Discovering microRNAs from deep sequencing data using miRDeep (original) (raw)
Bushati, N. & Cohen, S.M. microRNA Functions. Annu. Rev. Cell Dev. Biol.23, 175–205 (2007). ArticleCAS Google Scholar
Bartel, D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell116, 281–297 (2004). ArticleCAS Google Scholar
Miranda, K.C. et al. A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell126, 1203–1217 (2006). ArticleCAS Google Scholar
Aravin, A. & Tuschl, T. Identification and characterization of small RNAs involved in RNA silencing. FEBS Lett.579, 5830–5840 (2005). ArticleCAS Google Scholar
Landgraf, P. et al. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell129, 1401–1414 (2007). ArticleCAS Google Scholar
Bentwich, I. Prediction and validation of microRNAs and their targets. FEBS Lett.579, 5904–5910 (2005). ArticleCAS Google Scholar
Lau, N.C. et al. Characterization of the piRNA complex from rat testes. Science313, 363–367 (2006). ArticleCAS Google Scholar
Ruby, J.G. et al. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans.Cell127, 1193–1207 (2006). ArticleCAS Google Scholar
Berezikov, E. et al. Diversity of microRNAs in human and chimpanzee brain. Nat. Genet.38, 1375–1377 (2006). ArticleCAS Google Scholar
Aravin, A.A., Sachidanandam, R., Girard, A., Fejes-Toth, K. & Hannon, G.J. Developmentally regulated piRNA clusters implicate MILI in transposon control. Science316, 744–747 (2007). ArticleCAS Google Scholar
Girard, A., Sachidanandam, R., Hannon, G.J. & Carmell, M.A. A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature442, 199–202 (2006). Article Google Scholar
Pak, J. & Fire, A. Distinct populations of primary and secondary effectors during RNAi in C. elegans.Science315, 241–244 (2007). ArticleCAS Google Scholar
Brennecke, J. et al. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila.Cell128, 1089–1103 (2007). ArticleCAS Google Scholar
Houwing, S. et al. A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in Zebrafish. Cell129, 69–82 (2007). ArticleCAS Google Scholar
Tarasov, V. et al. Differential regulation of microRNAs by p53 revealed by massively parallel sequencing: miR-34a is a p53 target that induces apoptosis and G1-arrest. Cell Cycle6, 1586–1593 (2007). ArticleCAS Google Scholar
Chen, K. & Rajewsky, N. The evolution of gene regulation by transcription factors and microRNAs. Nat. Rev. Genet.8, 93–103 (2007). ArticleCAS Google Scholar
Grishok, A. et al. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell106, 23–34 (2001). ArticleCAS Google Scholar
Hutvagner, G. et al. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science293, 834–838 (2001). ArticleCAS Google Scholar
Filipowicz, W., Bhattacharyya, S.N. & Sonenberg, N. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat. Rev. Genet.9, 102–114 (2008). ArticleCAS Google Scholar
Rajewsky, N. microRNA target predictions in animals. Nat. Genet.38 Suppl, S8–S13 (2006). ArticleCAS Google Scholar
Bonnet, E., Wuyts, J., Rouze, P. & Van de Peer, Y. Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics20, 2911–2917 (2004). ArticleCAS Google Scholar
Pasquinelli, A.E. et al. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature408, 86–89 (2000). ArticleCAS Google Scholar
Chen, K. & Rajewsky, N. Deep conservation of microRNA-target relationships and 3′UTR motifs in vertebrates, flies, and nematodes. Cold Spring Harb. Symp. Quant. Biol.71, 149–156 (2006). ArticleCAS Google Scholar
Griffiths-Jones, S., Grocock, R.J., van Dongen, S., Bateman, A. & Enright, A.J. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res.34, D140–D144 (2006). ArticleCAS Google Scholar
Berezikov, E. et al. Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis. Genome Res.16, 1289–1298 (2006). ArticleCAS Google Scholar
Vagin, V.V. et al. A distinct small RNA pathway silences selfish genetic elements in the germline. Science313, 320–324 (2006). ArticleCAS Google Scholar
Wightman, B., Ha, I. & Ruvkun, G. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell, 75, 855–862 (1993). ArticleCAS Google Scholar
Lee, R.C., Feinbaum, R.L. & Ambros, V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell75, 843–854 (1993). ArticleCAS Google Scholar
Ambros, V., Lee, R.C., Lavanway, A., Williams, P.T. & Jewell, D. MicroRNAs and other tiny endogenous RNAs in C. elegans.Curr. Biol.13, 807–818 (2003). ArticleCAS Google Scholar
Ohler, U., Yekta, S., Lim, L.P., Bartel, D.P. & Burge, C.B. Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification. RNA10, 1309–1322 (2004). ArticleCAS Google Scholar
Berezikov, E. et al. Phylogenetic shadowing and computational identification of human microRNA genes. Cell120, 21–24 (2005). ArticleCAS Google Scholar
Lindblad-Toh, K. et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature438, 803–819 (2005). ArticleCAS Google Scholar
Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. Basic local alignment search tool. J. Mol. Biol.215, 403–410 (1990). ArticleCAS Google Scholar
Palakodeti, D., Smielewska, M. & Graveley, B.R. MicroRNAs from the Planarian Schmidtea mediterranea: a model system for stem cell biology. RNA12, 1640–1649 (2006). ArticleCAS Google Scholar
Rettig, M.P. et al. Evaluation of biochemical changes during in vivo erythrocyte senescence in the dog. Blood93, 376–384 (1999). CASPubMed Google Scholar
Chomczynski, P. & Sacchi, N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal. Biochem.162, 156–159 (1987). ArticleCAS Google Scholar
Lagos-Quintana, M., Rauhut, R., Lendeckel, W. & Tuschl, T. Identification of novel genes coding for small expressed RNAs. Science294, 853–858 (2001). ArticleCAS Google Scholar
Karolchik, D. et al. The UCSC Genome Browser Database. Nucleic Acids Res.31, 51–54 (2003). ArticleCAS Google Scholar
Griffiths-Jones, S. et al. Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res.33, D121–D124 (2005). ArticleCAS Google Scholar
Altschul, S.F., Bundschuh, R., Olsen, R. & Hwa, T. The estimation of statistical parameters for local alignment score distributions. Nucleic Acids Res.29, 351–361 (2001). ArticleCAS Google Scholar