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For: Yang Z, Michailidis G. A non-negative matrix factorization method for detecting modules in heterogeneous omics multi-modal data. Bioinformatics 2016;32:1-8. [PMID: 26377073 PMCID: PMC5006236 DOI: 10.1093/bioinformatics/btv544] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 09/08/2015] [Accepted: 09/09/2015] [Indexed: 12/15/2022]  Open
Number Cited by Other Article(s)
51
Zhang X, Zhou Z, Xu H, Liu CT. Integrative clustering methods for multi-omics data. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL STATISTICS 2022;14. [PMID: 35573155 PMCID: PMC9097984 DOI: 10.1002/wics.1553] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
52
Yuan D, Gaynanova I. Double-matched matrix decomposition for multi-view data. J Comput Graph Stat 2022. [DOI: 10.1080/10618600.2022.2067860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
53
Vahabi N, Michailidis G. Unsupervised Multi-Omics Data Integration Methods: A Comprehensive Review. Front Genet 2022;13:854752. [PMID: 35391796 PMCID: PMC8981526 DOI: 10.3389/fgene.2022.854752] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 02/28/2022] [Indexed: 12/26/2022]  Open
54
Qian K, Fu S, Li H, Li WV. scINSIGHT for interpreting single-cell gene expression from biologically heterogeneous data. Genome Biol 2022;23:82. [PMID: 35313930 PMCID: PMC8935111 DOI: 10.1186/s13059-022-02649-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 03/07/2022] [Indexed: 12/30/2022]  Open
55
Lock EF, Park JY, Hoadley KA. BIDIMENSIONAL LINKED MATRIX FACTORIZATION FOR PAN-OMICS PAN-CANCER ANALYSIS. Ann Appl Stat 2022;16:193-215. [PMID: 35505906 PMCID: PMC9060567 DOI: 10.1214/21-aoas1495] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
56
Multi-Omics Profiling of the Tumor Microenvironment. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022;1361:283-326. [DOI: 10.1007/978-3-030-91836-1_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
57
Nakazawa MA, Tamada Y, Tanaka Y, Ikeguchi M, Higashihara K, Okuno Y. Novel cancer subtyping method based on patient-specific gene regulatory network. Sci Rep 2021;11:23653. [PMID: 34880275 PMCID: PMC8654869 DOI: 10.1038/s41598-021-02394-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 11/12/2021] [Indexed: 12/11/2022]  Open
58
Carmichael I, Calhoun BC, Hoadley KA, Troester MA, Geradts J, Couture HD, Olsson L, Perou CM, Niethammer M, Hannig J, Marron JS. JOINT AND INDIVIDUAL ANALYSIS OF BREAST CANCER HISTOLOGIC IMAGES AND GENOMIC COVARIATES. Ann Appl Stat 2021;15:1697-1722. [PMID: 35432688 PMCID: PMC9007558 DOI: 10.1214/20-aoas1433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
59
Nguyen H, Tran D, Tran B, Roy M, Cassell A, Dascalu S, Draghici S, Nguyen T. SMRT: Randomized Data Transformation for Cancer Subtyping and Big Data Analysis. Front Oncol 2021;11:725133. [PMID: 34745946 PMCID: PMC8563705 DOI: 10.3389/fonc.2021.725133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/28/2021] [Indexed: 12/25/2022]  Open
60
Miao Z, Humphreys BD, McMahon AP, Kim J. Multi-omics integration in the age of million single-cell data. Nat Rev Nephrol 2021;17:710-724. [PMID: 34417589 PMCID: PMC9191639 DOI: 10.1038/s41581-021-00463-x] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2021] [Indexed: 02/06/2023]
61
Shiga M, Seno S, Onizuka M, Matsuda H. SC-JNMF: single-cell clustering integrating multiple quantification methods based on joint non-negative matrix factorization. PeerJ 2021;9:e12087. [PMID: 34532161 PMCID: PMC8404576 DOI: 10.7717/peerj.12087] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 08/07/2021] [Indexed: 11/20/2022]  Open
62
Heo YJ, Hwa C, Lee GH, Park JM, An JY. Integrative Multi-Omics Approaches in Cancer Research: From Biological Networks to Clinical Subtypes. Mol Cells 2021;44:433-443. [PMID: 34238766 PMCID: PMC8334347 DOI: 10.14348/molcells.2021.0042] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/09/2021] [Accepted: 05/12/2021] [Indexed: 11/27/2022]  Open
63
Ding Q, Sun Y, Shang J, Li F, Zhang Y, Liu JX. NMFNA: A Non-negative Matrix Factorization Network Analysis Method for Identifying Modules and Characteristic Genes of Pancreatic Cancer. Front Genet 2021;12:678642. [PMID: 34367241 PMCID: PMC8340025 DOI: 10.3389/fgene.2021.678642] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/03/2021] [Indexed: 01/15/2023]  Open
