• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (5075949)   Today's Articles (53)
For: Lin Y, Li H, Xiao X, Zhang L, Wang K, Zhao J, Wang M, Zheng F, Zhang M, Yang W, Han J, Yu R. DAISM-DNNXMBD: Highly accurate cell type proportion estimation with in silico data augmentation and deep neural networks. Patterns (N Y) 2022;3:100440. [PMID: 35510186 PMCID: PMC9058910 DOI: 10.1016/j.patter.2022.100440] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/29/2021] [Accepted: 01/06/2022] [Indexed: 12/31/2022]
Number Cited by Other Article(s)
1
Davidson NR, Zhang F, Greene CS. BuDDI: Bulk Deconvolution with Domain Invariance to predict cell-type-specific perturbations from bulk. PLoS Comput Biol 2025;21:e1012742. [PMID: 39823522 PMCID: PMC11790236 DOI: 10.1371/journal.pcbi.1012742] [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: 06/20/2024] [Revised: 02/03/2025] [Accepted: 12/20/2024] [Indexed: 01/19/2025]  Open
2
Xiong X, Liu Y, Pu D, Yang Z, Bi Z, Tian L, Li X. DeSide: A unified deep learning approach for cellular deconvolution of tumor microenvironment. Proc Natl Acad Sci U S A 2024;121:e2407096121. [PMID: 39514318 PMCID: PMC11573681 DOI: 10.1073/pnas.2407096121] [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: 04/09/2024] [Accepted: 09/23/2024] [Indexed: 11/16/2024]  Open
3
White BS, de Reyniès A, Newman AM, Waterfall JJ, Lamb A, Petitprez F, Lin Y, Yu R, Guerrero-Gimenez ME, Domanskyi S, Monaco G, Chung V, Banerjee J, Derrick D, Valdeolivas A, Li H, Xiao X, Wang S, Zheng F, Yang W, Catania CA, Lang BJ, Bertus TJ, Piermarocchi C, Caruso FP, Ceccarelli M, Yu T, Guo X, Bletz J, Coller J, Maecker H, Duault C, Shokoohi V, Patel S, Liliental JE, Simon S, Saez-Rodriguez J, Heiser LM, Guinney J, Gentles AJ. Community assessment of methods to deconvolve cellular composition from bulk gene expression. Nat Commun 2024;15:7362. [PMID: 39191725 PMCID: PMC11350143 DOI: 10.1038/s41467-024-50618-0] [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: 08/28/2023] [Accepted: 07/11/2024] [Indexed: 08/29/2024]  Open
4
Görtler F, Mensching-Buhr M, Skaar Ø, Schrod S, Sterr T, Schäfer A, Beißbarth T, Joshi A, Zacharias HU, Grellscheid SN, Altenbuchinger M. Adaptive digital tissue deconvolution. Bioinformatics 2024;40:i100-i109. [PMID: 38940181 PMCID: PMC11256946 DOI: 10.1093/bioinformatics/btae263] [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] [Indexed: 06/29/2024]  Open
5
Nguyen H, Nguyen H, Tran D, Draghici S, Nguyen T. Fourteen years of cellular deconvolution: methodology, applications, technical evaluation and outstanding challenges. Nucleic Acids Res 2024;52:4761-4783. [PMID: 38619038 PMCID: PMC11109966 DOI: 10.1093/nar/gkae267] [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: 10/26/2023] [Revised: 03/01/2024] [Accepted: 04/02/2024] [Indexed: 04/16/2024]  Open
6
Davidson NR, Zhang F, Greene CS. BuDDI: BulkDeconvolution withDomainInvariance to predict cell-type-specific perturbations from bulk. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.20.549951. [PMID: 37503097 PMCID: PMC10370205 DOI: 10.1101/2023.07.20.549951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
7
Chen G, Yu R, Chen X. Editorial: Integrative analysis of single-cell and/or bulk multi-omics sequencing data. Front Genet 2023;13:1121999. [PMID: 36685891 PMCID: PMC9845394 DOI: 10.3389/fgene.2022.1121999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 01/05/2023]  Open
8
Xiao X, Guo Q, Cui C, Lin Y, Zhang L, Ding X, Li Q, Wang M, Yang W, Kong Y, Yu R. Multiplexed imaging mass cytometry reveals distinct tumor-immune microenvironments linked to immunotherapy responses in melanoma. COMMUNICATIONS MEDICINE 2022;2:131. [PMID: 36281356 PMCID: PMC9587266 DOI: 10.1038/s43856-022-00197-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 09/30/2022] [Indexed: 11/08/2022]  Open
9
Lin Y, Wu S, Xiao X, Zhao J, Wang M, Li H, Wang K, Zhang M, Zheng F, Yang W, Zhang L, Han J, Yu R. Protocol to estimate cell type proportions from bulk RNA-seq using DAISM-DNNXMBD. STAR Protoc 2022;3:101587. [PMID: 35942344 PMCID: PMC9356155 DOI: 10.1016/j.xpro.2022.101587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]  Open
10
Tegner JN, Gomez-Cabrero D. Data-driven bioinformatics to disentangle cells within a tissue microenvironment. Trends Cell Biol 2022;32:467-469. [DOI: 10.1016/j.tcb.2022.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 03/30/2022] [Indexed: 10/18/2022]
PrevPage 1 of 1 1Next
© 2004-2025 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA