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For: Kim S, Oesterreich S, Kim S, Park Y, Tseng GC. Integrative clustering of multi-level omics data for disease subtype discovery using sequential double regularization. Biostatistics 2017;18:165-179. [PMID: 27549122 PMCID: PMC5255053 DOI: 10.1093/biostatistics/kxw039] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 04/21/2016] [Accepted: 06/29/2016] [Indexed: 11/12/2022]  Open
Number Cited by Other Article(s)
1
Zhu B, Zhang Z, Leung SY, Fan X. NetMIM: network-based multi-omics integration with block missingness for biomarker selection and disease outcome prediction. Brief Bioinform 2024;25:bbae454. [PMID: 39288230 PMCID: PMC11407451 DOI: 10.1093/bib/bbae454] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 07/24/2024] [Accepted: 08/30/2024] [Indexed: 09/19/2024]  Open
2
Courbariaux M, De Santiago K, Dalmasso C, Danjou F, Bekadar S, Corvol JC, Martinez M, Szafranski M, Ambroise C. A Sparse Mixture-of-Experts Model With Screening of Genetic Associations to Guide Disease Subtyping. Front Genet 2022;13:859462. [PMID: 35734430 PMCID: PMC9207464 DOI: 10.3389/fgene.2022.859462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/21/2022] [Indexed: 11/27/2022]  Open
3
Ma Y, Sun Z, Zeng P, Zhang W, Lin Z. JSNMF enables effective and accurate integrative analysis of single-cell multiomics data. Brief Bioinform 2022;23:6563185. [PMID: 35380624 DOI: 10.1093/bib/bbac105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 02/25/2022] [Accepted: 03/02/2022] [Indexed: 01/18/2023]  Open
4
Demirel HC, Arici MK, Tuncbag N. Computational approaches leveraging integrated connections of multi-omic data toward clinical applications. Mol Omics 2021;18:7-18. [PMID: 34734935 DOI: 10.1039/d1mo00158b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
5
Liñares-Blanco J, Pazos A, Fernandez-Lozano C. Machine learning analysis of TCGA cancer data. PeerJ Comput Sci 2021;7:e584. [PMID: 34322589 PMCID: PMC8293929 DOI: 10.7717/peerj-cs.584] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/17/2021] [Indexed: 06/13/2023]
6
Wu M, Yi H, Ma S. Vertical integration methods for gene expression data analysis. Brief Bioinform 2021;22:bbaa169. [PMID: 32793970 PMCID: PMC8138889 DOI: 10.1093/bib/bbaa169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/18/2020] [Accepted: 07/04/2020] [Indexed: 12/12/2022]  Open
7
Liu S, Zhang Y, Shang X, Zhang Z. ProTICS reveals prognostic impact of tumor infiltrating immune cells in different molecular subtypes. Brief Bioinform 2021;22:6271999. [PMID: 33963834 DOI: 10.1093/bib/bbab164] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/05/2021] [Accepted: 04/02/2021] [Indexed: 12/15/2022]  Open
8
Nazarov PV, Kreis S. Integrative approaches for analysis of mRNA and microRNA high-throughput data. Comput Struct Biotechnol J 2021;19:1154-1162. [PMID: 33680358 PMCID: PMC7895676 DOI: 10.1016/j.csbj.2021.01.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/11/2022]  Open
9
Wu M, Jiang Y, Ma S. Integration of Proteomics and Other Omics Data. Methods Mol Biol 2021;2361:307-324. [PMID: 34236669 DOI: 10.1007/978-1-0716-1641-3_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
10
Afrin K, Iquebal AS, Karimi M, Souris A, Lee SY, Mallick BK. Directionally dependent multi-view clustering using copula model. PLoS One 2020;15:e0238996. [PMID: 33095785 PMCID: PMC7584221 DOI: 10.1371/journal.pone.0238996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 08/27/2020] [Indexed: 11/23/2022]  Open
11
Gao X, Lee S, Li G, Jung S. Covariate-driven factorization by thresholding for multiblock data. Biometrics 2020;77:1011-1023. [PMID: 32799349 DOI: 10.1111/biom.13352] [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: 12/12/2019] [Revised: 08/03/2020] [Accepted: 08/07/2020] [Indexed: 11/30/2022]
12
Pucher BM, Zeleznik OA, Thallinger GG. Comparison and evaluation of integrative methods for the analysis of multilevel omics data: a study based on simulated and experimental cancer data. Brief Bioinform 2020;20:671-681. [PMID: 29688321 DOI: 10.1093/bib/bby027] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/02/2018] [Indexed: 12/12/2022]  Open
