• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (4833559)   Today's Articles (5707)
For: Papili Gao N, Ud-Dean SMM, Gandrillon O, Gunawan R. SINCERITIES: inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles. Bioinformatics 2017;34:258-266. [PMID: 28968704 PMCID: PMC5860204 DOI: 10.1093/bioinformatics/btx575] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 06/12/2017] [Accepted: 09/13/2017] [Indexed: 11/13/2022]  Open
Number Cited by Other Article(s)
1
da Silva JEH, Bernardino HS, de Oliveira IL, Camata JJ. A survey of the methodological process of modeling, inference, and evaluation of gene regulatory networks using scRNA-Seq data. Biosystems 2025;253:105464. [PMID: 40409400 DOI: 10.1016/j.biosystems.2025.105464] [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: 03/11/2024] [Revised: 03/20/2025] [Accepted: 04/17/2025] [Indexed: 05/25/2025]
2
Zhao W, Larschan E, Sandstede B, Singh R. Optimal transport reveals dynamic gene regulatory networks via gene velocity estimation. PLoS Comput Biol 2025;21:e1012476. [PMID: 40341271 DOI: 10.1371/journal.pcbi.1012476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Accepted: 04/10/2025] [Indexed: 05/10/2025]  Open
3
Pan Q, Ding L, Hladyshau S, Yao X, Zhou J, Yan L, Dhungana Y, Shi H, Qian C, Dong X, Burdyshaw C, Veloso JP, Khatamian A, Xie Z, Risch I, Yang X, Yang J, Huang X, Fang J, Jain A, Jain A, Rusch M, Brewer M, Peng J, Yan KK, Chi H, Yu J. scMINER: a mutual information-based framework for clustering and hidden driver inference from single-cell transcriptomics data. Nat Commun 2025;16:4305. [PMID: 40341143 PMCID: PMC12062461 DOI: 10.1038/s41467-025-59620-6] [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: 01/17/2025] [Accepted: 04/28/2025] [Indexed: 05/10/2025]  Open
4
Wang JC, Chen YJ, Zou Q. GRACE: Unveiling Gene Regulatory Networks With Causal Mechanistic Graph Neural Networks in Single-Cell RNA-Sequencing Data. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2025;36:9005-9017. [PMID: 38896510 DOI: 10.1109/tnnls.2024.3412753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
5
Li H, Zhang Z, Squires M, Chen X, Zhang X. scMultiSim: simulation of single-cell multi-omics and spatial data guided by gene regulatory networks and cell-cell interactions. Nat Methods 2025;22:982-993. [PMID: 40247122 DOI: 10.1038/s41592-025-02651-0] [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: 08/27/2023] [Accepted: 03/07/2025] [Indexed: 04/19/2025]
6
Su G, Wang H, Zhang Y, Wilkins MR, Canete PF, Yu D, Yang Y, Zhang W. Inferring gene regulatory networks by hypergraph generative model. CELL REPORTS METHODS 2025;5:101026. [PMID: 40220759 DOI: 10.1016/j.crmeth.2025.101026] [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: 06/23/2024] [Revised: 01/16/2025] [Accepted: 03/20/2025] [Indexed: 04/14/2025]
7
Abe H, Lin P, Zhou D, Ruderfer DM, Gamazon ER. Mapping dynamic regulation of gene expression using single-cell transcriptomics and application to complex disease genetics. HGG ADVANCES 2025;6:100397. [PMID: 39741416 PMCID: PMC11830375 DOI: 10.1016/j.xhgg.2024.100397] [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: 04/20/2024] [Revised: 12/24/2024] [Accepted: 12/24/2024] [Indexed: 01/03/2025]  Open
8
Chen L, Dautle M, Gao R, Zhang S, Chen Y. Inferring gene regulatory networks from time-series scRNA-seq data via GRANGER causal recurrent autoencoders. Brief Bioinform 2025;26:bbaf089. [PMID: 40062616 PMCID: PMC11891664 DOI: 10.1093/bib/bbaf089] [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: 10/31/2024] [Revised: 01/26/2025] [Accepted: 02/18/2025] [Indexed: 05/13/2025]  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
Yuan Q, Duren Z. Inferring gene regulatory networks from single-cell multiome data using atlas-scale external data. Nat Biotechnol 2025;43:247-257. [PMID: 38609714 PMCID: PMC11825371 DOI: 10.1038/s41587-024-02182-7] [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: 08/04/2023] [Accepted: 02/26/2024] [Indexed: 04/14/2024]
11
