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Number Cited by Other Article(s)
1
Wang Z, Meng J, Li H, Dai Q, Lin X, Luan Y. Attention-augmented multi-domain cooperative graph representation learning for molecular interaction prediction. Neural Netw 2025;186:107265. [PMID: 39987715 DOI: 10.1016/j.neunet.2025.107265] [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: 08/23/2024] [Revised: 01/23/2025] [Accepted: 02/07/2025] [Indexed: 02/25/2025]
2
Hu B, Su Y, Tian X, Chen C, Chen C, Lv X. GMAMDA: Predicting Metabolite-Disease Associations Based on Adaptive Hardness Negative Sampling and Adaptive Graph Multiple Convolution. J Chem Inf Model 2025;65:5242-5254. [PMID: 40372801 DOI: 10.1021/acs.jcim.5c00694] [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: 05/17/2025]
3
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]
4
Lu Q, Zhou Z, Wang Q. Multi-layer graph attention neural networks for accurate drug-target interaction mapping. Sci Rep 2024;14:26119. [PMID: 39478027 PMCID: PMC11525987 DOI: 10.1038/s41598-024-75742-1] [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: 02/02/2024] [Accepted: 10/08/2024] [Indexed: 11/02/2024]  Open
5
Pang H, Wei S, Du Z, Zhao Y, Cai S, Zhao Y. Graph Representation Learning Based on Specific Subgraphs for Biomedical Interaction Prediction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024;21:1552-1564. [PMID: 38767994 DOI: 10.1109/tcbb.2024.3402741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
6
Li M, Wang Z, Liu L, Liu X, Zhang W. Subgraph-Aware Graph Kernel Neural Network for Link Prediction in Biological Networks. IEEE J Biomed Health Inform 2024;28:4373-4381. [PMID: 38630566 DOI: 10.1109/jbhi.2024.3390092] [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: 04/19/2024]
7
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
8
Ma Y, Zhao Y, Ma Y. Kernel Bayesian nonlinear matrix factorization based on variational inference for human-virus protein-protein interaction prediction. Sci Rep 2024;14:5693. [PMID: 38454139 PMCID: PMC10920681 DOI: 10.1038/s41598-024-56208-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: 09/16/2023] [Accepted: 03/04/2024] [Indexed: 03/09/2024]  Open
9
Lei S, Lei X, Chen M, Pan Y. Drug Repositioning Based on Deep Sparse Autoencoder and Drug-Disease Similarity. Interdiscip Sci 2024;16:160-175. [PMID: 38103130 DOI: 10.1007/s12539-023-00593-9] [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: 07/19/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 12/17/2023]
10
Xuan P, Xiu J, Cui H, Zhang X, Nakaguchi T, Zhang T. Complementary feature learning across multiple heterogeneous networks and multimodal attribute learning for predicting disease-related miRNAs. iScience 2024;27:108639. [PMID: 38303724 PMCID: PMC10831890 DOI: 10.1016/j.isci.2023.108639] [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: 07/18/2023] [Revised: 11/02/2023] [Accepted: 12/01/2023] [Indexed: 02/03/2024]  Open
11
Luo H, Zhu C, Wang J, Zhang G, Luo J, Yan C. Prediction of drug-disease associations based on reinforcement symmetric metric learning and graph convolution network. Front Pharmacol 2024;15:1337764. [PMID: 38384286 PMCID: PMC10879308 DOI: 10.3389/fphar.2024.1337764] [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: 11/13/2023] [Accepted: 01/18/2024] [Indexed: 02/23/2024]  Open
12
Ma Y, Zhong J, Zhu N. Weighted hypergraph learning and adaptive inductive matrix completion for SARS-CoV-2 drug repositioning. Methods 2023;219:102-110. [PMID: 37804962 DOI: 10.1016/j.ymeth.2023.10.002] [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: 07/03/2022] [Revised: 09/14/2023] [Accepted: 10/03/2023] [Indexed: 10/09/2023]  Open
13
Binatlı OC, Gönen M. MOKPE: drug-target interaction prediction via manifold optimization based kernel preserving embedding. BMC Bioinformatics 2023;24:276. [PMID: 37407927 DOI: 10.1186/s12859-023-05401-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/25/2023] [Indexed: 07/07/2023]  Open
14
