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For: Jin D, Lee H. A computational approach to identifying gene-microRNA modules in cancer. PLoS Comput Biol 2015;11:e1004042. [PMID: 25611546 PMCID: PMC4303261 DOI: 10.1371/journal.pcbi.1004042] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 11/16/2014] [Indexed: 11/21/2022]  Open
Number Cited by Other Article(s)
1
Khemka N, Morris G, Kazemzadeh L, Costard LS, Neubert V, Bauer S, Rosenow F, Venø MT, Kjems J, Henshall DC, Prehn JHM, Connolly NMC. Integrative network analysis of miRNA-mRNA expression profiles during epileptogenesis in rats reveals therapeutic targets after emergence of first spontaneous seizure. Sci Rep 2024;14:15313. [PMID: 38961125 PMCID: PMC11222454 DOI: 10.1038/s41598-024-66117-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 06/27/2024] [Indexed: 07/05/2024]  Open
2
Arora A, Tsigelny IF, Kouznetsova VL. Laryngeal cancer diagnosis via miRNA-based decision tree model. Eur Arch Otorhinolaryngol 2024;281:1391-1399. [PMID: 38147113 DOI: 10.1007/s00405-023-08383-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 11/27/2023] [Indexed: 12/27/2023]
3
Chen J, Han G, Xu A, Akutsu T, Cai H. Identifying miRNA-Gene Common and Specific Regulatory Modules for Cancer Subtyping by a High-Order Graph Matching Model. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:421-431. [PMID: 35320104 DOI: 10.1109/tcbb.2022.3161635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
4
Lu L, Xu A, Gao F, Tian C, Wang H, Zhang J, Xie Y, Liu P, Liu S, Yang C, Ye Z, Wu X. Mesenchymal Stem Cell-Derived Exosomes as a Novel Strategy for the Treatment of Intervertebral Disc Degeneration. Front Cell Dev Biol 2022;9:770510. [PMID: 35141231 PMCID: PMC8818990 DOI: 10.3389/fcell.2021.770510] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/31/2021] [Indexed: 12/15/2022]  Open
5
Zhu F, Li J, Liu J, Min W. Network-based cancer genomic data integration for pattern discovery. BMC Genom Data 2021;22:54. [PMID: 34886811 PMCID: PMC8662848 DOI: 10.1186/s12863-021-01004-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
6
Soremekun O, Ezenwa C, Paimo O, Madu C, Omotoso O, Akinifesi O, Ntuenibok N. Integrative analysis of microRNA expression level profile identifies microRNAs associated with prostate cancer. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
7
Wani N, Barh D, Raza K. Modular network inference between miRNA-mRNA expression profiles using weighted co-expression network analysis. J Integr Bioinform 2021;18:20210029. [PMID: 34800012 PMCID: PMC8709739 DOI: 10.1515/jib-2021-0029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/20/2021] [Accepted: 10/28/2021] [Indexed: 12/14/2022]  Open
8
TSCCA: A tensor sparse CCA method for detecting microRNA-gene patterns from multiple cancers. PLoS Comput Biol 2021;17:e1009044. [PMID: 34061840 PMCID: PMC8195367 DOI: 10.1371/journal.pcbi.1009044] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 06/11/2021] [Accepted: 05/05/2021] [Indexed: 12/22/2022]  Open
9
Fang R, Yang H, Gao Y, Cao H, Goode EL, Cui Y. Gene-based mediation analysis in epigenetic studies. Brief Bioinform 2021;22:bbaa113. [PMID: 32608480 PMCID: PMC8660163 DOI: 10.1093/bib/bbaa113] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 04/07/2020] [Accepted: 05/12/2020] [Indexed: 12/15/2022]  Open
10
Paul S. RFCM3: Computational Method for Identification of miRNA-mRNA Regulatory Modules in Cervical Cancer. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020;17:1729-1740. [PMID: 30990434 DOI: 10.1109/tcbb.2019.2910851] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
11
Huang J, Chen J, Zhang B, Zhu L, Cai H. Evaluation of gene-drug common module identification methods using pharmacogenomics data. Brief Bioinform 2020;22:5860683. [PMID: 32591780 DOI: 10.1093/bib/bbaa087] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/06/2020] [Accepted: 04/23/2020] [Indexed: 01/21/2023]  Open
12
