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For: Wang J, Chen Y, Zou Q. Inferring gene regulatory network from single-cell transcriptomes with graph autoencoder model. PLoS Genet 2023;19:e1010942. [PMID: 37703293 PMCID: PMC10519590 DOI: 10.1371/journal.pgen.1010942] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 09/25/2023] [Accepted: 08/29/2023] [Indexed: 09/15/2023]  Open
Number Cited by Other Article(s)
1
Doost PA, Moghadam SS, Khezri E, Basem A, Trik M. A new intrusion detection method using ensemble classification and feature selection. Sci Rep 2025;15:13642. [PMID: 40254667 PMCID: PMC12009975 DOI: 10.1038/s41598-025-98604-w] [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: 10/07/2024] [Accepted: 04/14/2025] [Indexed: 04/22/2025]  Open
2
Lam T, Quach HT, Hall L, Abou Chakra M, Wong AP. A multidisciplinary approach towards modeling of a virtual human lung. NPJ Syst Biol Appl 2025;11:38. [PMID: 40251169 PMCID: PMC12008392 DOI: 10.1038/s41540-025-00517-x] [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: 12/27/2024] [Accepted: 04/08/2025] [Indexed: 04/20/2025]  Open
3
Tan C, Yuan Z, Xu F, Xie D. Optimized Feature Selection and Deep Neural Networks to Improve Heart Disease Prediction. JOURNAL OF IMAGING INFORMATICS IN MEDICINE 2025:10.1007/s10278-025-01435-4. [PMID: 40240654 DOI: 10.1007/s10278-025-01435-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2024] [Revised: 01/23/2025] [Accepted: 01/30/2025] [Indexed: 04/18/2025]
4
Hsu CY, Buñay Guaman JS, Ved A, Yadav A, Ezhilarasan G, Rameshbabu A, Alkhayyat A, Aulakh D, Choudhury S, Sunori SK, Ranjbar F. Prediction of methane hydrate equilibrium in saline water solutions based on support vector machine and decision tree techniques. Sci Rep 2025;15:11723. [PMID: 40188155 PMCID: PMC11972364 DOI: 10.1038/s41598-025-95969-w] [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: 02/10/2025] [Accepted: 03/25/2025] [Indexed: 04/07/2025]  Open
5
Guo J, Liao J, Chen Y, Wen L, Cheng S. New Machine Learning Method for Medical Image and Microarray Data Analysis for Heart Disease Classification. JOURNAL OF IMAGING INFORMATICS IN MEDICINE 2025:10.1007/s10278-025-01492-9. [PMID: 40169470 DOI: 10.1007/s10278-025-01492-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/02/2025] [Revised: 03/09/2025] [Accepted: 03/19/2025] [Indexed: 04/03/2025]
6
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
7
Yu W, Lin Z, Lan M, Ou-Yang L. GCLink: a graph contrastive link prediction framework for gene regulatory network inference. Bioinformatics 2025;41:btaf074. [PMID: 39960893 PMCID: PMC11881698 DOI: 10.1093/bioinformatics/btaf074] [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: 07/23/2024] [Revised: 01/10/2025] [Accepted: 02/13/2025] [Indexed: 03/06/2025]  Open
8
Ru Y, Gruninger M, Dou Y. Robust self supervised symmetric nonnegative matrix factorization to the graph clustering. Sci Rep 2025;15:7350. [PMID: 40025198 PMCID: PMC11873141 DOI: 10.1038/s41598-025-92564-x] [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: 12/02/2024] [Accepted: 02/28/2025] [Indexed: 03/04/2025]  Open
9
Wang C, Liu ZP. Diffusion-based generation of gene regulatory networks from scRNA-seq data with DigNet. Genome Res 2025;35:340-354. [PMID: 39694856 PMCID: PMC11874984 DOI: 10.1101/gr.279551.124] [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: 05/06/2024] [Accepted: 12/10/2024] [Indexed: 12/20/2024]
10
Liu J, Ma L, Ju F, Zhao C, Yu L. SpaCcLink: exploring downstream signaling regulations with graph attention network for systematic inference of spatial cell-cell communication. BMC Biol 2025;23:44. [PMID: 39939849 PMCID: PMC11823213 DOI: 10.1186/s12915-025-02141-x] [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: 04/22/2024] [Accepted: 01/23/2025] [Indexed: 02/14/2025]  Open
11