Gao Z, Ma H, Zhang X, Wang Y, Wu Z. Similarity measures-based graph co-contrastive learning for drug-disease association prediction. Bioinformatics 2023;39:btad357. [PMID: 37261859 PMCID: PMC10275904 DOI: 10.1093/bioinformatics/btad357] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 03/14/2023] [Accepted: 05/31/2023] [Indexed: 06/02/2023]  Open
15
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
16
Xie X, Wang Y, He K, Sheng N. Predicting miRNA-disease associations based on PPMI and attention network. BMC Bioinformatics 2023;24:113. [PMID: 36959547 PMCID: PMC10037801 DOI: 10.1186/s12859-023-05152-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/17/2023] [Indexed: 03/25/2023]  Open
17
Hyperbolic matrix factorization improves prediction of drug-target associations. Sci Rep 2023;13:959. [PMID: 36653463 PMCID: PMC9849222 DOI: 10.1038/s41598-023-27995-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 01/11/2023] [Indexed: 01/19/2023]  Open
18
Zhang J, Xie M. Graph regularized non-negative matrix factorization with prior knowledge consistency constraint for drug-target interactions prediction. BMC Bioinformatics 2022;23:564. [PMID: 36581822 PMCID: PMC9798666 DOI: 10.1186/s12859-022-05119-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/20/2022] [Indexed: 12/30/2022]  Open
19
Lei S, Lei X, Liu L. Drug repositioning based on heterogeneous networks and variational graph autoencoders. Front Pharmacol 2022;13:1056605. [PMID: 36618933 PMCID: PMC9812491 DOI: 10.3389/fphar.2022.1056605] [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: 09/29/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]  Open
20
Li P, Tiwari P, Xu J, Qian Y, Ai C, Ding Y, Guo F. Sparse regularized joint projection model for identifying associations of non-coding RNAs and human diseases. Knowl Based Syst 2022. [DOI: 10.1016/j.knosys.2022.110044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
21
Liu BM, Gao YL, Zhang DJ, Zhou F, Wang J, Zheng CH, Liu JX. A new framework for drug-disease association prediction combing light-gated message passing neural network and gated fusion mechanism. Brief Bioinform 2022;23:6775584. [PMID: 36305457 DOI: 10.1093/bib/bbac457] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 09/07/2022] [Accepted: 09/23/2022] [Indexed: 12/14/2022]  Open
22
Gao M, Liu S, Qi Y, Guo X, Shang X. GAE-LGA: integration of multi-omics data with graph autoencoders to identify lncRNA-PCG associations. Brief Bioinform 2022;23:6775590. [PMID: 36305456 DOI: 10.1093/bib/bbac452] [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: 07/14/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 12/14/2022]  Open
23
Mariappan R, Jayagopal A, Sien HZ, Rajan V. Neural Collective Matrix Factorization for integrated analysis of heterogeneous biomedical data. Bioinformatics 2022;38:4554-4561. [PMID: 35929808 DOI: 10.1093/bioinformatics/btac543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/30/2022] [Accepted: 08/03/2022] [Indexed: 12/24/2022]  Open
24
Xie X, Wang Y, Sheng N, Zhang S, Cao Y, Fu Y. Predicting miRNA-disease associations based on multi-view information fusion. Front Genet 2022;13:979815. [PMID: 36238163 PMCID: PMC9552014 DOI: 10.3389/fgene.2022.979815] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/16/2022] [Indexed: 11/13/2022]  Open
25
Liu B, Papadopoulos D, Malliaros FD, Tsoumakas G, Papadopoulos AN. Multiple similarity drug-target interaction prediction with random walks and matrix factorization. Brief Bioinform 2022;23:6692553. [PMID: 36070659 DOI: 10.1093/bib/bbac353] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/11/2022] [Accepted: 07/27/2022] [Indexed: 11/14/2022]  Open
26
Sharma VS, Fossati A, Ciuffa R, Buljan M, Williams EG, Chen Z, Shao W, Pedrioli PGA, Purcell AW, Martínez MR, Song J, Manica M, Aebersold R, Li C. PCfun: a hybrid computational framework for systematic characterization of protein complex function. Brief Bioinform 2022;23:6611913. [PMID: 35724564 PMCID: PMC9310514 DOI: 10.1093/bib/bbac239] [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: 02/24/2022] [Revised: 05/05/2022] [Accepted: 05/21/2022] [Indexed: 11/14/2022]  Open
