Lei Deng - RankMe

136 papers A* 1B 1Journal 89Unranked 45

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	DeepLMI: deep feature mining with a globally enhanced graph convolutional network for robust lncRNA-miRNA interaction prediction. Bioinform. Zhijian Huang, Kai Chen, Xianshu Wang, Junheng Wang, Siyuan Shen, Yuanpeng Zhang, Min Wu, Lei Deng
2026	J	`jnl`	HECLCDA:CircRNA-Drug Sensitivity Prediction via Heterogeneous Cross-Scale Contrastive Learning. IEEE Trans. Comput. Biol. Bioinform. Jinmiao Song, Bin Xu, Lei Deng, Qimeng Yang, Qiguo Dai, Shengwei Tian
2026	J	`jnl`	HHGSynergy: An Adaptive Heterogeneous Hypergraph Representation Learning Method for Anticancer Drug Synergy Prediction. IEEE Trans. Comput. Biol. Bioinform. Jinmiao Song, Yang Meng, Lei Deng, Qimeng Yang, Qiguo Dai, Shengwei Tian
2026	A*	`conf`	Hierarchical Structure-Property Alignment for Data-Efficient Molecular Generation and Editing. AAAI Ziyu Fan, Zhijian Huang, Yahan Li, Xiaowen Hu, Siyuan Shen, Yunliang Wang, Zeyu Zhong, Shuhong Liu, Shuning Yang, Shangqian Wu, Min Wu, Lei Deng
2026	J	`jnl`	ME-PFP: An Ensemble Learning Approach Fusing Multi-Source Features for Protein Function Prediction. J. Chem. Inf. Model. Haoxing Luo, Yue Hu, Chaolin Song, Xinhui Li, Yuyin Ma, Yurong Qian, Lei Deng
2026	J	`jnl`	MM-GHiNet: A multimodal graph hierarchical network for brain disease diagnosis. Expert Syst. Appl. Chao Li, Jiangtao Xu, Zhijian Huang, Lei Deng
2026	J	`jnl`	TwistDAN: Twisted Domain Adversarial Network for Synthetic Accessibility Assessment. J. Chem. Inf. Model. Qahtan Adnan Aljanabi, Zhijian Huang, Ziyu Fan, Shangqian Wu, Shuhong Liu, Meng Chen, Hang Chen, Yuanpeng Zhang, Jiangtao Xu, Lei Deng
2025	—	`conf`	A Modular Framework for Multimorbidity Prediction with MNAR-Aware Imputation and Label-Enhanced Transformers. BIBM Huamei Qi, Chen Cao, Zhenzhen Rao, Lei Deng
2025	J	`jnl`	AGCLNDA: Enhancing the Prediction of ncRNA-Drug Resistance Association Using Adaptive Graph Contrastive Learning. IEEE J. Biomed. Health Informatics Yanhao Fan, Che Zhang, Xiaowen Hu, Zhijian Huang, Lei Deng
2025	J	`jnl`	AGDNGDA: Unraveling Drug-Associated Genes with Adaptive Graph Diffusion Networks. J. Chem. Inf. Model. Xiaowen Hu, Che Zhang, Yanhao Fan, Kerui Wu, Lei Deng
2025	—	`conf`	ASRSMA: Atomic-Scale and Structure-Based Modeling for RNA-Small Molecule Binding Affinity Prediction via Contrastive Pretraining. BIBM Yahan Li, Zhijian Huang, Song Chen, Yucheng Wang, Min Wu, Lei Deng
2025	J	`jnl`	CircGO: Predicting circRNA Functions Through Self-Supervised Learning of Heterogeneous Networks. IEEE Trans. Comput. Biol. Bioinform. Zhijian Huang, Rongtao Zheng, Siyuan Shen, Kai Chen, Min Wu, Lei Deng
2025	J	`jnl`	Contrastive hypergraph collaborative filtering for transfer RNA-disease association prediction. Briefings Bioinform. Tianxiang Ouyang, Yuanpeng Zhang, Zhijian Huang, Lei Deng
2025	—	`conf`	DSSA: Dual-Stream Synthetic Accessibility Framework for Organic Compounds. BIBM Qahtan Adnan Aljanabi, Zhijian Huang, Gebremedhin Assefa Girmay, Zhengkang Wang, Yuanpeng Zhang, Lei Deng
2025	—	`conf`	DeepBindAffinity: A ResNet-Augmented Hybrid CNN-Transformer for Protein-Ligand Binding Affinity Prediction. BIBM Gebremedhin Assefa Girmay, Qahtan Adnan Aljanabi, Lei Deng
