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Volumn 822, Issue , 2012, Pages 233-248

DeepBase: Annotation and discovery of MicroRNAs and other noncoding RNAs from deep-sequencing data

Author keywords

Deep sequencing; Expression pattern; MicroRNA; ncRNA; Next generation sequencing; Small RNA

Indexed keywords

MICRORNA; UNTRANSLATED RNA;

EID: 84862946513     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-427-8_16     Document Type: Article
Times cited : (22)

References (27)
  • 1
    • 52949096084 scopus 로고    scopus 로고
    • Next-generation DNA sequencing methods
    • Mardis, E. R. (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9, 387-402.
    • (2008) Annu Rev Genomics Hum Genet , vol.9 , pp. 387-402
    • Mardis E, R.1
  • 2
    • 39649117755 scopus 로고    scopus 로고
    • The impact of nextgeneration sequencing technology on genetics
    • Mardis, E. R. (2008) The impact of nextgeneration sequencing technology on genetics. Trends Genet 24, 133-41.
    • (2008) Trends Genet , vol.24 , pp. 133-41
    • Mardis E, R.1
  • 3
    • 62349102325 scopus 로고    scopus 로고
    • Next is now: New technologies for sequencing of genomes, transcriptomes, and beyond
    • Lister, R., Gregory, B. D., and Ecker, J. R. (2009) Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond. Curr Opin Plant Biol 12, 107-18.
    • (2009) Curr Opin Plant Biol , vol.12 , pp. 107-18
    • Lister, R.1    Gregory, B.D.2    Ecker, J.R.3
  • 4
    • 50149095122 scopus 로고    scopus 로고
    • Endogenous small interfering RNAs in animals
    • Okamura, K., and Lai, E. C. (2008) Endogenous small interfering RNAs in animals. Nat Rev Mol Cell Biol 9, 673-8.
    • (2008) Nat Rev Mol Cell Biol , vol.9 , pp. 673-8
    • Okamura, K.1    Lai, E.C.2
  • 5
    • 58449134534 scopus 로고    scopus 로고
    • Small silencing RNAs: An expanding universe
    • Ghildiyal, M., and Zamore, P. D. (2009) Small silencing RNAs: an expanding universe. Nat Rev Genet 10, 94-108.
    • (2009) Nat Rev Genet , vol.10 , pp. 94-108
    • Ghildiyal, M.1    Zamore, P.D.2
  • 6
    • 58849112575 scopus 로고    scopus 로고
    • Biogenesis of small RNAs in animals
    • Kim, V. N., Han, J., and Siomi, M. C. (2009) Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol 10, 126-39.
    • (2009) Nat Rev Mol Cell Biol , vol.10 , pp. 126-39
    • Kim, V.N.1    Han, J.2    Siomi, M.C.3
  • 7
    • 34247525481 scopus 로고    scopus 로고
    • PiRNAs in the germ line
    • Lin, H. (2007) piRNAs in the germ line. Science 316, 397.
    • (2007) Science , vol.316 , pp. 397
    • Lin, H.1
  • 8
    • 75549084786 scopus 로고    scopus 로고
    • DeepBase: A database for deeply annotating and mining deep sequencing data
    • Yang, J. H., Shao, P., Zhou, H., Chen, Y. Q., and Qu, L. H. (2010) deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res 38, D123-30.
    • (2010) Nucleic Acids Res , vol.38
    • Yang, J.H.1    Shao, P.2    Zhou, H.3    Chen, Y.Q.4    Qu, L.H.5
  • 10
    • 33751009398 scopus 로고    scopus 로고
    • SnoSeeker: An advanced computational package for screening of guide and orphan snoRNA genes in the human genome
    • Yang, J. H., Zhang, X. C., Huang, Z. P., Zhou, H., Huang, M. B., Zhang, S., et al (2006) snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome. Nucleic Acids Res 34, 5112-23.
    • (2006) Nucleic Acids Res , vol.34 , pp. 5112-23
    • Yang, J.H.1    Zhang, X.C.2    Huang, Z.P.3    Zhou, H.4    Huang, M.B.5    Zhang, S.6
  • 11
    • 59649103076 scopus 로고    scopus 로고
    • A distinct class of small RNAs arises from pre-miRNA-proximal regions in a simple chordate
    • Shi, W., Hendrix, D., Levine, M., and Haley, B. (2009) A distinct class of small RNAs arises from pre-miRNA-proximal regions in a simple chordate. Nat Struct Mol Biol 16, 183-9.
    • (2009) Nat Struct Mol Biol , vol.16 , pp. 183-9
    • Shi, W.1    Hendrix, D.2    Levine, M.3    Haley, B.4
  • 12
    • 72749089855 scopus 로고    scopus 로고
    • A novel class of small RNAs: TRNAderived RNA fragments (tRFs)
    • Lee, Y. S., Shibata, Y., Malhotra, A., and Dutta, A. (2009) A novel class of small RNAs: tRNAderived RNA fragments (tRFs). Genes Dev 23, 2639-49.
