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For: Zhang W, Hou J, Liu B. iPiDA-LTR: Identifying piwi-interacting RNA-disease associations based on Learning to Rank. PLoS Comput Biol 2022;18:e1010404. [PMID: 35969645 PMCID: PMC9410559 DOI: 10.1371/journal.pcbi.1010404] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 08/25/2022] [Accepted: 07/18/2022] [Indexed: 12/01/2022]  Open
Number Cited by Other Article(s)
1
Hu X, Sun H, Shan L, Ma C, Quan H, Zhang Y, Zhang J, Fan Z, Tang Y, Deng L. Unraveling Disease-Associated PIWI-Interacting RNAs with a Contrastive Learning Methods. J Chem Inf Model 2025;65:4687-4697. [PMID: 40263714 DOI: 10.1021/acs.jcim.5c00173] [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: 04/24/2025]
2
Wei H, Hou J, Liu Y, Shaytan AK, Liu B, Wu H. iPiDA-LGE: a local and global graph ensemble learning framework for identifying piRNA-disease associations. BMC Biol 2025;23:119. [PMID: 40346532 PMCID: PMC12065364 DOI: 10.1186/s12915-025-02221-y] [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: 05/05/2024] [Accepted: 04/23/2025] [Indexed: 05/11/2025]  Open
3
Guo C, Wang X, Ren H. Databases and computational methods for the identification of piRNA-related molecules: A survey. Comput Struct Biotechnol J 2024;23:813-833. [PMID: 38328006 PMCID: PMC10847878 DOI: 10.1016/j.csbj.2024.01.011] [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: 09/11/2023] [Revised: 12/31/2023] [Accepted: 01/15/2024] [Indexed: 02/09/2024]  Open
4
Liu Y, Zhang F, Ding Y, Fei R, Li J, Wu FX. MRDPDA: A multi-Laplacian regularized deepFM model for predicting piRNA-disease associations. J Cell Mol Med 2024;28:e70046. [PMID: 39228010 PMCID: PMC11371490 DOI: 10.1111/jcmm.70046] [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: 04/18/2024] [Revised: 07/15/2024] [Accepted: 08/16/2024] [Indexed: 09/05/2024]  Open
5
Sun W, Guo C, Wan J, Ren H. piRNA-disease association prediction based on multi-channel graph variational autoencoder. PeerJ Comput Sci 2024;10:e2216. [PMID: 39145234 PMCID: PMC11323097 DOI: 10.7717/peerj-cs.2216] [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: 10/30/2023] [Accepted: 07/03/2024] [Indexed: 08/16/2024]
6
Zhang J, Lang M, Zhou Y, Zhang Y. Predicting RNA structures and functions by artificial intelligence. Trends Genet 2023;40:S0168-9525(23)00229-9. [PMID: 39492264 DOI: 10.1016/j.tig.2023.10.001] [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: 05/25/2023] [Revised: 08/22/2023] [Accepted: 10/03/2023] [Indexed: 11/05/2024]
7
Hou J, Wei H, Liu B. iPiDA-SWGCN: Identification of piRNA-disease associations based on Supplementarily Weighted Graph Convolutional Network. PLoS Comput Biol 2023;19:e1011242. [PMID: 37339125 DOI: 10.1371/journal.pcbi.1011242] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 06/05/2023] [Indexed: 06/22/2023]  Open
8
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
9
Meng X, Shang J, Ge D, Yang Y, Zhang T, Liu JX. ETGPDA: identification of piRNA-disease associations based on embedding transformation graph convolutional network. BMC Genomics 2023;24:279. [PMID: 37226081 PMCID: PMC10210294 DOI: 10.1186/s12864-023-09380-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/15/2023] [Indexed: 05/26/2023]  Open
10
Zhang L, Bai T, Wu H. sgRNA-2wPSM: Identify sgRNAs on-target activity by combining two-window-based position specific mismatch and synthetic minority oversampling technique. Comput Biol Med 2023;155:106489. [PMID: 36841059 DOI: 10.1016/j.compbiomed.2022.106489] [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: 11/22/2022] [Accepted: 12/27/2022] [Indexed: 12/30/2022]
11
Shi H, Wu C, Bai T, Chen J, Li Y, Wu H. Identify essential genes based on clustering based synthetic minority oversampling technique. Comput Biol Med 2023;153:106523. [PMID: 36652869 DOI: 10.1016/j.compbiomed.2022.106523] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/13/2022] [Accepted: 12/31/2022] [Indexed: 01/03/2023]
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