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For: Chen X, Xie D, Wang L, Zhao Q, You ZH, Liu H. BNPMDA: Bipartite Network Projection for MiRNA-Disease Association prediction. Bioinformatics 2019;34:3178-3186. [PMID: 29701758 DOI: 10.1093/bioinformatics/bty333] [Citation(s) in RCA: 235] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 04/24/2018] [Indexed: 12/16/2022]  Open
Number Cited by Other Article(s)
1
Ha J. DeepWalk-Based Graph Embeddings for miRNA-Disease Association Prediction Using Deep Neural Network. Biomedicines 2025;13:536. [PMID: 40149513 PMCID: PMC11940379 DOI: 10.3390/biomedicines13030536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2025] [Revised: 02/17/2025] [Accepted: 02/17/2025] [Indexed: 03/29/2025]  Open
2
Ha J. Graph Convolutional Network with Neural Collaborative Filtering for Predicting miRNA-Disease Association. Biomedicines 2025;13:136. [PMID: 39857720 PMCID: PMC11762804 DOI: 10.3390/biomedicines13010136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2024] [Revised: 01/01/2025] [Accepted: 01/07/2025] [Indexed: 01/27/2025]  Open
3
Zhu R, Wang Y, Dai LY. CLHGNNMDA: Hypergraph Neural Network Model Enhanced by Contrastive Learning for miRNA-Disease Association Prediction. J Comput Biol 2025;32:47-63. [PMID: 39602201 DOI: 10.1089/cmb.2024.0720] [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] [Indexed: 11/29/2024]  Open
4
Xia H, Dong C, Chen X, Wei Z, Gu L, Zhu X. SGTCDA: Prediction of circRNA-drug sensitivity associations with interpretable graph transformers and effective assessment. BMC Genomics 2024;25:1113. [PMID: 39567908 PMCID: PMC11577602 DOI: 10.1186/s12864-024-11022-6] [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: 06/07/2024] [Accepted: 11/08/2024] [Indexed: 11/22/2024]  Open
5
Sun W, Ren C, Xu J, Zhang P. SAGCN: Using Graph Convolutional Network With Subgraph-Aware for circRNA-Drug Sensitivity Identification. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024;21:1765-1774. [PMID: 38885113 DOI: 10.1109/tcbb.2024.3415058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
6
Jalali P, Aliyari S, Etesami M, Saeedi Niasar M, Taher S, Kavousi K, Nazemalhosseini Mojarad E, Salehi Z. GUCA2A dysregulation as a promising biomarker for accurate diagnosis and prognosis of colorectal cancer. Clin Exp Med 2024;24:251. [PMID: 39485546 PMCID: PMC11530487 DOI: 10.1007/s10238-024-01512-y] [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: 06/05/2024] [Accepted: 10/21/2024] [Indexed: 11/03/2024]
7
Ouyang D, Miao R, Zeng J, Li X, Ai N, Wang P, Hou J, Zheng J. SPLHRNMTF: robust orthogonal non-negative matrix tri-factorization with self-paced learning and dual hypergraph regularization for predicting miRNA-disease associations. BMC Genomics 2024;25:885. [PMID: 39304826 DOI: 10.1186/s12864-024-10729-w] [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: 03/21/2024] [Accepted: 08/20/2024] [Indexed: 09/22/2024]  Open
8
Chen Z, Zhang L, Li J, Chen H. Microbe-disease associations prediction by graph regularized non-negative matrix factorization with L 2 , 1 $$ {L}_{2,1} $$ norm regularization terms. J Cell Mol Med 2024;28:e18553. [PMID: 39239860 PMCID: PMC11377990 DOI: 10.1111/jcmm.18553] [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: 05/15/2024] [Revised: 06/19/2024] [Accepted: 07/09/2024] [Indexed: 09/07/2024]  Open
9
Chu S, Duan G, Yan C. PGCNMDA: Learning node representations along paths with graph convolutional network for predicting miRNA-disease associations. Methods 2024;229:71-81. [PMID: 38909974 DOI: 10.1016/j.ymeth.2024.06.007] [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: 04/30/2024] [Revised: 05/26/2024] [Accepted: 06/16/2024] [Indexed: 06/25/2024]  Open
10
Sun W, Zhang P, Zhang W, Xu J, Huang Y, Li L. Synchronous Mutual Learning Network and Asynchronous Multi-Scale Embedding Network for miRNA-Disease Association Prediction. Interdiscip Sci 2024;16:532-553. [PMID: 38310628 DOI: 10.1007/s12539-023-00602-x] [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: 10/09/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 02/06/2024]
11
Salooja CM, Sanker A, Deepthi K, Jereesh AS. An ensemble approach for circular RNA-disease association prediction using variational autoencoder and genetic algorithm. J Bioinform Comput Biol 2024;22:2450018. [PMID: 39215523 DOI: 10.1142/s0219720024500185] [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] [Indexed: 09/04/2024]
12