2025	J	`jnl`	DeepExpDR: Drug Response Prediction through Molecular Topological Grouping and Substructure-Aware Expert. J. Chem. Inf. Model. Yuanpeng Zhang, Zhijian Huang, Yurong Qian, Peng Xie, Ziyu Fan, Min Wu, Lei Deng
2025	J	`jnl`	DeepHeteroCDA: circRNA-drug sensitivity associations prediction via multi-scale heterogeneous network and graph attention mechanism. Briefings Bioinform. Zhijian Huang, Kai Chen, Xiaojun Xiao, Ziyu Fan, Yuanpeng Zhang, Lei Deng
2025	J	`jnl`	Enhancing Predictions of Drug Solubility Through Multidimensional Structural Characterization Exploitation. IEEE J. Biomed. Health Informatics Ziyu Fan, Linying Chen, Xinyi Wu, Zhijian Huang, Lei Deng
2025	J	`jnl`	GEP-DNN4Mol: automatic chemical molecular design based on deep neural networks and gene expression programming. Health Inf. Sci. Syst. Wen Zheng, Zhongji Li, Yuanyuan Chen, Wenjia Liao, Lei Deng, Hao Zhang, Yanmei Lin, Yuzhong Peng
2025	—	`conf`	GroupTransUNet: Group Transformer UNet for Medical Image Segmentation. BIBM Yunliang Wang, Ziyu Fan, Zhijian Huang, Jinmiao Song, Lei Deng
2025	J	`jnl`	HCoVDB: a comprehensive database encompassing viral genomes, drug targets, and therapeutics of human coronaviruses. Database J. Biol. Databases Curation Pan Zhang, Tianxiang Ouyang, Xiaowen Hu, Jie Huang, Biao Xiao, Zhijian Huang, Xingyang Shi, Xinyi Wu, Linying Chen, Yongkang Wu, Hanyue Wang, Ying Zhang, Guangdi Li, Hui Liu, Lei Deng
2025	J	`jnl`	HLN-DDI: hierarchical molecular representation learning with co-attention mechanism for drug-drug interaction prediction. BMC Bioinform. Yue Luo, Lei Deng, Zhijian Huang
2025	J	`jnl`	Hierarchical Structure-Property Alignment for Data-Efficient Molecular Generation and Editing. CoRR Ziyu Fan, Zhijian Huang, Yahan Li, Xiaowen Hu, Siyuan Shen, Yunliang Wang, Zeyu Zhong, Shuhong Liu, Shuning Yang, Shangqian Wu, Min Wu, Lei Deng
2025	—	`conf`	MVFDSP: A Multi-View Fusion Framework for Drug Side-Effect Frequency Prediction. BIBM Zhengkang Wang, Zhijian Huang, Yurong Qian, Yuanpeng Zhang, Yahan Li, Qahtan Adnan Aljanabi, Jinmiao Song, Lei Deng
2025	J	`jnl`	MVRBind: multi-view learning for RNA-small molecule binding site prediction. Briefings Bioinform. Song Chen, Zhijian Huang, Yucheng Wang, Yahan Li, Yaw Sing Tan, Lei Deng, Min Wu
2025	J	`jnl`	MolCL-SP: a multimodal contrastive learning framework with non-overlapping substructure perturbations for molecular property prediction. Bioinform. Yue Luo, Lei Deng
2025	—	`conf`	MutDTA: Interpretable Transfer Learning for Predicting Mutation Effects on Drug Binding Affinity in Viral Proteins. BIBM Xiaowen Hu, Pan Zhang, Min Wu, Guangdi Li, Zizhang Sheng, Lei Deng
2025	J	`jnl`	Partner-RBR: Predicting Multitype RNA-Binding Residues Based on Mutual Learning. J. Chem. Inf. Model. Zhijian Huang, Yihan Dong, Wenjuan Nie, Hang Chen, Qahtan Adnan Aljanabi, Lei Deng
2025	J	`jnl`	Precise prediction of hotspot residues in protein-RNA complexes using graph attention networks and pretrained protein language models. Bioinform. Siyuan Shen, Jie Chen, Zhijian Huang, Yuanpeng Zhang, Ziyu Fan, Yuting Kong, Lei Deng
2025	J	`jnl`	SeekTP: identifying multifunctional therapeutic peptides via graph attention and deep property integration. Briefings Bioinform. Guolun Zhong, Lei Deng
