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For: Zeng X, Zhang X, Zou Q. Integrative approaches for predicting microRNA function and prioritizing disease-related microRNA using biological interaction networks. Brief Bioinform 2015;17:193-203. [PMID: 26059461 DOI: 10.1093/bib/bbv033] [Citation(s) in RCA: 261] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Indexed: 12/21/2022]  Open
Number Cited by Other Article(s)
1
Zhao J, Liu H, Kang L, Gao W, Lu Q, Rao Y, Yue Z. deep-AMPpred: A Deep Learning Method for Identifying Antimicrobial Peptides and Their Functional Activities. J Chem Inf Model 2025;65:997-1008. [PMID: 39792442 DOI: 10.1021/acs.jcim.4c01913] [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: 01/12/2025]
2
Chen JY, Wang JF, Hu Y, Li XH, Qian YR, Song CL. Evaluating the advancements in protein language models for encoding strategies in protein function prediction: a comprehensive review. Front Bioeng Biotechnol 2025;13:1506508. [PMID: 39906415 PMCID: PMC11790633 DOI: 10.3389/fbioe.2025.1506508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2024] [Accepted: 01/02/2025] [Indexed: 02/06/2025]  Open
3
Gouda W, Ahmed AEH, El-Hamd H. Mohamed A, Abou-Ellail M, Afify M, Hamimy W, Abdelmaksoud MD. Evaluation of the association of some circulating miRNA molecules in the metabolic syndrome. Qatar Med J 2024;2024:71. [PMID: 39925821 PMCID: PMC11806720 DOI: 10.5339/qmj.2024.71] [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: 05/15/2024] [Accepted: 10/01/2024] [Indexed: 02/11/2025]  Open
4
Ke S, Huang Y, Wang D, Jiang Q, Luo Z, Li B, Yan D, Zhou J. BreCML: identifying breast cancer cell state in scRNA-seq via machine learning. Front Med (Lausanne) 2024;11:1482726. [PMID: 39574916 PMCID: PMC11579858 DOI: 10.3389/fmed.2024.1482726] [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: 08/18/2024] [Accepted: 10/15/2024] [Indexed: 11/24/2024]  Open
5
Yu S, Liu L, Wang H, Yan S, Zheng S, Ning J, Luo R, Fu X, Deng X. AtML: An Arabidopsis thaliana root cell identity recognition tool for medicinal ingredient accumulation. Methods 2024;231:61-69. [PMID: 39293728 DOI: 10.1016/j.ymeth.2024.09.010] [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: 07/07/2024] [Revised: 08/05/2024] [Accepted: 09/12/2024] [Indexed: 09/20/2024]  Open
6
Qiu Y, Chen W, Ching WK, Cai H, Jiang H, Zou Q. AGML: Adaptive Graph-Based Multi-Label Learning for Prediction of RBP and as Event Associations During EMT. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024;21:2113-2122. [PMID: 39133592 DOI: 10.1109/tcbb.2024.3440913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2025]
7
Yang Y, Sun Y, Li F, Guan B, Liu JX, Shang J. MGCNRF: Prediction of Disease-Related miRNAs Based on Multiple Graph Convolutional Networks and Random Forest. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2024;35:15701-15709. [PMID: 37459265 DOI: 10.1109/tnnls.2023.3289182] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2024]
8
Feng H, Ke C, Zou Q, Zhu Z, Liu T. Prediction of Potential miRNA-Disease Associations Based on a Masked Graph Autoencoder. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024;21:1874-1885. [PMID: 38954583 DOI: 10.1109/tcbb.2024.3421924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
9
Wang XF, Huang L, Wang Y, Guan RC, You ZH, Sheng N, Xie XP, Yang QX. A multichannel graph neural network based on multisimilarity modality hypergraph contrastive learning for predicting unknown types of cancer biomarkers. Brief Bioinform 2024;25:bbae575. [PMID: 39523624 PMCID: PMC11551052 DOI: 10.1093/bib/bbae575] [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: 08/05/2024] [Revised: 10/19/2024] [Accepted: 11/01/2024] [Indexed: 11/16/2024]  Open
10
Liu L, Huang Y, Zheng Y, Liao Y, Ma S, Wang Q. ScnML models single-cell transcriptome to predict spinal cord neuronal cell status. Front Genet 2024;15:1413484. [PMID: 38894722 PMCID: PMC11183327 DOI: 10.3389/fgene.2024.1413484] [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: 04/07/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024]  Open
11
Sulaimany S, Farahmandi K, Mafakheri A. Computational prediction of new therapeutic effects of probiotics. Sci Rep 2024;14:11932. [PMID: 38789535 PMCID: PMC11126595 DOI: 10.1038/s41598-024-62796-4] [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: 12/12/2023] [Accepted: 05/21/2024] [Indexed: 05/26/2024]  Open
12
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]
13
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
14
Tian Z, Han C, Xu L, Teng Z, Song W. MGCNSS: miRNA-disease association prediction with multi-layer graph convolution and distance-based negative sample selection strategy. Brief Bioinform 2024;25:bbae168. [PMID: 38622356 PMCID: PMC11018511 DOI: 10.1093/bib/bbae168] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/14/2024] [Accepted: 03/31/2024] [Indexed: 04/17/2024]  Open
15
Bryant CJ, McCool MA, Rosado González G, Abriola L, Surovtseva Y, Baserga S. Discovery of novel microRNA mimic repressors of ribosome biogenesis. Nucleic Acids Res 2024;52:1988-2011. [PMID: 38197221 PMCID: PMC10899765 DOI: 10.1093/nar/gkad1235] [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: 02/20/2023] [Revised: 12/03/2023] [Accepted: 12/16/2023] [Indexed: 01/11/2024]  Open
16
Wu W, Ma X, Wang Q, Gong M, Gao Q. Learning deep representation and discriminative features for clustering of multi-layer networks. Neural Netw 2024;170:405-416. [PMID: 38029721 DOI: 10.1016/j.neunet.2023.11.053] [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: 05/19/2023] [Revised: 09/29/2023] [Accepted: 11/22/2023] [Indexed: 12/01/2023]
17
Liao Q, Fu X, Zhuo L, Chen H. An efficient model for predicting human diseases through miRNA based on multiple-types of contrastive learning. Front Microbiol 2023;14:1325001. [PMID: 38163075 PMCID: PMC10755968 DOI: 10.3389/fmicb.2023.1325001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 11/16/2023] [Indexed: 01/03/2024]  Open
18
Wang H, Lin YN, Yan S, Hong JP, Tan JR, Chen YQ, Cao YS, Fang W. NRTPredictor: identifying rice root cell state in single-cell RNA-seq via ensemble learning. PLANT METHODS 2023;19:119. [PMID: 37925413 PMCID: PMC10625708 DOI: 10.1186/s13007-023-01092-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 10/15/2023] [Indexed: 11/06/2023]
19
Bryant CJ, McCool MA, Rosado-González GT, Abriola L, Surovtseva YV, Baserga SJ. Discovery of novel microRNA mimic repressors of ribosome biogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.17.526327. [PMID: 36824951 PMCID: PMC9949135 DOI: 10.1101/2023.02.17.526327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
20
Naderi Yeganeh P, Teo YY, Karagkouni D, Pita-Juárez Y, Morgan SL, Slack FJ, Vlachos IS, Hide WA. PanomiR: a systems biology framework for analysis of multi-pathway targeting by miRNAs. Brief Bioinform 2023;24:bbad418. [PMID: 37985452 PMCID: PMC10661971 DOI: 10.1093/bib/bbad418] [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: 08/08/2023] [Revised: 10/16/2023] [Accepted: 10/20/2023] [Indexed: 11/22/2023]  Open
21
Zhou F, Yin MM, Jiao CN, Zhao JX, Zheng CH, Liu JX. Predicting miRNA-Disease Associations Through Deep Autoencoder With Multiple Kernel Learning. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2023;34:5570-5579. [PMID: 34860656 DOI: 10.1109/tnnls.2021.3129772] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
22
Zhou Z, Du Z, Wei J, Zhuo L, Pan S, Fu X, Lian X. MHAM-NPI: Predicting ncRNA-protein interactions based on multi-head attention mechanism. Comput Biol Med 2023;163:107143. [PMID: 37339574 DOI: 10.1016/j.compbiomed.2023.107143] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/20/2023] [Accepted: 06/06/2023] [Indexed: 06/22/2023]
23
Wu W, Gong M, Ma X. Clustering of Multilayer Networks Using Joint Learning Algorithm With Orthogonality and Specificity of Features. IEEE TRANSACTIONS ON CYBERNETICS 2023;53:4972-4985. [PMID: 35286272 DOI: 10.1109/tcyb.2022.3152723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
24
Chen R, Li F, Guo X, Bi Y, Li C, Pan S, Coin LJM, Song J. ATTIC is an integrated approach for predicting A-to-I RNA editing sites in three species. Brief Bioinform 2023;24:bbad170. [PMID: 37150785 PMCID: PMC10565902 DOI: 10.1093/bib/bbad170] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/12/2023] [Accepted: 04/14/2023] [Indexed: 05/09/2023]  Open
25