Rahmanian S, Murad R, Breschi A, Zeng W, Mackiewicz M, Williams B, Davis CA, Roberts B, Meadows S, Moore D, Trout D, Zaleski C, Dobin A, Sei LH, Drenkow J, Scavelli A, Gingeras TR, Wold BJ, Myers RM, Guigó R, Mortazavi A. Dynamics of microRNA expression during mouse prenatal development. Genome Res 2019;29:1900-1909. [PMID: 31645363 PMCID: PMC6836743 DOI: 10.1101/gr.248997.119] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 08/29/2019] [Indexed: 12/15/2022]
13
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
14
Xiao Q, Luo J, Liang C, Cai J, Li G, Cao B. CeModule: an integrative framework for discovering regulatory patterns from genomic data in cancer. BMC Bioinformatics 2019;20:67. [PMID: 30732558 PMCID: PMC6367773 DOI: 10.1186/s12859-019-2654-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 01/24/2019] [Indexed: 12/14/2022]  Open
15
Zhang Y, Liu C, Wang J, Li X. Application of Monte Carlo cross-validation to identify pathway cross-talk in neonatal sepsis. Exp Biol Med (Maywood) 2018;243:444-450. [PMID: 29513099 PMCID: PMC5882034 DOI: 10.1177/1535370218759635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 01/17/2018] [Indexed: 01/06/2023]  Open
16
Luo J, Huang W, Cao B. A novel approach to identify the miRNA-mRNA causal regulatory modules in Cancer. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018;15:309-315. [PMID: 28113985 DOI: 10.1109/tcbb.2016.2612199] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
17
Jin D, Lee H. FGMD: A novel approach for functional gene module detection in cancer. PLoS One 2017;12:e0188900. [PMID: 29244808 PMCID: PMC5731741 DOI: 10.1371/journal.pone.0188900] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 11/15/2017] [Indexed: 12/26/2022]  Open
18
Seo J, Jin D, Choi CH, Lee H. Integration of MicroRNA, mRNA, and Protein Expression Data for the Identification of Cancer-Related MicroRNAs. PLoS One 2017;12:e0168412. [PMID: 28056026 PMCID: PMC5215789 DOI: 10.1371/journal.pone.0168412] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 11/29/2016] [Indexed: 12/20/2022]  Open
19
Prioritizing cancer-related microRNAs by integrating microRNA and mRNA datasets. Sci Rep 2016;6:35350. [PMID: 27734929 PMCID: PMC5062133 DOI: 10.1038/srep35350] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 09/28/2016] [Indexed: 12/29/2022]  Open
20
Walsh CJ, Hu P, Batt J, Dos Santos CC. Discovering MicroRNA-Regulatory Modules in Multi-Dimensional Cancer Genomic Data: A Survey of Computational Methods. Cancer Inform 2016;15:25-42. [PMID: 27721651 PMCID: PMC5051584 DOI: 10.4137/cin.s39369] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/14/2016] [Accepted: 08/16/2016] [Indexed: 12/20/2022]  Open
21
Sridharan K, Gogtay NJ. Therapeutic nucleic acids: current clinical status. Br J Clin Pharmacol 2016;82:659-72. [PMID: 27111518 DOI: 10.1111/bcp.12987] [Citation(s) in RCA: 165] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 04/20/2016] [Accepted: 04/21/2016] [Indexed: 02/06/2023]  Open
22
A Two-Stage Method to Identify Joint Modules From Matched MicroRNA and mRNA Expression Data. IEEE Trans Nanobioscience 2016. [DOI: 10.1109/tnb.2016.2556744] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
23
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] [Abstract] [MESH Headings] [Grants] [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
24
Yao X, Yan J, Kim S, Nho K, Risacher SL, Inlow M, Moore JH, Saykin AJ, Shen L, for the Alzheimer’s Disease Neuroimaging Initiative**. Two-dimensional Enrichment Analysis for Mining High-level Imaging Genetic Associations. BRAIN INFORMATICS AND HEALTH : 8TH INTERNATIONAL CONFERENCE, BIH 2015, LONDON, UK, AUGUST 30-SEPTEMBER 2, 2015 : PROCEEDINGS. BIH (CONFERENCE) (8TH : 2015 : LONDON, ENGLAND) 2015;9250:115-124. [PMID: 26568986 PMCID: PMC4640356 DOI: 10.1007/978-3-319-23344-4_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
25
Integrative Analysis with Monte Carlo Cross-Validation Reveals miRNAs Regulating Pathways Cross-Talk in Aggressive Breast Cancer. BIOMED RESEARCH INTERNATIONAL 2015;2015:831314. [PMID: 26240829 PMCID: PMC4512830 DOI: 10.1155/2015/831314] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/31/2015] [Accepted: 06/08/2015] [Indexed: 12/11/2022]
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