2025	—	`conf`	TabNet-Based Autoencoder Enhanced with Dynamic Masking for Multiple Imputation of Medical Table Data. BIBM Huamei Qi, Yuchen Yan, Zhenzhen Rao, Lei Deng
2025	J	`jnl`	Unraveling Disease-Associated PIWI-Interacting RNAs with a Contrastive Learning Methods. J. Chem. Inf. Model. Xiaowen Hu, Hao Sun, Linchao Shan, Chenxi Ma, Hanming Quan, Yuanpeng Zhang, Jiaxuan Zhang, Ziyu Fan, Yongjun Tang, Lei Deng
2024	—	`conf`	A Self-Attention Synthesizing Model with Privacy-Preserving(ACCT-GAN) for Medical Tabular Data. BIBM Huamei Qi, Wenqin Zou, Sen Fu, Lei Deng
2024	—	`conf`	ADiffGDA: Exploring Gene-Drug Associations via Adaptive Graph Diffusion Networks. BIBM Che Zhang, Yanhao Fan, Xiaowen Hu, Yurong Qian, Lei Deng
2024	J	`jnl`	AntiViralDL: Computational Antiviral Drug Repurposing Using Graph Neural Network and Self-Supervised Learning. IEEE J. Biomed. Health Informatics Pan Zhang, Xiaowen Hu, Guangdi Li, Lei Deng
2024	J	`jnl`	DPMGCDA: Deciphering circRNA-Drug Sensitivity Associations with Dual Perspective Learning and Path-Masked Graph Autoencoder. J. Chem. Inf. Model. Yue Luo, Lei Deng
2024	—	`conf`	DTA-Net: Dual-Task Attention Network for Medical Image Segmentation and Classification. BIBM Haifeng Qi, Siyuan Shen, Zhijian Huang, Lei Deng
2024	J	`jnl`	DeepFusionCDR: Employing Multi-Omics Integration and Molecule-Specific Transformers for Enhanced Prediction of Cancer Drug Responses. IEEE J. Biomed. Health Informatics Xiaowen Hu, Pan Zhang, Jiaxuan Zhang, Lei Deng
2024	J	`jnl`	DeepRSMA: a cross-fusion-based deep learning method for RNA-small molecule binding affinity prediction. Bioinform. Zhijian Huang, Yucheng Wang, Song Chen, Yaw Sing Tan, Lei Deng, Min Wu
2024	—	`conf`	Enhancing miRNA-Disease Prediction with Attention-Based Multi-View Contrastive Learning. BIBM Tianxiang Ouyang, Zhijian Huang, Lei Deng
2024	J	`jnl`	Exploring ncRNA-Drug Sensitivity Associations via Graph Contrastive Learning. IEEE ACM Trans. Comput. Biol. Bioinform. Xiaowen Hu, Ying Jiang, Lei Deng
2024	—	`conf`	GATBind: Accurate protein-RNA binding sites prediction via graph attention networks with pre-trained language model. BIBM Siyuan Shen, Shangqian Wu, Jie Chen, Zhijian Huang, Lei Deng
2024	—	`conf`	HGTRDA: Enhancing Prediction of ncRNA-Mediated Drug Resistance with Hypergraph Transformer. BIBM Che Zhang, Ruohui He, Yanhao Fan, Xiaowen Hu, Yurong Qian, Lei Deng
2024	—	`conf`	Hierarchical Molecular Structure Network with Co-attention Mechanism for Drug-Drug Interaction Prediction. BIBM Yue Luo, Lei Deng
2024	J	`jnl`	IGCNSDA: unraveling disease-associated snoRNAs with an interpretable graph convolutional network. Briefings Bioinform. Xiaowen Hu, Pan Zhang, Dayun Liu, Jiaxuan Zhang, Yuanpeng Zhang, Yihan Dong, Yanhao Fan, Lei Deng
2024	—	`conf`	Imputation of incomplete medical data using missing neighborhood perturbation denoising autoencoder. BIBM Huamei Qi, Wenhui Yang, Sen Fu, Lei Deng
2024	—	`conf`	LSNSCDA: Unraveling CircRNA-Drug Sensitivity via Local Smoothing Graph Neural Network and Credible Negative Samples. BIBM Ziyu Fan, Yuanpeng Zhang, Yahan Li, Zeyu Zhong, Lei Deng
