Lei Deng

Publication Activity (10 Years)

Years Active: 2011-2024
Publications (10 Years): 52

Top Topics

Solvent Accessibility

Protein Structural

Top Venues

IEEE ACM Trans. Comput. Biol. Bioinform.

Briefings Bioinform.

Publications

Pan Zhang, Xiaowen Hu, Guangdi Li, Lei Deng
AntiViralDL: Computational Antiviral Drug Repurposing Using Graph Neural Network and Self-Supervised Learning. IEEE J. Biomed. Health Informatics 28 (1) (2024)
Ru Zhang, Yanmei Lin, Yijia Wu, Lei Deng, Hao Zhang, Mingzhi Liao, Yuzhong Peng
MvMRL: a multi-view molecular representation learning method for molecular property prediction. Briefings Bioinform. 25 (4) (2024)
Xinhui Li, Yurong Qian, Yue Hu, Jiaying Chen, Haitao Yue, Lei Deng
MSF-PFP: A Novel Multisource Feature Fusion Model for Protein Function Prediction. J. Chem. Inf. Model. 64 (5) (2024)
Huamei Qi, Yuxuan Hu, Ruohao Fan, Lei Deng
Tab-Cox: An Interpretable Deep Survival Analysis Model for Patients With Nasopharyngeal Carcinoma Based on TabNet. IEEE J. Biomed. Health Informatics 28 (8) (2024)
Zhijian Huang, Pan Zhang, Lei Deng
DeepCoVDR: deep transfer learning with graph transformer and cross-attention for predicting COVID-19 drug response. Bioinform. 39 (Supplement-1) (2023)
Rongtao Zheng, Zhijian Huang, Lei Deng
Large-scale predicting protein functions through heterogeneous feature fusion. Briefings Bioinform. 24 (4) (2023)
Yuanpeng Zhang, Yurong Qian, Xiaojun Xiao, Xiaowen Hu, Zhijian Huang, Lei Deng
PTDA-SWGCL: Predicting tRNA-Disease Associations using Supplementarily Weighted Graph Contrastive Learning. BIBM (2023)
Xiaojun Xiao, Yurong Qian, Zhijian Huang, Rongtao Zheng, Lei Deng
Predicting Associations between circRNAs and Drug Sensitivity using Heterogeneous Graphs and Graph Attention Networks. BIBM (2023)
Yurong Qian, Jingjing Zheng, Ying Jiang, Shaoqiu Li, Lei Deng
Prediction of circRNA-MiRNA Association Using Singular Value Decomposition and Graph Neural Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (6) (2023)
Jiwen Liu, Zhufang Kuang, Lei Deng
GCNPCA: miRNA-Disease Associations Prediction Algorithm Based on Graph Convolutional Neural Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (2) (2023)
Yihan Dong, Xiaowen Hu, Zhijian Huang, Lei Deng
TGC-ARG: Predicting Antibiotic Resistance through Transformer-based Modeling and Contrastive Learning. BIBM (2023)
Lei Deng, Ying Jiang, Xiaowen Hu, Rongtao Zheng, Zhijian Huang, Jingpu Zhang
ABLNCPP: Attention Mechanism-Based Bidirectional Long Short-Term Memory for Noncoding RNA Coding Potential Prediction. J. Chem. Inf. Model. 63 (12) (2023)
Jie Chen, Yurong Qian, Zhijian Huang, Xiaojun Xiao, Lei Deng
Enhancing Protein Solubility Prediction through Pre-trained Language Models and Graph Convolutional Neural Networks. BIBM (2023)
Dayun Liu, Xianghui Li, Liangliang Zhang, Xiaowen Hu, Jiaxuan Zhang, Zhirong Liu, Lei Deng
HGNNLDA: Predicting lncRNA-Drug Sensitivity Associations via a Dual Channel Hypergraph Neural Network. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (6) (2023)
Zhihao Ma, Zhufang Kuang, Lei Deng
NGCICM: A Novel Deep Learning-Based Method for Predicting circRNA-miRNA Interactions. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (5) (2023)
Wenjuan Nie, Lei Deng
TSNAPred: predicting type-specific nucleic acid binding residues via an ensemble approach. Briefings Bioinform. 23 (4) (2022)
Genwei Han, Zhufang Kuang, Lei Deng
MSCNE: Predict miRNA-Disease Associations Using Neural Network Based on Multi-Source Biological Information. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (5) (2022)
Haojie Huang, Gongming Zhou, Xuejun Liu, Lei Deng, Chen Wu, Dachuan Zhang, Hui Liu
Contrastive learning-based computational histopathology predict differential expression of cancer driver genes. CoRR (2022)