27
Ma Y, Liu Q. Generalized matrix factorization based on weighted hypergraph learning for microbe-drug association prediction. Comput Biol Med 2022;145:105503. [DOI: 10.1016/j.compbiomed.2022.105503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/28/2022] [Accepted: 04/04/2022] [Indexed: 11/03/2022]
28
Li X, Liu LP, Hassoun S. Boost-RS: boosted embeddings for recommender systems and its application to enzyme-substrate interaction prediction. Bioinformatics 2022;38:2832-2838. [PMID: 35561204 PMCID: PMC9113267 DOI: 10.1093/bioinformatics/btac201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 02/06/2022] [Accepted: 04/07/2022] [Indexed: 11/17/2022]  Open
29
Long Y, Wu M, Liu Y, Fang Y, Kwoh CK, Chen J, Luo J, Li X. Pre-training graph neural networks for link prediction in biomedical networks. Bioinformatics 2022;38:2254-2262. [PMID: 35171981 DOI: 10.1093/bioinformatics/btac100] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/15/2022] [Accepted: 02/14/2022] [Indexed: 02/03/2023]  Open
30
Ma Y. DeepMNE: Deep Multi-network Embedding for lncRNA-Disease Association prediction. IEEE J Biomed Health Inform 2022;26:3539-3549. [PMID: 35180094 DOI: 10.1109/jbhi.2022.3152619] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
31
Targets preliminary screening for the fresh natural drug molecule based on Cosine-correlation and similarity-comparison of local network. J Transl Med 2022;20:67. [PMID: 35115019 PMCID: PMC8812203 DOI: 10.1186/s12967-022-03279-w] [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: 11/05/2021] [Accepted: 01/24/2022] [Indexed: 11/30/2022]  Open
32
Ding Y, Tang J, Guo F, Zou Q. Identification of drug-target interactions via multiple kernel-based triple collaborative matrix factorization. Brief Bioinform 2022;23:6520305. [PMID: 35134117 DOI: 10.1093/bib/bbab582] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/02/2021] [Accepted: 12/19/2021] [Indexed: 12/15/2022]  Open
33
Yang H, Ding Y, Tang J, Guo F. Inferring human microbe–drug associations via multiple kernel fusion on graph neural network. Knowl Based Syst 2022. [DOI: 10.1016/j.knosys.2021.107888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
34
Fu H, Huang F, Liu X, Qiu Y, Zhang W. MVGCN: data integration through multi-view graph convolutional network for predicting links in biomedical bipartite networks. Bioinformatics 2022;38:426-434. [PMID: 34499148 DOI: 10.1093/bioinformatics/btab651] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 08/07/2021] [Accepted: 09/06/2021] [Indexed: 02/05/2023]  Open
35
Ma Y, Ma Y. Hypergraph-based logistic matrix factorization for metabolite-disease interaction prediction. Bioinformatics 2022;38:435-443. [PMID: 34499104 DOI: 10.1093/bioinformatics/btab652] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/08/2021] [Accepted: 09/06/2021] [Indexed: 02/03/2023]  Open
36
Zhou S, Sun W, Zhang P, Li L. Predicting Pseudogene-miRNA Associations Based on Feature Fusion and Graph Auto-Encoder. Front Genet 2021;12:781277. [PMID: 34966413 PMCID: PMC8710693 DOI: 10.3389/fgene.2021.781277] [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: 09/22/2021] [Accepted: 11/16/2021] [Indexed: 11/13/2022]  Open
37
Zhang G, Li M, Deng H, Xu X, Liu X, Zhang W. SGNNMD: signed graph neural network for predicting deregulation types of miRNA-disease associations. Brief Bioinform 2021;23:6455665. [PMID: 34875683 DOI: 10.1093/bib/bbab464] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 11/13/2022]  Open
38
Ou-Yang L, Lu F, Zhang ZC, Wu M. Matrix factorization for biomedical link prediction and scRNA-seq data imputation: an empirical survey. Brief Bioinform 2021;23:6447434. [PMID: 34864871 DOI: 10.1093/bib/bbab479] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/25/2021] [Accepted: 10/18/2021] [Indexed: 02/02/2023]  Open
39