2024	—	`conf`	MFF-LncLoc: Subcellular Localization Prediction of lncRNAs Based on Multi-Feature Fusion Using Transformers. BIBM Ziyu Fan, Ying Jiang, Shuning Yang, Lei Deng
2024	J	`jnl`	MSF-PFP: A Novel Multisource Feature Fusion Model for Protein Function Prediction. J. Chem. Inf. Model. Xinhui Li, Yurong Qian, Yue Hu, Jiaying Chen, Haitao Yue, Lei Deng
2024	J	`jnl`	MolMVC: Enhancing molecular representations for drug-related tasks through multi-view contrastive learning. Bioinform. Zhijian Huang, Ziyu Fan, Siyuan Shen, Min Wu, Lei Deng
2024	J	`jnl`	MvMRL: a multi-view molecular representation learning method for molecular property prediction. Briefings Bioinform. Ru Zhang, Yanmei Lin, Yijia Wu, Lei Deng, Hao Zhang, Mingzhi Liao, Yuzhong Peng
2024	J	`jnl`	SGCLDGA: unveiling drug-gene associations through simple graph contrastive learning. Briefings Bioinform. Yanhao Fan, Che Zhang, Xiaowen Hu, Zhijian Huang, Jiameng Xue, Lei Deng
2024	J	`jnl`	Tab-Cox: An Interpretable Deep Survival Analysis Model for Patients With Nasopharyngeal Carcinoma Based on TabNet. IEEE J. Biomed. Health Informatics Huamei Qi, Yuxuan Hu, Ruohao Fan, Lei Deng
2023	J	`jnl`	A comprehensive review and evaluation of graph neural networks for non-coding RNA and complex disease associations. Briefings Bioinform. Xiaowen Hu, Dayun Liu, Jiaxuan Zhang, Yanhao Fan, Tianxiang Ouyang, Yue Luo, Yuanpeng Zhang, Lei Deng
2023	J	`jnl`	ABLNCPP: Attention Mechanism-Based Bidirectional Long Short-Term Memory for Noncoding RNA Coding Potential Prediction. J. Chem. Inf. Model. Lei Deng, Ying Jiang, Xiaowen Hu, Rongtao Zheng, Zhijian Huang, Jingpu Zhang
2023	—	`conf`	CLPiDA: A Contrastive Learning Approach for Predicting Potential PiRNA-Disease Associations. BIBM Xiaowen Hu, Yuanpeng Zhang, Jiaxuan Zhang, Lei Deng
2023	J	`jnl`	DeepCoVDR: deep transfer learning with graph transformer and cross-attention for predicting COVID-19 drug response. Bioinform. Zhijian Huang, Pan Zhang, Lei Deng
2023	—	`conf`	Enhancing Protein Solubility Prediction through Pre-trained Language Models and Graph Convolutional Neural Networks. BIBM Jie Chen, Yurong Qian, Zhijian Huang, Xiaojun Xiao, Lei Deng
2023	J	`jnl`	GCNPCA: miRNA-Disease Associations Prediction Algorithm Based on Graph Convolutional Neural Networks. IEEE ACM Trans. Comput. Biol. Bioinform. Jiwen Liu, Zhufang Kuang, Lei Deng
2023	J	`jnl`	HGCLMDA: Predicting mRNA-Drug Sensitivity Associations via Hypergraph Contrastive Learning. J. Chem. Inf. Model. Xiaowen Hu, Yihan Dong, Jiaxuan Zhang, Lei Deng
2023	J	`jnl`	HGNNLDA: Predicting lncRNA-Drug Sensitivity Associations via a Dual Channel Hypergraph Neural Network. IEEE ACM Trans. Comput. Biol. Bioinform. Dayun Liu, Xianghui Li, Liangliang Zhang, Xiaowen Hu, Jiaxuan Zhang, Zhirong Liu, Lei Deng
2023	J	`jnl`	Large-scale predicting protein functions through heterogeneous feature fusion. Briefings Bioinform. Rongtao Zheng, Zhijian Huang, Lei Deng
2023	J	`jnl`	NGCICM: A Novel Deep Learning-Based Method for Predicting circRNA-miRNA Interactions. IEEE ACM Trans. Comput. Biol. Bioinform. Zhihao Ma, Zhufang Kuang, Lei Deng
2023	—	`conf`	PTDA-SWGCL: Predicting tRNA-Disease Associations using Supplementarily Weighted Graph Contrastive Learning. BIBM Yuanpeng Zhang, Yurong Qian, Xiaojun Xiao, Xiaowen Hu, Zhijian Huang, Lei Deng