Soylu NN, Sefer E. BERT2OME: Prediction of 2'-O-Methylation Modifications From RNA Sequence by Transformer Architecture Based on BERT. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:2177-2189. [PMID: 37819796 DOI: 10.1109/tcbb.2023.3237769] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
26
Yan W, Chen Y, Hu G, Shi T, Liu X, Li J, Sun L, Qian F, Chen W. MiR-200/183 family-mediated module biomarker for gastric cancer progression: an AI-assisted bioinformatics method with experimental functional survey. J Transl Med 2023;21:163. [PMID: 36864416 PMCID: PMC9983275 DOI: 10.1186/s12967-023-04010-z] [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: 09/19/2022] [Accepted: 02/18/2023] [Indexed: 03/04/2023]  Open
27
Ha J. SMAP: Similarity-based matrix factorization framework for inferring miRNA-disease association. Knowl Based Syst 2023. [DOI: 10.1016/j.knosys.2023.110295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
28
van Wijk N, Zohar K, Linial M. Challenging Cellular Homeostasis: Spatial and Temporal Regulation of miRNAs. Int J Mol Sci 2022;23:16152. [PMID: 36555797 PMCID: PMC9787707 DOI: 10.3390/ijms232416152] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/11/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]  Open
29
Wang Y, Sun Z, He Q, Li J, Ni M, Yang M. Self-supervised graph representation learning integrates multiple molecular networks and decodes gene-disease relationships. PATTERNS (NEW YORK, N.Y.) 2022;4:100651. [PMID: 36699743 PMCID: PMC9868676 DOI: 10.1016/j.patter.2022.100651] [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: 04/04/2022] [Revised: 05/19/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022]
30
Zhang H, Wang Y, Pan Z, Sun X, Mou M, Zhang B, Li Z, Li H, Zhu F. ncRNAInter: a novel strategy based on graph neural network to discover interactions between lncRNA and miRNA. Brief Bioinform 2022;23:6747810. [PMID: 36198065 DOI: 10.1093/bib/bbac411] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/04/2022] [Accepted: 08/23/2022] [Indexed: 12/14/2022]  Open
31
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
32
Lu X, Li J, Zhu Z, Yuan Y, Chen G, He K. Predicting miRNA-Disease Associations via Combining Probability Matrix Feature Decomposition With Neighbor Learning. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:3160-3170. [PMID: 34260356 DOI: 10.1109/tcbb.2021.3097037] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
33
Li M, Fan Y, Zhang Y, Lv Z. Using Sequence Similarity Based on CKSNP Features and a Graph Neural Network Model to Identify miRNA-Disease Associations. Genes (Basel) 2022;13:1759. [PMID: 36292644 PMCID: PMC9602123 DOI: 10.3390/genes13101759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 01/12/2024]  Open
34
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
35
Xu L, Li X, Yang Q, Tan L, Liu Q, Liu Y. Application of Bidirectional Generative Adversarial Networks to Predict Potential miRNAs Associated With Diseases. Front Genet 2022;13:936823. [PMID: 35903359 PMCID: PMC9314862 DOI: 10.3389/fgene.2022.936823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 06/08/2022] [Indexed: 11/18/2022]  Open
36
Ouyang D, Miao R, Wang J, Liu X, Xie S, Ai N, Dang Q, Liang Y. Predicting Multiple Types of Associations Between miRNAs and Diseases Based on Graph Regularized Weighted Tensor Decomposition. Front Bioeng Biotechnol 2022;10:911769. [PMID: 35910021 PMCID: PMC9335924 DOI: 10.3389/fbioe.2022.911769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/04/2022] [Indexed: 11/23/2022]  Open
37
Ai C, Yang H, Ding Y, Tang J, Guo F. A multi-layer multi-kernel neural network for determining associations between non-coding RNAs and diseases. Neurocomputing 2022. [DOI: 10.1016/j.neucom.2022.04.068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
38
Ni J, Li L, Wang Y, Ji C, Zheng C. MDSCMF: Matrix Decomposition and Similarity-Constrained Matrix Factorization for miRNA-Disease Association Prediction. Genes (Basel) 2022;13:1021. [PMID: 35741782 PMCID: PMC9223216 DOI: 10.3390/genes13061021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 11/16/2022]  Open
39
