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For: Chen CJ, Servant N, Toedling J, Sarazin A, Marchais A, Duvernois-Berthet E, Cognat V, Colot V, Voinnet O, Heard E, Ciaudo C, Barillot E. ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data. Bioinformatics 2012;28:3147-9. [PMID: 23044543 DOI: 10.1093/bioinformatics/bts587] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]  Open
Number Cited by Other Article(s)
51
Alidjinou EK, Engelmann I, Bossu J, Villenet C, Figeac M, Romond MB, Sané F, Hober D. Persistence of Coxsackievirus B4 in pancreatic ductal-like cells results in cellular and viral changes. Virulence 2017;8:1229-1244. [PMID: 28112573 DOI: 10.1080/21505594.2017.1284735] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
52
Han Y, He X. Integrating Epigenomics into the Understanding of Biomedical Insight. Bioinform Biol Insights 2016;10:267-289. [PMID: 27980397 PMCID: PMC5138066 DOI: 10.4137/bbi.s38427] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 11/01/2016] [Accepted: 11/06/2016] [Indexed: 12/13/2022]  Open
53
Barau J, Teissandier A, Zamudio N, Roy S, Nalesso V, Hérault Y, Guillou F, Bourc’his D. The DNA methyltransferase DNMT3C protects male germ cells from transposon activity. Science 2016;354:909-912. [DOI: 10.1126/science.aah5143] [Citation(s) in RCA: 210] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 10/19/2016] [Indexed: 12/23/2022]
54
Becker E, Bengs S, Aluri S, Opitz L, Atrott K, Stanzel C, Castro PAR, Rogler G, Frey-Wagner I. Doxycycline, metronidazole and isotretinoin: Do they modify microRNA/mRNA expression profiles and function in murine T-cells? Sci Rep 2016;6:37082. [PMID: 27853192 PMCID: PMC5113073 DOI: 10.1038/srep37082] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 10/18/2016] [Indexed: 12/19/2022]  Open
55
Woldemichael BT, Jawaid A, Kremer EA, Gaur N, Krol J, Marchais A, Mansuy IM. The microRNA cluster miR-183/96/182 contributes to long-term memory in a protein phosphatase 1-dependent manner. Nat Commun 2016;7:12594. [PMID: 27558292 PMCID: PMC5007330 DOI: 10.1038/ncomms12594] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 07/13/2016] [Indexed: 12/24/2022]  Open
56
Li HK, Mai RT, Huang HD, Chou CH, Chang YA, Chang YW, You LR, Chen CM, Lee YHW. DDX3 Represses Stemness by Epigenetically Modulating Tumor-suppressive miRNAs in Hepatocellular Carcinoma. Sci Rep 2016;6:28637. [PMID: 27344963 PMCID: PMC4921922 DOI: 10.1038/srep28637] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 06/06/2016] [Indexed: 12/16/2022]  Open
57
Hepatitis C Virus-Induced Upregulation of MicroRNA miR-146a-5p in Hepatocytes Promotes Viral Infection and Deregulates Metabolic Pathways Associated with Liver Disease Pathogenesis. J Virol 2016;90:6387-6400. [PMID: 27147737 DOI: 10.1128/jvi.00619-16] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 04/23/2016] [Indexed: 12/12/2022]  Open
58
RNA Bioinformatics for Precision Medicine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016;939:21-38. [DOI: 10.1007/978-981-10-1503-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
59
The Lin28/let-7 axis is critical for myelination in the peripheral nervous system. Nat Commun 2015;6:8584. [PMID: 26466203 PMCID: PMC4634210 DOI: 10.1038/ncomms9584] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 09/04/2015] [Indexed: 12/31/2022]  Open
60
Branscheid A, Marchais A, Schott G, Lange H, Gagliardi D, Andersen SU, Voinnet O, Brodersen P. SKI2 mediates degradation of RISC 5'-cleavage fragments and prevents secondary siRNA production from miRNA targets in Arabidopsis. Nucleic Acids Res 2015;43:10975-88. [PMID: 26464441 PMCID: PMC4678812 DOI: 10.1093/nar/gkv1014] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 09/24/2015] [Indexed: 12/19/2022]  Open
61
Afonso-Grunz F, Müller S. Principles of miRNA-mRNA interactions: beyond sequence complementarity. Cell Mol Life Sci 2015;72:3127-41. [PMID: 26037721 PMCID: PMC11114000 DOI: 10.1007/s00018-015-1922-2] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 04/26/2015] [Accepted: 05/04/2015] [Indexed: 11/24/2022]
62
Lopez JP, Diallo A, Cruceanu C, Fiori LM, Laboissiere S, Guillet I, Fontaine J, Ragoussis J, Benes V, Turecki G, Ernst C. Biomarker discovery: quantification of microRNAs and other small non-coding RNAs using next generation sequencing. BMC Med Genomics 2015;8:35. [PMID: 26130076 PMCID: PMC4487992 DOI: 10.1186/s12920-015-0109-x] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/16/2015] [Indexed: 02/08/2023]  Open
63
Cha DJ, Franklin JL, Dou Y, Liu Q, Higginbotham JN, Demory Beckler M, Weaver AM, Vickers K, Prasad N, Levy S, Zhang B, Coffey RJ, Patton JG. KRAS-dependent sorting of miRNA to exosomes. eLife 2015;4:e07197. [PMID: 26132860 PMCID: PMC4510696 DOI: 10.7554/elife.07197] [Citation(s) in RCA: 283] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 06/29/2015] [Indexed: 12/13/2022]  Open