Dayun Liu, Junyi Liu, Yi Luo, Qihua He, Lei Deng
MGATMDA: Predicting Microbe-Disease Associations via Multi-Component Graph Attention Network. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (6) (2022)
Guolun Zhong, Lei Deng
inACP: An integrated approach to the prediction of anticancer peptides. BIBM (2022)
Lei Deng, Ziyu Fan, Xiaojun Xiao, Hui Liu, Jiaxuan Zhang
Dual-Channel Heterogeneous Graph Neural Network for Predicting microRNA-Mediated Drug Sensitivity. J. Chem. Inf. Model. 62 (23) (2022)
Lei Deng, Dayun Liu, Yizhan Li, Runqi Wang, Junyi Liu, Jiaxuan Zhang, Hui Liu
MSPCD: predicting circRNA-disease associations via integrating multi-source data and hierarchical neural network. BMC Bioinform. (3) (2022)
Hui Liu, Yibiao Huang, Xuejun Liu, Lei Deng
Attention-wise masked graph contrastive learning for predicting molecular property. Briefings Bioinform. 23 (5) (2022)
Jinxian Wang, Xuejun Liu, Siyuan Shen, Lei Deng, Hui Liu
DeepDDS: deep graph neural network with attention mechanism to predict synergistic drug combinations. Briefings Bioinform. 23 (1) (2022)
Haojie Huang, Gongming Zhou, Xuejun Liu, Lei Deng, Chen Wu, Dachuan Zhang, Hui Liu
Contrastive learning-based computational histopathology predict differential expression of cancer driver genes. Briefings Bioinform. 23 (5) (2022)
Hui Liu, Yibiao Huang, Xuejun Liu, Lei Deng
Attention-wise masked graph contrastive learning for predicting molecular property. CoRR (2022)
Lei Deng, Zixuan Liu, Yurong Qian, Jingpu Zhang
Predicting circRNA-drug sensitivity associations via graph attention auto-encoder. BMC Bioinform. 23 (1) (2022)
Jinxian Wang, Ying Zhang, Wenjuan Nie, Yi Luo, Lei Deng
Computational anti-COVID-19 drug design: progress and challenges. Briefings Bioinform. 23 (1) (2022)
Jingjing Zheng, Yurong Qian, Jie He, Zerui Kang, Lei Deng
Graph Neural Network with Self-Supervised Learning for Noncoding RNA-Drug Resistance Association Prediction. J. Chem. Inf. Model. 62 (15) (2022)
Lei Deng, Yibiao Huang, Xuejun Liu, Hui Liu
Graph2MDA: a multi-modal variational graph embedding model for predicting microbe-drug associations. Bioinform. 38 (4) (2022)
Liang Shu, Cheng Zhou, Xinxu Yuan, Jingpu Zhang, Lei Deng
MSCFS: inferring circRNA functional similarity based on multiple data sources. BMC Bioinform. (10) (2021)
Lei Deng, Yibiao Huang, Xuejun Liu, Hui Liu
Graph2MDA: a multi-modal variational graph embedding model for predicting microbe-drug associations. CoRR (2021)
Lei Deng, Wenkai Li, Jingpu Zhang
LDAH2V: Exploring Meta-Paths Across Multiple Networks for lncRNA-Disease Association Prediction. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (4) (2021)
Yuanyuan Deng, Song Yu, Lei Deng, Hui Liu, Xuejun Liu, Yi Luo
A multi-task graph convolutional network modeling of drug-drug interactions and synergistic efficacy. BIBM (2021)
Jinxian Wang, Xuejun Liu, Siyuan Shen, Lei Deng, Hui Liu
DeepDDS: deep graph neural network with attention mechanism to predict synergistic drug combinations. CoRR (2021)
Junyi Liu, Siyu Liu, Chenzhe Liu, Yaping Zhang, Yuliang Pan, Zixiang Wang, Jiacheng Wang, Ting Wen, Lei Deng
Nabe: an energetic database of amino acid mutations in protein-nucleic acid binding interfaces. Database J. Biol. Databases Curation 2021 (2021)
Lei Deng, Wei Lin, Jiacheng Wang, Jingpu Zhang
DeepciRGO: functional prediction of circular RNAs through hierarchical deep neural networks using heterogeneous network features. BMC Bioinform. 21 (1) (2020)
Lei Deng, Jing Yang, Hui Liu
Predicting circRNA-disease associations using meta path-based representation learning on heterogenous network. BIBM (2020)
Lei Deng, Yong Gao
Gammachirp filter banks applied in roust speaker recognition based on GMM-UBM classifier. Int. Arab J. Inf. Technol. 17 (2) (2020)
Lei Deng, Xin Sun, Wei Lin, Jingpu Zhang
DKCirc2GO: Predicting Gene Ontology of circRNAs Using Dual KATZ Approach. BIBM (2019)
Jingpu Zhang, Zuping Zhang, Zhigang Chen, Lei Deng
Integrating Multiple Heterogeneous Networks for Novel LncRNA-Disease Association Inference. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (2) (2019)
Lei Deng, Guolun Zhong, Chenzhe Liu, Judong Luo, Hui Liu
MADOKA: an ultra-fast approach for large-scale protein structure similarity searching. BMC Bioinform. (19) (2019)
Lei Deng, Danyi Ye, Junmin Zhao, Jingpu Zhang
MultiSourcDSim: an integrated approach for exploring disease similarity. BMC Medical Informatics Decis. Mak. (6) (2019)
Zuping Zhang, Jingpu Zhang, Chao Fan, Yongjun Tang, Lei Deng
KATZLGO: Large-Scale Prediction of LncRNA Functions by Using the KATZ Measure Based on Multiple Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (2) (2019)
Lei Deng, Danyi Ye, Junmin Zhao, Jingpu Zhang
Exploring Disease Similarity by Integrating Multiple Data Sources. BIBM (2018)
Lei Deng, Hongjie Wu, Chuyao Liu, Weihua Zhan, Jingpu Zhang
Probing the functions of long non-coding RNAs by exploiting the topology of global association and interaction network. Comput. Biol. Chem. 74 (2018)
Jingpu Zhang, Zuping Zhang, Zixiang Wang, Yuting Liu, Lei Deng
Ontological function annotation of long non-coding RNAs through hierarchical multi-label classification. Bioinform. 34 (10) (2018)
Lei Deng, Chao Fan, Zhiwen Zeng
A sparse autoencoder-based deep neural network for protein solvent accessibility and contact number prediction. BMC Bioinform. 18 (16) (2017)
Yongjun Tang, Diwei Liu, Zixiang Wang, Ting Wen, Lei Deng
A boosting approach for prediction of protein-RNA binding residues. BMC Bioinform. 18 (S-13) (2017)
Jingpu Zhang, Shuai Zou, Lei Deng
BiRWLGO: A global network-based strategy for lncRNA function annotation using bi-random walk. BIBM (2017)
Diwei Liu, Yongjun Tang, Chao Fan, Zhigang Chen, Lei Deng
PredRBR: Accurate Prediction of RNA-Binding Residues in proteins using Gradient Tree Boosting. BIBM (2016)
Chao Fan, Diwei Liu, Rui Huang, Zhigang Chen, Lei Deng
PredRSA: a gradient boosted regression trees approach for predicting protein solvent accessibility. BMC Bioinform. 17 (S-1) (2016)
Lei Deng, Zhigang Chen
An Integrated Framework for Functional Annotation of Protein Structural Domains. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (4) (2015)
Yang Meng, Lei Deng, Zhigang Chen, Cheng Zhou, Diwei Liu, Chao Fan, Ting Yan
A Multi-Instance Multi-Label Learning Approach for Protein Domain Annotation. ICIC (3) (2014)
Lei Deng, Qiangfeng Cliff Zhang, Zhigang Chen, Yang Meng, Jihong Guan, Shuigeng Zhou
PredHS: a web server for predicting protein-protein interaction hot spots by using structural neighborhood properties. Nucleic Acids Res. 42 (Webserver-Issue) (2014)
Yong Gao, Weilin Hao, Zhigang Chen, Lei Deng
Structure-Based Prediction of Protein Phosphorylation Sites Using an Ensemble Approach. ICIC (3) (2014)
Qiangfeng Cliff Zhang, Donald Petrey, José Ignacio Garzón, Lei Deng, Barry Honig
PrePPI: a structure-informed database of protein-protein interactions. Nucleic Acids Res. 41 (Database-Issue) (2013)
Lei Deng, Jihong Guan, Xiaoming Wei, Yuan Yi, Qiangfeng Cliff Zhang, Shuigeng Zhou
Boosting Prediction Performance of Protein-Protein Interaction Hot Spots by Using Structural Neighborhood Properties. J. Comput. Biol. 20 (11) (2013)
Qiangfeng Cliff Zhang, Lei Deng, Markus Fisher, Jihong Guan, Barry Honig, Donald Petrey
PredUs: a web server for predicting protein interfaces using structural neighbors. Nucleic Acids Res. 39 (Web-Server-Issue) (2011)