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For: Kana O, Nault R, Filipovic D, Marri D, Zacharewski T, Bhattacharya S. Generative modeling of single-cell gene expression for dose-dependent chemical perturbations. Patterns (N Y) 2023;4:100817. [PMID: 37602218 PMCID: PMC10436058 DOI: 10.1016/j.patter.2023.100817] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/07/2022] [Accepted: 07/14/2023] [Indexed: 08/22/2023]
Number Cited by Other Article(s)
1
Wu Y, Liu J, Xiao Y, Zhang S, Li L. CoupleVAE: coupled variational autoencoders for predicting perturbational single-cell RNA sequencing data. Brief Bioinform 2025;26:bbaf126. [PMID: 40178283 PMCID: PMC11966612 DOI: 10.1093/bib/bbaf126] [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: 10/24/2024] [Revised: 01/21/2025] [Accepted: 03/03/2025] [Indexed: 04/05/2025]  Open
2
Monfort-Lanzas P, Rungger K, Madersbacher L, Hackl H. Machine learning to dissect perturbations in complex cellular systems. Comput Struct Biotechnol J 2025;27:832-842. [PMID: 40103613 PMCID: PMC11915099 DOI: 10.1016/j.csbj.2025.02.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Revised: 02/24/2025] [Accepted: 02/25/2025] [Indexed: 03/20/2025]  Open
3
Gavriilidis GI, Vasileiou V, Orfanou A, Ishaque N, Psomopoulos F. A mini-review on perturbation modelling across single-cell omic modalities. Comput Struct Biotechnol J 2024;23:1886-1896. [PMID: 38721585 PMCID: PMC11076269 DOI: 10.1016/j.csbj.2024.04.058] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/23/2024] [Accepted: 04/23/2024] [Indexed: 01/06/2025]  Open
4
Qi X, Zhao L, Tian C, Li Y, Chen ZL, Huo P, Chen R, Liu X, Wan B, Yang S, Zhao Y. Predicting transcriptional responses to novel chemical perturbations using deep generative model for drug discovery. Nat Commun 2024;15:9256. [PMID: 39462106 PMCID: PMC11513139 DOI: 10.1038/s41467-024-53457-1] [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: 03/11/2024] [Accepted: 10/11/2024] [Indexed: 10/28/2024]  Open
5
Gao Y, Wei Z, Dong K, Chen K, Yang J, Chuai G, Liu Q. Toward subtask-decomposition-based learning and benchmarking for predicting genetic perturbation outcomes and beyond. NATURE COMPUTATIONAL SCIENCE 2024;4:773-785. [PMID: 39333790 DOI: 10.1038/s43588-024-00698-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 08/29/2024] [Indexed: 09/30/2024]
6
Deshpande S, Georgaka S, Haley M, Sellers R, Minshull J, Nallala J, Fergie M, Stone N, Rajpoot N, Baker SM, Iqbal M, Couper K, Roncaroli F, Minhas F. Ouroboros: cross-linking protein expression perturbations and cancer histology imaging with generative-predictive modeling. Bioinformatics 2024;40:ii174-ii181. [PMID: 39230703 PMCID: PMC11373318 DOI: 10.1093/bioinformatics/btae399] [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: 09/05/2024]  Open
7
Li C, Shao X, Zhang S, Wang Y, Jin K, Yang P, Lu X, Fan X, Wang Y. scRank infers drug-responsive cell types from untreated scRNA-seq data using a target-perturbed gene regulatory network. Cell Rep Med 2024;5:101568. [PMID: 38754419 PMCID: PMC11228399 DOI: 10.1016/j.xcrm.2024.101568] [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: 05/05/2023] [Revised: 12/27/2023] [Accepted: 04/21/2024] [Indexed: 05/18/2024]
8
Filipovic D, Kana O, Marri D, Bhattacharya S. Unique challenges and best practices for single cell transcriptomic analysis in toxicology. CURRENT OPINION IN TOXICOLOGY 2024;38:100475. [PMID: 38645720 PMCID: PMC11027889 DOI: 10.1016/j.cotox.2024.100475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
9
Jiang Q, Chen S, Chen X, Jiang R. scPRAM accurately predicts single-cell gene expression perturbation response based on attention mechanism. Bioinformatics 2024;40:btae265. [PMID: 38625746 PMCID: PMC11076148 DOI: 10.1093/bioinformatics/btae265] [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: 12/07/2023] [Revised: 04/06/2024] [Accepted: 04/13/2024] [Indexed: 04/17/2024]  Open
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