Sun Y, Gao J. HGATLink: single-cell gene regulatory network inference via the fusion of heterogeneous graph attention networks and transformer. BMC Bioinformatics 2025;26:49. [PMID: 39934680 PMCID: PMC11817978 DOI: 10.1186/s12859-025-06071-x] [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: 08/15/2024] [Accepted: 01/29/2025] [Indexed: 02/13/2025]  Open
12
Ma L, Liu J, Sun W, Zhao C, Yu L. scMFG: a single-cell multi-omics integration method based on feature grouping. BMC Genomics 2025;26:132. [PMID: 39934664 PMCID: PMC11817349 DOI: 10.1186/s12864-025-11319-0] [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: 08/20/2024] [Accepted: 02/03/2025] [Indexed: 02/13/2025]  Open
13
Yang M, Xiao J, Zhong Q. Modeling of parameters affecting the removal of chromium using polysulfone/graphene oxide membrane via response surface methodology. ENVIRONMENTAL MONITORING AND ASSESSMENT 2025;197:180. [PMID: 39841272 DOI: 10.1007/s10661-025-13616-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Accepted: 01/03/2025] [Indexed: 01/23/2025]
14
Cao G, Chen D. Unveiling Long Non-coding RNA Networks from Single-Cell Omics Data Through Artificial Intelligence. Methods Mol Biol 2025;2883:257-279. [PMID: 39702712 DOI: 10.1007/978-1-0716-4290-0_11] [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: 12/21/2024]
15
Weng G, Martin P, Kim H, Won KJ. Integrating Prior Knowledge Using Transformer for Gene Regulatory Network Inference. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025;12:e2409990. [PMID: 39605181 PMCID: PMC11744656 DOI: 10.1002/advs.202409990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2024] [Revised: 10/23/2024] [Indexed: 11/29/2024]
16
Cui W, Long Q, Liu W, Fang C, Wang X, Wang P, Zhou Y. Hierarchical Graph Transformer With Contrastive Learning for Gene Regulatory Network Inference. IEEE J Biomed Health Inform 2025;29:690-699. [PMID: 39401117 DOI: 10.1109/jbhi.2024.3476490] [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]
17
Wu CY, Xu ZX, Li N, Qi DY, Hao ZH, Wu HY, Gao R, Jin YT. Accurately identifying positive and negative regulation of apoptosis using fusion features and machine learning methods. Comput Biol Chem 2024;113:108207. [PMID: 39265463 DOI: 10.1016/j.compbiolchem.2024.108207] [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: 06/28/2024] [Revised: 08/20/2024] [Accepted: 09/06/2024] [Indexed: 09/14/2024]
18
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
19
Sun Y, Pan Z, Wang Z, Wang H, Wei L, Cui F, Zou Q, Zhang Z. Single-cell transcriptome analysis reveals immune microenvironment changes and insights into the transition from DCIS to IDC with associated prognostic genes. J Transl Med 2024;22:894. [PMID: 39363164 PMCID: PMC11448450 DOI: 10.1186/s12967-024-05706-6] [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: 06/27/2024] [Accepted: 09/25/2024] [Indexed: 10/05/2024]  Open
20
K Lodi M, Chernikov A, Ghosh P. COFFEE: consensus single cell-type specific inference for gene regulatory networks. Brief Bioinform 2024;25:bbae457. [PMID: 39311699 PMCID: PMC11418232 DOI: 10.1093/bib/bbae457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/22/2024] [Accepted: 09/02/2024] [Indexed: 09/26/2024]  Open
21
Yuan L, Zhao L, Jiang Y, Shen Z, Zhang Q, Zhang M, Zheng CH, Huang DS. scMGATGRN: a multiview graph attention network-based method for inferring gene regulatory networks from single-cell transcriptomic data. Brief Bioinform 2024;25:bbae526. [PMID: 39417321 PMCID: PMC11484520 DOI: 10.1093/bib/bbae526] [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: 05/20/2024] [Revised: 07/09/2024] [Accepted: 10/03/2024] [Indexed: 10/19/2024]  Open
22
Johnston KG, Grieco SF, Nie Q, Theis FJ, Xu X. Small data methods in omics: the power of one. Nat Methods 2024;21:1597-1602. [PMID: 39174710 PMCID: PMC12067744 DOI: 10.1038/s41592-024-02390-8] [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: 08/19/2023] [Accepted: 07/24/2024] [Indexed: 08/24/2024]
23
Xiang L, Rao J, Yuan J, Xie T, Yan H. Single-Cell RNA-Sequencing: Opening New Horizons for Breast Cancer Research. Int J Mol Sci 2024;25:9482. [PMID: 39273429 PMCID: PMC11395021 DOI: 10.3390/ijms25179482] [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: 07/31/2024] [Revised: 08/25/2024] [Accepted: 08/29/2024] [Indexed: 09/15/2024]  Open
24
Cervantes-Pérez SA, Zogli P, Amini S, Thibivilliers S, Tennant S, Hossain MS, Xu H, Meyer I, Nooka A, Ma P, Yao Q, Naldrett MJ, Farmer A, Martin O, Bhattacharya S, Kläver J, Libault M. Single-cell transcriptome atlases of soybean root and mature nodule reveal new regulatory programs that control the nodulation process. PLANT COMMUNICATIONS 2024;5:100984. [PMID: 38845198 PMCID: PMC11369782 DOI: 10.1016/j.xplc.2024.100984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/21/2024] [Accepted: 06/03/2024] [Indexed: 07/14/2024]
25
Moeckel C, Mouratidis I, Chantzi N, Uzun Y, Georgakopoulos-Soares I. Advances in computational and experimental approaches for deciphering transcriptional regulatory networks: Understanding the roles of cis-regulatory elements is essential, and recent research utilizing MPRAs, STARR-seq, CRISPR-Cas9, and machine learning has yielded valuable insights. Bioessays 2024;46:e2300210. [PMID: 38715516 PMCID: PMC11444527 DOI: 10.1002/bies.202300210] [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: 10/31/2023] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
26
Si Y, Zou J, Gao Y, Chuai G, Liu Q, Chen L. Foundation models in molecular biology. BIOPHYSICS REPORTS 2024;10:135-151. [PMID: 39027316 PMCID: PMC11252241 DOI: 10.52601/bpr.2024.240006] [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: 01/23/2024] [Accepted: 03/04/2024] [Indexed: 07/20/2024]  Open
27
Gan Y, Yu J, Xu G, Yan C, Zou G. Inferring gene regulatory networks from single-cell transcriptomics based on graph embedding. Bioinformatics 2024;40:btae291. [PMID: 38810116 PMCID: PMC11142726 DOI: 10.1093/bioinformatics/btae291] [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: 01/12/2024] [Revised: 03/06/2024] [Accepted: 05/28/2024] [Indexed: 05/31/2024]  Open
28
Sun N, Shao H, Zhang Y, Ci B, Yao H, Bai B, Tan T. Establishing a 3D culture system for early organogenesis of monkey embryos ex vivo and single-cell transcriptome analysis of cultured embryos. STAR Protoc 2024;5:102835. [PMID: 38224493 PMCID: PMC10826423 DOI: 10.1016/j.xpro.2023.102835] [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: 10/09/2023] [Revised: 11/30/2023] [Accepted: 12/27/2023] [Indexed: 01/17/2024]  Open
29
Cui X, Lin Q, Chen M, Wang Y, Wang Y, Wang Y, Tao J, Yin H, Zhao T. Long-read sequencing unveils novel somatic variants and methylation patterns in the genetic information system of early lung cancer. Comput Biol Med 2024;171:108174. [PMID: 38442557 DOI: 10.1016/j.compbiomed.2024.108174] [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: 01/07/2024] [Revised: 01/25/2024] [Accepted: 02/18/2024] [Indexed: 03/07/2024]
30
Peng L, Yang Y, Yang C, Li Z, Cheong N. HRGCNLDA: Forecasting of lncRNA-disease association based on hierarchical refinement graph convolutional neural network. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2024;21:4814-4834. [PMID: 38872515 DOI: 10.3934/mbe.2024212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
31
Lodi MK, Chernikov A, Ghosh P. COFFEE: Consensus Single Cell-Type Specific Inference for Gene Regulatory Networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.05.574445. [PMID: 38260386 PMCID: PMC10802453 DOI: 10.1101/2024.01.05.574445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
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