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For: Ronen R, Gan I, Modai S, Sukacheov A, Dror G, Halperin E, Shomron N. miRNAkey: a software for microRNA deep sequencing analysis. ACTA ACUST UNITED AC 2010;26:2615-6. [PMID: 20801911 DOI: 10.1093/bioinformatics/btq493] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Number Cited by Other Article(s)
1
Chen JW, Shrestha L, Green G, Leier A, Marquez-Lago TT. The hitchhikers' guide to RNA sequencing and functional analysis. Brief Bioinform 2023;24:bbac529. [PMID: 36617463 PMCID: PMC9851315 DOI: 10.1093/bib/bbac529] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/18/2022] [Accepted: 11/07/2022] [Indexed: 01/10/2023]  Open
2
Diendorfer A, Khamina K, Pultar M, Hackl M. miND (miRNA NGS Discovery pipeline): a small RNA-seq analysis pipeline and report generator for microRNA biomarker discovery studies. F1000Res 2022. [DOI: 10.12688/f1000research.94159.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
3
La Ferlita A, Alaimo S, Di Bella S, Martorana E, Laliotis GI, Bertoni F, Cascione L, Tsichlis PN, Ferro A, Bosotti R, Pulvirenti A. RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis. BMC Bioinformatics 2021;22:298. [PMID: 34082707 PMCID: PMC8173825 DOI: 10.1186/s12859-021-04211-7] [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: 11/08/2020] [Accepted: 05/20/2021] [Indexed: 12/13/2022]  Open
4
MicroRNAs Regulating Autophagy in Neurodegeneration. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021;1208:191-264. [PMID: 34260028 DOI: 10.1007/978-981-16-2830-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
5
Kaur M, Kumar A, Siddaraju NK, Fairoze MN, Chhabra P, Ahlawat S, Vijh RK, Yadav A, Arora R. Differential expression of miRNAs in skeletal muscles of Indian sheep with diverse carcass and muscle traits. Sci Rep 2020;10:16332. [PMID: 33004825 PMCID: PMC7529745 DOI: 10.1038/s41598-020-73071-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 09/03/2020] [Indexed: 12/15/2022]  Open
6
Liu Q, Ding C, Lang X, Guo G, Chen J, Su X. Small noncoding RNA discovery and profiling with sRNAtools based on high-throughput sequencing. Brief Bioinform 2019;22:463-473. [PMID: 31885040 PMCID: PMC7820841 DOI: 10.1093/bib/bbz151] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/24/2019] [Accepted: 11/01/2019] [Indexed: 02/05/2023]  Open
7
Di Bella S, La Ferlita A, Carapezza G, Alaimo S, Isacchi A, Ferro A, Pulvirenti A, Bosotti R. A benchmarking of pipelines for detecting ncRNAs from RNA-Seq data. Brief Bioinform 2019;21:1987-1998. [PMID: 31740918 DOI: 10.1093/bib/bbz110] [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: 05/28/2019] [Revised: 07/12/2019] [Accepted: 08/01/2019] [Indexed: 12/18/2022]  Open
8
Computational Resources for Prediction and Analysis of Functional miRNA and Their Targetome. Methods Mol Biol 2019;1912:215-250. [PMID: 30635896 DOI: 10.1007/978-1-4939-8982-9_9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
9
HIV-1 infection increases microRNAs that inhibit Dicer1, HRB and HIV-EP2, thereby reducing viral replication. PLoS One 2019;14:e0211111. [PMID: 30682089 PMCID: PMC6347224 DOI: 10.1371/journal.pone.0211111] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 01/08/2019] [Indexed: 01/18/2023]  Open
10
Xue J, Zhou D, Poulsen O, Hartley I, Imamura T, Xie EX, Haddad GG. Exploring miRNA-mRNA regulatory network in cardiac pathology in Na+/H+ exchanger isoform 1 transgenic mice. Physiol Genomics 2018;50:846-861. [PMID: 30029588 DOI: 10.1152/physiolgenomics.00048.2018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]  Open
11
Baños-Lara MDR, Zabaleta J, Garai J, Baddoo M, Guerrero-Plata A. Comparative analysis of miRNA profile in human dendritic cells infected with respiratory syncytial virus and human metapneumovirus. BMC Res Notes 2018;11:432. [PMID: 29970194 PMCID: PMC6029031 DOI: 10.1186/s13104-018-3541-0] [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: 05/09/2018] [Accepted: 06/26/2018] [Indexed: 12/12/2022]  Open
