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For: Huang YA, Hu P, Chan KCC, You ZH. Graph convolution for predicting associations between miRNA and drug resistance. Bioinformatics 2020;36:851-858. [PMID: 31397851 DOI: 10.1093/bioinformatics/btz621] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 07/17/2019] [Accepted: 08/08/2019] [Indexed: 12/19/2022]  Open
Number Cited by Other Article(s)
1
Du X, Li J, Wang B, Zhang J, Wang T, Wang J. NRGCNMDA: Microbe-Drug Association Prediction Based on Residual Graph Convolutional Networks and Conditional Random Fields. Interdiscip Sci 2025;17:344-358. [PMID: 39775537 DOI: 10.1007/s12539-024-00678-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 11/08/2024] [Accepted: 11/18/2024] [Indexed: 01/11/2025]
2
Sheng N, Liu Y, Gao L, Wang L, Si C, Huang L, Wang Y. Deep-Learning-Based Integration of Sequence and Structure Information for Efficiently Predicting miRNA-Drug Associations. J Chem Inf Model 2025. [PMID: 40380921 DOI: 10.1021/acs.jcim.5c00038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2025]
3
Lei C, Lei X. Predicting Drug-miRNA Associations Combining SDNE with BiGRU. IEEE J Biomed Health Inform 2025;29:3805-3816. [PMID: 40030943 DOI: 10.1109/jbhi.2024.3525266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2025]
4
Liu Z, Dai Q, Yu X, Duan X, Wang C. Predicting circRNA-Drug Resistance Associations Based on a Multimodal Graph Representation Learning Framework. IEEE J Biomed Health Inform 2025;29:1838-1848. [PMID: 37498762 DOI: 10.1109/jbhi.2023.3299423] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
5
Ren Z, Zeng X, Lao Y, Zheng H, You Z, Xiang H, Zou Q. A spatial hierarchical network learning framework for drug repositioning allowing interpretation from macro to micro scale. Commun Biol 2024;7:1413. [PMID: 39478146 PMCID: PMC11525566 DOI: 10.1038/s42003-024-07107-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 10/21/2024] [Indexed: 11/02/2024]  Open
6
Zhou Z, Du Z, Jiang X, Zhuo L, Xu Y, Fu X, Liu M, Zou Q. GAM-MDR: probing miRNA-drug resistance using a graph autoencoder based on random path masking. Brief Funct Genomics 2024;23:475-483. [PMID: 38391194 DOI: 10.1093/bfgp/elae005] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/15/2024] [Accepted: 01/31/2024] [Indexed: 02/24/2024]  Open
7
Zhang W, Zhang P, Sun W, Xu J, Liao L, Cao Y, Han Y. Improving plant miRNA-target prediction with self-supervised k-mer embedding and spectral graph convolutional neural network. PeerJ 2024;12:e17396. [PMID: 38799058 PMCID: PMC11122044 DOI: 10.7717/peerj.17396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/25/2024] [Indexed: 05/29/2024]  Open
8
Zhang Y, Li X. Empowering Graph Neural Networks with Block-Based Dual Adaptive Deep Adjustment for Drug Resistance-Related NcRNA Discovery. J Chem Inf Model 2024;64:3537-3547. [PMID: 38523272 PMCID: PMC11040722 DOI: 10.1021/acs.jcim.3c01973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 03/12/2024] [Accepted: 03/12/2024] [Indexed: 03/26/2024]
9
Zhang P, Zhang W, Sun W, Xu J, Hu H, Wang L, Wong L. Identification of gene biomarkers for brain diseases via multi-network topological semantics extraction and graph convolutional network. BMC Genomics 2024;25:175. [PMID: 38350848 PMCID: PMC10865627 DOI: 10.1186/s12864-024-09967-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/03/2024] [Indexed: 02/15/2024]  Open
10
Qu J, Ni J, Ni TG, Bian ZK, Liang JZ. Prediction of Human Microbe-Drug Association based on Layer Attention Graph Convolutional Network. Curr Med Chem 2024;31:5097-5109. [PMID: 39225188 DOI: 10.2174/0109298673249941231108091326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 08/20/2023] [Accepted: 10/19/2023] [Indexed: 09/04/2024]
11
Sharma V, Giammona M, Zubarev D, Tek A, Nugyuen K, Sundberg L, Congiu D, La YH. Formulation Graphs for Mapping Structure-Composition of Battery Electrolytes to Device Performance. J Chem Inf Model 2023;63:6998-7010. [PMID: 37948621 PMCID: PMC10685446 DOI: 10.1021/acs.jcim.3c01030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 11/12/2023]
12