13
Integrative Deep Learning for Identifying Differentially Expressed (DE) Biomarkers. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2019;2019:8418760. [PMID: 31915462 PMCID: PMC6935456 DOI: 10.1155/2019/8418760] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/19/2019] [Accepted: 08/04/2019] [Indexed: 11/17/2022]
14
Fang Z, Ma T, Tang G, Zhu L, Yan Q, Wang T, Celedón JC, Chen W, Tseng GC. Bayesian integrative model for multi-omics data with missingness. Bioinformatics 2019;34:3801-3808. [PMID: 30184058 DOI: 10.1093/bioinformatics/bty775] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 08/31/2018] [Indexed: 01/14/2023]  Open
15
Duan R, Gao L, Xu H, Song K, Hu Y, Wang H, Dong Y, Zhang C, Jia S. CEPICS: A Comparison and Evaluation Platform for Integration Methods in Cancer Subtyping. Front Genet 2019;10:966. [PMID: 31649733 PMCID: PMC6792302 DOI: 10.3389/fgene.2019.00966] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 09/10/2019] [Indexed: 11/17/2022]  Open
16
Majellano EC, Clark VL, Winter NA, Gibson PG, McDonald VM. Approaches to the assessment of severe asthma: barriers and strategies. J Asthma Allergy 2019;12:235-251. [PMID: 31692528 PMCID: PMC6712210 DOI: 10.2147/jaa.s178927] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 07/25/2019] [Indexed: 12/12/2022]  Open
17
Kim H, Kim Y, Han B, Jang JY, Kim Y. Clinically Applicable Deep Learning Algorithm Using Quantitative Proteomic Data. J Proteome Res 2019;18:3195-3202. [DOI: 10.1021/acs.jproteome.9b00268] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
18
Mirza B, Wang W, Wang J, Choi H, Chung NC, Ping P. Machine Learning and Integrative Analysis of Biomedical Big Data. Genes (Basel) 2019;10:E87. [PMID: 30696086 PMCID: PMC6410075 DOI: 10.3390/genes10020087] [Citation(s) in RCA: 182] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 01/08/2019] [Accepted: 01/21/2019] [Indexed: 12/11/2022]  Open
19
Wu C, Zhou F, Ren J, Li X, Jiang Y, Ma S. A Selective Review of Multi-Level Omics Data Integration Using Variable Selection. High Throughput 2019;8:E4. [PMID: 30669303 PMCID: PMC6473252 DOI: 10.3390/ht8010004] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/24/2018] [Accepted: 01/10/2019] [Indexed: 01/02/2023]  Open
20
Min EJ, Chang C, Long Q. Generalized Bayesian Factor Analysis for Integrative Clustering with Applications to Multi-Omics Data. PROCEEDINGS OF THE ... INTERNATIONAL CONFERENCE ON DATA SCIENCE AND ADVANCED ANALYTICS. IEEE INTERNATIONAL CONFERENCE ON DATA SCIENCE AND ADVANCED ANALYTICS 2018;2018:109-119. [PMID: 31106307 PMCID: PMC6521881 DOI: 10.1109/dsaa.2018.00021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
21
Sidhaye VK, Nishida K, Martinez FJ. Precision medicine in COPD: where are we and where do we need to go? Eur Respir Rev 2018;27:180022. [PMID: 30068688 PMCID: PMC6156790 DOI: 10.1183/16000617.0022-2018] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/18/2018] [Indexed: 12/15/2022]  Open
22
Ma T, Song C, Tseng GC. Discussant paper on ‘Statistical contributions to bioinformatics: Design, modelling, structure learning and integration’. STAT MODEL 2017. [DOI: 10.1177/1471082x17705992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
23
Node-Structured Integrative Gaussian Graphical Model Guided by Pathway Information. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2017;2017:8520480. [PMID: 28487748 PMCID: PMC5405575 DOI: 10.1155/2017/8520480] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 02/20/2017] [Accepted: 03/06/2017] [Indexed: 12/23/2022]
24
Kim S, Jhong JH, Lee J, Koo JY. Meta-analytic support vector machine for integrating multiple omics data. BioData Min 2017;10:2. [PMID: 28149325 PMCID: PMC5270233 DOI: 10.1186/s13040-017-0126-8] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 01/11/2017] [Indexed: 11/10/2022]  Open
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