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For: Grabski IN, Irizarry RA. A probabilistic gene expression barcode for annotation of cell types from single-cell RNA-seq data. Biostatistics 2022;23:1150-1164. [PMID: 35770795 PMCID: PMC9802389 DOI: 10.1093/biostatistics/kxac021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 05/10/2022] [Accepted: 05/22/2022] [Indexed: 01/07/2023]  Open
Number Cited by Other Article(s)
1
Maurer K, Grabski IN, Houot R, Gohil SH, Miura S, Redd R, Lyu H, Lu W, Arihara Y, Budka J, McDonough M, Ansuinelli M, Reynolds C, Jacene H, Li S, Livak KJ, Ritz J, Miles B, Mattie M, Neuberg DS, Irizarry RA, Armand P, Wu CJ, Jacobson C. Baseline immune state and T-cell clonal kinetics are associated with durable response to CAR-T therapy in large B-cell lymphoma. Blood 2024;144:2490-2502. [PMID: 39241199 PMCID: PMC11952007 DOI: 10.1182/blood.2024024381] [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: 02/23/2024] [Revised: 07/30/2024] [Accepted: 08/12/2024] [Indexed: 09/08/2024]  Open
2
Ji L, Wang A, Sonthalia S, Naiman DQ, Younes L, Colantuoni C, Geman D. CellCover Captures Neural Stem Cell Progression in Mammalian Neocortical Development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.06.535943. [PMID: 37383947 PMCID: PMC10299349 DOI: 10.1101/2023.04.06.535943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
3
Gonzalez-Ferrer J, Lehrer J, O'Farrell A, Paten B, Teodorescu M, Haussler D, Jonsson VD, Mostajo-Radji MA. SIMS: A deep-learning label transfer tool for single-cell RNA sequencing analysis. CELL GENOMICS 2024;4:100581. [PMID: 38823397 PMCID: PMC11228957 DOI: 10.1016/j.xgen.2024.100581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 04/02/2024] [Accepted: 05/09/2024] [Indexed: 06/03/2024]
4
Gonzalez-Ferrer J, Lehrer J, O’Farrell A, Paten B, Teodorescu M, Haussler D, Jonsson VD, Mostajo-Radji MA. Unraveling Neuronal Identities Using SIMS: A Deep Learning Label Transfer Tool for Single-Cell RNA Sequencing Analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.28.529615. [PMID: 36909548 PMCID: PMC10002667 DOI: 10.1101/2023.02.28.529615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
5
Aybey B, Zhao S, Brors B, Staub E. Immune cell type signature discovery and random forest classification for analysis of single cell gene expression datasets. Front Immunol 2023;14:1194745. [PMID: 37609075 PMCID: PMC10441575 DOI: 10.3389/fimmu.2023.1194745] [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: 03/27/2023] [Accepted: 07/14/2023] [Indexed: 08/24/2023]  Open
6
Grabski IN, Street K, Irizarry RA. Significance analysis for clustering with single-cell RNA-sequencing data. Nat Methods 2023;20:1196-1202. [PMID: 37429993 PMCID: PMC11282907 DOI: 10.1038/s41592-023-01933-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 06/01/2023] [Indexed: 07/12/2023]
7
Covert I, Gala R, Wang T, Svoboda K, Sümbül U, Lee SI. Predictive and robust gene selection for spatial transcriptomics. Nat Commun 2023;14:2091. [PMID: 37045821 PMCID: PMC10097645 DOI: 10.1038/s41467-023-37392-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 03/16/2023] [Indexed: 04/14/2023]  Open
8
Yang F, Wang W, Wang F, Fang Y, Tang D, Huang J, Lu H, Yao J. scBERT as a large-scale pretrained deep language model for cell type annotation of single-cell RNA-seq data. NAT MACH INTELL 2022. [DOI: 10.1038/s42256-022-00534-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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