Zhong Y, Shen C, Xi X, Luo Y, Ding P, Luo L. Multitask joint learning with graph autoencoders for predicting potential MiRNA-drug associations. Artif Intell Med 2023;145:102665. [PMID: 37925217 DOI: 10.1016/j.artmed.2023.102665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 06/14/2023] [Accepted: 09/14/2023] [Indexed: 11/06/2023]
13
Ye S, Zhao W, Shen X, Jiang X, He T. An effective multi-task learning framework for drug repurposing based on graph representation learning. Methods 2023;218:48-56. [PMID: 37516260 DOI: 10.1016/j.ymeth.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 07/04/2023] [Accepted: 07/20/2023] [Indexed: 07/31/2023]  Open
14
Sun J, Xu M, Ru J, James-Bott A, Xiong D, Wang X, Cribbs AP. Small molecule-mediated targeting of microRNAs for drug discovery: Experiments, computational techniques, and disease implications. Eur J Med Chem 2023;257:115500. [PMID: 37262996 PMCID: PMC11554572 DOI: 10.1016/j.ejmech.2023.115500] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/05/2023] [Accepted: 05/15/2023] [Indexed: 06/03/2023]
15
Ma Z, Kuang Z, Deng L. NGCICM: A Novel Deep Learning-Based Method for Predicting circRNA-miRNA Interactions. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:3080-3092. [PMID: 37027645 DOI: 10.1109/tcbb.2023.3248787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
16
Zhang P, Wang Z, Sun W, Xu J, Zhang W, Wu K, Wong L, Li L. RDRGSE: A Framework for Noncoding RNA-Drug Resistance Discovery by Incorporating Graph Skeleton Extraction and Attentional Feature Fusion. ACS OMEGA 2023;8:27386-27397. [PMID: 37546619 PMCID: PMC10398708 DOI: 10.1021/acsomega.3c02763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 07/06/2023] [Indexed: 08/08/2023]
17
Yang H, Liu Y, Chen L, Zhao J, Guo M, Zhao X, Wen Z, He Z, Chen C, Xu L. MiRNA-Based Therapies for Lung Cancer: Opportunities and Challenges? Biomolecules 2023;13:877. [PMID: 37371458 DOI: 10.3390/biom13060877] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/13/2023] [Accepted: 05/19/2023] [Indexed: 06/29/2023]  Open
18
Gao M, Shang X. Identification of associations between lncRNA and drug resistance based on deep learning and attention mechanism. Front Microbiol 2023;14:1147778. [PMID: 37180267 PMCID: PMC10169643 DOI: 10.3389/fmicb.2023.1147778] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/04/2023] [Indexed: 05/16/2023]  Open
19
Jha K, Karmakar S, Saha S. Graph-BERT and language model-based framework for protein-protein interaction identification. Sci Rep 2023;13:5663. [PMID: 37024543 PMCID: PMC10079975 DOI: 10.1038/s41598-023-31612-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/14/2023] [Indexed: 04/08/2023]  Open
20
Tian Z, Fang H, Teng Z, Ye Y. GOGCN: Graph Convolutional Network on Gene Ontology for Functional Similarity Analysis of Genes. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:1053-1064. [PMID: 35687647 DOI: 10.1109/tcbb.2022.3181300] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
21
Wang MN, Li Y, Lei LL, Ding DW, Xie XJ. Combining non-negative matrix factorization with graph Laplacian regularization for predicting drug-miRNA associations based on multi-source information fusion. Front Pharmacol 2023;14:1132012. [PMID: 36817132 PMCID: PMC9931722 DOI: 10.3389/fphar.2023.1132012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023]  Open
22
Luo Y, Peng L, Shan W, Sun M, Luo L, Liang W. Machine learning in the development of targeting microRNAs in human disease. Front Genet 2023;13:1088189. [PMID: 36685965 PMCID: PMC9845262 DOI: 10.3389/fgene.2022.1088189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/12/2022] [Indexed: 01/05/2023]  Open
23
Deng L, Fan Z, Xiao X, Liu H, Zhang J. Dual-Channel Heterogeneous Graph Neural Network for Predicting microRNA-Mediated Drug Sensitivity. J Chem Inf Model 2022;62:5929-5937. [PMID: 36413746 DOI: 10.1021/acs.jcim.2c01060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
24
Das B, Kutsal M, Das R. A geometric deep learning model for display and prediction of potential drug-virus interactions against SARS-CoV-2. CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS : AN INTERNATIONAL JOURNAL SPONSORED BY THE CHEMOMETRICS SOCIETY 2022;229:104640. [PMID: 36042844 PMCID: PMC9400382 DOI: 10.1016/j.chemolab.2022.104640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/17/2022] [Accepted: 08/19/2022] [Indexed: 05/04/2023]