2023	—	`conf`	Predicting Associations between circRNAs and Drug Sensitivity using Heterogeneous Graphs and Graph Attention Networks. BIBM Xiaojun Xiao, Yurong Qian, Zhijian Huang, Rongtao Zheng, Lei Deng
2023	J	`jnl`	Prediction of circRNA-MiRNA Association Using Singular Value Decomposition and Graph Neural Networks. IEEE ACM Trans. Comput. Biol. Bioinform. Yurong Qian, Jingjing Zheng, Ying Jiang, Shaoqiu Li, Lei Deng
2023	—	`conf`	TGC-ARG: Predicting Antibiotic Resistance through Transformer-based Modeling and Contrastive Learning. BIBM Yihan Dong, Xiaowen Hu, Zhijian Huang, Lei Deng
2022	J	`jnl`	Attention-wise masked graph contrastive learning for predicting molecular property. Briefings Bioinform. Hui Liu, Yibiao Huang, Xuejun Liu, Lei Deng
2022	J	`jnl`	Attention-wise masked graph contrastive learning for predicting molecular property. CoRR Hui Liu, Yibiao Huang, Xuejun Liu, Lei Deng
2022	J	`jnl`	Computational anti-COVID-19 drug design: progress and challenges. Briefings Bioinform. Jinxian Wang, Ying Zhang, Wenjuan Nie, Yi Luo, Lei Deng
2022	J	`jnl`	Contrastive learning-based computational histopathology predict differential expression of cancer driver genes. Briefings Bioinform. Haojie Huang, Gongming Zhou, Xuejun Liu, Lei Deng, Chen Wu, Dachuan Zhang, Hui Liu
2022	J	`jnl`	Contrastive learning-based computational histopathology predict differential expression of cancer driver genes. CoRR Haojie Huang, Gongming Zhou, Xuejun Liu, Lei Deng, Chen Wu, Dachuan Zhang, Hui Liu
2022	J	`jnl`	DeepDDS: deep graph neural network with attention mechanism to predict synergistic drug combinations. Briefings Bioinform. Jinxian Wang, Xuejun Liu, Siyuan Shen, Lei Deng, Hui Liu
2022	—	`conf`	DeepFusionGO: Protein function prediction by fusing heterogeneous features through deep learning. BIBM Zhijian Huang, Rongtao Zheng, Lei Deng
2022	J	`jnl`	Dual-Channel Heterogeneous Graph Neural Network for Predicting microRNA-Mediated Drug Sensitivity. J. Chem. Inf. Model. Lei Deng, Ziyu Fan, Xiaojun Xiao, Hui Liu, Jiaxuan Zhang
2022	J	`jnl`	Graph Neural Network with Self-Supervised Learning for Noncoding RNA-Drug Resistance Association Prediction. J. Chem. Inf. Model. Jingjing Zheng, Yurong Qian, Jie He, Zerui Kang, Lei Deng
2022	J	`jnl`	Graph2MDA: a multi-modal variational graph embedding model for predicting microbe-drug associations. Bioinform. Lei Deng, Yibiao Huang, Xuejun Liu, Hui Liu
2022	J	`jnl`	MGATMDA: Predicting Microbe-Disease Associations via Multi-Component Graph Attention Network. IEEE ACM Trans. Comput. Biol. Bioinform. Dayun Liu, Junyi Liu, Yi Luo, Qihua He, Lei Deng
2022	J	`jnl`	MSCNE: Predict miRNA-Disease Associations Using Neural Network Based on Multi-Source Biological Information. IEEE ACM Trans. Comput. Biol. Bioinform. Genwei Han, Zhufang Kuang, Lei Deng
2022	J	`jnl`	MSPCD: predicting circRNA-disease associations via integrating multi-source data and hierarchical neural network. BMC Bioinform. Lei Deng, Dayun Liu, Yizhan Li, Runqi Wang, Junyi Liu, Jiaxuan Zhang, Hui Liu
2022	J	`jnl`	Predicting circRNA-drug sensitivity associations via graph attention auto-encoder. BMC Bioinform. Lei Deng, Zixuan Liu, Yurong Qian, Jingpu Zhang
