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For: Bouland GA, Mahfouz A, Reinders MJT. Differential analysis of binarized single-cell RNA sequencing data captures biological variation. NAR Genom Bioinform 2021;3:lqab118. [PMID: 34988441 PMCID: PMC8693570 DOI: 10.1093/nargab/lqab118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 11/04/2021] [Accepted: 12/03/2021] [Indexed: 12/11/2022]  Open
Number Cited by Other Article(s)
1
Jansma A, Yao Y, Wolfe J, Del Debbio L, Beentjes SV, Ponting CP, Khamseh A. High order expression dependencies finely resolve cryptic states and subtypes in single cell data. Mol Syst Biol 2025;21:173-207. [PMID: 39748128 PMCID: PMC11790937 DOI: 10.1038/s44320-024-00074-1] [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: 01/09/2024] [Revised: 10/24/2024] [Accepted: 10/31/2024] [Indexed: 01/04/2025]  Open
2
Sharifi MN, Shi Y, Chrostek MR, Callahan SC, Shang T, Berg TJ, Helzer KT, Bootsma ML, Sjöström M, Josefsson A, Feng FY, Huffman LB, Schulte C, Blitzer GC, Sodji QH, Morris ZS, Ma VT, Meimetis L, Kosoff D, Taylor AK, LeBeau AM, Lang JM, Zhao SG. Clinical cell-surface targets in metastatic and primary solid cancers. JCI Insight 2024;9:e183674. [PMID: 39315546 PMCID: PMC11457844 DOI: 10.1172/jci.insight.183674] [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] [Indexed: 09/25/2024]  Open
3
Yu D, Li M, Linghu G, Hu Y, Hajdarovic KH, Wang A, Singh R, Webb AE. CellBiAge: Improved single-cell age classification using data binarization. Cell Rep 2023;42:113500. [PMID: 38032797 PMCID: PMC10791072 DOI: 10.1016/j.celrep.2023.113500] [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: 05/04/2023] [Revised: 10/20/2023] [Accepted: 11/13/2023] [Indexed: 12/02/2023]  Open
4
Gilis J, Perin L, Malfait M, Van den Berge K, Takele Assefa A, Verbist B, Risso D, Clement L. Differential detection workflows for multi-sample single-cell RNA-seq data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.17.572043. [PMID: 38187695 PMCID: PMC10769270 DOI: 10.1101/2023.12.17.572043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
5
Bouland GA, Mahfouz A, Reinders MJT. Consequences and opportunities arising due to sparser single-cell RNA-seq datasets. Genome Biol 2023;24:86. [PMID: 37085823 PMCID: PMC10120229 DOI: 10.1186/s13059-023-02933-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 04/10/2023] [Indexed: 04/23/2023]  Open
6
Doyle JJ. Cell types as species: Exploring a metaphor. FRONTIERS IN PLANT SCIENCE 2022;13:868565. [PMID: 36072310 PMCID: PMC9444152 DOI: 10.3389/fpls.2022.868565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 07/29/2022] [Indexed: 06/05/2023]
7
Gagnon J, Pi L, Ryals M, Wan Q, Hu W, Ouyang Z, Zhang B, Li K. Recommendations of scRNA-seq Differential Gene Expression Analysis Based on Comprehensive Benchmarking. LIFE (BASEL, SWITZERLAND) 2022;12:life12060850. [PMID: 35743881 PMCID: PMC9225332 DOI: 10.3390/life12060850] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/31/2022] [Accepted: 06/04/2022] [Indexed: 12/13/2022]
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