Peng H, Xu J, Liu K, Liu F, Zhang A, Zhang X. EIEPCF: accurate inference of functional gene regulatory networks by eliminating indirect effects from confounding factors. Brief Funct Genomics 2024;23:373-383. [PMID: 37642217 DOI: 10.1093/bfgp/elad040] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/07/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023]  Open
13
Xuan P, Wang X, Cui H, Meng X, Nakaguchi T, Zhang T. Meta-Path Semantic and Global-Local Representation Learning Enhanced Graph Convolutional Model for Disease-Related miRNA Prediction. IEEE J Biomed Health Inform 2024;28:4306-4316. [PMID: 38709611 DOI: 10.1109/jbhi.2024.3397003] [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: 05/08/2024]
14
Biyu H, Mengshan L, Yuxin H, Ming Z, Nan W, Lixin G. A miRNA-disease association prediction model based on tree-path global feature extraction and fully connected artificial neural network with multi-head self-attention mechanism. BMC Cancer 2024;24:683. [PMID: 38840078 PMCID: PMC11151537 DOI: 10.1186/s12885-024-12420-5] [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: 11/18/2023] [Accepted: 05/23/2024] [Indexed: 06/07/2024]  Open
15
Jia C, Wang F, Xing B, Li S, Zhao Y, Li Y, Wang Q. DGAMDA: Predicting miRNA-disease association based on dynamic graph attention network. INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING 2024;40:e3809. [PMID: 38472636 DOI: 10.1002/cnm.3809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 01/22/2024] [Accepted: 01/27/2024] [Indexed: 03/14/2024]
16
Sheng N, Xie X, Wang Y, Huang L, Zhang S, Gao L, Wang H. A Survey of Deep Learning for Detecting miRNA- Disease Associations: Databases, Computational Methods, Challenges, and Future Directions. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024;21:328-347. [PMID: 38194377 DOI: 10.1109/tcbb.2024.3351752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
17
Wang T, Wang W, Jiang X, Mao J, Zhuo L, Liu M, Fu X, Yao X. ML-NPI: Predicting Interactions between Noncoding RNA and Protein Based on Meta-Learning in a Large-Scale Dynamic Graph. J Chem Inf Model 2024;64:2912-2920. [PMID: 37920888 DOI: 10.1021/acs.jcim.3c01238] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
18
Ouyang D, Liang Y, Wang J, Li L, Ai N, Feng J, Lu S, Liao S, Liu X, Xie S. HGCLAMIR: Hypergraph contrastive learning with attention mechanism and integrated multi-view representation for predicting miRNA-disease associations. PLoS Comput Biol 2024;20:e1011927. [PMID: 38652712 PMCID: PMC11037542 DOI: 10.1371/journal.pcbi.1011927] [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: 09/20/2023] [Accepted: 02/19/2024] [Indexed: 04/25/2024]  Open
19
Peng L, Yang Y, Yang C, Li Z, Cheong N. HRGCNLDA: Forecasting of lncRNA-disease association based on hierarchical refinement graph convolutional neural network. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2024;21:4814-4834. [PMID: 38872515 DOI: 10.3934/mbe.2024212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
20
Chen Z, Zhang L, Li J, Fu M. MLFLHMDA: predicting human microbe-disease association based on multi-view latent feature learning. Front Microbiol 2024;15:1353278. [PMID: 38371933 PMCID: PMC10869561 DOI: 10.3389/fmicb.2024.1353278] [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: 12/10/2023] [Accepted: 01/17/2024] [Indexed: 02/20/2024]  Open
21
Chang Z, Zhu R, Liu J, Shang J, Dai L. HGSMDA: miRNA-Disease Association Prediction Based on HyperGCN and Sørensen-Dice Loss. Noncoding RNA 2024;10:9. [PMID: 38392964 PMCID: PMC10893088 DOI: 10.3390/ncrna10010009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024]  Open
22
Bai T, Yan K, Liu B. DAmiRLocGNet: miRNA subcellular localization prediction by combining miRNA-disease associations and graph convolutional networks. Brief Bioinform 2023:bbad212. [PMID: 37332057 DOI: 10.1093/bib/bbad212] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 06/20/2023]  Open
23
Gu C, Li X. Prediction of disease-related miRNAs by voting with multiple classifiers. BMC Bioinformatics 2023;24:177. [PMID: 37122001 PMCID: PMC10150488 DOI: 10.1186/s12859-023-05308-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 04/26/2023] [Indexed: 05/02/2023]  Open
24
Qu Q, Chen X, Ning B, Zhang X, Nie H, Zeng L, Chen H, Fu X. Prediction of miRNA-disease associations by neural network-based deep matrix factorization. Methods 2023;212:1-9. [PMID: 36813017 DOI: 10.1016/j.ymeth.2023.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/17/2023] [Accepted: 02/10/2023] [Indexed: 02/23/2023]  Open