2022	J	`jnl`	TSNAPred: predicting type-specific nucleic acid binding residues via an ensemble approach. Briefings Bioinform. Wenjuan Nie, Lei Deng
2022	—	`conf`	inACP: An integrated approach to the prediction of anticancer peptides. BIBM Guolun Zhong, Lei Deng
2021	—	`conf`	A multi-task graph convolutional network modeling of drug-drug interactions and synergistic efficacy. BIBM Yuanyuan Deng, Song Yu, Lei Deng, Hui Liu, Xuejun Liu, Yi Luo
2021	—	`conf`	Accurately Predicting circRNA-disease Associations Using Variational Graph Auto-encoders and LightGBM. BIBM Siyuan Shen, Yurong Qian, Jingjing Zheng, Junyi Liu, Lei Deng
2021	—	`conf`	CMIVGSD: circRNA-miRNA Interaction Prediction Based on Variational Graph Auto-Encoder and Singular Value Decomposition. BIBM Yurong Qian, Jingjing Zheng, Zhe Zhang, Ying Jiang, Jiaxuan Zhang, Lei Deng
2021	J	`jnl`	CRPGCN: predicting circRNA-disease associations using graph convolutional network based on heterogeneous network. BMC Bioinform. Zhihao Ma, Zhufang Kuang, Lei Deng
2021	J	`jnl`	DeepDDS: deep graph neural network with attention mechanism to predict synergistic drug combinations. CoRR Jinxian Wang, Xuejun Liu, Siyuan Shen, Lei Deng, Hui Liu
2021	—	`conf`	GCNSDA: Predicting snoRNA-disease associations via graph convolutional network. BIBM Dayun Liu, Yi Luo, Jingjing Zheng, Hanlin Xu, Jiaxuan Zhang, Lei Deng
2021	J	`jnl`	Graph2MDA: a multi-modal variational graph embedding model for predicting microbe-drug associations. CoRR Lei Deng, Yibiao Huang, Xuejun Liu, Hui Liu
2021	J	`jnl`	LDAH2V: Exploring Meta-Paths Across Multiple Networks for lncRNA-Disease Association Prediction. IEEE ACM Trans. Comput. Biol. Bioinform. Lei Deng, Wenkai Li, Jingpu Zhang
2021	—	`conf`	LGCMDS: Predicting miRNA-Drug Sensitivity based on Light Graph Convolution Network. BIBM Song Yu, Hanlin Xu, Yizhan Li, Dayun Liu, Lei Deng
2021	J	`jnl`	MSCFS: inferring circRNA functional similarity based on multiple data sources. BMC Bioinform. Liang Shu, Cheng Zhou, Xinxu Yuan, Jingpu Zhang, Lei Deng
2021	J	`jnl`	Nabe: an energetic database of amino acid mutations in protein-nucleic acid binding interfaces. Database J. Biol. Databases Curation Junyi Liu, Siyu Liu, Chenzhe Liu, Yaping Zhang, Yuliang Pan, Zixiang Wang, Jiacheng Wang, Ting Wen, Lei Deng
2021	J	`jnl`	SMALF: miRNA-disease associations prediction based on stacked autoencoder and XGBoost. BMC Bioinform. Dayun Liu, Yibiao Huang, Wenjuan Nie, Jiaxuan Zhang, Lei Deng
2021	—	`conf`	iPiDA-GBNN: Identification of Piwi-interacting RNA-disease associations based on gradient boosting neural network. BIBM Yurong Qian, Qihua He, Lei Deng
2020	—	`conf`	DeepARC: An Attention-based Hybrid Model for Predicting Transcription Factor Binding Sites from Positional Embedded DNA Sequence. BIBM Jialong Chen, Lei Deng
2020	J	`jnl`	DeepciRGO: functional prediction of circular RNAs through hierarchical deep neural networks using heterogeneous network features. BMC Bioinform. Lei Deng, Wei Lin, Jiacheng Wang, Jingpu Zhang
2020	J	`jnl`	DrugCombDB: a comprehensive database of drug combinations toward the discovery of combinatorial therapy. Nucleic Acids Res. Hui Liu, Wenhao Zhang, Bo Zou, Jinxian Wang, Yuanyuan Deng, Lei Deng
2020	J	`jnl`	Gammachirp filter banks applied in roust speaker recognition based on GMM-UBM classifier. Int. Arab J. Inf. Technol. Lei Deng, Yong Gao
