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For: Sass S, Dietmann S, Burk UC, Brabletz S, Lutter D, Kowarsch A, Mayer KF, Brabletz T, Ruepp A, Theis FJ, Wang Y. MicroRNAs coordinately regulate protein complexes. BMC Syst Biol 2011;5:136. [PMID: 21867514 PMCID: PMC3170341 DOI: 10.1186/1752-0509-5-136] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 08/25/2011] [Indexed: 02/06/2023]
Number Cited by Other Article(s)
1
Yang T, He Y, Wang Y. Introducing TEC-LncMir for prediction of lncRNA-miRNA interactions through deep learning of RNA sequences. Brief Bioinform 2024;26:bbaf046. [PMID: 39927859 PMCID: PMC11808807 DOI: 10.1093/bib/bbaf046] [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: 09/18/2024] [Revised: 12/30/2024] [Accepted: 01/22/2025] [Indexed: 02/11/2025]  Open
2
Yang T, Wang Y, He Y. TEC-miTarget: enhancing microRNA target prediction based on deep learning of ribonucleic acid sequences. BMC Bioinformatics 2024;25:159. [PMID: 38643080 PMCID: PMC11032603 DOI: 10.1186/s12859-024-05780-z] [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: 10/16/2023] [Accepted: 04/12/2024] [Indexed: 04/22/2024]  Open
3
The EMT activator ZEB1 accelerates endosomal trafficking to establish a polarity axis in lung adenocarcinoma cells. Nat Commun 2021;12:6354. [PMID: 34732702 PMCID: PMC8566461 DOI: 10.1038/s41467-021-26677-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 09/20/2021] [Indexed: 12/15/2022]  Open
4
Fishman ES, Louie M, Miltner AM, Cheema SK, Wong J, Schlaeger NM, Moshiri A, Simó S, Tarantal AF, La Torre A. MicroRNA Signatures of the Developing Primate Fovea. Front Cell Dev Biol 2021;9:654385. [PMID: 33898453 PMCID: PMC8060505 DOI: 10.3389/fcell.2021.654385] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 03/16/2021] [Indexed: 11/22/2022]  Open
5
Liu N, Wei S, Zhao R. Integrated miRNA-mRNA Analysis Reveals Potential Biomarkers of Chemoresistance in Ovarian Cancer. J BIOMATER TISS ENG 2021. [DOI: 10.1166/jbt.2021.2508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
6
Yoon S, Nguyen HCT, Jo W, Kim J, Chi SM, Park J, Kim SY, Nam D. Biclustering analysis of transcriptome big data identifies condition-specific microRNA targets. Nucleic Acids Res 2019;47:e53. [PMID: 30820547 PMCID: PMC6511842 DOI: 10.1093/nar/gkz139] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 02/19/2019] [Indexed: 12/26/2022]  Open
7
Lei H, Liu W, Si J, Wang J, Zhang T. Analyzing the regulation of miRNAs on protein-protein interaction network in Hodgkin lymphoma. BMC Bioinformatics 2019;20:449. [PMID: 31477006 PMCID: PMC6720096 DOI: 10.1186/s12859-019-3041-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/21/2019] [Indexed: 12/28/2022]  Open
8
Kinetic Modelling of Competition and Depletion of Shared miRNAs by Competing Endogenous RNAs. Methods Mol Biol 2019;1912:367-409. [PMID: 30635902 DOI: 10.1007/978-1-4939-8982-9_15] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
9
In silico identification of microRNAs predicted to regulate N-myristoyltransferase and Methionine Aminopeptidase 2 functions in cancer and infectious diseases. PLoS One 2018;13:e0194612. [PMID: 29579063 PMCID: PMC5868815 DOI: 10.1371/journal.pone.0194612] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 03/06/2018] [Indexed: 01/16/2023]  Open
10
Lu M, Xu X, Xi B, Dai Q, Li C, Su L, Zhou X, Tang M, Yao Y, Yang J. Molecular Network-Based Identification of Competing Endogenous RNAs in Thyroid Carcinoma. Genes (Basel) 2018;9:E44. [PMID: 29351231 PMCID: PMC5793195 DOI: 10.3390/genes9010044] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 01/10/2018] [Accepted: 01/11/2018] [Indexed: 12/14/2022]  Open
11
Boone DK, Weisz HA, Bi M, Falduto MT, Torres KEO, Willey HE, Volsko CM, Kumar AM, Micci MA, Dewitt DS, Prough DS, Hellmich HL. Evidence linking microRNA suppression of essential prosurvival genes with hippocampal cell death after traumatic brain injury. Sci Rep 2017;7:6645. [PMID: 28751711 PMCID: PMC5532254 DOI: 10.1038/s41598-017-06341-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 06/13/2017] [Indexed: 01/09/2023]  Open
12
He SJ, Xiang CQ, Zhang Y, Lu XT, Chen HW, Xiong LX. Recent progress on the effects of microRNAs and natural products on tumor epithelial-mesenchymal transition. Onco Targets Ther 2017;10:3435-3451. [PMID: 28744148 PMCID: PMC5513877 DOI: 10.2147/ott.s139546] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
