: a multi-view molecular representation learning method for molecular property prediction.

Ru Zhang, Yanmei Lin, Yijia Wu, Lei Deng, Hao Zhang, Mingzhi Liao, Yuzhong Peng

Briefings Bioinform., 2024

2023

Large-scale predicting protein functions through heterogeneous feature fusion.

Rongtao Zheng, Zhijian Huang, Lei Deng

Briefings Bioinform., July, 2023

ABLNCPP: Attention Mechanism-Based Bidirectional Long Short-Term Memory for Noncoding RNA Coding Potential Prediction.

Lei Deng, Ying Jiang, Xiaowen Hu, Rongtao Zheng, Zhijian Huang, Jingpu Zhang

J. Chem. Inf. Model., June, 2023

Prediction of circRNA-MiRNA Association Using Singular Value Decomposition and Graph Neural Networks.

Yurong Qian, Jingjing Zheng, Ying Jiang, Shaoqiu Li, Lei Deng

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

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

IEEE ACM Trans. Comput. Biol. Bioinform., 2023

GCNPCA: miRNA-Disease Associations Prediction Algorithm Based on Graph Convolutional Neural Networks.

Jiwen Liu, Zhufang Kuang, Lei Deng

IEEE ACM Trans. Comput. Biol. Bioinform., 2023

DeepCoVDR: deep transfer learning with graph transformer and cross-attention for predicting COVID-19 drug response.

Zhijian Huang, Pan Zhang, Lei Deng

Bioinform., 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

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 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

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2023

TGC-ARG: Predicting Antibiotic Resistance through Transformer-based Modeling and Contrastive Learning.

Yihan Dong, Xiaowen Hu, Zhijian Huang, Lei Deng

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2023

Enhancing Protein Solubility Prediction through Pre-trained Language Models and Graph Convolutional Neural Networks.

Jie Chen, Yurong Qian, Zhijian Huang, Xiaojun Xiao, Lei Deng

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2023

2022

MGATMDA: Predicting Microbe-Disease Associations via Multi-Component Graph Attention Network.

Dayun Liu, Junyi Liu, Yi Luo, Qihua He, Lei Deng

IEEE ACM Trans. Comput. Biol. Bioinform., 2022

MSCNE: Predict miRNA-Disease Associations Using Neural Network Based on Multi-Source Biological Information.

Genwei Han, Zhufang Kuang, Lei Deng

IEEE ACM Trans. Comput. Biol. Bioinform., 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

J. Chem. Inf. Model., 2022

Dual-Channel Heterogeneous Graph Neural Network for Predicting microRNA-Mediated Drug Sensitivity.

Lei Deng, Ziyu Fan, Xiaojun Xiao, Hui Liu, Jiaxuan Zhang

J. Chem. Inf. Model., 2022

Predicting circRNA-drug sensitivity associations via graph attention auto-encoder.

Lei Deng, Zixuan Liu, Yurong Qian, Jingpu Zhang

BMC Bioinform., 2022

MSPCD: predicting circRNA-disease associations via integrating multi-source data and hierarchical neural network.

Lei Deng, Dayun Liu, Yizhan Li, Runqi Wang, Junyi Liu, Jiaxuan Zhang, Hui Liu

BMC Bioinform., 2022

Graph2MDA: a multi-modal variational graph embedding model for predicting microbe-drug associations.

Lei Deng, Yibiao Huang, Xuejun Liu, Hui Liu

Bioinform., 2022

Computational anti-COVID-19 drug design: progress and challenges.

Jinxian Wang, Ying Zhang, Wenjuan Nie, Yi Luo, Lei Deng

Briefings Bioinform., 2022

DeepDDS: deep graph neural network with attention mechanism to predict synergistic drug combinations.

Jinxian Wang, Xuejun Liu, Siyuan Shen, Lei Deng, Hui Liu

Briefings Bioinform., 2022

TSNAPred: predicting type-specific nucleic acid binding residues via an ensemble approach.

Wenjuan Nie, Lei Deng

Briefings Bioinform., 2022

Attention-wise masked graph contrastive learning for predicting molecular property.

Hui Liu, Yibiao Huang, Xuejun Liu, Lei Deng

Briefings Bioinform., 2022

Contrastive learning-based computational histopathology predict differential expression of cancer driver genes.

Haojie Huang, Gongming Zhou, Xuejun Liu, Lei Deng, Chen Wu, Dachuan Zhang, Hui Liu

Briefings Bioinform., 2022

inACP: An integrated approach to the prediction of anticancer peptides.

Guolun Zhong, Lei Deng

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022

DeepFusionGO: Protein function prediction by fusing heterogeneous features through deep learning.