64
Moon S, Lee H. JDSNMF: Joint Deep Semi-Non-Negative Matrix Factorization for Learning Integrative Representation of Molecular Signals in Alzheimer's Disease. J Pers Med 2021;11:jpm11080686. [PMID: 34442330 PMCID: PMC8400727 DOI: 10.3390/jpm11080686] [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: 06/02/2021] [Revised: 07/16/2021] [Accepted: 07/18/2021] [Indexed: 12/14/2022]  Open
65
Song D, Li K, Hemminger Z, Wollman R, Li JJ. scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling. Bioinformatics 2021;37:i358-i366. [PMID: 34252925 PMCID: PMC8275345 DOI: 10.1093/bioinformatics/btab273] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]  Open
66
Zhao S, Tsibris A. Leveraging Novel Integrated Single-Cell Analyses to Define HIV-1 Latency Reversal. Viruses 2021;13:1197. [PMID: 34206546 PMCID: PMC8310207 DOI: 10.3390/v13071197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/11/2021] [Accepted: 06/16/2021] [Indexed: 01/24/2023]  Open
67
Picard M, Scott-Boyer MP, Bodein A, Périn O, Droit A. Integration strategies of multi-omics data for machine learning analysis. Comput Struct Biotechnol J 2021;19:3735-3746. [PMID: 34285775 PMCID: PMC8258788 DOI: 10.1016/j.csbj.2021.06.030] [Citation(s) in RCA: 246] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 12/25/2022]  Open
68
Okochi Y, Sakaguchi S, Nakae K, Kondo T, Naoki H. Model-based prediction of spatial gene expression via generative linear mapping. Nat Commun 2021;12:3731. [PMID: 34140477 PMCID: PMC8211835 DOI: 10.1038/s41467-021-24014-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 05/27/2021] [Indexed: 11/17/2022]  Open
69
Chen T, Philip M, Lê Cao KA, Tyagi S. A multi-modal data harmonisation approach for discovery of COVID-19 drug targets. Brief Bioinform 2021;22:6279836. [PMID: 34036326 PMCID: PMC8194516 DOI: 10.1093/bib/bbab185] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 03/09/2021] [Accepted: 04/22/2021] [Indexed: 12/27/2022]  Open
70
Adossa N, Khan S, Rytkönen KT, Elo LL. Computational strategies for single-cell multi-omics integration. Comput Struct Biotechnol J 2021;19:2588-2596. [PMID: 34025945 PMCID: PMC8114078 DOI: 10.1016/j.csbj.2021.04.060] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/23/2021] [Accepted: 04/24/2021] [Indexed: 02/06/2023]  Open
71
Wang B, Ma X, Xie M, Wu Y, Wang Y, Duan R, Zhang C, Yu L, Guo X, Gao L. CBP-JMF: An Improved Joint Matrix Tri-Factorization Method for Characterizing Complex Biological Processes of Diseases. Front Genet 2021;12:665416. [PMID: 33968140 PMCID: PMC8103031 DOI: 10.3389/fgene.2021.665416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/01/2021] [Indexed: 11/13/2022]  Open
72
Liang L, Zhu K, Tao J, Lu S. ORN: Inferring patient-specific dysregulation status of pathway modules in cancer with OR-gate Network. PLoS Comput Biol 2021;17:e1008792. [PMID: 33819263 PMCID: PMC8049496 DOI: 10.1371/journal.pcbi.1008792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 04/15/2021] [Accepted: 02/15/2021] [Indexed: 01/26/2023]  Open
73
Auslander N, Gussow AB, Koonin EV. Incorporating Machine Learning into Established Bioinformatics Frameworks. Int J Mol Sci 2021;22:2903. [PMID: 33809353 PMCID: PMC8000113 DOI: 10.3390/ijms22062903] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/08/2021] [Accepted: 03/10/2021] [Indexed: 12/23/2022]  Open
74
Identifying multimodal signatures underlying the somatic comorbidity of psychosis: the COMMITMENT roadmap. Mol Psychiatry 2021;26:722-724. [PMID: 33060817 PMCID: PMC7910206 DOI: 10.1038/s41380-020-00915-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/16/2020] [Accepted: 10/02/2020] [Indexed: 11/25/2022]
75
Wang M, Allen GI. Integrative Generalized Convex Clustering Optimization and Feature Selection for Mixed Multi-View Data. JOURNAL OF MACHINE LEARNING RESEARCH : JMLR 2021;22:55. [PMID: 34744522 PMCID: PMC8570363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
76
Zhu H, Li G, Lock EF. Generalized integrative principal component analysis for multi-type data with block-wise missing structure. Biostatistics 2020;21:302-318. [PMID: 30247540 DOI: 10.1093/biostatistics/kxy052] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 08/15/2018] [Indexed: 12/19/2022]  Open