    • (2009) Genes Dev , vol.23 , pp. 2639-49
    • Lee, Y.S.1    Shibata, Y.2    Malhotra, A.3    Dutta, A.4
  • 14
    • 77952368550 scopus 로고    scopus 로고
    • Mammalian microRNAs: Experimental evaluation of novel and previously annotated genes
    • Chiang, H. R., Schoenfeld, L. W., Ruby, J. G., Auyeung, V. C., Spies, N., Baek, D., et al (2010) Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes Dev 24, 992-1009.
    • (2010) Genes Dev , vol.24 , pp. 992-1009
    • Chiang, H.R.1    Schoenfeld, L.W.2    Ruby, J.G.3    Auyeung, V.C.4    Spies, N.5    Baek, D.6
  • 15
    • 73349122299 scopus 로고    scopus 로고
    • Evolutionary fl ux of canonical microRNAs and mirtrons in Drosophila
    • author reply 9-10
    • Berezikov, E., Liu, N., Flynt, A. S., Hodges, E., Rooks, M., Hannon, G. J., et al (2010) Evolutionary fl ux of canonical microRNAs and mirtrons in Drosophila. Nat Genet 42, 6-9; author reply 9-10.
    • (2010) Nat Genet , vol.42 , pp. 6-9
    • Berezikov, E.1    Liu, N.2    Flynt, A.S.3    Hodges, E.4    Rooks, M.5    Hannon, G.J.6
  • 17
    • 41649106136 scopus 로고    scopus 로고
    • Application of massively parallel sequencing to microRNA profi ling and discovery in human embryonic stem cells
    • Morin, R. D., O'Connor, M. D., Griffi th, M., Kuchenbauer, F., Delaney, A., Prabhu, A. L., et al (2008) Application of massively parallel sequencing to microRNA profi ling and discovery in human embryonic stem cells. Genome Res 18, 610-21.
    • (2008) Genome Res , vol.18 , pp. 610-21
    • Morin, R.D.1    O'connor, M.D.2    Griffi Th, M.3    Kuchenbauer, F.4    Delaney, A.5    Prabhu, A.L.6
  • 19
    • 77950547534 scopus 로고    scopus 로고
    • MiRTRAP, a computational method for the systematic identifi cation of miRNAs from high throughput sequencing data
    • Hendrix, D., Levine, M., and Shi, W. miRTRAP, a computational method for the systematic identifi cation of miRNAs from high throughput sequencing data. Genome Biol 11, R39.
    • Genome Biol , vol.11
    • Hendrix, D.1    Levine, M.2    Shi, W.3
  • 20
    • 33845436047 scopus 로고    scopus 로고
    • Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans
    • Ruby, J. G., Jan, C., Player, C., Axtell, M. J., Lee, W., Nusbaum, C. (2006) Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127, 1193-207.
    • (2006) Cell , vol.127 , pp. 1193-207
    • Ruby, J.G.1    Jan, C.2    Player, C.3    Axtell, M.J.4    Lee, W.5    Nusbaum, C.6
  • 21
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memoryeffi cient alignment of short DNA sequences to the human genome
    • Langmead, B., Trapnell, C., Pop, M., and Salzberg, S. L. (2009) Ultrafast and memoryeffi cient alignment of short DNA sequences to the human genome. Genome Biol 10, R25.
    • (2009) Genome Biol , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 22
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li, H., and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-60.
    • (2009) Bioinformatics , vol.25 , pp. 1754-60
    • Li, H.1    Durbin, R.2
  • 23
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA secondary structure server
    • Hofacker, I. L. (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31, 3429-31.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3429-31
    • Hofacker I, L.1
  • 24
    • 0019876473 scopus 로고
    • Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
    • Zuker, M., and Stiegler, P. (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res 9, 133-48.
    • (1981) Nucleic Acids Res , vol.9 , pp. 133-48
    • Zuker, M.1    Stiegler, P.2
  • 26
  • 27
    • 38149071979 scopus 로고    scopus 로고
    • Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs
    • Ruby, J. G., Stark, A., Johnston, W. K., Kellis, M., Bartel, D. P., and Lai, E. C. (2007) Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res 17, 1850 - 64.
    • (2007) Genome Res , vol.17 , pp. 1850-1864
    • Ruby, J.G.1    Stark, A.2    Johnston, W.K.3    Kellis, M.4    Bartel, D.P.5    Lai, E.C.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.