Literature DB >> 22161567

Identification of novel and known miRNAs in deep-sequencing data with miRDeep2.

Sebastian D Mackowiak1.   

Abstract

miRNAs comprise an abundant class of small non-coding RNAs that play important roles in a wide range of biological processes by post-transcriptional regulation of a large fraction of animal genes. High-throughput sequencing machines and the availability of completely sequenced genomes make it possible to reliably identify miRNAs with computational methods. This unit documents how to use the miRDeep2 software package to identify novel and known microRNAs in small RNA deep-sequencing data. Moreover, the usage of miRDeep2 to profile miRNA expression across samples is illustrated.
© 2011 by John Wiley & Sons, Inc.

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Year:  2011        PMID： 22161567     DOI： 10.1002/0471250953.bi1210s36

Source DB:  PubMed          Journal:  Curr Protoc Bioinformatics        ISSN： 1934-3396


  51 in total

1.  Detecting miRNAs in deep-sequencing data: a software performance comparison and evaluation.

Authors:  Vernell Williamson; Albert Kim; Bin Xie; G Omari McMichael; Yuan Gao; Vladimir Vladimirov
Journal:  Brief Bioinform       Date:  2012-03-24       Impact factor: 11.622

2.  Effects of Pasteurella multocida on Histopathology, miRNA and mRNA Expression Dynamics in Lung of Goats.

Authors:  Wencan Zhang; Zizhuo Jiao; Huixian Huang; Yanru Wu; Haotian Wu; Zhiyong Liu; Zhenxing Zhang; Qi An; Yiwen Cheng; Si Chen; Churiga Man; Li Du; Fengyang Wang; Qiaoling Chen
Journal:  Animals (Basel)       Date:  2022-06-13       Impact factor: 3.231

3.  Circulating miRNAs associated with bone mineral density in healthy adult baboons.

Authors:  Ellen E Quillen; Jaydee Foster; Anne Sheldrake; Maggie Stainback; Jeremy Glenn; Laura A Cox; Todd L Bredbenner
Journal:  J Orthop Res       Date:  2021-11-19       Impact factor: 3.102

4.  Discovery of microRNAs and transcript targets related to witches' broom disease in Paulownia fortunei by high-throughput sequencing and degradome approach.

Authors:  Suyan Niu; Guoqiang Fan; Minjie Deng; Zhenli Zhao; Enkai Xu; Lin Cao
Journal:  Mol Genet Genomics       Date:  2015-08-05       Impact factor: 3.291

5.  Evolution of small RNA expression following hybridization and allopolyploidization: insights from Spartina species (Poaceae, Chloridoideae).

Authors:  Armand Cavé-Radet; Delphine Giraud; Oscar Lima; Abdelhak El Amrani; Malika Aïnouche; Armel Salmon
Journal:  Plant Mol Biol       Date:  2019-11-20       Impact factor: 4.076

6.  Identification and functional analysis of microRNAs and their targets in Platanus acerifolia under lead (Pb) stress.

Authors:  Yuanlong Wang; Zhenli Zhao; Minjie Deng; Rongning Liu; Suyan Niu; Guoqiang Fan
Journal:  Int J Mol Sci       Date:  2015-03-30       Impact factor: 5.923

7.  High-throughput data integration of RNA-miRNA-circRNA reveals novel insights into mechanisms of benzo[a]pyrene-induced carcinogenicity.

Authors:  Florian Caiment; Stan Gaj; Sandra Claessen; Jos Kleinjans
Journal:  Nucleic Acids Res       Date:  2015-02-17       Impact factor: 16.971

8.  High-throughput sequencing reveals extraordinary fluidity of miRNA, piRNA, and siRNA pathways in nematodes.

Authors:  Zhen Shi; Taiowa A Montgomery; Yan Qi; Gary Ruvkun
Journal:  Genome Res       Date:  2013-01-30       Impact factor: 9.043

9.  Next generation sequencing reveals the expression of a unique miRNA profile in response to a gram-positive bacterial infection.

Authors:  Nathan Lawless; Amir B K Foroushani; Matthew S McCabe; Cliona O'Farrelly; David J Lynn
Journal:  PLoS One       Date:  2013-03-05       Impact factor: 3.240

10.  Exosomal miR-218-5p/miR-363-3p from Endothelial Progenitor Cells Ameliorate Myocardial Infarction by Targeting the p53/JMY Signaling Pathway.

Authors:  Xiao Ke; Rongfeng Yang; Fang Wu; Xing Wang; Jiawen Liang; Xun Hu; Chengheng Hu
Journal:  Oxid Med Cell Longev       Date:  2021-07-16       Impact factor: 6.543
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