Liu P, Luo J, Chen X. miRCom: Tensor Completion Integrating Multi-View Information to Deduce the Potential Disease-Related miRNA-miRNA Pairs. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:1747-1759. [PMID: 33180730 DOI: 10.1109/tcbb.2020.3037331] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
40
Zhao A, Li D, Mao X, Yang M, Deng W, Hu W, Chen C, Yang G, Li L. GNG2 acts as a tumor suppressor in breast cancer through stimulating MRAS signaling. Cell Death Dis 2022;13:260. [PMID: 35322009 PMCID: PMC8943035 DOI: 10.1038/s41419-022-04690-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 02/10/2022] [Accepted: 02/24/2022] [Indexed: 01/02/2023]
41
Han H, Zhu R, Liu JX, Dai LY. Predicting miRNA-disease associations via layer attention graph convolutional network model. BMC Med Inform Decis Mak 2022;22:69. [PMID: 35305630 PMCID: PMC8934489 DOI: 10.1186/s12911-022-01807-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/09/2022] [Indexed: 12/03/2022]  Open
42
Yu L, Zheng Y, Ju B, Ao C, Gao L. Research progress of miRNA-disease association prediction and comparison of related algorithms. Brief Bioinform 2022;23:6542222. [PMID: 35246678 DOI: 10.1093/bib/bbac066] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/30/2022] [Accepted: 02/08/2022] [Indexed: 11/13/2022]  Open
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Gao Z, Wang YT, Wu QW, Li L, Ni JC, Zheng CH. A New Method Based on Matrix Completion and Non-Negative Matrix Factorization for Predicting Disease-Associated miRNAs. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:763-772. [PMID: 32991287 DOI: 10.1109/tcbb.2020.3027444] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
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Predicting miRNA-Disease Association Based on Neural Inductive Matrix Completion with Graph Autoencoders and Self-Attention Mechanism. Biomolecules 2022;12:biom12010064. [PMID: 35053212 PMCID: PMC8774034 DOI: 10.3390/biom12010064] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 12/29/2021] [Accepted: 12/31/2021] [Indexed: 02/06/2023]  Open
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Saxena R, Bishnoi R, Singla D. Gene Ontology: application and importance in functional annotation of the genomic data. Bioinformatics 2022. [DOI: 10.1016/b978-0-323-89775-4.00015-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]  Open
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RFLMDA: A Novel Reinforcement Learning-Based Computational Model for Human MicroRNA-Disease Association Prediction. Biomolecules 2021;11:biom11121835. [PMID: 34944479 PMCID: PMC8699433 DOI: 10.3390/biom11121835] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 11/23/2022]  Open
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Ao C, Zou Q, Yu L. NmRF: identification of multispecies RNA 2'-O-methylation modification sites from RNA sequences. Brief Bioinform 2021;23:6446272. [PMID: 34850821 DOI: 10.1093/bib/bbab480] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/05/2021] [Accepted: 10/18/2021] [Indexed: 12/12/2022]  Open
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Zeng M, Lu C, Fei Z, Wu FX, Li Y, Wang J, Li M. DMFLDA: A Deep Learning Framework for Predicting lncRNA-Disease Associations. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021;18:2353-2363. [PMID: 32248123 DOI: 10.1109/tcbb.2020.2983958] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
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Luo J, Shen C, Lai Z, Cai J, Ding P. Incorporating Clinical, Chemical and Biological Information for Predicting Small Molecule-microRNA Associations Based on Non-Negative Matrix Factorization. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021;18:2535-2545. [PMID: 32092012 DOI: 10.1109/tcbb.2020.2975780] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
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Wang YT, Li L, Ji CM, Zheng CH, Ni JC. ILPMDA: Predicting miRNA-Disease Association Based on Improved Label Propagation. Front Genet 2021;12:743665. [PMID: 34659364 PMCID: PMC8514753 DOI: 10.3389/fgene.2021.743665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 08/30/2021] [Indexed: 12/21/2022]  Open
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