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For: Treppner M, Binder H, Hess M. Interpretable generative deep learning: an illustration with single cell gene expression data. Hum Genet 2022;141:1481-1498. [PMID: 34988661 PMCID: PMC9360114 DOI: 10.1007/s00439-021-02417-6] [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: 05/14/2021] [Accepted: 08/06/2021] [Indexed: 11/26/2022]
Number Cited by Other Article(s)
1
Hackenberg M, Brunn N, Vogel T, Binder H. Infusing structural assumptions into dimensionality reduction for single-cell RNA sequencing data to identify small gene sets. Commun Biol 2025;8:414. [PMID: 40069486 PMCID: PMC11897155 DOI: 10.1038/s42003-025-07872-9] [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: 04/15/2024] [Accepted: 03/03/2025] [Indexed: 03/15/2025]  Open
2
Rivero-Garcia I, Torres M, Sánchez-Cabo F. Deep generative models in single-cell omics. Comput Biol Med 2024;176:108561. [PMID: 38749321 DOI: 10.1016/j.compbiomed.2024.108561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/30/2024] [Accepted: 05/05/2024] [Indexed: 05/31/2024]
3
Salido-Guadarrama I, Romero-Cordoba SL, Rueda-Zarazua B. Multi-Omics Mining of lncRNAs with Biological and Clinical Relevance in Cancer. Int J Mol Sci 2023;24:16600. [PMID: 38068923 PMCID: PMC10706612 DOI: 10.3390/ijms242316600] [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: 09/28/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023]  Open
4
Fouché A, Zinovyev A. Omics data integration in computational biology viewed through the prism of machine learning paradigms. FRONTIERS IN BIOINFORMATICS 2023;3:1191961. [PMID: 37600970 PMCID: PMC10436311 DOI: 10.3389/fbinf.2023.1191961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 07/26/2023] [Indexed: 08/22/2023]  Open
5
Mohammed MA, Abdulkareem KH, Dinar AM, Zapirain BG. Rise of Deep Learning Clinical Applications and Challenges in Omics Data: A Systematic Review. Diagnostics (Basel) 2023;13:664. [PMID: 36832152 PMCID: PMC9955380 DOI: 10.3390/diagnostics13040664] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/05/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023]  Open
6
Brombacher E, Hackenberg M, Kreutz C, Binder H, Treppner M. The performance of deep generative models for learning joint embeddings of single-cell multi-omics data. Front Mol Biosci 2022;9:962644. [PMID: 36387277 PMCID: PMC9643784 DOI: 10.3389/fmolb.2022.962644] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2023]  Open
7
Watson DS. Interpretable machine learning for genomics. Hum Genet 2022;141:1499-1513. [PMID: 34669035 PMCID: PMC8527313 DOI: 10.1007/s00439-021-02387-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 10/08/2021] [Indexed: 12/19/2022]
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