64
Cha DJ, Franklin JL, Dou Y, Liu Q, Higginbotham JN, Demory Beckler M, Weaver AM, Vickers K, Prasad N, Levy S, Zhang B, Coffey RJ, Patton JG. KRAS-dependent sorting of miRNA to exosomes. eLife 2015. [PMID: 26132860 DOI: 10.7554/elife07197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
65
Veneziano D, Nigita G, Ferro A. Computational Approaches for the Analysis of ncRNA through Deep Sequencing Techniques. Front Bioeng Biotechnol 2015;3:77. [PMID: 26090362 PMCID: PMC4453482 DOI: 10.3389/fbioe.2015.00077] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 05/14/2015] [Indexed: 11/13/2022]  Open
66
Biryukova I, Ye T. Endogenous siRNAs and piRNAs derived from transposable elements and genes in the malaria vector mosquito Anopheles gambiae. BMC Genomics 2015;16:278. [PMID: 25879960 PMCID: PMC4423592 DOI: 10.1186/s12864-015-1436-1] [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: 11/16/2014] [Accepted: 03/06/2015] [Indexed: 12/24/2022]  Open
67
Integrated analyses to reconstruct microRNA-mediated regulatory networks in mouse liver using high-throughput profiling. BMC Genomics 2015;16 Suppl 2:S12. [PMID: 25707768 PMCID: PMC4331712 DOI: 10.1186/1471-2164-16-s2-s12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
68
Biryukova I, Ye T, Levashina E. Transcriptome-wide analysis of microRNA expression in the malaria mosquito Anopheles gambiae. BMC Genomics 2014;15:557. [PMID: 24997592 PMCID: PMC4112208 DOI: 10.1186/1471-2164-15-557] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 06/25/2014] [Indexed: 12/29/2022]  Open
69
Coruh C, Shahid S, Axtell MJ. Seeing the forest for the trees: annotating small RNA producing genes in plants. CURRENT OPINION IN PLANT BIOLOGY 2014;18:87-95. [PMID: 24632306 PMCID: PMC4001702 DOI: 10.1016/j.pbi.2014.02.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 01/28/2014] [Accepted: 02/14/2014] [Indexed: 05/09/2023]
70
The intestinal microbiota interferes with the microRNA response upon oral Listeria infection. mBio 2013;4:e00707-13. [PMID: 24327339 PMCID: PMC3870255 DOI: 10.1128/mbio.00707-13] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
71
Luo GZ, Yang W, Ma YK, Wang XJ. ISRNA: an integrative online toolkit for short reads from high-throughput sequencing data. ACTA ACUST UNITED AC 2013;30:434-6. [PMID: 24300438 DOI: 10.1093/bioinformatics/btt678] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
72
Maillard PV, Ciaudo C, Marchais A, Li Y, Jay F, Ding SW, Voinnet O. Antiviral RNA interference in mammalian cells. Science 2013;342:235-8. [PMID: 24115438 DOI: 10.1126/science.1241930] [Citation(s) in RCA: 316] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
73
Ciaudo C, Jay F, Okamoto I, Chen CJ, Sarazin A, Servant N, Barillot E, Heard E, Voinnet O. RNAi-dependent and independent control of LINE1 accumulation and mobility in mouse embryonic stem cells. PLoS Genet 2013;9:e1003791. [PMID: 24244175 PMCID: PMC3820764 DOI: 10.1371/journal.pgen.1003791] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 07/29/2013] [Indexed: 01/04/2023]  Open
74
Chen CJ, Heard E. Small RNAs derived from structural non-coding RNAs. Methods 2013;63:76-84. [DOI: 10.1016/j.ymeth.2013.05.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2013] [Revised: 04/12/2013] [Accepted: 05/06/2013] [Indexed: 12/25/2022]  Open
75
Jay F, Ciaudo C. An RNA tool kit to study the status of mouse ES cells: Sex determination and stemness. Methods 2013;63:85-92. [DOI: 10.1016/j.ymeth.2013.02.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 02/08/2013] [Accepted: 02/12/2013] [Indexed: 10/27/2022]  Open
76
Müller S, Rycak L, Winter P, Kahl G, Koch I, Rotter B. omiRas: a Web server for differential expression analysis of miRNAs derived from small RNA-Seq data. Bioinformatics 2013;29:2651-2. [DOI: 10.1093/bioinformatics/btt457] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]  Open
77
Wu J, Liu Q, Wang X, Zheng J, Wang T, You M, Sheng Sun Z, Shi Q. mirTools 2.0 for non-coding RNA discovery, profiling, and functional annotation based on high-throughput sequencing. RNA Biol 2013;10:1087-92. [PMID: 23778453 DOI: 10.4161/rna.25193] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
78
Castro-Vega LJ, Jouravleva K, Liu WY, Martinez C, Gestraud P, Hupé P, Servant N, Albaud B, Gentien D, Gad S, Richard S, Bacchetti S, Londoño-Vallejo A. Telomere crisis in kidney epithelial cells promotes the acquisition of a microRNA signature retrieved in aggressive renal cell carcinomas. Carcinogenesis 2013;34:1173-80. [PMID: 23358853 DOI: 10.1093/carcin/bgt029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]  Open
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