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For: Dai X, Xu F, Wang S, Mundra PA, Zheng J. PIKE-R2P: Protein-protein interaction network-based knowledge embedding with graph neural network for single-cell RNA to protein prediction. BMC Bioinformatics 2021;22:139. [PMID: 34078261 PMCID: PMC8170782 DOI: 10.1186/s12859-021-04022-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 02/11/2021] [Indexed: 12/05/2022]  Open
Number Cited by Other Article(s)
1
Sheinin R, Sharan R, Madi A. scNET: learning context-specific gene and cell embeddings by integrating single-cell gene expression data with protein-protein interactions. Nat Methods 2025;22:708-716. [PMID: 40097811 PMCID: PMC11978505 DOI: 10.1038/s41592-025-02627-0] [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: 04/25/2024] [Accepted: 02/07/2025] [Indexed: 03/19/2025]
2
Li S, Hua H, Chen S. Graph neural networks for single-cell omics data: a review of approaches and applications. Brief Bioinform 2025;26:bbaf109. [PMID: 40091193 PMCID: PMC11911123 DOI: 10.1093/bib/bbaf109] [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: 12/04/2024] [Revised: 02/09/2025] [Accepted: 02/25/2025] [Indexed: 03/19/2025]  Open
3
Zhu P, Li J, Wang Y, Xiao B, Zhao S, Hu Q. Collaborative Decision-Reinforced Self-Supervision for Attributed Graph Clustering. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2023;34:10851-10863. [PMID: 35584075 DOI: 10.1109/tnnls.2022.3171583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
4
Lee M. Recent Advances in Deep Learning for Protein-Protein Interaction Analysis: A Comprehensive Review. Molecules 2023;28:5169. [PMID: 37446831 DOI: 10.3390/molecules28135169] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/30/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023]  Open
5
A graph neural network model for deciphering the biological mechanisms of plant electrical signal classification. Appl Soft Comput 2023. [DOI: 10.1016/j.asoc.2023.110153] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
6
Panditrao G, Bhowmick R, Meena C, Sarkar RR. Emerging landscape of molecular interaction networks: Opportunities, challenges and prospects. J Biosci 2022. [PMID: 36210749 PMCID: PMC9018971 DOI: 10.1007/s12038-022-00253-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
7
Xu W, He H, Guo Z, Li W. Evaluation of machine learning models on protein level inference from prioritized RNA features. Brief Bioinform 2022;23:6555405. [PMID: 35352096 DOI: 10.1093/bib/bbac091] [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: 11/01/2021] [Revised: 02/16/2022] [Accepted: 02/23/2022] [Indexed: 11/12/2022]  Open
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