Jung S. Advances in modeling cellular state dynamics: integrating omics data and predictive techniques. Anim Cells Syst (Seoul) 2025;29:72-83. [PMID: 39807350 PMCID: PMC11727055 DOI: 10.1080/19768354.2024.2449518] [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: 10/15/2024] [Revised: 12/19/2024] [Accepted: 12/29/2024] [Indexed: 01/16/2025]  Open
12
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]
13
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]
14
Peng D, Cahan P. OneSC: a computational platform for recapitulating cell state transitions. Bioinformatics 2024;40:btae703. [PMID: 39570626 PMCID: PMC11630913 DOI: 10.1093/bioinformatics/btae703] [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: 05/31/2024] [Revised: 11/13/2024] [Accepted: 11/19/2024] [Indexed: 11/22/2024]  Open
15
Li R, Wu J, Li G, Liu J, Liu J, Xuan J, Deng Z. SIGRN: Inferring Gene Regulatory Network with Soft Introspective Variational Autoencoders. Int J Mol Sci 2024;25:12741. [PMID: 39684451 DOI: 10.3390/ijms252312741] [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: 10/04/2024] [Revised: 11/21/2024] [Accepted: 11/25/2024] [Indexed: 12/18/2024]  Open
16
Huang W, Hu Y, Wang L, Wu G, Zhang C, Shi Q. Spatially aligned graph transfer learning for characterizing spatial regulatory heterogeneity. Brief Bioinform 2024;26:bbaf021. [PMID: 39841593 PMCID: PMC11752617 DOI: 10.1093/bib/bbaf021] [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: 10/22/2024] [Revised: 12/26/2024] [Accepted: 01/08/2025] [Indexed: 01/24/2025]  Open
17
Karamveer, Uzun Y. Approaches for Benchmarking Single-Cell Gene Regulatory Network Methods. Bioinform Biol Insights 2024;18:11779322241287120. [PMID: 39502448 PMCID: PMC11536393 DOI: 10.1177/11779322241287120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 09/10/2024] [Indexed: 11/08/2024]  Open
18
Wang Y, Zheng P, Cheng YC, Wang Z, Aravkin A. WENDY: Covariance dynamics based gene regulatory network inference. Math Biosci 2024;377:109284. [PMID: 39168402 DOI: 10.1016/j.mbs.2024.109284] [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: 03/25/2024] [Revised: 06/25/2024] [Accepted: 08/16/2024] [Indexed: 08/23/2024]
19
Dong J, Li J, Wang F. Deep Learning in Gene Regulatory Network Inference: A Survey. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024;21:2089-2101. [PMID: 39137088 DOI: 10.1109/tcbb.2024.3442536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
20
Graham J, Zhang Y, He L, Gonzalez-Fernandez T. CRISPR-GEM: A Novel Machine Learning Model for CRISPR Genetic Target Discovery and Evaluation. ACS Synth Biol 2024;13:3413-3429. [PMID: 39375864 PMCID: PMC11494708 DOI: 10.1021/acssynbio.4c00473] [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: 07/09/2024] [Revised: 09/17/2024] [Accepted: 09/27/2024] [Indexed: 10/09/2024]
21
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
22
Loers JU, Vermeirssen V. A single-cell multimodal view on gene regulatory network inference from transcriptomics and chromatin accessibility data. Brief Bioinform 2024;25:bbae382. [PMID: 39207727 PMCID: PMC11359808 DOI: 10.1093/bib/bbae382] [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: 04/05/2024] [Revised: 06/27/2024] [Accepted: 07/23/2024] [Indexed: 09/04/2024]  Open
23
Chang Z, Xu Y, Dong X, Gao Y, Wang C. Single-cell and spatial multiomic inference of gene regulatory networks using SCRIPro. Bioinformatics 2024;40:btae466. [PMID: 39024032 PMCID: PMC11288411 DOI: 10.1093/bioinformatics/btae466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 06/05/2024] [Accepted: 07/17/2024] [Indexed: 07/20/2024]  Open
24
Graham JP, Zhang Y, He L, Gonzalez-Fernandez T. CRISPR-GEM: A Novel Machine Learning Model for CRISPR Genetic Target Discovery and Evaluation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.01.601587. [PMID: 39005295 PMCID: PMC11244939 DOI: 10.1101/2024.07.01.601587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
25
Zhou X, Pan J, Chen L, Zhang S, Chen Y. DeepIMAGER: Deeply Analyzing Gene Regulatory Networks from scRNA-seq Data. Biomolecules 2024;14:766. [PMID: 39062480 PMCID: PMC11274664 DOI: 10.3390/biom14070766] [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: 05/11/2024] [Revised: 06/22/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024]  Open
26