25
Ha J, Park S. NCMD: Node2vec-Based Neural Collaborative Filtering for Predicting MiRNA-Disease Association. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:1257-1268. [PMID: 35849666 DOI: 10.1109/tcbb.2022.3191972] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
26
Feng H, Jin D, Li J, Li Y, Zou Q, Liu T. Matrix reconstruction with reliable neighbors for predicting potential MiRNA-disease associations. Brief Bioinform 2023;24:6960615. [PMID: 36567252 DOI: 10.1093/bib/bbac571] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/16/2022] [Accepted: 11/23/2022] [Indexed: 12/27/2022]  Open
27
Yang B, Chen H. Predicting circRNA-drug sensitivity associations by learning multimodal networks using graph auto-encoders and attention mechanism. Brief Bioinform 2023;24:6972879. [PMID: 36617209 DOI: 10.1093/bib/bbac596] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/11/2022] [Accepted: 12/04/2022] [Indexed: 01/09/2023]  Open
28
Liu ZH, Ji CM, Ni JC, Wang YT, Qiao LJ, Zheng CH. Convolution Neural Networks Using Deep Matrix Factorization for Predicting Circrna-Disease Association. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:277-284. [PMID: 34951853 DOI: 10.1109/tcbb.2021.3138339] [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]
29
Peng L, Yang J, Wang M, Zhou L. Editorial: Machine learning-based methods for RNA data analysis—Volume II. Front Genet 2022;13:1010089. [DOI: 10.3389/fgene.2022.1010089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/20/2022] [Indexed: 12/02/2022]  Open
30
Huang L, Zhang L, Chen X. Updated review of advances in microRNAs and complex diseases: experimental results, databases, webservers and data fusion. Brief Bioinform 2022;23:6696143. [PMID: 36094095 DOI: 10.1093/bib/bbac397] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/19/2022] [Accepted: 08/15/2022] [Indexed: 12/14/2022]  Open
31
Peng L, Tu Y, Huang L, Li Y, Fu X, Chen X. DAESTB: inferring associations of small molecule-miRNA via a scalable tree boosting model based on deep autoencoder. Brief Bioinform 2022;23:6827720. [PMID: 36377749 DOI: 10.1093/bib/bbac478] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 09/28/2022] [Accepted: 10/08/2022] [Indexed: 11/16/2022]  Open
32
Huang L, Zhang L, Chen X. Updated review of advances in microRNAs and complex diseases: towards systematic evaluation of computational models. Brief Bioinform 2022;23:6712303. [PMID: 36151749 DOI: 10.1093/bib/bbac407] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 08/11/2022] [Accepted: 08/20/2022] [Indexed: 12/14/2022]  Open
33
Ouyang D, Liang Y, Wang J, Liu X, Xie S, Miao R, Ai N, Li L, Dang Q. Predicting multiple types of miRNA-disease associations using adaptive weighted nonnegative tensor factorization with self-paced learning and hypergraph regularization. Brief Bioinform 2022;23:6720405. [PMID: 36168938 DOI: 10.1093/bib/bbac390] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 12/14/2022]  Open
34
Yan C, Ding C, Duan G. PMMS: Predicting essential miRNAs based on multi-head self-attention mechanism and sequences. Front Med (Lausanne) 2022;9:1015278. [DOI: 10.3389/fmed.2022.1015278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/25/2022] [Indexed: 11/18/2022]  Open
35
Chen L, Lin D, Xu H, Li J, Lin L. WLLP: A weighted reconstruction-based linear label propagation algorithm for predicting potential therapeutic agents for COVID-19. Front Microbiol 2022;13:1040252. [PMID: 36466666 PMCID: PMC9713947 DOI: 10.3389/fmicb.2022.1040252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/06/2022] [Indexed: 11/18/2022]  Open
36
Cao B, Li R, Xiao S, Deng S, Zhou X, Zhou L. Predicting miRNA-disease association through combining miRNA function and network topological similarities based on MINE. iScience 2022;25:105299. [DOI: 10.1016/j.isci.2022.105299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/08/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022]  Open
37
Li L, Gao Z, Zheng CH, Qi R, Wang YT, Ni JC. Predicting miRNA-Disease Association Based on Improved Graph Regression. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:3604-3613. [PMID: 34757912 DOI: 10.1109/tcbb.2021.3127017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
38