12
miR-MaGiC improves quantification accuracy for small RNA-seq. BMC Res Notes 2018;11:296. [PMID: 29764489 PMCID: PMC5952827 DOI: 10.1186/s13104-018-3418-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/09/2018] [Indexed: 12/17/2022]  Open
13
Nair VB, Manasa VG, Sinto MS, Jayasree K, James FV, Kannan S. Differential Expression of MicroRNAs in Uterine Cervical Cancer and Its Implications in Carcinogenesis; An Integrative Approach. Int J Gynecol Cancer 2018;28:553-562. [PMID: 29466255 DOI: 10.1097/igc.0000000000001203] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
14
Bisgin H, Gong B, Wang Y, Tong W. Evaluation of Bioinformatics Approaches for Next-Generation Sequencing Analysis of microRNAs with a Toxicogenomics Study Design. Front Genet 2018;9:22. [PMID: 29467792 PMCID: PMC5808213 DOI: 10.3389/fgene.2018.00022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 01/17/2018] [Indexed: 12/18/2022]  Open
15
Shin SJ, Lee JH, Kwon HB. Genome-wide identification and characterization of drought responsive MicroRNAs in Solanum tuberosum L. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0586-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
16
Kappel A, Keller A. miRNA assays in the clinical laboratory: workflow, detection technologies and automation aspects. Clin Chem Lab Med 2017;55:636-647. [PMID: 27987355 DOI: 10.1515/cclm-2016-0467] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 11/01/2016] [Indexed: 12/27/2022]
17
Zhao S, Gordon W, Du S, Zhang C, He W, Xi L, Mathur S, Agostino M, Paradis T, von Schack D, Vincent M, Zhang B. QuickMIRSeq: a pipeline for quick and accurate quantification of both known miRNAs and isomiRs by jointly processing multiple samples from microRNA sequencing. BMC Bioinformatics 2017;18:180. [PMID: 28320324 PMCID: PMC5359966 DOI: 10.1186/s12859-017-1601-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 03/14/2017] [Indexed: 12/21/2022]  Open
18
Kfir-Erenfeld S, Haggiag N, Biton M, Stepensky P, Assayag-Asherie N, Yefenof E. miR-103 inhibits proliferation and sensitizes hemopoietic tumor cells for glucocorticoid-induced apoptosis. Oncotarget 2017;8:472-489. [PMID: 27888798 PMCID: PMC5352135 DOI: 10.18632/oncotarget.13447] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 11/12/2016] [Indexed: 11/25/2022]  Open
19
Amirkhah R, Meshkin HN, Farazmand A, Rasko JEJ, Schmitz U. Computational and Experimental Identification of Tissue-Specific MicroRNA Targets. Methods Mol Biol 2017;1580:127-147. [PMID: 28439832 DOI: 10.1007/978-1-4939-6866-4_11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
20
Veneziano D, Di Bella S, Nigita G, Laganà A, Ferro A, Croce CM. Noncoding RNA: Current Deep Sequencing Data Analysis Approaches and Challenges. Hum Mutat 2016;37:1283-1298. [PMID: 27516218 DOI: 10.1002/humu.23066] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/09/2016] [Indexed: 02/06/2023]
21
Ziemann M, Kaspi A, El-Osta A. Evaluation of microRNA alignment techniques. RNA (NEW YORK, N.Y.) 2016;22:1120-38. [PMID: 27284164 PMCID: PMC4931105 DOI: 10.1261/rna.055509.115] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 05/04/2016] [Indexed: 05/26/2023]
22
miARma-Seq: a comprehensive tool for miRNA, mRNA and circRNA analysis. Sci Rep 2016;6:25749. [PMID: 27167008 PMCID: PMC4863143 DOI: 10.1038/srep25749] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/21/2016] [Indexed: 01/21/2023]  Open
23
Urgese G, Paciello G, Acquaviva A, Ficarra E. isomiR-SEA: an RNA-Seq analysis tool for miRNAs/isomiRs expression level profiling and miRNA-mRNA interaction sites evaluation. BMC Bioinformatics 2016;17:148. [PMID: 27036505 PMCID: PMC4815201 DOI: 10.1186/s12859-016-0958-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 02/19/2016] [Indexed: 01/01/2023]  Open
24