13
Martirosyan A, De Martino A, Pagnani A, Marinari E. ceRNA crosstalk stabilizes protein expression and affects the correlation pattern of interacting proteins. Sci Rep 2017;7:43673. [PMID: 28266541 PMCID: PMC5339858 DOI: 10.1038/srep43673] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 01/27/2017] [Indexed: 12/14/2022]  Open
14
Bracken CP, Scott HS, Goodall GJ. A network-biology perspective of microRNA function and dysfunction in cancer. Nat Rev Genet 2016;17:719-732. [DOI: 10.1038/nrg.2016.134] [Citation(s) in RCA: 529] [Impact Index Per Article: 58.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
15
Tkatchenko AV, Luo X, Tkatchenko TV, Vaz C, Tanavde VM, Maurer-Stroh S, Zauscher S, Gonzalez P, Young TL. Large-Scale microRNA Expression Profiling Identifies Putative Retinal miRNA-mRNA Signaling Pathways Underlying Form-Deprivation Myopia in Mice. PLoS One 2016;11:e0162541. [PMID: 27622715 PMCID: PMC5021328 DOI: 10.1371/journal.pone.0162541] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 08/24/2016] [Indexed: 12/16/2022]  Open
16
Lai M, Gonzalez-Martin A, Cooper AB, Oda H, Jin HY, Shepherd J, He L, Zhu J, Nemazee D, Xiao C. Regulation of B-cell development and tolerance by different members of the miR-17∼92 family microRNAs. Nat Commun 2016;7:12207. [PMID: 27481093 PMCID: PMC4974641 DOI: 10.1038/ncomms12207] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 06/10/2016] [Indexed: 12/19/2022]  Open
17
Preusse M, Marr C, Saunders S, Maticzka D, Lickert H, Backofen R, Theis F. SimiRa: A tool to identify coregulation between microRNAs and RNA-binding proteins. RNA Biol 2016;12:998-1009. [PMID: 26383775 PMCID: PMC4615630 DOI: 10.1080/15476286.2015.1068496] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
18
MicroRNA-Target Network Inference and Local Network Enrichment Analysis Identify Two microRNA Clusters with Distinct Functions in Head and Neck Squamous Cell Carcinoma. Int J Mol Sci 2015;16:30204-22. [PMID: 26694379 PMCID: PMC4691172 DOI: 10.3390/ijms161226230] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 12/08/2015] [Accepted: 12/09/2015] [Indexed: 12/23/2022]  Open
19
Zhang J, Le TD, Liu L, He J, Li J. A novel framework for inferring condition-specific TF and miRNA co-regulation of protein-protein interactions. Gene 2015;577:55-64. [PMID: 26611531 DOI: 10.1016/j.gene.2015.11.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 10/16/2015] [Accepted: 11/17/2015] [Indexed: 12/11/2022]
20
Meyer SU, Sass S, Mueller NS, Krebs S, Bauersachs S, Kaiser S, Blum H, Thirion C, Krause S, Theis FJ, Pfaffl MW. Integrative Analysis of MicroRNA and mRNA Data Reveals an Orchestrated Function of MicroRNAs in Skeletal Myocyte Differentiation in Response to TNF-α or IGF1. PLoS One 2015;10:e0135284. [PMID: 26270642 PMCID: PMC4536022 DOI: 10.1371/journal.pone.0135284] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 07/20/2015] [Indexed: 12/23/2022]  Open
21
Benlhabib H, Guo W, Pierce BM, Mendelson CR. The miR-200 family and its targets regulate type II cell differentiation in human fetal lung. J Biol Chem 2015. [PMID: 26203191 DOI: 10.1074/jbc.m114.636068] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
22
Mitra R, Lin CC, Eischen CM, Bandyopadhyay S, Zhao Z. Concordant dysregulation of miR-5p and miR-3p arms of the same precursor microRNA may be a mechanism in inducing cell proliferation and tumorigenesis: a lung cancer study. RNA (NEW YORK, N.Y.) 2015;21:1055-1065. [PMID: 25852169 PMCID: PMC4436660 DOI: 10.1261/rna.048132.114] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 02/11/2015] [Indexed: 05/29/2023]
23
Bajan S, Hutvagner G. Regulation of miRNA processing and miRNA mediated gene repression in cancer. Microrna 2015;3:10-7. [PMID: 25069508 PMCID: PMC4260356 DOI: 10.2174/2211536602666140110234046] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 12/13/2013] [Accepted: 12/20/2013] [Indexed: 12/19/2022]
24
Ulfenborg B, Jurcevic S, Lindlöf A, Klinga-Levan K, Olsson B. miREC: a database of miRNAs involved in the development of endometrial cancer. BMC Res Notes 2015;8:104. [PMID: 25889518 PMCID: PMC4383082 DOI: 10.1186/s13104-015-1052-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 03/11/2015] [Indexed: 12/19/2022]  Open