Peng D, Cahan P. OneSC: A computational platform for recapitulating cell state transitions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596831. [PMID: 38895453 PMCID: PMC11185539 DOI: 10.1101/2024.05.31.596831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
27
Wan R, Zhang Y, Peng Y, Tian F, Gao G, Tang F, Jia J, Ge H. Unveiling gene regulatory networks during cellular state transitions without linkage across time points. Sci Rep 2024;14:12355. [PMID: 38811747 PMCID: PMC11137113 DOI: 10.1038/s41598-024-62850-1] [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: 01/24/2024] [Accepted: 05/22/2024] [Indexed: 05/31/2024]  Open
28
Lei Y, Huang XT, Guo X, Hang Katie Chan K, Gao L. DeepGRNCS: deep learning-based framework for jointly inferring gene regulatory networks across cell subpopulations. Brief Bioinform 2024;25:bbae334. [PMID: 38980373 PMCID: PMC11232306 DOI: 10.1093/bib/bbae334] [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: 03/11/2024] [Revised: 06/03/2024] [Accepted: 07/01/2024] [Indexed: 07/10/2024]  Open
29
Singh R, Wu AP, Mudide A, Berger B. Causal gene regulatory analysis with RNA velocity reveals an interplay between slow and fast transcription factors. Cell Syst 2024;15:462-474.e5. [PMID: 38754366 DOI: 10.1016/j.cels.2024.04.005] [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: 04/14/2023] [Revised: 08/25/2023] [Accepted: 04/18/2024] [Indexed: 05/18/2024]
30
Zinati Y, Takiddeen A, Emad A. GRouNdGAN: GRN-guided simulation of single-cell RNA-seq data using causal generative adversarial networks. Nat Commun 2024;15:4055. [PMID: 38744843 PMCID: PMC11525796 DOI: 10.1038/s41467-024-48516-6] [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: 07/31/2023] [Accepted: 05/01/2024] [Indexed: 05/16/2024]  Open
31
Raharinirina NA, Sunkara V, von Kleist M, Fackeldey K, Weber M. Multi-Input data ASsembly for joint Analysis (MIASA): A framework for the joint analysis of disjoint sets of variables. PLoS One 2024;19:e0302425. [PMID: 38728301 PMCID: PMC11086896 DOI: 10.1371/journal.pone.0302425] [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: 11/01/2023] [Accepted: 04/04/2024] [Indexed: 05/12/2024]  Open
32
Lee J, Kim N, Cho KH. Decoding the principle of cell-fate determination for its reverse control. NPJ Syst Biol Appl 2024;10:47. [PMID: 38710700 PMCID: PMC11074314 DOI: 10.1038/s41540-024-00372-2] [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: 12/11/2023] [Accepted: 04/16/2024] [Indexed: 05/08/2024]  Open
33
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
34
Stock M, Popp N, Fiorentino J, Scialdone A. Topological benchmarking of algorithms to infer gene regulatory networks from single-cell RNA-seq data. Bioinformatics 2024;40:btae267. [PMID: 38627250 PMCID: PMC11096270 DOI: 10.1093/bioinformatics/btae267] [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: 05/16/2023] [Revised: 02/28/2024] [Accepted: 04/16/2024] [Indexed: 05/18/2024]  Open
35
Fiorentino J, Armaos A, Colantoni A, Tartaglia G. Prediction of protein-RNA interactions from single-cell transcriptomic data. Nucleic Acids Res 2024;52:e31. [PMID: 38364867 PMCID: PMC11014251 DOI: 10.1093/nar/gkae076] [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: 07/17/2023] [Revised: 01/12/2024] [Accepted: 01/26/2024] [Indexed: 02/18/2024]  Open
36
Pan X, Zhang X. Studying temporal dynamics of single cells: expression, lineage and regulatory networks. Biophys Rev 2024;16:57-67. [PMID: 38495440 PMCID: PMC10937865 DOI: 10.1007/s12551-023-01090-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/27/2023] [Indexed: 03/19/2024]  Open
37
Li S, Liu Y, Shen LC, Yan H, Song J, Yu DJ. GMFGRN: a matrix factorization and graph neural network approach for gene regulatory network inference. Brief Bioinform 2024;25:bbad529. [PMID: 38261340 PMCID: PMC10805180 DOI: 10.1093/bib/bbad529] [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: 09/29/2023] [Revised: 12/08/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024]  Open
38
Louarn M, Collet G, Barré È, Fest T, Dameron O, Siegel A, Chatonnet F. Regulus infers signed regulatory relations from few samples' information using discretization and likelihood constraints. PLoS Comput Biol 2024;20:e1011816. [PMID: 38252636 PMCID: PMC10833539 DOI: 10.1371/journal.pcbi.1011816] [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: 12/16/2022] [Revised: 02/01/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024]  Open