Zhijian Huang, Rongtao Zheng, Lei Deng

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022

2021

LDAH2V: Exploring Meta-Paths Across Multiple Networks for lncRNA-Disease Association Prediction.

Lei Deng, Wenkai Li, Jingpu Zhang

IEEE ACM Trans. Comput. Biol. Bioinform., 2021

MSCFS: inferring circRNA functional similarity based on multiple data sources.

Liang Shu, Cheng Zhou, Xinxu Yuan, Jingpu Zhang, Lei Deng

BMC Bioinform., 2021

CRPGCN: predicting circRNA-disease associations using graph convolutional network based on heterogeneous network.

Zhihao Ma, Zhufang Kuang, Lei Deng

BMC Bioinform., 2021

SMALF: miRNA-disease associations prediction based on stacked autoencoder and XGBoost.

Dayun Liu, Yibiao Huang, Wenjuan Nie, Jiaxuan Zhang, Lei Deng

BMC Bioinform., 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

Database J. Biol. Databases Curation, 2021

LGCMDS: Predicting miRNA-Drug Sensitivity based on Light Graph Convolution Network.

Song Yu, Hanlin Xu, Yizhan Li, Dayun Liu, Lei Deng

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021

Accurately Predicting circRNA-disease Associations Using Variational Graph Auto-encoders and LightGBM.

Siyuan Shen, Yurong Qian, Jingjing Zheng, Junyi Liu, Lei Deng

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 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

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021

iPiDA-GBNN: Identification of Piwi-interacting RNA-disease associations based on gradient boosting neural network.

Yurong Qian, Qihua He, Lei Deng

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021

GCNSDA: Predicting snoRNA-disease associations via graph convolutional network.

Dayun Liu, Yi Luo, Jingjing Zheng, Hanlin Xu, Jiaxuan Zhang, Lei Deng

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021

A multi-task graph convolutional network modeling of drug-drug interactions and synergistic efficacy.

Yuanyuan Deng, Song Yu, Lei Deng, Hui Liu, Xuejun Liu, Yi Luo

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021

2020

DrugCombDB: a comprehensive database of drug combinations toward the discovery of combinatorial therapy.

Hui Liu, Wenhao Zhang, Bo Zou, Jinxian Wang, Yuanyuan Deng, Lei Deng

Nucleic Acids Res., 2020

HNet-DNN: Inferring New Drug-Disease Associations with Deep Neural Network Based on Heterogeneous Network Features.

Hui Liu, Wenhao Zhang, Yinglong Song, Lei Deng, Shuigeng Zhou

J. Chem. Inf. Model., 2020

Pathway-Guided Deep Neural Network toward Interpretable and Predictive Modeling of Drug Sensitivity.

Lei Deng, Yideng Cai, Wenhao Zhang, Wenyi Yang, Bo Gao, Hui Liu

J. Chem. Inf. Model., 2020

Gammachirp filter banks applied in roust speaker recognition based on GMM-UBM classifier.

Lei Deng, Yong Gao

Int. Arab J. Inf. Technol., 2020

DeepciRGO: functional prediction of circular RNAs through hierarchical deep neural networks using heterogeneous network features.

Lei Deng, Wei Lin, Jiacheng Wang, Jingpu Zhang

BMC Bioinform., 2020

Machine learning-based methods and novel data models to predict adverse drug reaction.

Jinxian Wang, Yuanyuan Deng, Liang Shu, Lei Deng

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2020

Predict the Protein-protein Interaction between Virus and Host through Hybrid Deep Neural Network.

Lei Deng, Jiaojiao Zhao, Jingpu Zhang

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2020

DeepARC: An Attention-based Hybrid Model for Predicting Transcription Factor Binding Sites from Positional Embedded DNA Sequence.

Jialong Chen, Lei Deng

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2020

Predicting circRNA-disease associations using meta path-based representation learning on heterogenous network.

Lei Deng, Jing Yang, Hui Liu

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2020

2019

KATZLGO: Large-Scale Prediction of LncRNA Functions by Using the KATZ Measure Based on Multiple Networks.

Zuping Zhang, Jingpu Zhang, Chao Fan, Yongjun Tang, Lei Deng

IEEE ACM Trans. Comput. Biol. Bioinform., 2019

Integrating Multiple Heterogeneous Networks for Novel LncRNA-Disease Association Inference.

Jingpu Zhang, Zuping Zhang, Zhigang Chen, Lei Deng

IEEE ACM Trans. Comput. Biol. Bioinform., 2019

MultiSourcDSim: an integrated approach for exploring disease similarity.

Lei Deng, Danyi Ye, Junmin Zhao, Jingpu Zhang

BMC Medical Informatics Decis. Mak., 2019

MADOKA: an ultra-fast approach for large-scale protein structure similarity searching.