Guo R, Chen H, Wang W, Wu G, Lv F. Predicting potential miRNA-disease associations based on more reliable negative sample selection. BMC Bioinformatics 2022;23:432. [PMID: 36253735 PMCID: PMC9575264 DOI: 10.1186/s12859-022-04978-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/06/2022] [Indexed: 11/10/2022]  Open
39
Wang B, Wang X, Zheng X, Han Y, Du X. JSCSNCP-LMA: a method for predicting the association of lncRNA-miRNA. Sci Rep 2022;12:17030. [PMID: 36220862 PMCID: PMC9552706 DOI: 10.1038/s41598-022-21243-y] [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: 05/24/2022] [Accepted: 09/26/2022] [Indexed: 12/29/2022]  Open
40
MHDMF: Prediction of miRNA-disease associations based on Deep Matrix Factorization with Multi-source Graph Convolutional Network. Comput Biol Med 2022;149:106069. [PMID: 36115300 DOI: 10.1016/j.compbiomed.2022.106069] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/31/2022] [Accepted: 08/27/2022] [Indexed: 11/24/2022]
41
Peng L, Wang C, Tian G, Liu G, Li G, Lu Y, Yang J, Chen M, Li Z. Analysis of CT scan images for COVID-19 pneumonia based on a deep ensemble framework with DenseNet, Swin transformer, and RegNet. Front Microbiol 2022;13:995323. [PMID: 36212877 PMCID: PMC9539545 DOI: 10.3389/fmicb.2022.995323] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/22/2022] [Indexed: 12/15/2022]  Open
42
Huang L, Zhang L, Chen X. Updated review of advances in microRNAs and complex diseases: taxonomy, trends and challenges of computational models. Brief Bioinform 2022;23:6686738. [PMID: 36056743 DOI: 10.1093/bib/bbac358] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/24/2022] [Accepted: 07/30/2022] [Indexed: 12/12/2022]  Open
43
Ma M, Na S, Zhang X, Chen C, Xu J. SFGAE: a self-feature-based graph autoencoder model for miRNA-disease associations prediction. Brief Bioinform 2022;23:6678419. [PMID: 36037084 DOI: 10.1093/bib/bbac340] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022]  Open
44
Rao Y, Xie M, Wang H. Predict potential miRNA-disease associations based on bounded nuclear norm regularization. Front Genet 2022;13:978975. [PMID: 36072658 PMCID: PMC9441603 DOI: 10.3389/fgene.2022.978975] [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: 06/27/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022]  Open
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Wang W, Chen H. Predicting miRNA-disease associations based on graph attention networks and dual Laplacian regularized least squares. Brief Bioinform 2022;23:6645486. [PMID: 35849099 DOI: 10.1093/bib/bbac292] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/23/2022] [Accepted: 06/26/2022] [Indexed: 01/05/2023]  Open
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Yang Y, Shang J, Sun Y, Li F, Zhang Y, Kong XZ, Li S, Liu JX. TLNPMD: Prediction of miRNA-Disease Associations Based on miRNA-Drug-Disease Three-Layer Heterogeneous Network. Molecules 2022;27:4371. [PMID: 35889243 PMCID: PMC9324587 DOI: 10.3390/molecules27144371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/06/2022] [Indexed: 12/10/2022]  Open
47
Chen B, Wang T, Zhang J, Zhang S, Shang X. Identification of Colon Cancer-Related RNAs Based on Heterogeneous Networks and Random Walk. BIOLOGY 2022;11:1003. [PMID: 36101384 PMCID: PMC9312154 DOI: 10.3390/biology11071003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/25/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022]
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Ji C, Wang Y, Gao Z, Li L, Ni J, Zheng C. A Semi-Supervised Learning Method for MiRNA-Disease Association Prediction Based on Variational Autoencoder. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:2049-2059. [PMID: 33735084 DOI: 10.1109/tcbb.2021.3067338] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
49
Paolini A, Baldassarre A, Bruno SP, Felli C, Muzi C, Ahmadi Badi S, Siadat SD, Sarshar M, Masotti A. Improving the Diagnostic Potential of Extracellular miRNAs Coupled to Multiomics Data by Exploiting the Power of Artificial Intelligence. Front Microbiol 2022;13:888414. [PMID: 35756065 PMCID: PMC9218639 DOI: 10.3389/fmicb.2022.888414] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/11/2022] [Indexed: 12/15/2022]  Open
50
Li G, Fang T, Zhang Y, Liang C, Xiao Q, Luo J. Predicting miRNA-disease associations based on graph attention network with multi-source information. BMC Bioinformatics 2022;23:244. [PMID: 35729531 PMCID: PMC9215044 DOI: 10.1186/s12859-022-04796-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/15/2022] [Indexed: 11/10/2022]  Open
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