77
Park M, Kim D, Moon K, Park T. Integrative Analysis of Multi-Omics Data Based on Blockwise Sparse Principal Components. Int J Mol Sci 2020;21:E8202. [PMID: 33147797 PMCID: PMC7663540 DOI: 10.3390/ijms21218202] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/27/2020] [Accepted: 10/31/2020] [Indexed: 01/14/2023]  Open
78
Fantini D, Vidimar V, Yu Y, Condello S, Meeks JJ. MutSignatures: an R package for extraction and analysis of cancer mutational signatures. Sci Rep 2020;10:18217. [PMID: 33106540 PMCID: PMC7589488 DOI: 10.1038/s41598-020-75062-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 10/09/2020] [Indexed: 12/31/2022]  Open
79
Li J, Lu Q, Wen Y. Multi-kernel linear mixed model with adaptive lasso for prediction analysis on high-dimensional multi-omics data. Bioinformatics 2020;36:1785-1794. [PMID: 31693075 DOI: 10.1093/bioinformatics/btz822] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 10/08/2019] [Accepted: 11/01/2019] [Indexed: 12/11/2022]  Open
80
Ishikawa Y, Nakai K. A hypothetical trivalent epigenetic code that affects the nature of human ESCs. PLoS One 2020;15:e0238742. [PMID: 32911515 PMCID: PMC7482980 DOI: 10.1371/journal.pone.0238742] [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: 05/29/2020] [Accepted: 08/21/2020] [Indexed: 02/07/2023]  Open
81
Fan J, Slowikowski K, Zhang F. Single-cell transcriptomics in cancer: computational challenges and opportunities. Exp Mol Med 2020;52:1452-1465. [PMID: 32929226 PMCID: PMC8080633 DOI: 10.1038/s12276-020-0422-0] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 02/26/2020] [Accepted: 03/10/2020] [Indexed: 02/07/2023]  Open
82
Hu X, Hu Y, Wu F, Leung RWT, Qin J. Integration of single-cell multi-omics for gene regulatory network inference. Comput Struct Biotechnol J 2020;18:1925-1938. [PMID: 32774787 PMCID: PMC7385034 DOI: 10.1016/j.csbj.2020.06.033] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 06/17/2020] [Accepted: 06/20/2020] [Indexed: 12/20/2022]  Open
83
Chen T, Tyagi S. Integrative computational epigenomics to build data-driven gene regulation hypotheses. Gigascience 2020;9:giaa064. [PMID: 32543653 PMCID: PMC7297091 DOI: 10.1093/gigascience/giaa064] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 12/20/2022]  Open
84
Hu J, Zeng T, Xia Q, Huang L, Zhang Y, Zhang C, Zeng Y, Liu H, Zhang S, Huang G, Wan W, Ding Y, Hu F, Yang C, Chen L, Wang W. Identification of Key Genes for the Ultrahigh Yield of Rice Using Dynamic Cross-tissue Network Analysis. GENOMICS, PROTEOMICS & BIOINFORMATICS 2020;18:256-270. [PMID: 32736037 PMCID: PMC7801251 DOI: 10.1016/j.gpb.2019.11.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 08/26/2019] [Accepted: 11/08/2019] [Indexed: 11/29/2022]
85
Godichon-Baggioni A, Maugis-Rabusseau C, Rau A. Multiview cluster aggregation and splitting, with an application to multiomic breast cancer data. Ann Appl Stat 2020. [DOI: 10.1214/19-aoas1317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
86
Chen G, Wang L, Diao T, Chen Y, Cao C, Zhang X. Analysis of immune-related signatures of colorectal cancer identifying two different immune phenotypes: Evidence for immune checkpoint inhibitor therapy. Oncol Lett 2020;20:517-524. [PMID: 32565977 PMCID: PMC7285802 DOI: 10.3892/ol.2020.11605] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 02/05/2020] [Indexed: 12/24/2022]  Open
87
Esposito F, Boccarelli A, Del Buono N. An NMF-Based Methodology for Selecting Biomarkers in the Landscape of Genes of Heterogeneous Cancer-Associated Fibroblast Populations. Bioinform Biol Insights 2020;14:1177932220906827. [PMID: 32425511 PMCID: PMC7218276 DOI: 10.1177/1177932220906827] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 01/22/2020] [Indexed: 01/27/2023]  Open
88
Serra A, Fratello M, Cattelani L, Liampa I, Melagraki G, Kohonen P, Nymark P, Federico A, Kinaret PAS, Jagiello K, Ha MK, Choi JS, Sanabria N, Gulumian M, Puzyn T, Yoon TH, Sarimveis H, Grafström R, Afantitis A, Greco D. Transcriptomics in Toxicogenomics, Part III: Data Modelling for Risk Assessment. NANOMATERIALS (BASEL, SWITZERLAND) 2020;10:E708. [PMID: 32276469 PMCID: PMC7221955 DOI: 10.3390/nano10040708] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 03/25/2020] [Accepted: 03/26/2020] [Indexed: 12/30/2022]