Lei Deng, Guolun Zhong, Chenzhe Liu, Judong Luo, Hui Liu

BMC Bioinform., 2019

D2VCB: A Hybrid Deep Neural Network for the Prediction of in-vivo Protein-DNA Binding from Combined DNA Sequence.

Lei Deng, Hui Wu, Hui Liu

Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019

DKCirc2GO: Predicting Gene Ontology of circRNAs Using Dual KATZ Approach.

Lei Deng, Xin Sun, Wei Lin, Jingpu Zhang

Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019

A deep neural network approach using distributed representations of RNA sequence and structure for identifying binding site of RNA-binding proteins.

Lei Deng, Youzhi Liu, Yechuan Shi, Hui Liu

Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019

2018

Probing the functions of long non-coding RNAs by exploiting the topology of global association and interaction network.

Lei Deng, Hongjie Wu, Chuyao Liu, Weihua Zhan, Jingpu Zhang

Comput. Biol. Chem., 2018

PDRLGB: precise DNA-binding residue prediction using a light gradient boosting machine.

Lei Deng, Juan Pan, Xiaojie Xu, Wenyi Yang, Chuyao Liu, Hui Liu

BMC Bioinform., 2018

Ontological function annotation of long non-coding RNAs through hierarchical multi-label classification.

Jingpu Zhang, Zuping Zhang, Zixiang Wang, Yuting Liu, Lei Deng

Bioinform., 2018

XPredRBR: Accurate and Fast Prediction of RNA-Binding Residues in Proteins Using eXtreme Gradient Boosting.

Lei Deng, Zuojin Dong, Hui Liu

Proceedings of the Bioinformatics Research and Applications - 14th International Symposium, 2018

Exploring Disease Similarity by Integrating Multiple Data Sources.

Lei Deng, Danyi Ye, Junmin Zhao, Jingpu Zhang

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

2017

A boosting approach for prediction of protein-RNA binding residues.

Yongjun Tang, Diwei Liu, Zixiang Wang, Ting Wen, Lei Deng

BMC Bioinform., 2017

A sparse autoencoder-based deep neural network for protein solvent accessibility and contact number prediction.

Lei Deng, Chao Fan, Zhiwen Zeng

BMC Bioinform., 2017

BiRWLGO: A global network-based strategy for lncRNA function annotation using bi-random walk.

Jingpu Zhang, Shuai Zou, Lei Deng

Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017

2016

PredRSA: a gradient boosted regression trees approach for predicting protein solvent accessibility.

Chao Fan, Diwei Liu, Rui Huang, Zhigang Chen, Lei Deng

BMC Bioinform., 2016

PredRBR: Accurate Prediction of RNA-Binding Residues in proteins using Gradient Tree Boosting.

Diwei Liu, Yongjun Tang, Chao Fan, Zhigang Chen, Lei Deng

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

2015

An Integrated Framework for Functional Annotation of Protein Structural Domains.

Lei Deng, Zhigang Chen

IEEE ACM Trans. Comput. Biol. Bioinform., 2015

2014

PredHS: a web server for predicting protein-protein interaction hot spots by using structural neighborhood properties.

Lei Deng, Qiangfeng Cliff Zhang, Zhigang Chen, Yang Meng, Jihong Guan, Shuigeng Zhou

Nucleic Acids Res., 2014

A Multi-Instance Multi-Label Learning Approach for Protein Domain Annotation.

Yang Meng, Lei Deng, Zhigang Chen, Cheng Zhou, Diwei Liu, Chao Fan, Ting Yan

Proceedings of the Intelligent Computing in Bioinformatics - 10th International Conference, 2014

Structure-Based Prediction of Protein Phosphorylation Sites Using an Ensemble Approach.

Yong Gao, Weilin Hao, Zhigang Chen, Lei Deng

Proceedings of the Intelligent Computing in Bioinformatics - 10th International Conference, 2014

2013

PrePPI: a structure-informed database of protein-protein interactions.

Qiangfeng Cliff Zhang, Donald Petrey, José Ignacio Garzón, Lei Deng, Barry Honig

Nucleic Acids Res., 2013

Boosting Prediction Performance of Protein-Protein Interaction Hot Spots by Using Structural Neighborhood Properties.

Lei Deng, Jihong Guan, Xiaoming Wei, Yuan Yi, Qiangfeng Cliff Zhang, Shuigeng Zhou

J. Comput. Biol., 2013

2011

PredUs: a web server for predicting protein interfaces using structural neighbors.

Qiangfeng Cliff Zhang, Lei Deng, Markus Fisher, Jihong Guan, Barry Honig, Donald Petrey

Nucleic Acids Res., 2011