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For: Ruohan W, Yuwei Z, Mengbo W, Xikang F, Jianping W, Shuai Cheng L. Resolving single-cell copy number profiling for large datasets. Brief Bioinform 2022;23:6633647. [PMID: 35801503 DOI: 10.1093/bib/bbac264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/29/2022] [Accepted: 06/06/2022] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
1
Wang J, Ye F, Chai H, Jiang Y, Wang T, Ran X, Xia Q, Xu Z, Fu Y, Zhang G, Wu H, Guo G, Guo H, Ruan Y, Wang Y, Xing D, Xu X, Zhang Z. Advances and applications in single-cell and spatial genomics. SCIENCE CHINA. LIFE SCIENCES 2025;68:1226-1282. [PMID: 39792333 DOI: 10.1007/s11427-024-2770-x] [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: 08/20/2024] [Accepted: 10/10/2024] [Indexed: 01/12/2025]
2
Song M, Ma S, Wang G, Wang Y, Yang Z, Xie B, Guo T, Huang X, Zhang L. Benchmarking copy number aberrations inference tools using single-cell multi-omics datasets. Brief Bioinform 2025;26:bbaf076. [PMID: 40037644 PMCID: PMC11879432 DOI: 10.1093/bib/bbaf076] [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: 10/21/2024] [Revised: 12/21/2024] [Accepted: 02/12/2025] [Indexed: 03/06/2025]  Open
3
Kuipers J, Tuncel MA, Ferreira PF, Jahn K, Beerenwinkel N. Single-cell copy number calling and event history reconstruction. Bioinformatics 2025;41:btaf072. [PMID: 39946094 PMCID: PMC11897432 DOI: 10.1093/bioinformatics/btaf072] [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: 06/18/2024] [Revised: 01/06/2025] [Accepted: 02/11/2025] [Indexed: 03/14/2025]  Open
4
Weiner S, Li B, Nabavi S. Improved allele-specific single-cell copy number estimation in low-coverage DNA-sequencing. Bioinformatics 2024;40:btae506. [PMID: 39133157 PMCID: PMC11346770 DOI: 10.1093/bioinformatics/btae506] [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: 04/03/2024] [Revised: 07/12/2024] [Accepted: 08/09/2024] [Indexed: 08/13/2024]  Open
5
Zhang L, Zhou XM, Mallory X. SCCNAInfer: a robust and accurate tool to infer the absolute copy number on scDNA-seq data. BIOINFORMATICS (OXFORD, ENGLAND) 2024;40:btae454. [PMID: 39067018 DOI: 10.1093/bioinformatics/btae454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 06/13/2024] [Accepted: 07/26/2024] [Indexed: 07/30/2024]
6
Liu F, Shi F, Du F, Cao X, Yu Z. CoT: a transformer-based method for inferring tumor clonal copy number substructure from scDNA-seq data. Brief Bioinform 2024;25:bbae187. [PMID: 38670159 PMCID: PMC11052634 DOI: 10.1093/bib/bbae187] [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: 12/06/2023] [Revised: 03/08/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024]  Open
7
Liu F, Shi F, Yu Z. Inferring single-cell copy number profiles through cross-cell segmentation of read counts. BMC Genomics 2024;25:25. [PMID: 38166601 PMCID: PMC10762977 DOI: 10.1186/s12864-023-09901-5] [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: 05/17/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024]  Open
8
Zhang L, Bass HW, Irianto J, Mallory X. Integrating SNVs and CNAs on a phylogenetic tree from single-cell DNA sequencing data. Genome Res 2023;33:2002-2017. [PMID: 37993137 PMCID: PMC10760445 DOI: 10.1101/gr.277249.122] [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: 08/26/2022] [Accepted: 10/25/2023] [Indexed: 11/24/2023]
9
Liu Y, Wu G. The utilization of single-cell sequencing technology in investigating the immune microenvironment of ccRCC. Front Immunol 2023;14:1276658. [PMID: 38090562 PMCID: PMC10715415 DOI: 10.3389/fimmu.2023.1276658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/07/2023] [Indexed: 12/18/2023]  Open
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