메뉴 건너뛰기




Volumn 26, Issue 18, 2010, Pages

Classification of ncRNAs using position and size information in deep sequencing data

Author keywords

[No Author keywords available]

Indexed keywords

UNTRANSLATED RNA;

EID: 77956531066     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq363     Document Type: Article
Times cited : (23)

References (30)
  • 1
    • 0035838369 scopus 로고    scopus 로고
    • Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline
    • Aravin,A.A. et al. (2001) Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline. Curr. Biol., 11, 1017-1027.
    • (2001) Curr. Biol. , vol.11 , pp. 1017-1027
    • Aravin, A.A.1
  • 2
    • 54349104464 scopus 로고    scopus 로고
    • Mouse ES cells express endogenous shRNAs, siRNAs, and other microprocessor-independent, dicer-dependent small RNAs
    • Babiarz,J.E. et al. (2008) Mouse ES cells express endogenous shRNAs, siRNAs, and other microprocessor-independent, dicer-dependent small RNAs. Genes Dev., 22, 2773-2785.
    • (2008) Genes Dev. , vol.22 , pp. 2773-2785
    • Babiarz, J.E.1
  • 3
    • 0036703184 scopus 로고    scopus 로고
    • The expanding snoRNA world
    • Bachellerie,J.P. et al. (2002) The expanding snoRNA world. Biochimie, 84, 775-790.
    • (2002) Biochimie , vol.84 , pp. 775-790
    • Bachellerie, J.P.1
  • 4
    • 0347444723 scopus 로고    scopus 로고
    • MicroRNAs: genomics, biogenesis, mechanism, and function
    • Bartel,D.P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116, 281-297.
    • (2004) Cell , vol.116 , pp. 281-297
    • Bartel, D.P.1
  • 5
    • 26944498633 scopus 로고    scopus 로고
    • Prediction and validation of microRNAs and their targets
    • Bentwich,I. (2005) Prediction and validation of microRNAs and their targets. FEBS Lett., 579, 5904-5910.
    • (2005) FEBS Lett. , vol.579 , pp. 5904-5910
    • Bentwich, I.1
  • 6
    • 58149189877 scopus 로고    scopus 로고
    • GtRNAdb: a database of transfer RNA genes detected in genomic sequence
    • Chan,P.P. and Lowe,T.M. (2009) GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res., 37, D93-D97.
    • (2009) Nucleic Acids Res. , vol.37
    • Chan, P.P.1    Lowe, T.M.2
  • 7
    • 44349104241 scopus 로고    scopus 로고
    • An endogenous small interfering RNA pathway in Drosophila
    • Czech,B. et al. (2008) An endogenous small interfering RNA pathway in Drosophila. Nature, 453, 798-802.
    • (2008) Nature , vol.453 , pp. 798-802
    • Czech, B.1
  • 8
    • 13344279384 scopus 로고    scopus 로고
    • Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction
    • Doshi,K.J. et al. (2004) Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction. BMC Bioinformatics, 5, 105.
    • (2004) BMC Bioinformatics , vol.5 , pp. 105
    • Doshi, K.J.1
  • 9
    • 13244260785 scopus 로고    scopus 로고
    • Evaluation of several lightweight stochastic contextfree grammars for RNA secondary structure prediction
    • Dowell,R.D. and Eddy,S.R. (2004) Evaluation of several lightweight stochastic contextfree grammars for RNA secondary structure prediction. BMC Bioinformatics, 5, 71.
    • (2004) BMC Bioinformatics , vol.5 , pp. 71
    • Dowell, R.D.1    Eddy, S.R.2
  • 11
    • 41849084855 scopus 로고    scopus 로고
    • Discovering microRNAs from deep sequencing data using miRDeep
    • Friedlander,M.R. et al. (2008) Discovering microRNAs from deep sequencing data using miRDeep. Nat. Biotechnol., 26, 407-415.
    • (2008) Nat. Biotechnol. , vol.26 , pp. 407-415
    • Friedlander, M.R.1
  • 12
    • 77449145877 scopus 로고    scopus 로고
    • The scaRNA2 is produced by an independent transcription unit and its processing is directed by the encoding region
    • Gerard,M.A. et al. (2010) The scaRNA2 is produced by an independent transcription unit and its processing is directed by the encoding region. Nucleic Acids Res., 38, 370-381.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 370-381
    • Gerard, M.A.1
  • 13
    • 0020484488 scopus 로고
    • An improved algorithm for matching biological sequences
    • Gotoh,O. (1982) An improved algorithm for matching biological sequences. J. Mol. Biol., 162, 705-708.
    • (1982) J. Mol. Biol. , vol.162 , pp. 705-708
    • Gotoh, O.1
  • 14
    • 38549150275 scopus 로고    scopus 로고
    • miRBase: tools for microRNA genomics
    • Griffiths-Jones,S. et al. (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res., 36, D154-D158.
    • (2008) Nucleic Acids Res. , vol.36
    • Griffiths-Jones, S.1
  • 15
    • 34250805982 scopus 로고    scopus 로고
    • MicroRNA targeting specificity in mammals: determinants beyond seed pairing
    • Grimson,A. et al. (2007) MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol. Cell, 27, 91-105.
    • (2007) Mol. Cell , vol.27 , pp. 91-105