39
Xin J, Wang M, Qu L, Chen Q, Wang W, Wang Z. BIC-LP: A Hybrid Higher-Order Dynamic Bayesian Network Score Function for Gene Regulatory Network Reconstruction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024;21:188-199. [PMID: 38127613 DOI: 10.1109/tcbb.2023.3345317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
40
Kim H, Choi H, Lee D, Kim J. A review on gene regulatory network reconstruction algorithms based on single cell RNA sequencing. Genes Genomics 2024;46:1-11. [PMID: 38032470 DOI: 10.1007/s13258-023-01473-8] [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: 09/23/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023]
41
Abe H, Lin P, Zhou D, Ruderfer DM, Gamazon ER. Mapping the landscape of lineage-specific dynamic regulation of gene expression using single-cell transcriptomics and application to genetics of complex disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.24.23297476. [PMID: 37961453 PMCID: PMC10635195 DOI: 10.1101/2023.10.24.23297476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
42
Cheng J, Cheng M, Lusis AJ, Yang X. Gene Regulatory Networks in Coronary Artery Disease. Curr Atheroscler Rep 2023;25:1013-1023. [PMID: 38008808 PMCID: PMC11466510 DOI: 10.1007/s11883-023-01170-7] [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] [Accepted: 11/09/2023] [Indexed: 11/28/2023]
43
Badia-I-Mompel P, Wessels L, Müller-Dott S, Trimbour R, Ramirez Flores RO, Argelaguet R, Saez-Rodriguez J. Gene regulatory network inference in the era of single-cell multi-omics. Nat Rev Genet 2023;24:739-754. [PMID: 37365273 DOI: 10.1038/s41576-023-00618-5] [Citation(s) in RCA: 124] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2023] [Indexed: 06/28/2023]
44
Velten B, Stegle O. Principles and challenges of modeling temporal and spatial omics data. Nat Methods 2023;20:1462-1474. [PMID: 37710019 DOI: 10.1038/s41592-023-01992-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/31/2023] [Indexed: 09/16/2023]
45
Shojaee A, Huang SSC. Robust discovery of gene regulatory networks from single-cell gene expression data by Causal Inference Using Composition of Transactions. Brief Bioinform 2023;24:bbad370. [PMID: 37897702 PMCID: PMC10612495 DOI: 10.1093/bib/bbad370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 09/06/2023] [Accepted: 09/29/2023] [Indexed: 10/30/2023]  Open
46
Mao G, Pang Z, Zuo K, Wang Q, Pei X, Chen X, Liu J. Predicting gene regulatory links from single-cell RNA-seq data using graph neural networks. Brief Bioinform 2023;24:bbad414. [PMID: 37985457 PMCID: PMC10661972 DOI: 10.1093/bib/bbad414] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/22/2023]  Open
47
Zeng Y, He Y, Zheng R, Li M. Inferring single-cell gene regulatory network by non-redundant mutual information. Brief Bioinform 2023;24:bbad326. [PMID: 37715282 DOI: 10.1093/bib/bbad326] [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: 04/19/2023] [Revised: 07/12/2023] [Accepted: 08/08/2023] [Indexed: 09/17/2023]  Open
48
Li H, Zhang Z, Squires M, Chen X, Zhang X. scMultiSim: simulation of single cell multi-omics and spatial data guided by gene regulatory networks and cell-cell interactions. RESEARCH SQUARE 2023:rs.3.rs-3301625. [PMID: 37790516 PMCID: PMC10543280 DOI: 10.21203/rs.3.rs-3301625/v1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
49
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] [Abstract] [MESH Headings] [Grants] [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
50
Dautle M, Zhang S, Chen Y. scTIGER: A Deep-Learning Method for Inferring Gene Regulatory Networks from Case versus Control scRNA-seq Datasets. Int J Mol Sci 2023;24:13339. [PMID: 37686146 PMCID: PMC10488287 DOI: 10.3390/ijms241713339] [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: 07/02/2023] [Revised: 08/06/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023]  Open
PrevPage 1 of 3 123Next
© 2004-2025 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA