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For: Zhang S, Shao J, Yu D, Qiu X, Zhang J. MatchMixeR: a cross-platform normalization method for gene expression data integration. Bioinformatics 2020;36:2486-2491. [PMID: 31904810 DOI: 10.1093/bioinformatics/btz974] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 09/19/2019] [Accepted: 12/31/2019] [Indexed: 01/18/2023]  Open
Number Cited by Other Article(s)
1
Feldman S, Ner-Gaon H, Treister E, Shay T. Comparison and development of cross-study normalization methods for inter-species transcriptional analysis. PLoS One 2024;19:e0307997. [PMID: 39255285 PMCID: PMC11386461 DOI: 10.1371/journal.pone.0307997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 07/16/2024] [Indexed: 09/12/2024]  Open
2
Terranova N, Renard D, Shahin MH, Menon S, Cao Y, Hop CECA, Hayes S, Madrasi K, Stodtmann S, Tensfeldt T, Vaddady P, Ellinwood N, Lu J. Artificial Intelligence for Quantitative Modeling in Drug Discovery and Development: An Innovation and Quality Consortium Perspective on Use Cases and Best Practices. Clin Pharmacol Ther 2024;115:658-672. [PMID: 37716910 DOI: 10.1002/cpt.3053] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/11/2023] [Indexed: 09/18/2023]
3
Borisov N, Tkachev V, Simonov A, Sorokin M, Kim E, Kuzmin D, Karademir-Yilmaz B, Buzdin A. Uniformly shaped harmonization combines human transcriptomic data from different platforms while retaining their biological properties and differential gene expression patterns. Front Mol Biosci 2023;10:1237129. [PMID: 37745690 PMCID: PMC10511763 DOI: 10.3389/fmolb.2023.1237129] [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: 06/08/2023] [Accepted: 08/28/2023] [Indexed: 09/26/2023]  Open
4
Ai N, Yang Z, Yuan H, Ouyang D, Miao R, Ji Y, Liang Y. A distributed sparse logistic regression with $$L_{1/2}$$ regularization for microarray biomarker discovery in cancer classification. Soft comput 2022. [DOI: 10.1007/s00500-022-07551-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
5
Borisov N, Buzdin A. Transcriptomic Harmonization as the Way for Suppressing Cross-Platform Bias and Batch Effect. Biomedicines 2022;10:2318. [PMID: 36140419 PMCID: PMC9496268 DOI: 10.3390/biomedicines10092318] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022]  Open
6
Zhang Y, Sun H, Mandava A, Aevermann BD, Kollmann TR, Scheuermann RH, Qiu X, Qian Y. FastMix: a versatile data integration pipeline for cell type-specific biomarker inference. Bioinformatics 2022;38:4735-4744. [PMID: 36018232 PMCID: PMC9801972 DOI: 10.1093/bioinformatics/btac585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 08/18/2022] [Accepted: 08/25/2022] [Indexed: 01/07/2023]  Open
7
Junet V, Farrés J, Mas JM, Daura X. CuBlock: a cross-platform normalization method for gene-expression microarrays. Bioinformatics 2021;37:2365-2373. [PMID: 33609102 PMCID: PMC8388031 DOI: 10.1093/bioinformatics/btab105] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 02/04/2021] [Accepted: 02/16/2021] [Indexed: 12/28/2022]  Open
8
Lung PY, Zhong D, Pang X, Li Y, Zhang J. Maximizing the reusability of gene expression data by predicting missing metadata. PLoS Comput Biol 2020;16:e1007450. [PMID: 33156882 PMCID: PMC7673503 DOI: 10.1371/journal.pcbi.1007450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/18/2020] [Accepted: 10/09/2020] [Indexed: 11/18/2022]  Open
9
Jiang A, Hilton LK, Tang J, Rushton CK, Grande BM, Scott DW, Morin RD. PRPS-ST: A protocol-agnostic self-training method for gene expression-based classification of blood cancers. Blood Cancer Discov 2020;1:244-257. [PMID: 33392514 DOI: 10.1158/2643-3230.bcd-20-0076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
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