25
Duan T, Kuang Z, Deng L. SVMMDR: Prediction of miRNAs-drug resistance using support vector machines based on heterogeneous network. Front Oncol 2022;12:987609. [PMID: 36338674 PMCID: PMC9632662 DOI: 10.3389/fonc.2022.987609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/14/2022] [Indexed: 11/21/2022]  Open
26
Graph Neural Network for Protein-Protein Interaction Prediction: A Comparative Study. MOLECULES (BASEL, SWITZERLAND) 2022;27:molecules27186135. [PMID: 36144868 PMCID: PMC9501426 DOI: 10.3390/molecules27186135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/17/2022]
27
Guan YJ, Yu CQ, Li LP, You ZH, Ren ZH, Pan J, Li YC. BNEMDI: A Novel MicroRNA–Drug Interaction Prediction Model Based on Multi-Source Information With a Large-Scale Biological Network. Front Genet 2022;13:919264. [PMID: 35910223 PMCID: PMC9334674 DOI: 10.3389/fgene.2022.919264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/30/2022] [Indexed: 12/03/2022]  Open
28
Feng H, Xiang Y, Wang X, Xue W, Yue Z. MTAGCN: predicting miRNA-target associations in Camellia sinensis var. assamica through graph convolution neural network. BMC Bioinformatics 2022;23:271. [PMID: 35820798 PMCID: PMC9275082 DOI: 10.1186/s12859-022-04819-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 07/01/2022] [Indexed: 11/10/2022]  Open
29
Jha K, Saha S, Singh H. Prediction of protein-protein interaction using graph neural networks. Sci Rep 2022;12:8360. [PMID: 35589837 PMCID: PMC9120162 DOI: 10.1038/s41598-022-12201-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/18/2022] [Indexed: 01/09/2023]  Open
30
Li G, Wang D, Zhang Y, Liang C, Xiao Q, Luo J. Using Graph Attention Network and Graph Convolutional Network to Explore Human CircRNA-Disease Associations Based on Multi-Source Data. Front Genet 2022;13:829937. [PMID: 35198012 PMCID: PMC8859418 DOI: 10.3389/fgene.2022.829937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/10/2022] [Indexed: 11/13/2022]  Open
31
Niu Y, Song C, Gong Y, Zhang W. MiRNA-Drug Resistance Association Prediction Through the Attentive Multimodal Graph Convolutional Network. Front Pharmacol 2022;12:799108. [PMID: 35095506 PMCID: PMC8790023 DOI: 10.3389/fphar.2021.799108] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022]  Open
32
Ma Z, Kuang Z, Deng L. CRPGCN: predicting circRNA-disease associations using graph convolutional network based on heterogeneous network. BMC Bioinformatics 2021;22:551. [PMID: 34772332 PMCID: PMC8588735 DOI: 10.1186/s12859-021-04467-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/01/2021] [Indexed: 12/16/2022]  Open
33
Li Y, Wang R, Zhang S, Xu H, Deng L. LRGCPND: Predicting Associations between ncRNA and Drug Resistance via Linear Residual Graph Convolution. Int J Mol Sci 2021;22:10508. [PMID: 34638849 PMCID: PMC8508984 DOI: 10.3390/ijms221910508] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/25/2021] [Accepted: 09/27/2021] [Indexed: 01/08/2023]  Open
34
Zhang XM, Liang L, Liu L, Tang MJ. Graph Neural Networks and Their Current Applications in Bioinformatics. Front Genet 2021;12:690049. [PMID: 34394185 PMCID: PMC8360394 DOI: 10.3389/fgene.2021.690049] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 05/28/2021] [Indexed: 12/22/2022]  Open
35
ACHP: A Web Server for Predicting Anti-Cancer Peptide and Anti-Hypertensive Peptide. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10222-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
36
Long Y, Wu M, Kwoh CK, Luo J, Li X. Predicting human microbe-drug associations via graph convolutional network with conditional random field. Bioinformatics 2020;36:4918-4927. [PMID: 32597948 PMCID: PMC7559035 DOI: 10.1093/bioinformatics/btaa598] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/31/2020] [Accepted: 06/20/2020] [Indexed: 12/23/2022]  Open
37
Yuan M, Zhao S, Chen R, Wang G, Bie Y, Wu Q, Cheng J. MicroRNA-138 inhibits tumor growth and enhances chemosensitivity in human cervical cancer by targeting H2AX. Exp Ther Med 2019;19:630-638. [PMID: 31853324 PMCID: PMC6909785 DOI: 10.3892/etm.2019.8238] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 09/20/2019] [Indexed: 12/11/2022]  Open
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