Pirrò S, Zanella L, Kenzo M, Montesano C, Minutolo A, Potestà M, Sobze MS, Canini A, Cirilli M, Muleo R, Colizzi V, Galgani A. MicroRNA from Moringa oleifera: Identification by High Throughput Sequencing and Their Potential Contribution to Plant Medicinal Value. PLoS One 2016;11:e0149495. [PMID: 26930203 PMCID: PMC4773123 DOI: 10.1371/journal.pone.0149495] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 02/02/2016] [Indexed: 12/19/2022]  Open
25
Quek C, Jung CH, Bellingham SA, Lonie A, Hill AF. iSRAP - a one-touch research tool for rapid profiling of small RNA-seq data. J Extracell Vesicles 2015;4:29454. [PMID: 26561006 PMCID: PMC4641893 DOI: 10.3402/jev.v4.29454] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 10/12/2015] [Accepted: 10/14/2015] [Indexed: 12/23/2022]  Open
26
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
27
Tam S, Tsao MS, McPherson JD. Optimization of miRNA-seq data preprocessing. Brief Bioinform 2015;16:950-63. [PMID: 25888698 PMCID: PMC4652620 DOI: 10.1093/bib/bbv019] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Indexed: 12/05/2022]  Open
28
Han TS, Hur K, Xu G, Choi B, Okugawa Y, Toiyama Y, Oshima H, Oshima M, Lee HJ, Kim VN, Chang AN, Goel A, Yang HK. MicroRNA-29c mediates initiation of gastric carcinogenesis by directly targeting ITGB1. Gut 2015;64:203-14. [PMID: 24870620 PMCID: PMC4384419 DOI: 10.1136/gutjnl-2013-306640] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
29
Zhang B, Wang Q. MicroRNA-based biotechnology for plant improvement. J Cell Physiol 2015;230:1-15. [PMID: 24909308 DOI: 10.1002/jcp.24685] [Citation(s) in RCA: 164] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 05/21/2014] [Indexed: 12/19/2022]
30
Radovich M, Ragoussis J. Methods of quantifying microRNAs for hypoxia research: classic and next generation. Antioxid Redox Signal 2014;21:1239-48. [PMID: 24328936 DOI: 10.1089/ars.2013.5716] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
31
Wang H, Zhang Q, Fang X. Transcriptomics and proteomics in stem cell research. Front Med 2014;8:433-44. [PMID: 24972645 DOI: 10.1007/s11684-014-0336-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 03/14/2014] [Indexed: 12/20/2022]
32
Rudnicki A, Isakov O, Ushakov K, Shivatzki S, Weiss I, Friedman LM, Shomron N, Avraham KB. Next-generation sequencing of small RNAs from inner ear sensory epithelium identifies microRNAs and defines regulatory pathways. BMC Genomics 2014;15:484. [PMID: 24942165 PMCID: PMC4073505 DOI: 10.1186/1471-2164-15-484] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Accepted: 06/13/2014] [Indexed: 01/21/2023]  Open
33
Sun Z, Evans J, Bhagwate A, Middha S, Bockol M, Yan H, Kocher JP. CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data. BMC Genomics 2014;15:423. [PMID: 24894665 PMCID: PMC4070549 DOI: 10.1186/1471-2164-15-423] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Accepted: 05/27/2014] [Indexed: 01/21/2023]  Open
34
Yuan T, Huang X, Dittmar RL, Du M, Kohli M, Boardman L, Thibodeau SN, Wang L. eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing. BMC Genomics 2014;15:176. [PMID: 24593312 PMCID: PMC4029068 DOI: 10.1186/1471-2164-15-176] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 02/26/2014] [Indexed: 01/19/2023]  Open
35
Mehta JP. Sequencing small RNA: introduction and data analysis fundamentals. Methods Mol Biol 2014;1182:93-103. [PMID: 25055904 DOI: 10.1007/978-1-4939-1062-5_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
36
Patra D, Fasold M, Langenberger D, Steger G, Grosse I, Stadler PF. plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants. FRONTIERS IN PLANT SCIENCE 2014;5:708. [PMID: 25566282 PMCID: PMC4274896 DOI: 10.3389/fpls.2014.00708] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 11/26/2014] [Indexed: 05/11/2023]
37
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]
38