Sorkhi AG, Abbasi Z, Mobarakeh MI, Pirgazi J. Drug-target interaction prediction using unifying of graph regularized nuclear norm with bilinear factorization. BMC Bioinformatics 2021;22:555. [PMID: 34789169 PMCID: PMC8597250 DOI: 10.1186/s12859-021-04464-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/29/2021] [Indexed: 12/27/2022]  Open
40
Identification of drug-target interactions via multi-view graph regularized link propagation model. Neurocomputing 2021. [DOI: 10.1016/j.neucom.2021.05.100] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
41
Yi HC, You ZH, Huang DS, Kwoh CK. Graph representation learning in bioinformatics: trends, methods and applications. Brief Bioinform 2021;23:6361044. [PMID: 34471921 DOI: 10.1093/bib/bbab340] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/18/2021] [Accepted: 08/02/2021] [Indexed: 12/12/2022]  Open
42
Tang X, Luo J, Shen C, Lai Z. Multi-view Multichannel Attention Graph Convolutional Network for miRNA-disease association prediction. Brief Bioinform 2021;22:6271996. [PMID: 33963829 DOI: 10.1093/bib/bbab174] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 12/11/2022]  Open
43
Ma Y, Liu L, Chen Q, Ma Y. An Inductive Logistic Matrix Factorization Model for Predicting Drug-Metabolite Association With Vicus Regularization. Front Microbiol 2021;12:650366. [PMID: 33868209 PMCID: PMC8047063 DOI: 10.3389/fmicb.2021.650366] [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: 01/07/2021] [Accepted: 03/08/2021] [Indexed: 11/28/2022]  Open
44
Long Y, Wu M, Liu Y, Zheng J, Kwoh CK, Luo J, Li X. Graph contextualized attention network for predicting synthetic lethality in human cancers. Bioinformatics 2021;37:2432-2440. [PMID: 33609108 DOI: 10.1093/bioinformatics/btab110] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 02/09/2021] [Accepted: 02/16/2021] [Indexed: 11/13/2022]  Open
45
Long Y, Luo J. Association Mining to Identify Microbe Drug Interactions Based on Heterogeneous Network Embedding Representation. IEEE J Biomed Health Inform 2021;25:266-275. [PMID: 32750918 DOI: 10.1109/jbhi.2020.2998906] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
46
Shen C, Luo J, Ouyang W, Ding P, Chen X. IDDkin: Network-based influence deep diffusion model for enhancing prediction of kinase inhibitors. Bioinformatics 2020;36:5481-5491. [PMID: 33367525 DOI: 10.1093/bioinformatics/btaa1058] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/09/2020] [Accepted: 12/10/2020] [Indexed: 01/01/2023]  Open
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Lei X, Mudiyanselage TB, Zhang Y, Bian C, Lan W, Yu N, Pan Y. A comprehensive survey on computational methods of non-coding RNA and disease association prediction. Brief Bioinform 2020;22:6042241. [PMID: 33341893 DOI: 10.1093/bib/bbaa350] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/20/2020] [Accepted: 11/01/2020] [Indexed: 02/06/2023]  Open
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Ata SK, Wu M, Fang Y, Ou-Yang L, Kwoh CK, Li XL. Recent advances in network-based methods for disease gene prediction. Brief Bioinform 2020;22:6023077. [PMID: 33276376 DOI: 10.1093/bib/bbaa303] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/29/2020] [Accepted: 10/10/2020] [Indexed: 01/28/2023]  Open
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Wang L, Chen Y, Zhang N, Chen W, Zhang Y, Gao R. QIMCMDA: MiRNA-Disease Association Prediction by q-Kernel Information and Matrix Completion. Front Genet 2020;11:594796. [PMID: 33193744 PMCID: PMC7643770 DOI: 10.3389/fgene.2020.594796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 09/21/2020] [Indexed: 12/27/2022]  Open
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Yu Z, Huang F, Zhao X, Xiao W, Zhang W. Predicting drug-disease associations through layer attention graph convolutional network. Brief Bioinform 2020;22:5918381. [PMID: 33078832 DOI: 10.1093/bib/bbaa243] [Citation(s) in RCA: 183] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/16/2020] [Accepted: 08/31/2020] [Indexed: 12/23/2022]  Open
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