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For: 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] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 08/31/2018] [Indexed: 01/14/2023]  Open
Number Cited by Other Article(s)
1
Mukherjee A, Abraham S, Singh A, Balaji S, Mukunthan KS. From Data to Cure: A Comprehensive Exploration of Multi-omics Data Analysis for Targeted Therapies. Mol Biotechnol 2025;67:1269-1289. [PMID: 38565775 PMCID: PMC11928429 DOI: 10.1007/s12033-024-01133-6] [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: 12/27/2023] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
2
Canida T, Ke H, Chen S, Ye Z, Ma T. Multivariate Bayesian variable selection for multi-trait genetic fine mapping. J R Stat Soc Ser C Appl Stat 2025;74:331-351. [PMID: 40092670 PMCID: PMC11905884 DOI: 10.1093/jrsssc/qlae055] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/21/2024] [Accepted: 10/01/2024] [Indexed: 03/19/2025]
3
Kidenya BR, Mboowa G. Unlocking the future of complex human diseases prediction: multi-omics risk score breakthrough. FRONTIERS IN BIOINFORMATICS 2024;4:1510352. [PMID: 39737249 PMCID: PMC11682975 DOI: 10.3389/fbinf.2024.1510352] [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: 10/12/2024] [Accepted: 11/29/2024] [Indexed: 01/01/2025]  Open
4
Tao L, Xie Y, Deng JD, Shen H, Deng HW, Zhou W, Zhao C. SGUQ: Staged Graph Convolution Neural Network for Alzheimer's Disease Diagnosis using Multi-Omics Data. ARXIV 2024:arXiv:2410.11046v1. [PMID: 39483351 PMCID: PMC11527097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/03/2024]
5
Hernández-Lemus E, Ochoa S. Methods for multi-omic data integration in cancer research. Front Genet 2024;15:1425456. [PMID: 39364009 PMCID: PMC11446849 DOI: 10.3389/fgene.2024.1425456] [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: 04/29/2024] [Accepted: 08/28/2024] [Indexed: 10/05/2024]  Open
6
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
7
Gutierrez Reyes CD, Alejo-Jacuinde G, Perez Sanchez B, Chavez Reyes J, Onigbinde S, Mogut D, Hernández-Jasso I, Calderón-Vallejo D, Quintanar JL, Mechref Y. Multi Omics Applications in Biological Systems. Curr Issues Mol Biol 2024;46:5777-5793. [PMID: 38921016 PMCID: PMC11202207 DOI: 10.3390/cimb46060345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/31/2024] [Accepted: 06/05/2024] [Indexed: 06/27/2024]  Open
8
Zhao C, Liu A, Zhang X, Cao X, Ding Z, Sha Q, Shen H, Deng HW, Zhou W. CLCLSA: Cross-omics linked embedding with contrastive learning and self attention for integration with incomplete multi-omics data. Comput Biol Med 2024;170:108058. [PMID: 38295477 PMCID: PMC10959569 DOI: 10.1016/j.compbiomed.2024.108058] [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: 08/23/2023] [Revised: 12/30/2023] [Accepted: 01/26/2024] [Indexed: 02/02/2024]
9
Zhao C, Liu A, Zhang X, Cao X, Ding Z, Sha Q, Shen H, Deng HW, Zhou W. CLCLSA: Cross-omics Linked embedding with Contrastive Learning and Self Attention for multi-omics integration with incomplete multi-omics data. RESEARCH SQUARE 2023:rs.3.rs-2768563. [PMID: 37205427 PMCID: PMC10187371 DOI: 10.21203/rs.3.rs-2768563/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
10
Zhao C, Liu A, Zhang X, Cao X, Ding Z, Sha Q, Shen H, Deng HW, Zhou W. CLCLSA: Cross-omics Linked embedding with Contrastive Learning and Self Attention for multi-omics integration with incomplete multi-omics data. ARXIV 2023:arXiv:2304.05542v1. [PMID: 37090237 PMCID: PMC10120753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