Jia J, Parikh H, Xiao W, Hoskins JW, Pflicke H, Liu X, Collins I, Zhou W, Wang Z, Powell J, Thorgeirsson SS, Rudloff U, Petersen GM, Amundadottir LT. An integrated transcriptome and epigenome analysis identifies a novel candidate gene for pancreatic cancer. BMC Med Genomics 2013;6:33. [PMID: 24053169 PMCID: PMC3849454 DOI: 10.1186/1755-8794-6-33] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 09/16/2013] [Indexed: 12/17/2022]  Open
39
Mor E, Shomron N. Species-specific microRNA regulation influences phenotypic variability: perspectives on species-specific microRNA regulation. Bioessays 2013;35:881-8. [PMID: 23864354 DOI: 10.1002/bies.201200157] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
40
miReader: Discovering Novel miRNAs in Species without Sequenced Genome. PLoS One 2013;8:e66857. [PMID: 23805282 PMCID: PMC3689854 DOI: 10.1371/journal.pone.0066857] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 05/11/2013] [Indexed: 12/26/2022]  Open
41
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
42
Metpally RPR, Nasser S, Malenica I, Courtright A, Carlson E, Ghaffari L, Villa S, Tembe W, Van Keuren-Jensen K. Comparison of Analysis Tools for miRNA High Throughput Sequencing Using Nerve Crush as a Model. Front Genet 2013;4:20. [PMID: 23459507 PMCID: PMC3585423 DOI: 10.3389/fgene.2013.00020] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 02/06/2013] [Indexed: 12/31/2022]  Open
43
Uva P, Da Sacco L, Del Cornò M, Baldassarre A, Sestili P, Orsini M, Palma A, Gessani S, Masotti A. Rat mir-155 generated from the lncRNA Bic is 'hidden' in the alternate genomic assembly and reveals the existence of novel mammalian miRNAs and clusters. RNA (NEW YORK, N.Y.) 2013;19:365-79. [PMID: 23329697 PMCID: PMC3677247 DOI: 10.1261/rna.035394.112] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
44
Chou CH, Lin FM, Chou MT, Hsu SD, Chang TH, Weng SL, Shrestha S, Hsiao CC, Hung JH, Huang HD. A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing. BMC Genomics 2013;14 Suppl 1:S2. [PMID: 23368412 PMCID: PMC3549799 DOI: 10.1186/1471-2164-14-s1-s2] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]  Open
45
Jorge NAN, Ferreira CG, Passetti F. Bioinformatics of Cancer ncRNA in High Throughput Sequencing: Present State and Challenges. Front Genet 2012;3:287. [PMID: 23251139 PMCID: PMC3523245 DOI: 10.3389/fgene.2012.00287] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 11/22/2012] [Indexed: 12/24/2022]  Open
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An J, Lai J, Lehman ML, Nelson CC. miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res 2012;41:727-37. [PMID: 23221645 PMCID: PMC3553977 DOI: 10.1093/nar/gks1187] [Citation(s) in RCA: 171] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
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Cheng WC, Chung IF, Huang TS, Chang ST, Sun HJ, Tsai CF, Liang ML, Wong TT, Wang HW. YM500: a small RNA sequencing (smRNA-seq) database for microRNA research. Nucleic Acids Res 2012. [PMID: 23203880 PMCID: PMC3531161 DOI: 10.1093/nar/gks1238] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]  Open
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Mapleson D, Moxon S, Dalmay T, Moulton V. MirPlex: A Tool for Identifying miRNAs in High-Throughput sRNA Datasets Without a Genome. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2012. [DOI: 10.1002/jez.b.22483] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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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] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]  Open
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miR-BAG: bagging based identification of microRNA precursors. PLoS One 2012;7:e45782. [PMID: 23049860 PMCID: PMC3458082 DOI: 10.1371/journal.pone.0045782] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 08/23/2012] [Indexed: 12/21/2022]  Open
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