25
Aure MR, Jernström S, Krohn M, Vollan HKM, Due EU, Rødland E, Kåresen R, Ram P, Lu Y, Mills GB, Sahlberg KK, Børresen-Dale AL, Lingjærde OC, Kristensen VN. Integrated analysis reveals microRNA networks coordinately expressed with key proteins in breast cancer. Genome Med 2015;7:21. [PMID: 25873999 PMCID: PMC4396592 DOI: 10.1186/s13073-015-0135-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 01/19/2015] [Indexed: 01/20/2023]  Open
26
Obermayer B, Levine E. Exploring the miRNA regulatory network using evolutionary correlations. PLoS Comput Biol 2014;10:e1003860. [PMID: 25299225 PMCID: PMC4191876 DOI: 10.1371/journal.pcbi.1003860] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 08/18/2014] [Indexed: 01/01/2023]  Open
27
Yogev O, Lagos D, Enver T, Boshoff C. Kaposi's sarcoma herpesvirus microRNAs induce metabolic transformation of infected cells. PLoS Pathog 2014;10:e1004400. [PMID: 25255370 PMCID: PMC4177984 DOI: 10.1371/journal.ppat.1004400] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 08/14/2014] [Indexed: 02/01/2023]  Open
28
Ye Y, Li D, Ouyang D, Deng L, Zhang Y, Ma Y, Li Y. MicroRNA expression in the aging mouse thymus. Gene 2014;547:218-25. [DOI: 10.1016/j.gene.2014.06.039] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 06/05/2014] [Accepted: 06/19/2014] [Indexed: 01/03/2023]
29
Moyret-Lalle C, Ruiz E, Puisieux A. Epithelial-mesenchymal transition transcription factors and miRNAs: “Plastic surgeons” of breast cancer. World J Clin Oncol 2014;5:311-322. [PMID: 25114847 PMCID: PMC4127603 DOI: 10.5306/wjco.v5.i3.311] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 03/18/2014] [Accepted: 06/27/2014] [Indexed: 02/06/2023]  Open
30
Afshar AS, Xu J, Goutsias J. Integrative identification of deregulated miRNA/TF-mediated gene regulatory loops and networks in prostate cancer. PLoS One 2014;9:e100806. [PMID: 24968068 PMCID: PMC4072696 DOI: 10.1371/journal.pone.0100806] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 05/28/2014] [Indexed: 01/07/2023]  Open
31
Zhu W, Chen YPP. Computational developments in microRNA-regulated protein-protein interactions. BMC SYSTEMS BIOLOGY 2014;8:14. [PMID: 24507415 PMCID: PMC3922185 DOI: 10.1186/1752-0509-8-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 01/20/2014] [Indexed: 01/12/2023]
32
Alshalalfa M, D. Bader G, Bismar TA, Alhajj R. Coordinate microRNA-mediated regulation of protein complexes in prostate cancer. PLoS One 2013;8:e84261. [PMID: 24391925 PMCID: PMC3877262 DOI: 10.1371/journal.pone.0084261] [Citation(s) in RCA: 7] [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: 05/06/2013] [Accepted: 11/21/2013] [Indexed: 11/18/2022]  Open
33
Le HS, Bar-Joseph Z. Integrating sequence, expression and interaction data to determine condition-specific miRNA regulation. Bioinformatics 2013;29:i89-97. [PMID: 23813013 PMCID: PMC3694655 DOI: 10.1093/bioinformatics/btt231] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]  Open
34
Gorini G, Nunez YO, Mayfield RD. Integration of miRNA and protein profiling reveals coordinated neuroadaptations in the alcohol-dependent mouse brain. PLoS One 2013;8:e82565. [PMID: 24358208 PMCID: PMC3865091 DOI: 10.1371/journal.pone.0082565] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 10/24/2013] [Indexed: 12/12/2022]  Open
35
Alshalalfa M. miRNA regulation in the context of functional protein networks: principles and applications. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2013;6:189-99. [PMID: 24532562 DOI: 10.1002/wsbm.1251] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
36
Wang L, Tian WD, Xu X, Nie B, Lu J, Liu X, Zhang B, Dong Q, Sunwoo JB, Li G, Li XP. Epstein-Barr virus nuclear antigen 1 (EBNA1) protein induction of epithelial-mesenchymal transition in nasopharyngeal carcinoma cells. Cancer 2013;120:363-72. [PMID: 24190575 DOI: 10.1002/cncr.28418] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 09/03/2013] [Accepted: 09/04/2013] [Indexed: 12/16/2022]
37