89
Mallik S, Zhao Z. Graph- and rule-based learning algorithms: a comprehensive review of their applications for cancer type classification and prognosis using genomic data. Brief Bioinform 2020;21:368-394. [PMID: 30649169 PMCID: PMC7373185 DOI: 10.1093/bib/bby120] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/26/2018] [Accepted: 11/21/2018] [Indexed: 12/20/2022]  Open
90
Subramanian I, Verma S, Kumar S, Jere A, Anamika K. Multi-omics Data Integration, Interpretation, and Its Application. Bioinform Biol Insights 2020;14:1177932219899051. [PMID: 32076369 PMCID: PMC7003173 DOI: 10.1177/1177932219899051] [Citation(s) in RCA: 683] [Impact Index Per Article: 136.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 11/09/2019] [Indexed: 12/22/2022]  Open
91
Zhang L, Zhang S. Learning common and specific patterns from data of multiple interrelated biological scenarios with matrix factorization. Nucleic Acids Res 2020;47:6606-6617. [PMID: 31175825 PMCID: PMC6649783 DOI: 10.1093/nar/gkz488] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 05/11/2019] [Accepted: 05/22/2019] [Indexed: 11/18/2022]  Open
92
Park SJ, Onizuka S, Seki M, Suzuki Y, Iwata T, Nakai K. A systematic sequencing-based approach for microbial contaminant detection and functional inference. BMC Biol 2019;17:72. [PMID: 31519179 PMCID: PMC6743104 DOI: 10.1186/s12915-019-0690-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/20/2019] [Indexed: 12/16/2022]  Open
93
Abbas-Aghababazadeh F, Mo Q, Fridley BL. Statistical genomics in rare cancer. Semin Cancer Biol 2019;61:1-10. [PMID: 31437624 DOI: 10.1016/j.semcancer.2019.08.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/14/2019] [Accepted: 08/17/2019] [Indexed: 12/26/2022]
94
Su L, Liu G, Wang J, Xu D. A rectified factor network based biclustering method for detecting cancer-related coding genes and miRNAs, and their interactions. Methods 2019;166:22-30. [PMID: 31121299 PMCID: PMC6708461 DOI: 10.1016/j.ymeth.2019.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 04/14/2019] [Accepted: 05/13/2019] [Indexed: 12/12/2022]  Open
95
Wilk G, Braun R. Integrative analysis reveals disrupted pathways regulated by microRNAs in cancer. Nucleic Acids Res 2019;46:1089-1101. [PMID: 29294105 PMCID: PMC5814839 DOI: 10.1093/nar/gkx1250] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/01/2017] [Indexed: 02/06/2023]  Open
96
Welch JD, Kozareva V, Ferreira A, Vanderburg C, Martin C, Macosko EZ. Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity. Cell 2019;177:1873-1887.e17. [PMID: 31178122 PMCID: PMC6716797 DOI: 10.1016/j.cell.2019.05.006] [Citation(s) in RCA: 721] [Impact Index Per Article: 120.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 02/21/2019] [Accepted: 04/30/2019] [Indexed: 02/07/2023]
97
Esposito F, Gillis N, Del Buono N. Orthogonal joint sparse NMF for microarray data analysis. J Math Biol 2019;79:223-247. [PMID: 31004215 DOI: 10.1007/s00285-019-01355-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 03/29/2019] [Indexed: 12/20/2022]
98
Li Y, Wu FX, Ngom A. A review on machine learning principles for multi-view biological data integration. Brief Bioinform 2019;19:325-340. [PMID: 28011753 DOI: 10.1093/bib/bbw113] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Indexed: 01/08/2023]  Open
99
Systematical Identification of Breast Cancer-Related Circular RNA Modules for Deciphering circRNA Functions Based on the Non-Negative Matrix Factorization Algorithm. Int J Mol Sci 2019;20:ijms20040919. [PMID: 30791568 PMCID: PMC6412941 DOI: 10.3390/ijms20040919] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/03/2019] [Accepted: 02/12/2019] [Indexed: 01/22/2023]  Open
100
Yang Z, Michailidis G. Quantifying heterogeneity of expression data based on principal components. Bioinformatics 2019;35:553-559. [PMID: 30060088 DOI: 10.1093/bioinformatics/bty671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 07/05/2018] [Accepted: 07/27/2018] [Indexed: 11/12/2022]  Open
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