11
Donovan SM, Aghaeepour N, Andres A, Azad MB, Becker M, Carlson SE, Järvinen KM, Lin W, Lönnerdal B, Slupsky CM, Steiber AL, Raiten DJ. Evidence for human milk as a biological system and recommendations for study design-a report from "Breastmilk Ecology: Genesis of Infant Nutrition (BEGIN)" Working Group 4. Am J Clin Nutr 2023;117 Suppl 1:S61-S86. [PMID: 37173061 PMCID: PMC10356565 DOI: 10.1016/j.ajcnut.2022.12.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 05/15/2023]  Open
12
Flores JE, Claborne DM, Weller ZD, Webb-Robertson BJM, Waters KM, Bramer LM. Missing data in multi-omics integration: Recent advances through artificial intelligence. Front Artif Intell 2023;6:1098308. [PMID: 36844425 PMCID: PMC9949722 DOI: 10.3389/frai.2023.1098308] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/23/2023] [Indexed: 02/11/2023]  Open
13
Raufaste-Cazavieille V, Santiago R, Droit A. Multi-omics analysis: Paving the path toward achieving precision medicine in cancer treatment and immuno-oncology. Front Mol Biosci 2022;9:962743. [PMID: 36304921 PMCID: PMC9595279 DOI: 10.3389/fmolb.2022.962743] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022]  Open
14
Hung RJ, Khodayari Moez E, Kim SJ, Budhathoki S, Brooks JD. Considerations of biomarker application for cancer continuum in the era of precision medicine. CURR EPIDEMIOL REP 2022;9:200-211. [PMID: 36090700 PMCID: PMC9454320 DOI: 10.1007/s40471-022-00295-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2022] [Indexed: 11/25/2022]
15
Wolc A, Dekkers JCM. Application of Bayesian genomic prediction methods to genome-wide association analyses. Genet Sel Evol 2022;54:31. [PMID: 35562659 PMCID: PMC9103490 DOI: 10.1186/s12711-022-00724-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/27/2022] [Indexed: 11/19/2022]  Open
16
Das S, Mukhopadhyay I. TiMEG: an integrative statistical method for partially missing multi-omics data. Sci Rep 2021;11:24077. [PMID: 34911979 PMCID: PMC8674330 DOI: 10.1038/s41598-021-03034-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 11/24/2021] [Indexed: 11/25/2022]  Open
17
Park Y, Heider D, Hauschild AC. Integrative Analysis of Next-Generation Sequencing for Next-Generation Cancer Research toward Artificial Intelligence. Cancers (Basel) 2021;13:3148. [PMID: 34202427 PMCID: PMC8269018 DOI: 10.3390/cancers13133148] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/16/2021] [Accepted: 06/21/2021] [Indexed: 12/18/2022]  Open
18
Mirzaei A, Carter SR, Patanwala AE, Schneider CR. Missing data in surveys: Key concepts, approaches, and applications. Res Social Adm Pharm 2021;18:2308-2316. [PMID: 33775556 DOI: 10.1016/j.sapharm.2021.03.009] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/26/2021] [Accepted: 03/11/2021] [Indexed: 10/21/2022]
19
Espinosa C, Becker M, Marić I, Wong RJ, Shaw GM, Gaudilliere B, Aghaeepour N, Stevenson DK. Data-Driven Modeling of Pregnancy-Related Complications. Trends Mol Med 2021;27:762-776. [PMID: 33573911 DOI: 10.1016/j.molmed.2021.01.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/01/2020] [Accepted: 01/20/2021] [Indexed: 12/11/2022]
20
A network embedding based method for partial multi-omics integration in cancer subtyping. Methods 2020;192:67-76. [PMID: 32805397 DOI: 10.1016/j.ymeth.2020.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/18/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022]  Open
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