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For: Cabassi A, Kirk PDW. Multiple kernel learning for integrative consensus clustering of omic datasets. Bioinformatics 2021;36:4789-4796. [PMID: 32592464 PMCID: PMC7750932 DOI: 10.1093/bioinformatics/btaa593] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 05/18/2020] [Accepted: 06/19/2020] [Indexed: 12/19/2022]  Open
Number Cited by Other Article(s)
1
Ellington CN, Lengerich BJ, Watkins TBK, Yang J, Adduri AK, Mahbub S, Xiao H, Kellis M, Xing EP. Learning to estimate sample-specific transcriptional networks for 7,000 tumors. Proc Natl Acad Sci U S A 2025;122:e2411930122. [PMID: 40408406 DOI: 10.1073/pnas.2411930122] [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: 06/14/2024] [Accepted: 04/06/2025] [Indexed: 05/25/2025]  Open
2
Rao J, Kirk PDW. VICatMix: variational Bayesian clustering and variable selection for discrete biomedical data. BIOINFORMATICS ADVANCES 2025;5:vbaf055. [PMID: 40206332 PMCID: PMC11981716 DOI: 10.1093/bioadv/vbaf055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2025] [Accepted: 03/13/2025] [Indexed: 04/11/2025]
3
Duong HT, Huynh NCN, Nguyen CTK, Le LGH, Nguyen KD, Nguyen HT, Tu LNL, Tran NHB, Giang H, Nguyen HN, Ho CQ, Hoang HT, Dang THQ, Thai TA, Cao DV. Identify characteristics of Vietnamese oral squamous cell carcinoma patients by machine learning on transcriptome and clinical-histopathological analysis. J Dent Sci 2024;19:S81-S90. [PMID: 39807441 PMCID: PMC11725156 DOI: 10.1016/j.jds.2024.08.013] [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: 08/05/2024] [Revised: 08/19/2024] [Indexed: 01/16/2025]  Open
4
Qiu Y, Guo D, Zhao P, Zou Q. scMNMF: a novel method for single-cell multi-omics clustering based on matrix factorization. Brief Bioinform 2024;25:bbae228. [PMID: 38754408 PMCID: PMC11097994 DOI: 10.1093/bib/bbae228] [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: 01/31/2024] [Revised: 04/02/2024] [Accepted: 04/22/2024] [Indexed: 05/18/2024]  Open
5
Huang C, Kuan PF. intCC: An efficient weighted integrative consensus clustering of multimodal data. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2024;29:627-640. [PMID: 38160311 PMCID: PMC10764072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
6
Wu X, Han M, Song X, He S, Bo X, Zhu Y. COMMO: a web server for the identification and analysis of consensus gene modules across multiple methods. Bioinformatics 2023;39:btad708. [PMID: 37995293 PMCID: PMC10713113 DOI: 10.1093/bioinformatics/btad708] [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: 09/19/2023] [Revised: 11/05/2023] [Accepted: 11/22/2023] [Indexed: 11/25/2023]  Open
7
Marcos-Zambrano LJ, López-Molina VM, Bakir-Gungor B, Frohme M, Karaduzovic-Hadziabdic K, Klammsteiner T, Ibrahimi E, Lahti L, Loncar-Turukalo T, Dhamo X, Simeon A, Nechyporenko A, Pio G, Przymus P, Sampri A, Trajkovik V, Lacruz-Pleguezuelos B, Aasmets O, Araujo R, Anagnostopoulos I, Aydemir Ö, Berland M, Calle ML, Ceci M, Duman H, Gündoğdu A, Havulinna AS, Kaka Bra KHN, Kalluci E, Karav S, Lode D, Lopes MB, May P, Nap B, Nedyalkova M, Paciência I, Pasic L, Pujolassos M, Shigdel R, Susín A, Thiele I, Truică CO, Wilmes P, Yilmaz E, Yousef M, Claesson MJ, Truu J, Carrillo de Santa Pau E. A toolbox of machine learning software to support microbiome analysis. Front Microbiol 2023;14:1250806. [PMID: 38075858 PMCID: PMC10704913 DOI: 10.3389/fmicb.2023.1250806] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/11/2023] [Indexed: 05/14/2025]  Open
8
Chen W, Wang H, Liang C. Deep multi-view contrastive learning for cancer subtype identification. Brief Bioinform 2023;24:bbad282. [PMID: 37539822 DOI: 10.1093/bib/bbad282] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/29/2023] [Accepted: 07/19/2023] [Indexed: 08/05/2023]  Open
9
Cortes-Ciriano I, Steele CD, Piculell K, Al-Ibraheemi A, Eulo V, Bui MM, Chatzipli A, Dickson BC, Borcherding DC, Feber A, Galor A, Hart J, Jones KB, Jordan JT, Kim RH, Lindsay D, Miller C, Nishida Y, Proszek PZ, Serrano J, Sundby RT, Szymanski JJ, Ullrich NJ, Viskochil D, Wang X, Snuderl M, Park PJ, Flanagan AM, Hirbe AC, Pillay N, Miller DT, for the Genomics of MPNST (GeM) Consortium. Genomic Patterns of Malignant Peripheral Nerve Sheath Tumor (MPNST) Evolution Correlate with Clinical Outcome and Are Detectable in Cell-Free DNA. Cancer Discov 2023;13:654-671. [PMID: 36598417 PMCID: PMC9983734 DOI: 10.1158/2159-8290.cd-22-0786] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/09/2022] [Accepted: 12/16/2022] [Indexed: 01/05/2023]
10
Madhumita, Dwivedi A, Paul S. Recursive integration of synergised graph representations of multi-omics data for cancer subtypes identification. Sci Rep 2022;12:15629. [PMID: 36115864 PMCID: PMC9482647 DOI: 10.1038/s41598-022-17585-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 07/27/2022] [Indexed: 11/09/2022]  Open
11
Combining Molecular, Imaging, and Clinical Data Analysis for Predicting Cancer Prognosis. Cancers (Basel) 2022;14:cancers14133215. [PMID: 35804988 PMCID: PMC9265023 DOI: 10.3390/cancers14133215] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 02/04/2023]  Open
12
Brière G, Darbo É, Thébault P, Uricaru R. Consensus clustering applied to multi-omics disease subtyping. BMC Bioinformatics 2021;22:361. [PMID: 34229612 PMCID: PMC8259015 DOI: 10.1186/s12859-021-04279-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 06/28/2021] [Indexed: 11/10/2022]  Open
13
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
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