Chavali S, Bruhn S, Tiemann K, Sætrom P, Barrenäs F, Saito T, Kanduri K, Wang H, Benson M. MicroRNAs act complementarily to regulate disease-related mRNA modules in human diseases. RNA (NEW YORK, N.Y.) 2013;19:1552-1562. [PMID: 24062574 PMCID: PMC3851722 DOI: 10.1261/rna.038414.113] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 08/20/2013] [Indexed: 06/02/2023]
38
Singhal R, Bard JE, Nowak NJ, Buck MJ, Kandel ES. FOXO1 regulates expression of a microRNA cluster on X chromosome. Aging (Albany NY) 2013;5:347-56. [PMID: 23748164 PMCID: PMC3701110 DOI: 10.18632/aging.100558] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
39
Alshalalfa M, Alhajj R. Using context-specific effect of miRNAs to identify functional associations between miRNAs and gene signatures. BMC Bioinformatics 2013;14 Suppl 12:S1. [PMID: 24267745 PMCID: PMC3848857 DOI: 10.1186/1471-2105-14-s12-s1] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]  Open
40
Lemons D, Maurya MR, Subramaniam S, Mercola M. Developing microRNA screening as a functional genomics tool for disease research. Front Physiol 2013;4:223. [PMID: 23986717 PMCID: PMC3753477 DOI: 10.3389/fphys.2013.00223] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 08/02/2013] [Indexed: 02/04/2023]  Open
41
Sass S, Buettner F, Mueller NS, Theis FJ. A modular framework for gene set analysis integrating multilevel omics data. Nucleic Acids Res 2013;41:9622-33. [PMID: 23975194 PMCID: PMC3834824 DOI: 10.1093/nar/gkt752] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]  Open
42
Stankiewicz TR, Schroeder EK, Kelsey NA, Bouchard RJ, Linseman DA. C-terminal binding proteins are essential pro-survival factors that undergo caspase-dependent downregulation during neuronal apoptosis. Mol Cell Neurosci 2013;56:322-332. [PMID: 23859824 DOI: 10.1016/j.mcn.2013.07.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 06/25/2013] [Accepted: 07/08/2013] [Indexed: 12/20/2022]  Open
43
Complex-forming proteins escape the robust regulations of miRNA in human. FEBS Lett 2013;587:2284-7. [PMID: 23756149 DOI: 10.1016/j.febslet.2013.05.062] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/21/2013] [Accepted: 05/29/2013] [Indexed: 12/14/2022]
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Qabaja A, Alshalalfa M, Bismar TA, Alhajj R. Protein network-based Lasso regression model for the construction of disease-miRNA functional interactions. EURASIP JOURNAL ON BIOINFORMATICS & SYSTEMS BIOLOGY 2013;2013:3. [PMID: 23339438 PMCID: PMC3606436 DOI: 10.1186/1687-4153-2013-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 10/29/2012] [Indexed: 12/26/2022]
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A systematic screen reveals MicroRNA clusters that significantly regulate four major signaling pathways. PLoS One 2012;7:e48474. [PMID: 23144891 PMCID: PMC3493556 DOI: 10.1371/journal.pone.0048474] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 09/26/2012] [Indexed: 11/19/2022]  Open
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Alshalalfa M, Bader GD, Goldenberg A, Morris Q, Alhajj R. Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study. BMC SYSTEMS BIOLOGY 2012;6:112. [PMID: 22929553 PMCID: PMC3490713 DOI: 10.1186/1752-0509-6-112] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 08/14/2012] [Indexed: 11/10/2022]
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Sen K, Ghosh TC. Evolutionary conservation and disease gene association of the human genes composing pseudogenes. Gene 2012;501:164-70. [PMID: 22521745 DOI: 10.1016/j.gene.2012.04.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 02/09/2012] [Accepted: 04/05/2012] [Indexed: 01/16/2023]
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Gennarino VA, D'Angelo G, Dharmalingam G, Fernandez S, Russolillo G, Sanges R, Mutarelli M, Belcastro V, Ballabio A, Verde P, Sardiello M, Banfi S. Identification of microRNA-regulated gene networks by expression analysis of target genes. Genome Res 2012;22:1163-72. [PMID: 22345618 PMCID: PMC3371699 DOI: 10.1101/gr.130435.111] [Citation(s) in RCA: 148] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Goh WWB, Oikawa H, Sng JCG, Sergot M, Wong L. The role of miRNAs in complex formation and control. ACTA ACUST UNITED AC 2011;28:453-6. [PMID: 22180412 DOI: 10.1093/bioinformatics/btr693] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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