    • Grimson, A.1
  • 16
    • 77950202393 scopus 로고    scopus 로고
    • Human tRNA-derived small RNAs in the global regulation of RNA silencing
    • Haussecker,D. et al. (2010) Human tRNA-derived small RNAs in the global regulation of RNA silencing. RNA, 16, 673-695.
    • (2010) RNA , vol.16 , pp. 673-695
    • Haussecker, D.1
  • 17
    • 84957795647 scopus 로고
    • Thermodynamics of RNA folding. when is an RNA molecule in equilibrium?
    • Springer Berlin/Heidelberg
    • Higgs,P. and Morgan,S. (1995) Thermodynamics of RNA folding. when is an RNA molecule in equilibrium? In Advances in Artificial Life, Springer, Berlin/Heidelberg, pp. 852-861.
    • (1995) Advances in Artificial Life , pp. 852-861
    • Higgs, P.1    Morgan, S.2
  • 18
    • 34249772381 scopus 로고
    • Fast folding and comparison of RNA secondary structures
    • Hofacker,I.L. et al. (1994) Fast folding and comparison of RNA secondary structures. Monatsh. Chem. Chem. Mon., 125, 167-188.
    • (1994) Monatsh. Chem. Chem. Mon. , vol.125 , pp. 167-188
    • Hofacker, I.L.1
  • 19
    • 1042304206 scopus 로고    scopus 로고
    • Prediction of locally stable RNA secondary structures for genome-wide surveys
    • Hofacker,I.L. et al. (2004) Prediction of locally stable RNA secondary structures for genome-wide surveys. Bioinformatics, 20, 186-190.
    • (2004) Bioinformatics , vol.20 , pp. 186-190
    • Hofacker, I.L.1
  • 20
    • 67649663873 scopus 로고    scopus 로고
    • Dynamic expression of small non-coding RNAs, including novel microRNAs and piRNAs/21U-RNAs, during Caenorhabditis elegans development
    • Kato,M. et al. (2009) Dynamic expression of small non-coding RNAs, including novel microRNAs and piRNAs/21U-RNAs, during Caenorhabditis elegans development. Genome Biol., 10, R54.
    • (2009) Genome Biol. , vol.10
    • Kato, M.1
  • 21
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead,B. et al. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
    • (2009) Genome Biol. , vol.10
    • Langmead, B.1
  • 22
    • 72849117513 scopus 로고    scopus 로고
    • Characterization of viral and human RNAs smaller than canonical MicroRNAs
    • Li,Z. et al. (2009) Characterization of viral and human RNAs smaller than canonical MicroRNAs. J. Virol., 83, 12751-12758.
    • (2009) J. Virol. , vol.83 , pp. 12751-12758
    • Li, Z.1
  • 23
    • 34948901976 scopus 로고    scopus 로고
    • Structural determinants of RNA recognition and cleavage by Dicer
    • MacRae,I.J. et al. (2007). Structural determinants of RNA recognition and cleavage by Dicer. Nat. Struct. Mol. Biol., 14, 934-940.
    • (2007) Nat. Struct. Mol. Biol. , vol.14 , pp. 934-940
    • MacRae, I.J.1
  • 24
    • 41649106136 scopus 로고    scopus 로고
    • Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells
    • Morin,R.D. et al. (2008) Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res., 18, 610-621.
    • (2008) Genome Res. , vol.18 , pp. 610-621
    • Morin, R.D.1
  • 25
    • 67349135253 scopus 로고    scopus 로고
    • High throughput sequencing of microRNAs in chicken somites
    • Rathjen,T. et al. (2009) High throughput sequencing of microRNAs in chicken somites. FEBS Lett., 583, 1422-1426.
    • (2009) FEBS Lett. , vol.583 , pp. 1422-1426
    • Rathjen, T.1
  • 26
    • 59649103076 scopus 로고    scopus 로고
    • A distinct class of small RNAs arises from pre-miRNA-proximal regions in a simple chordate
    • Shi,W. et al. (2009) A distinct class of small RNAs arises from pre-miRNA-proximal regions in a simple chordate. Nat. Struct. Mol. Biol., 16, 183-189.
    • (2009) Nat. Struct. Mol. Biol. , vol.16 , pp. 183-189
    • Shi, W.1
  • 27
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
    • (1981) J. Mol. Biol. , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 28
    • 67650604265 scopus 로고    scopus 로고
    • Stressing out over tRNA cleavage
    • Thompson,D.M. and Parker,R. (2009) Stressing out over tRNA cleavage. Cell, 138, 215-219.
    • (2009) Cell , vol.138 , pp. 215-219
    • Thompson, D.M.1    Parker, R.2
  • 29
    • 34247598415 scopus 로고    scopus 로고
    • Inferring noncoding RNAfamilies and classes by means of genomescale structure-based clustering
    • Will,S. et al. (2007) Inferring noncoding RNAfamilies and classes by means of genomescale structure-based clustering. PLoS Comput. Biol., 3, e65.
    • (2007) PLoS Comput. Biol. , vol.3
    • Will, S.1
  • 30
    • 0033677331 scopus 로고    scopus 로고
    • A simple iterative approach to parameter optimization
    • Zien,A. et al. (2000) A simple iterative approach to parameter optimization. J. Comput. Biol., 7, 483-501.
    • (2000) J. Comput. Biol. , vol.7 , pp. 483-501
    • Zien, A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.