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For: 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] [What about the content of this article? (0)] [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
Number Cited by Other Article(s)
1
Chen J, Zhang L, Liang Z. Utilizing Dual-Channel Graph and Hypergraph Convolution Network to Discover Microbes Underlying Disease Traits. J Chem Inf Model 2025;65:5152-5162. [PMID: 40370041 DOI: 10.1021/acs.jcim.5c00224] [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: 05/16/2025]
2
Panghalia A, Singh V. Machine learning approaches for predicting the small molecule-miRNA associations: a comprehensive review. Mol Divers 2025:10.1007/s11030-025-11211-9. [PMID: 40392452 DOI: 10.1007/s11030-025-11211-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2025] [Accepted: 04/25/2025] [Indexed: 05/22/2025]
3
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]
4
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]
5
Li Y, Wang S, Zhang Y, Ren C, Liu T, Liu Y, Pang S. IRPCA: An Interpretable Robust Principal Component Analysis Framework for Inferring miRNA-Drug Associations. J Chem Inf Model 2025;65:2432-2442. [PMID: 39980166 DOI: 10.1021/acs.jcim.4c02385] [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: 02/22/2025]
6
Zhang B, Quan L, Zhang Z, Cao L, Chen Q, Peng L, Wang J, Jiang Y, Nie L, Li G, Wu T, Lyu Q. MVCL-DTI: Predicting Drug-Target Interactions Using a Multiview Contrastive Learning Model on a Heterogeneous Graph. J Chem Inf Model 2025;65:1009-1026. [PMID: 39812134 DOI: 10.1021/acs.jcim.4c02073] [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: 01/16/2025]
7
Li Z, Zeng Y, Jiang M, Wei B. Deep Drug-Target Binding Affinity Prediction Base on Multiple Feature Extraction and Fusion. ACS OMEGA 2025;10:2020-2032. [PMID: 39866608 PMCID: PMC11755178 DOI: 10.1021/acsomega.4c08048] [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: 09/02/2024] [Revised: 12/25/2024] [Accepted: 01/03/2025] [Indexed: 01/28/2025]
8
Wang Z, Chen Y, Ma H, Gao H, Zhu Y, Wang H, Zhang N. Accurate identification of snoRNA targets using variational graph autoencoder to advance the redevelopment of traditional medicines. Front Pharmacol 2025;15:1529128. [PMID: 39834830 PMCID: PMC11743687 DOI: 10.3389/fphar.2024.1529128] [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: 11/16/2024] [Accepted: 12/11/2024] [Indexed: 01/22/2025]  Open
9
Xie G, Li D, Lin Z, Gu G, Li W, Chen R, Liu Z. HPTRMF: Collaborative Matrix Factorization-Based Prediction Method for LncRNA-Disease Associations Using High-Order Perturbation and Flexible Trifactor Regularization. J Chem Inf Model 2024;64:9594-9608. [PMID: 39058598 DOI: 10.1021/acs.jcim.4c01070] [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: 07/28/2024]
10
Liu M, Meng X, Mao Y, Li H, Liu J. ReduMixDTI: Prediction of Drug-Target Interaction with Feature Redundancy Reduction and Interpretable Attention Mechanism. J Chem Inf Model 2024;64:8952-8962. [PMID: 39570771 DOI: 10.1021/acs.jcim.4c01554] [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: 12/10/2024]
11
Yang B, Wen F, Cui Y. Integrative transcriptome analysis identifies a crotonylation gene signature for predicting prognosis and drug sensitivity in hepatocellular carcinoma. J Cell Mol Med 2024;28:e70083. [PMID: 39428564 PMCID: PMC11491312 DOI: 10.1111/jcmm.70083] [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: 05/25/2024] [Revised: 08/29/2024] [Accepted: 09/03/2024] [Indexed: 10/22/2024]  Open
12
Xie J, Xu P, Lin Y, Zheng M, Jia J, Tan X, Sun J, Zhao Q. LncRNA-miRNA interactions prediction based on meta-path similarity and Gaussian kernel similarity. J Cell Mol Med 2024;28:e18590. [PMID: 39347925 PMCID: PMC11441278 DOI: 10.1111/jcmm.18590] [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: 05/04/2024] [Revised: 07/16/2024] [Accepted: 07/24/2024] [Indexed: 10/01/2024]  Open
13
Yin S, Xu P, Jiang Y, Yang X, Lin Y, Zheng M, Hu J, Zhao Q. Predicting the potential associations between circRNA and drug sensitivity using a multisource feature-based approach. J Cell Mol Med 2024;28:e18591. [PMID: 39347936 PMCID: PMC11441279 DOI: 10.1111/jcmm.18591] [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: 05/07/2024] [Revised: 07/16/2024] [Accepted: 07/24/2024] [Indexed: 10/01/2024]  Open
14
Chen J, Tao R, Qiu Y, Yuan Q. CMFHMDA: a prediction framework for human disease-microbe associations based on cross-domain matrix factorization. Brief Bioinform 2024;25:bbae481. [PMID: 39327064 PMCID: PMC11427075 DOI: 10.1093/bib/bbae481] [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: 06/23/2024] [Revised: 08/27/2024] [Accepted: 09/12/2024] [Indexed: 09/28/2024]  Open
15
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
16
Sun XY, Hou ZJ, Zhang WG, Chen Y, Yao HB. HTFSMMA: Higher-Order Topological Guided Small Molecule-MicroRNA Associations Prediction. J Comput Biol 2024;31:886-906. [PMID: 39109562 DOI: 10.1089/cmb.2024.0587] [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: 09/10/2024]  Open
17
Chen J, Zhu Y, Yuan Q. Predicting potential microbe-disease associations based on dual branch graph convolutional network. J Cell Mol Med 2024;28:e18571. [PMID: 39086148 PMCID: PMC11291560 DOI: 10.1111/jcmm.18571] [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: 05/15/2024] [Revised: 06/15/2024] [Accepted: 06/27/2024] [Indexed: 08/02/2024]  Open
18
Zhao R, Cheng S, Bai X, Zhang D, Fang H, Che W, Zhang W, Zhou Y, Duan W, Liang Q, Xiao L, Nie G, Hou Y. Development of an efficient liposomal DOX delivery formulation for HCC therapy by targeting CK2α. Biotechnol J 2024;19:e2400050. [PMID: 38651271 DOI: 10.1002/biot.202400050] [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: 01/30/2024] [Revised: 03/11/2024] [Accepted: 03/23/2024] [Indexed: 04/25/2024]
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