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For: Todorov H, Cannoodt R, Saelens W, Saeys Y. Network Inference from Single-Cell Transcriptomic Data. Methods Mol Biol 2019;1883:235-249. [PMID: 30547403 DOI: 10.1007/978-1-4939-8882-2_10] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Number Cited by Other Article(s)
1
Shin D, Cho KH. Critical transition and reversion of tumorigenesis. Exp Mol Med 2023;55:692-705. [PMID: 37009794 PMCID: PMC10167317 DOI: 10.1038/s12276-023-00969-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 04/04/2023]  Open
2
Subramanian A, Zakeri P, Mousa M, Alnaqbi H, Alshamsi FY, Bettoni L, Damiani E, Alsafar H, Saeys Y, Carmeliet P. Angiogenesis goes computational - The future way forward to discover new angiogenic targets? Comput Struct Biotechnol J 2022;20:5235-5255. [PMID: 36187917 PMCID: PMC9508490 DOI: 10.1016/j.csbj.2022.09.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/09/2022] [Accepted: 09/09/2022] [Indexed: 11/26/2022]  Open
3
Ding J, Sharon N, Bar-Joseph Z. Temporal modelling using single-cell transcriptomics. Nat Rev Genet 2022;23:355-368. [PMID: 35102309 DOI: 10.1038/s41576-021-00444-7] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2021] [Indexed: 12/16/2022]
4
Peterson JC, Kelder TP, Goumans MJTH, Jongbloed MRM, DeRuiter MC. The Role of Cell Tracing and Fate Mapping Experiments in Cardiac Outflow Tract Development, New Opportunities through Emerging Technologies. J Cardiovasc Dev Dis 2021;8:47. [PMID: 33925811 PMCID: PMC8146276 DOI: 10.3390/jcdd8050047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/18/2021] [Accepted: 04/22/2021] [Indexed: 02/07/2023]  Open
5
Kumar N, Mishra B, Athar M, Mukhtar S. Inference of Gene Regulatory Network from Single-Cell Transcriptomic Data Using pySCENIC. Methods Mol Biol 2021;2328:171-182. [PMID: 34251625 DOI: 10.1007/978-1-0716-1534-8_10] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
6
Osorio D, Zhong Y, Li G, Huang JZ, Cai JJ. scTenifoldNet: A Machine Learning Workflow for Constructing and Comparing Transcriptome-wide Gene Regulatory Networks from Single-Cell Data. PATTERNS (NEW YORK, N.Y.) 2020;1:100139. [PMID: 33336197 PMCID: PMC7733883 DOI: 10.1016/j.patter.2020.100139] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/29/2020] [Accepted: 10/12/2020] [Indexed: 02/02/2023]
7
Improved detection of tumor suppressor events in single-cell RNA-Seq data. NPJ Genom Med 2020;5:43. [PMID: 33083012 PMCID: PMC7541488 DOI: 10.1038/s41525-020-00151-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/21/2020] [Indexed: 12/17/2022]  Open
8
Charrout M, Reinders MJT, Mahfouz A. Untangling biological factors influencing trajectory inference from single cell data. NAR Genom Bioinform 2020;2:lqaa053. [PMID: 33575604 PMCID: PMC7671373 DOI: 10.1093/nargab/lqaa053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/17/2020] [Accepted: 07/07/2020] [Indexed: 12/14/2022]  Open
9
Zheng X, Huang Y, Zou X. scPADGRN: A preconditioned ADMM approach for reconstructing dynamic gene regulatory network using single-cell RNA sequencing data. PLoS Comput Biol 2020;16:e1007471. [PMID: 32716923 PMCID: PMC7410337 DOI: 10.1371/journal.pcbi.1007471] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 08/06/2020] [Accepted: 05/28/2020] [Indexed: 12/23/2022]  Open
10
Hie B, Peters J, Nyquist SK, Shalek AK, Berger B, Bryson BD. Computational Methods for Single-Cell RNA Sequencing. Annu Rev Biomed Data Sci 2020. [DOI: 10.1146/annurev-biodatasci-012220-100601] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
11
Efremova M, Vento-Tormo R, Park JE, Teichmann SA, James KR. Immunology in the Era of Single-Cell Technologies. Annu Rev Immunol 2020;38:727-757. [PMID: 32075461 DOI: 10.1146/annurev-immunol-090419-020340] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
12
Brückner DB, Fink A, Rädler JO, Broedersz CP. Disentangling the behavioural variability of confined cell migration. J R Soc Interface 2020;17:20190689. [PMCID: PMC7061702 DOI: 10.1098/rsif.2019.0689] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/17/2020] [Indexed: 12/30/2024]  Open
13
Chew G, Petretto E. Transcriptional Networks of Microglia in Alzheimer's Disease and Insights into Pathogenesis. Genes (Basel) 2019;10:E798. [PMID: 31614849 PMCID: PMC6826883 DOI: 10.3390/genes10100798] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/30/2019] [Accepted: 10/11/2019] [Indexed: 02/07/2023]  Open
14
Blencowe M, Arneson D, Ding J, Chen YW, Saleem Z, Yang X. Network modeling of single-cell omics data: challenges, opportunities, and progresses. Emerg Top Life Sci 2019;3:379-398. [PMID: 32270049 PMCID: PMC7141415 DOI: 10.1042/etls20180176] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/07/2019] [Accepted: 06/24/2019] [Indexed: 01/07/2023]
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