2020	J	`jnl`	HNet-DNN: Inferring New Drug-Disease Associations with Deep Neural Network Based on Heterogeneous Network Features. J. Chem. Inf. Model. Hui Liu, Wenhao Zhang, Yinglong Song, Lei Deng, Shuigeng Zhou
2020	—	`conf`	Machine learning-based methods and novel data models to predict adverse drug reaction. BIBM Jinxian Wang, Yuanyuan Deng, Liang Shu, Lei Deng
2020	J	`jnl`	Pathway-Guided Deep Neural Network toward Interpretable and Predictive Modeling of Drug Sensitivity. J. Chem. Inf. Model. Lei Deng, Yideng Cai, Wenhao Zhang, Wenyi Yang, Bo Gao, Hui Liu
2020	—	`conf`	Predict the Protein-protein Interaction between Virus and Host through Hybrid Deep Neural Network. BIBM Lei Deng, Jiaojiao Zhao, Jingpu Zhang
2020	—	`conf`	Predicting circRNA-disease associations using meta path-based representation learning on heterogenous network. BIBM Lei Deng, Jing Yang, Hui Liu
2019	—	`conf`	A deep neural network approach using distributed representations of RNA sequence and structure for identifying binding site of RNA-binding proteins. BIBM Lei Deng, Youzhi Liu, Yechuan Shi, Hui Liu
2019	—	`conf`	D2VCB: A Hybrid Deep Neural Network for the Prediction of in-vivo Protein-DNA Binding from Combined DNA Sequence. BIBM Lei Deng, Hui Wu, Hui Liu
2019	—	`conf`	DKCirc2GO: Predicting Gene Ontology of circRNAs Using Dual KATZ Approach. BIBM Lei Deng, Xin Sun, Wei Lin, Jingpu Zhang
2019	J	`jnl`	Integrating Multiple Heterogeneous Networks for Novel LncRNA-Disease Association Inference. IEEE ACM Trans. Comput. Biol. Bioinform. Jingpu Zhang, Zuping Zhang, Zhigang Chen, Lei Deng
2019	J	`jnl`	KATZLGO: Large-Scale Prediction of LncRNA Functions by Using the KATZ Measure Based on Multiple Networks. IEEE ACM Trans. Comput. Biol. Bioinform. Zuping Zhang, Jingpu Zhang, Chao Fan, Yongjun Tang, Lei Deng
2019	J	`jnl`	MADOKA: an ultra-fast approach for large-scale protein structure similarity searching. BMC Bioinform. Lei Deng, Guolun Zhong, Chenzhe Liu, Judong Luo, Hui Liu
2019	J	`jnl`	MultiSourcDSim: an integrated approach for exploring disease similarity. BMC Medical Informatics Decis. Mak. Lei Deng, Danyi Ye, Junmin Zhao, Jingpu Zhang
2018	J	`jnl`	Computational identification of binding energy hot spots in protein-RNA complexes using an ensemble approach. Bioinform. Yuliang Pan, Zixiang Wang, Weihua Zhan, Lei Deng
2018	—	`conf`	Exploring Disease Similarity by Integrating Multiple Data Sources. BIBM Lei Deng, Danyi Ye, Junmin Zhao, Jingpu Zhang
2018	J	`jnl`	Ontological function annotation of long non-coding RNAs through hierarchical multi-label classification. Bioinform. Jingpu Zhang, Zuping Zhang, Zixiang Wang, Yuting Liu, Lei Deng
2018	J	`jnl`	PDRLGB: precise DNA-binding residue prediction using a light gradient boosting machine. BMC Bioinform. Lei Deng, Juan Pan, Xiaojie Xu, Wenyi Yang, Chuyao Liu, Hui Liu
2018	J	`jnl`	Probing the functions of long non-coding RNAs by exploiting the topology of global association and interaction network. Comput. Biol. Chem. Lei Deng, Hongjie Wu, Chuyao Liu, Weihua Zhan, Jingpu Zhang
2018	J	`jnl`	SDADB: a functional annotation database of protein structural domains. Database J. Biol. Databases Curation Cheng Zeng, Weihua Zhan, Lei Deng
2018	—	`conf`	XPredRBR: Accurate and Fast Prediction of RNA-Binding Residues in Proteins Using eXtreme Gradient Boosting. ISBRA Lei Deng, Zuojin Dong, Hui Liu
2017	J	`jnl`	A boosting approach for prediction of protein-RNA binding residues. BMC Bioinform. Yongjun Tang, Diwei Liu, Zixiang Wang, Ting Wen, Lei Deng
2017	J	`jnl`	A sparse autoencoder-based deep neural network for protein solvent accessibility and contact number prediction. BMC Bioinform. Lei Deng, Chao Fan, Zhiwen Zeng
2017	—	`conf`	BiRWLGO: A global network-based strategy for lncRNA function annotation using bi-random walk. BIBM Jingpu Zhang, Shuai Zou, Lei Deng
2017	—	`conf`	Combining diffusion and HeteSim features for accurate prediction of protein-lncRNA interactions. BIBM Junqiang Wang, Yun Xiao, Zixiang Wang, Weihua Zhan, Lei Deng
2017	J	`jnl`	Revealing Dynamic Communities in networks using genetic algorithm with Merging and Splitting Operators. CoRR Weihua Zhan, Lei Deng, Jihong Guan, Jun Niu
2016	—	`conf`	PredRBR: Accurate Prediction of RNA-Binding Residues in proteins using Gradient Tree Boosting. BIBM Diwei Liu, Yongjun Tang, Chao Fan, Zhigang Chen, Lei Deng
2016	J	`jnl`	PredRSA: a gradient boosted regression trees approach for predicting protein solvent accessibility. BMC Bioinform. Chao Fan, Diwei Liu, Rui Huang, Zhigang Chen, Lei Deng
2015	J	`jnl`	An Integrated Framework for Functional Annotation of Protein Structural Domains. IEEE ACM Trans. Comput. Biol. Bioinform. Lei Deng, Zhigang Chen
2014	—	`conf`	A Multi-Instance Multi-Label Learning Approach for Protein Domain Annotation. ICIC (3) Yang Meng, Lei Deng, Zhigang Chen, Cheng Zhou, Diwei Liu, Chao Fan, Ting Yan
2014	J	`jnl`	PredHS: a web server for predicting protein-protein interaction hot spots by using structural neighborhood properties. Nucleic Acids Res. Lei Deng, Qiangfeng Cliff Zhang, Zhigang Chen, Yang Meng, Jihong Guan, Shuigeng Zhou
2014	—	`conf`	Structure-Based Prediction of Protein Phosphorylation Sites Using an Ensemble Approach. ICIC (3) Yong Gao, Weilin Hao, Zhigang Chen, Lei Deng
2013	B	`conf`	Boosting Prediction Performance of Protein-Protein Interaction Hot Spots by Using Structural Neighborhood Properties - (Extended Abstract). RECOMB Lei Deng, Jihong Guan, Xiaoming Wei, Yuan Yi, Shuigeng Zhou
2013	J	`jnl`	Boosting Prediction Performance of Protein-Protein Interaction Hot Spots by Using Structural Neighborhood Properties. J. Comput. Biol. Lei Deng, Jihong Guan, Xiaoming Wei, Yuan Yi, Qiangfeng Cliff Zhang, Shuigeng Zhou
2013	J	`jnl`	PrePPI: a structure-informed database of protein-protein interactions. Nucleic Acids Res. Qiangfeng Cliff Zhang, Donald Petrey, José Ignacio Garzón, Lei Deng, Barry Honig
2012	J	`jnl`	A semi-supervised boosting SVM for predicting hot spots at protein-protein Interfaces. BMC Syst. Biol. Bin Xu, Xiaoming Wei, Lei Deng, Jihong Guan, Shuigeng Zhou
2011	J	`jnl`	PredUs: a web server for predicting protein interfaces using structural neighbors. Nucleic Acids Res. Qiangfeng Cliff Zhang, Lei Deng, Markus Fisher, Jihong Guan, Barry Honig, Donald Petrey
2009	J	`jnl`	Prediction of protein-protein interaction sites using an ensemble method. BMC Bioinform. Lei Deng, Jihong Guan, Qiwen Dong, Shuigeng Zhou