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For: Kim H, Lee J, Kang K, Yoon S. MarkerCount: A stable, count-based cell type identifier for single-cell RNA-seq experiments. Comput Struct Biotechnol J 2022;20:3120-3132. [PMID: 35782735 PMCID: PMC9233224 DOI: 10.1016/j.csbj.2022.06.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/05/2022] [Accepted: 06/05/2022] [Indexed: 11/21/2022]  Open
Number Cited by Other Article(s)
1
Traversa D, Chiara M. Mapping Cell Identity from scRNA-seq: A primer on computational methods. Comput Struct Biotechnol J 2025;27:1559-1569. [PMID: 40270709 PMCID: PMC12017876 DOI: 10.1016/j.csbj.2025.03.051] [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: 11/15/2024] [Revised: 03/29/2025] [Accepted: 03/31/2025] [Indexed: 04/25/2025]  Open
2
Huang YA, Li YC, You ZH, Hu L, Hu PW, Wang L, Peng Y, Huang ZA. Consensus representation of multiple cell-cell graphs from gene signaling pathways for cell type annotation. BMC Biol 2025;23:23. [PMID: 39849579 PMCID: PMC11756145 DOI: 10.1186/s12915-025-02128-8] [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: 08/07/2024] [Accepted: 01/13/2025] [Indexed: 01/25/2025]  Open
3
Mondal S, Becskei A. Gene choice in cancer cells is exclusive in ion transport but concurrent in DNA replication. Comput Struct Biotechnol J 2024;23:2534-2547. [PMID: 38974885 PMCID: PMC11226983 DOI: 10.1016/j.csbj.2024.06.004] [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: 02/29/2024] [Revised: 06/04/2024] [Accepted: 06/04/2024] [Indexed: 07/09/2024]  Open
4
Chen H, Lu Y, Rao Y. A self-training interpretable cell type annotation framework using specific marker gene. Bioinformatics 2024;40:btae569. [PMID: 39312689 PMCID: PMC11488977 DOI: 10.1093/bioinformatics/btae569] [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: 04/11/2024] [Revised: 09/03/2024] [Accepted: 09/19/2024] [Indexed: 09/25/2024]  Open
5
Cao X, Huang YA, You ZH, Shang X, Hu L, Hu PW, Huang ZA. scPriorGraph: constructing biosemantic cell-cell graphs with prior gene set selection for cell type identification from scRNA-seq data. Genome Biol 2024;25:207. [PMID: 39103856 DOI: 10.1186/s13059-024-03357-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: 10/26/2023] [Accepted: 07/29/2024] [Indexed: 08/07/2024]  Open
6
Martini L, Amprimo G, Di Carlo S, Olmo G, Ferraris C, Savino A, Bardini R. Neuronal Spike Shapes (NSS): A straightforward approach to investigate heterogeneity in neuronal excitability states. Comput Biol Med 2024;168:107783. [PMID: 38056213 DOI: 10.1016/j.compbiomed.2023.107783] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/23/2023] [Accepted: 11/28/2023] [Indexed: 12/08/2023]
7
Kim H, Kim HK, Hong D, Kim M, Jang S, Yang CS, Yoon S. Identification of ulcerative colitis-specific immune cell signatures from public single-cell RNA-seq data. Genes Genomics 2023;45:957-967. [PMID: 37133723 DOI: 10.1007/s13258-023-01390-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/13/2023] [Indexed: 05/04/2023]
8
Cheng Y, Fan X, Zhang J, Li Y. A scalable sparse neural network framework for rare cell type annotation of single-cell transcriptome data. Commun Biol 2023;6:545. [PMID: 37210444 DOI: 10.1038/s42003-023-04928-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 05/11/2023] [Indexed: 05/22/2023]  Open
9
Lee J, Kim M, Kang K, Yang CS, Yoon S. Hierarchical cell-type identifier accurately distinguishes immune-cell subtypes enabling precise profiling of tissue microenvironment with single-cell RNA-sequencing. Brief Bioinform 2023;24:bbad006. [PMID: 36681937 PMCID: PMC10025442 DOI: 10.1093/bib/bbad006] [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: 10/07/2022] [Revised: 12/22/2022] [Accepted: 01/02/2023] [Indexed: 01/23/2023]  Open
10
Lee J, Kim H, Kim M, Yoon S, Lee S. Role of lymphoid lineage cells aberrantly expressing alarmins S100A8/A9 in determining the severity of COVID-19. Genes Genomics 2023;45:337-346. [PMID: 36107397 PMCID: PMC9476394 DOI: 10.1007/s13258-022-01285-2] [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: 04/27/2022] [Accepted: 07/08/2022] [Indexed: 01/09/2023]
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