메뉴 건너뛰기




Volumn 37, Issue 8, 2009, Pages 2419-2433

Survey and Summary: Current tools for the identification of miRNA genes and their targets

Author keywords

[No Author keywords available]

Indexed keywords

DICER; EXPORTIN 5; MESSENGER RNA; MICRORNA; PROTEIN DROSHA; RIBOSOME RNA; TRANSFER RNA; UNCLASSIFIED DRUG;

EID: 65849520676     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp145     Document Type: Review
Times cited : (198)

References (134)
  • 1
    • 0035955366 scopus 로고    scopus 로고
    • An extensive class of small RNAs in Caenorhabditis elegans
    • Lee,R.C. and Ambros,V. (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science, 294, 862-864.
    • (2001) Science , vol.294 , pp. 862-864
    • Lee, R.C.1    Ambros, V.2
  • 2
    • 0035955361 scopus 로고    scopus 로고
    • An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans
    • Lau,N.C., Lim,L.P., Weinstein,E.G. and Bartel,D.P. (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science, 294, 858-862.
    • (2001) Science , vol.294 , pp. 858-862
    • Lau, N.C.1    Lim, L.P.2    Weinstein, E.G.3    Bartel, D.P.4
  • 3
    • 0035966319 scopus 로고    scopus 로고
    • microRNAs: Tiny regulators with great potential
    • Ambros,V. (2001) microRNAs: Tiny regulators with great potential. Cell, 107, 823-826.
    • (2001) Cell , vol.107 , pp. 823-826
    • Ambros, V.1
  • 4
    • 0344232733 scopus 로고    scopus 로고
    • microRNAs: Runts of the genome assert themselves
    • Lai,E.C. (2003) microRNAs: Runts of the genome assert themselves. Curr. Biol., 13, R925-R936.
    • (2003) Curr. Biol , vol.13
    • Lai, E.C.1
  • 6
    • 0037009364 scopus 로고    scopus 로고
    • MicroRNA maturation: Stepwise processing and subcellular localization
    • Lee,Y., Jeon,K., Lee,J.-T., Kim,S. and Kim,V.N. (2002) MicroRNA maturation: Stepwise processing and subcellular localization. EMBO J. 21, 4663-4670.
    • (2002) EMBO J , vol.21 , pp. 4663-4670
    • Lee, Y.1    Jeon, K.2    Lee, J.-T.3    Kim, S.4    Kim, V.N.5
  • 7
    • 13944260434 scopus 로고    scopus 로고
    • Microarray proling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes
    • Baskerville,S. and Bartel,D.P. (2005) Microarray proling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA, 11, 241-247.
    • (2005) RNA , vol.11 , pp. 241-247
    • Baskerville, S.1    Bartel, D.P.2
  • 10
    • 6344281172 scopus 로고    scopus 로고
    • Identification of mammalian microRNA host genes and transcription units
    • Rodriguez,A., Griffiths-Jones,S., Ashurst,J.L. and Bradley,A. (2004) Identification of mammalian microRNA host genes and transcription units. Genome Res., 14, 1902-1910.
    • (2004) Genome Res , vol.14 , pp. 1902-1910
    • Rodriguez, A.1    Griffiths-Jones, S.2    Ashurst, J.L.3    Bradley, A.4
  • 11
    • 9344235449 scopus 로고    scopus 로고
    • Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs
    • Cai,X., Hagedorn,C.H. and Cullen,B.R. (2004) Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA, 10, 1957-1966.
    • (2004) RNA , vol.10 , pp. 1957-1966
    • Cai, X.1    Hagedorn, C.H.2    Cullen, B.R.3
  • 12
    • 19444367079 scopus 로고    scopus 로고
    • Mammalian microRNAs derived from genomic repeats
    • Smalheiser,N.R. and Torvik,V.I. (2005) Mammalian microRNAs derived from genomic repeats. Trends Genet., 21, 322-326.
    • (2005) Trends Genet , vol.21 , pp. 322-326
    • Smalheiser, N.R.1    Torvik, V.I.2
  • 16
    • 10944254152 scopus 로고    scopus 로고
    • Transcription and processing of human microRNA precursors
    • Cullen,B.R. (2004) Transcription and processing of human microRNA precursors. Mol. Cell, 16, 861-865.
    • (2004) Mol. Cell , vol.16 , pp. 861-865
    • Cullen, B.R.1
  • 18
    • 4444230672 scopus 로고    scopus 로고
    • Structural requirements for pre-microRNA binding and nuclear export by Exportin 5
    • Zeng,Y. and Cullen,B.R. (2004) Structural requirements for pre-microRNA binding and nuclear export by Exportin 5. Nucleic Acids Res., 32, 4776-4785.
    • (2004) Nucleic Acids Res , vol.32 , pp. 4776-4785
    • Zeng, Y.1    Cullen, B.R.2
  • 20
    • 0037144546 scopus 로고    scopus 로고
    • A microRNA in a multiple-turnover RNAi enzyme complex
    • Hutvágner,G. and Zamore,P.D. (2002) A microRNA in a multiple-turnover RNAi enzyme complex. Science, 297, 2056-2060.
    • (2002) Science , vol.297 , pp. 2056-2060
    • Hutvágner, G.1    Zamore, P.D.2
  • 21
    • 3142613181 scopus 로고    scopus 로고
    • Single processing center models for human Dicer and bacterial RNase III
    • Zhang,H., Kolb,F.A., Jaskiewicz,L., Westhof,E. and Filipowicz,W. (2004) Single processing center models for human Dicer and bacterial RNase III. Cell, 118, 57-68.
    • (2004) Cell , vol.118 , pp. 57-68
    • Zhang, H.1    Kolb, F.A.2    Jaskiewicz, L.3    Westhof, E.4    Filipowicz, W.5
  • 23
    • 0142165224 scopus 로고    scopus 로고
    • Functional siRNAs and miRNAs exhibit strand bias
    • Khvorova,A., Reynolds,A. and Jayasena,S.D. (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell, 115, 209-216.
    • (2003) Cell , vol.115 , pp. 209-216
    • Khvorova, A.1    Reynolds, A.2    Jayasena, S.D.3
  • 24
    • 4744357297 scopus 로고    scopus 로고
    • Structural features of microRNA (miRNA) precursors and their relevance to miRNA biogenesis and small interfering RNA/short hairpin RNA design
    • Krol,J., Sobczak,K., Wilczynska,U., Drath,M., Jasinska,A., Kaczynska,D. and Krzyzosiak,W.J. (2004) Structural features of microRNA (miRNA) precursors and their relevance to miRNA biogenesis and small interfering RNA/short hairpin RNA design. J. Biol. Chem., 279, 42230-42239.
    • (2004) J. Biol. Chem , vol.279 , pp. 42230-42239
    • Krol, J.1    Sobczak, K.2    Wilczynska, U.3    Drath, M.4    Jasinska, A.5    Kaczynska, D.6    Krzyzosiak, W.J.7
  • 25
    • 23844530681 scopus 로고    scopus 로고
    • Asymmetry of intronic pre-miRNA structures in functional RISC assembly
    • Lin,S.-L., Chang,D. and Ying,S.-Y. (2005) Asymmetry of intronic pre-miRNA structures in functional RISC assembly. Gene, 356, 32-38.
    • (2005) Gene , vol.356 , pp. 32-38
    • Lin, S.-L.1    Chang, D.2    Ying, S.-Y.3
  • 28
    • 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
  • 29
    • 0037782493 scopus 로고    scopus 로고
    • MicroRNAs: At the root of plant development?
    • Bartel,B. and Bartel,D.P. (2003) MicroRNAs: At the root of plant development? Plant Physiol., 132, 709-717.
    • (2003) Plant Physiol , vol.132 , pp. 709-717
    • Bartel, B.1    Bartel, D.P.2
  • 33
    • 11444251652 scopus 로고    scopus 로고
    • New human and mouse microRNA genes found by homology search
    • Weber,M.J. (2005) New human and mouse microRNA genes found by homology search. FEBS J., 272, 59-73.
    • (2005) FEBS J , vol.272 , pp. 59-73
    • Weber, M.J.1
  • 34
    • 34447097693 scopus 로고    scopus 로고
    • Intronic microRNA precursors that bypass Drosha processing
    • Ruby,J.G., Jan,C.H. and Bartel,D.P. (2007) Intronic microRNA precursors that bypass Drosha processing. Nature, 448, 83-86.
    • (2007) Nature , vol.448 , pp. 83-86
    • Ruby, J.G.1    Jan, C.H.2    Bartel, D.P.3
  • 35
    • 33846945735 scopus 로고    scopus 로고
    • Processing of intronic microRNAs
    • Kim,Y.-K. and Kim,V.N. (2007) Processing of intronic microRNAs. EMBO J., 26, 775-783.
    • (2007) EMBO J , vol.26 , pp. 775-783
    • Kim, Y.-K.1    Kim, V.N.2
  • 36
    • 0036544755 scopus 로고    scopus 로고
    • Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation
    • Lai,E.C. (2002) Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation. Nat. Genet. 30, 363-364.
    • (2002) Nat. Genet , vol.30 , pp. 363-364
    • Lai, E.C.1
  • 37
    • 13444312098 scopus 로고    scopus 로고
    • Substrate requirements for let-7 function in the developing zebrafish embryo
    • Kloosterman,W.P., Wienholds,E., Ketting,R.F. and Plasterk,R.H.A. (2004) Substrate requirements for let-7 function in the developing zebrafish embryo. Nucleic Acids Res., 32, 6284-6291.
    • (2004) Nucleic Acids Res , vol.32 , pp. 6284-6291
    • Kloosterman, W.P.1    Wienholds, E.2    Ketting, R.F.3    Plasterk, R.H.A.4
  • 38
    • 34547441263 scopus 로고    scopus 로고
    • Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5′ UTR as in the 3′ UTR
    • Lytle,J.R., Yario,T.A. and Steitz,J.A. (2007) Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5′ UTR as in the 3′ UTR. Proc. Natl Acad. Sci. USA, 104, 9667-9672.
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 9667-9672
    • Lytle, J.R.1    Yario, T.A.2    Steitz, J.A.3
  • 40
    • 28344440823 scopus 로고    scopus 로고
    • MicroRNA function: Multiple mechanisms for a tiny RNA?
    • Pillai,R.S. (2005) MicroRNA function: Multiple mechanisms for a tiny RNA? RNA, 11, 1753-1761.
    • (2005) RNA , vol.11 , pp. 1753-1761
    • Pillai, R.S.1
  • 41
    • 40349094597 scopus 로고    scopus 로고
    • MicroRNA-373 induces expression of genes with complementary promoter sequences
    • Place,R.F., Li,L.-C., Pookot,D., Noonan,E.J. and Dahiya,R. (2008) MicroRNA-373 induces expression of genes with complementary promoter sequences. Proc. Natl Acad. Sci. USA, 105, 1608-1613.
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 1608-1613
    • Place, R.F.1    Li, L.-C.2    Pookot, D.3    Noonan, E.J.4    Dahiya, R.5
  • 42
    • 36749026906 scopus 로고    scopus 로고
    • Switching from repression to activation: MicroRNAs can up-regulate translation
    • Vasudevan,S., Tong,Y. and Steitz,J.A. (2007) Switching from repression to activation: MicroRNAs can up-regulate translation. Science, 318, 1931-1934.
    • (2007) Science , vol.318 , pp. 1931-1934
    • Vasudevan, S.1    Tong, Y.2    Steitz, J.A.3
  • 45
    • 4043074968 scopus 로고    scopus 로고
    • Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis
    • Sunkar,R. and Zhu,J.-K. (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell, 16, 2001-2019.
    • (2004) Plant Cell , vol.16 , pp. 2001-2019
    • Sunkar, R.1    Zhu, J.-K.2
  • 46
    • 11244251011 scopus 로고    scopus 로고
    • Plant and animal microRNAs: Similarities and differences
    • Millar,A.A. and Waterhouse,P.M. (2005) Plant and animal microRNAs: similarities and differences. Funct. Integr. Genomics, 5, 129-135.
    • (2005) Funct. Integr. Genomics , vol.5 , pp. 129-135
    • Millar, A.A.1    Waterhouse, P.M.2
  • 47
    • 34547510962 scopus 로고    scopus 로고
    • Target mimics modulate miRNAs
    • Chitwood,D.H. and Timmermans,M.C.P. (2007) Target mimics modulate miRNAs. Nat. Genet., 39, 935-936.
    • (2007) Nat. Genet , vol.39 , pp. 935-936
    • Chitwood, D.H.1    Timmermans, M.C.P.2
  • 52
    • 0347906099 scopus 로고    scopus 로고
    • Towards a complete description of the microRNA complement of animal genomes
    • Brennecke,J. and Cohen,S.M. (2003) Towards a complete description of the microRNA complement of animal genomes. Genome Biol., 4, 228.
    • (2003) Genome Biol , vol.4 , pp. 228
    • Brennecke, J.1    Cohen, S.M.2
  • 55
    • 0842278323 scopus 로고    scopus 로고
    • Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification
    • Ohler,U., Yekta,S., Lim,L.P., Bartel,D.P. and Burge,C.B. (2004) Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification. RNA, 10, 1309-1322.
    • (2004) RNA , vol.10 , pp. 1309-1322
    • Ohler, U.1    Yekta, S.2    Lim, L.P.3    Bartel, D.P.4    Burge, C.B.5
  • 57
    • 38149071979 scopus 로고
    • Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs
    • 2007
    • 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, 1850-1864.
    • (1850) Genome Res , vol.17
    • Ruby, J.G.1    Stark, A.2    Johnston, W.K.3    Kellis, M.4    Bartel, D.P.5    Lai, E.C.6
  • 58
    • 43649096475 scopus 로고    scopus 로고
    • Identification of novel Drosophila melanogaster MicroRNAs
    • Sandmann,T. and Cohen,S.M. (2007) Identification of novel Drosophila melanogaster MicroRNAs. PLoS ONE, 2, e1265.
    • (2007) PLoS ONE , vol.2
    • Sandmann, T.1    Cohen, S.M.2
  • 60
    • 21844477027 scopus 로고    scopus 로고
    • Human microRNA prediction through a probabilistic co-learning model of sequence and structure
    • Nam,J.-W., Shin,K.-R., Han,J., Lee,Y., Kim,V.N. and Zhang,B.-T. (2005) Human microRNA prediction through a probabilistic co-learning model of sequence and structure. Nucleic Acids Res., 33, 3570-3581.
    • (2005) Nucleic Acids Res , vol.33 , pp. 3570-3581
    • Nam, J.-W.1    Shin, K.-R.2    Han, J.3    Lee, Y.4    Kim, V.N.5    Zhang, B.-T.6
  • 62
    • 30344447264 scopus 로고    scopus 로고
    • Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine
    • Xue,C., Li,F., He,T., Liu,G.-P., Li,Y. and Zhang,X. (2005) Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine. BMC Bioinformatics, 6, 310.
    • (2005) BMC Bioinformatics , vol.6 , pp. 310
    • Xue, C.1    Li, F.2    He, T.3    Liu, G.-P.4    Li, Y.5    Zhang, X.6
  • 63
    • 33747871855 scopus 로고    scopus 로고
    • Hairpins in a haystack: Recognizing microRNA precursors in comparative genomics data
    • Hertel,J. and Stadler,P.F. (2006) Hairpins in a haystack: Recognizing microRNA precursors in comparative genomics data. Bioinformatics, 22, e197-e202.
    • (2006) Bioinformatics , vol.22
    • Hertel, J.1    Stadler, P.F.2
  • 64
    • 34447309058 scopus 로고    scopus 로고
    • De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures
    • Ng,K.L.S. and Mishra,S.K. (2007) De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures. Bioinformatics, 23, 1321-1330.
    • (2007) Bioinformatics , vol.23 , pp. 1321-1330
    • Ng, K.L.S.1    Mishra, S.K.2
  • 65
    • 38349097919 scopus 로고    scopus 로고
    • MiRFinder: An improved approach and software implementation for genome-wide fast microRNA precursor scans
    • Huang,T., Fan,B., Rothschild,M., Hu,Z., Li,K. and Zhao,S. (2007) MiRFinder: An improved approach and software implementation for genome-wide fast microRNA precursor scans. BMC Bioinformatics, 8, 341.
    • (2007) BMC Bioinformatics , vol.8 , pp. 341
    • Huang, T.1    Fan, B.2    Rothschild, M.3    Hu, Z.4    Li, K.5    Zhao, S.6
  • 66
    • 41549152081 scopus 로고    scopus 로고
    • Mammalian MicroRNA prediction through a support vector machine model of sequence and structure
    • Sheng,Y., Engström,P.G. and Lenhard,B. (2007) Mammalian MicroRNA prediction through a support vector machine model of sequence and structure. PLoS ONE, 2, e946.
    • (2007) PLoS ONE , vol.2
    • Sheng, Y.1    Engström, P.G.2    Lenhard, B.3
  • 67
    • 33846650507 scopus 로고    scopus 로고
    • Reliable prediction of Drosha processing sites improves microRNA gene prediction
    • Helvik,S.A., Snøve,O. and Saetrom,P. (2007) Reliable prediction of Drosha processing sites improves microRNA gene prediction. Bioinformatics, 23, 142-149.
    • (2007) Bioinformatics , vol.23 , pp. 142-149
    • Helvik, S.A.1    Snøve, O.2    Saetrom, P.3
  • 68
    • 34547596338 scopus 로고    scopus 로고
    • MiPred: Classification of real and pseudo microRNA precursors using random forest prediction model with combined features
    • Jiang,P., Wu,H., Wang,W., Ma,W., Sun,X. and Lu,Z. (2007) MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Nucleic Acids Res. 35, W339-W344.
    • (2007) Nucleic Acids Res , vol.35
    • Jiang, P.1    Wu, H.2    Wang, W.3    Ma, W.4    Sun, X.5    Lu, Z.6
  • 69
    • 33745594057 scopus 로고    scopus 로고
    • Combining multi-species genomic data for microRNA identification using a Naive Bayes classifier
    • Yousef,M., Nebozhyn,M., Shatkay,H., Kanterakis,S., Showe,L.C. and Showe,M.K. (2006) Combining multi-species genomic data for microRNA identification using a Naive Bayes classifier. Bioinformatics, 22, 1325-1334.
    • (2006) Bioinformatics , vol.22 , pp. 1325-1334
    • Yousef, M.1    Nebozhyn, M.2    Shatkay, H.3    Kanterakis, S.4    Showe, L.C.5    Showe, M.K.6
  • 70
    • 39049169222 scopus 로고    scopus 로고
    • Ab initio identification of human microRNAs based on structure motifs
    • Brameier,M. and Wiuf,C. (2007) Ab initio identification of human microRNAs based on structure motifs. BMC Bioinformatics, 8, 478.
    • (2007) BMC Bioinformatics , vol.8 , pp. 478
    • Brameier, M.1    Wiuf, C.2
  • 71
    • 15244358503 scopus 로고    scopus 로고
    • Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals
    • Xie,X., Lu,J., Kulbokas,E.J., Golub,T.R., Mootha,V., Lindblad-Toh,K., Lander,E.S. and Kellis,M. (2005) Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature, 434, 338-345.
    • (2005) Nature , vol.434 , pp. 338-345
    • Xie, X.1    Lu, J.2    Kulbokas, E.J.3    Golub, T.R.4    Mootha, V.5    Lindblad-Toh, K.6    Lander, E.S.7    Kellis, M.8
  • 72
    • 34347355440 scopus 로고    scopus 로고
    • miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii
    • Molnár,A., Schwach,F., Studholme,D.J., Thuenemann,E.C. and Baulcombe,D.C. (2007) miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii. Nature, 447, 1126-1129.
    • (2007) Nature , vol.447 , pp. 1126-1129
    • Molnár, A.1    Schwach, F.2    Studholme, D.J.3    Thuenemann, E.C.4    Baulcombe, D.C.5
  • 75
    • 33745807260 scopus 로고    scopus 로고
    • An approach for the identification of microRNA with an application to Anopheles gambiae
    • Chatterjee,R. and Chaudhuri,K. (2006) An approach for the identification of microRNA with an application to Anopheles gambiae. Acta Biochim. Pol., 53, 303-309.
    • (2006) Acta Biochim. Pol , vol.53 , pp. 303-309
    • Chatterjee, R.1    Chaudhuri, K.2
  • 77
    • 39149087993 scopus 로고    scopus 로고
    • Computational prediction and experimental validation of Ciona intestinalis microRNA genes
    • Norden-Krichmar,T., Holtz,J., Pasquinelli,A. and Gaasterland,T. (2007) Computational prediction and experimental validation of Ciona intestinalis microRNA genes. BMC Genomics, 8, 445.
    • (2007) BMC Genomics , vol.8 , pp. 445
    • Norden-Krichmar, T.1    Holtz, J.2    Pasquinelli, A.3    Gaasterland, T.4
  • 78
    • 16344366331 scopus 로고    scopus 로고
    • Profile-based detection of microRNA precursors in animal genomes
    • Legendre,M., Lambert,A. and Gautheret,D. (2005) Profile-based detection of microRNA precursors in animal genomes. Bioinformatics, 21 841-845.
    • (2005) Bioinformatics , vol.21 , pp. 841-845
    • Legendre, M.1    Lambert, A.2    Gautheret, D.3
  • 79
    • 0035834489 scopus 로고    scopus 로고
    • Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles
    • Gautheret,D. and Lambert,A. (2001) Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles. J. Mol. Biol., 313, 1003-1011.
    • (2001) J. Mol. Biol , vol.313 , pp. 1003-1011
    • Gautheret, D.1    Lambert, A.2
  • 80
    • 24644476482 scopus 로고    scopus 로고
    • MicroRNA identification based on sequence and structure alignment
    • Wang,X., Zhang,J., Li,F., Gu,J., He,T., Zhang,X. and Li,Y. (2005) MicroRNA identification based on sequence and structure alignment. Bioinformatics, 21, 3610-3614.
    • (2005) Bioinformatics , vol.21 , pp. 3610-3614
    • Wang, X.1    Zhang, J.2    Li, F.3    Gu, J.4    He, T.5    Zhang, X.6    Li, Y.7
  • 81
    • 34247598415 scopus 로고    scopus 로고
    • Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering
    • Will,S., Reiche,K., Hofacker,I.L., Stadler,P.F. and Backofen,R. (2007) Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comput. Biol., 3, e65.
    • (2007) PLoS Comput. Biol , vol.3
    • Will, S.1    Reiche, K.2    Hofacker, I.L.3    Stadler, P.F.4    Backofen, R.5
  • 82
    • 33947728394 scopus 로고    scopus 로고
    • RNA stem-loops: To be or not to be cleaved by RNAse III
    • Ritchie,W., Legendre,M. and Gautheret,D. (2007) RNA stem-loops: To be or not to be cleaved by RNAse III. RNA, 13, 457-462.
    • (2007) RNA , vol.13 , pp. 457-462
    • Ritchie, W.1    Legendre, M.2    Gautheret, D.3
  • 83
    • 12744262431 scopus 로고    scopus 로고
    • Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets
    • Wang,X.-J., Reyes,J.L., Chua,N.-H. and Gaasterland,T. (2004) Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biol., 5, R65.
    • (2004) Genome Biol , vol.5
    • Wang, X.-J.1    Reyes, J.L.2    Chua, N.-H.3    Gaasterland, T.4
  • 84
    • 2942672580 scopus 로고    scopus 로고
    • Computational identification of plant microRNAs and their targets, including a stress-induced miRNA
    • Jones-Rhoades,M.W. and Bartel,D.P. (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell, 14, 787-799.
    • (2004) Mol. Cell , vol.14 , pp. 787-799
    • Jones-Rhoades, M.W.1    Bartel, D.P.2
  • 85
    • 3843089328 scopus 로고    scopus 로고
    • Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes
    • Bonnet,E., Wuyts,J., Rouze', P. and dePeer,Y.V. (2004) Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc. Natl Acad. Sci. USA 101, 11511-11516.
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 11511-11516
    • Bonnet, E.1    Wuyts, J.2    Rouze', P.3    dePeer, Y.V.4
  • 87
    • 25444490438 scopus 로고    scopus 로고
    • Computational evidence for hundreds of non-conserved plant microRNAs
    • Lindow,M. and Krogh,A. (2005) Computational evidence for hundreds of non-conserved plant microRNAs. BMC Genomics, 6, 119.
    • (2005) BMC Genomics , vol.6 , pp. 119
    • Lindow, M.1    Krogh, A.2
  • 88
    • 18844373063 scopus 로고    scopus 로고
    • Computational identification of novel family members of microRNA genes in Arabidopsis thaliana and Oryza sativa
    • Li,Y., Li,W. and Jin,Y.-X. (2005) Computational identification of novel family members of microRNA genes in Arabidopsis thaliana and Oryza sativa. Acta Biochim. Biophys. Sin., 37, 75-87.
    • (2005) Acta Biochim. Biophys. Sin , vol.37 , pp. 75-87
    • Li, Y.1    Li, W.2    Jin, Y.-X.3
  • 90
    • 33646830110 scopus 로고    scopus 로고
    • Conservation and divergence of plant microRNA genes
    • Zhang,B., Pan,X., Cannon,C.H., Cobb,G.P. and Anderson,T.A. (2006) Conservation and divergence of plant microRNA genes. Plant J., 46, 243-259.
    • (2006) Plant J , vol.46 , pp. 243-259
    • Zhang, B.1    Pan, X.2    Cannon, C.H.3    Cobb, G.P.4    Anderson, T.A.5
  • 91
    • 42149157716 scopus 로고    scopus 로고
    • Identification of novel and candidate miRNAs in rice by high throughput sequencing
    • Sunkar,R., Zhou,X., Zheng,Y., Zhang,W. and Zhu,J. (2008) Identification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biol., 8, 25.
    • (2008) BMC Plant Biol , vol.8 , pp. 25
    • Sunkar, R.1    Zhou, X.2    Zheng, Y.3    Zhang, W.4    Zhu, J.5
  • 92
    • 2142654329 scopus 로고    scopus 로고
    • MicroRNA-directed cleavage of HOXB8 mRNA
    • Yekta,S., Shih,I.-H. and Bartel,D.P. (2004) MicroRNA-directed cleavage of HOXB8 mRNA. Science, 304, 594-596.
    • (2004) Science , vol.304 , pp. 594-596
    • Yekta, S.1    Shih, I.-H.2    Bartel, D.P.3
  • 93
    • 0242361521 scopus 로고    scopus 로고
    • Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes
    • Aukerman,M.J. and Sakai,H. (2003) Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes. Plant Cell, 15, 2730-2741.
    • (2003) Plant Cell , vol.15 , pp. 2730-2741
    • Aukerman, M.J.1    Sakai, H.2
  • 94
    • 1642366133 scopus 로고    scopus 로고
    • A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development
    • Chen,X. (2004) A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science, 303, 2022-2025.
    • (2004) Science , vol.303 , pp. 2022-2025
    • Chen, X.1
  • 96
    • 22144437679 scopus 로고    scopus 로고
    • Silence from within: Endogenous siRNAs and miRNAs
    • Sontheimer,E.J. and Carthew,R.W. (2005) Silence from within: Endogenous siRNAs and miRNAs. Cell, 122, 9-12.
    • (2005) Cell , vol.122 , pp. 9-12
    • Sontheimer, E.J.1    Carthew, R.W.2
  • 97
    • 0041691111 scopus 로고    scopus 로고
    • MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms
    • Zeng,Y., Yi,R. and Cullen,B.R. (2003) MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms. Proc. Natl Acad. Sci. USA, 100, 9779-9784.
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 9779-9784
    • Zeng, Y.1    Yi, R.2    Cullen, B.R.3
  • 98
    • 13244278197 scopus 로고    scopus 로고
    • siRNA and miRNA: An insight into RISCs
    • Tang,G. (2005) siRNA and miRNA: An insight into RISCs. Trends Biochem. Sci., 30, 106-114.
    • (2005) Trends Biochem. Sci , vol.30 , pp. 106-114
    • Tang, G.1
  • 99
    • 0034101197 scopus 로고    scopus 로고
    • The 3′ untranslated region of messenger RNA: A molecular 'hotspot' for pathology?
    • Conne,B., Stutz,A. and Vassalli,J.D. (2000) The 3′ untranslated region of messenger RNA: A molecular 'hotspot' for pathology? Nat. Med., 6, 637-641.
    • (2000) Nat. Med , vol.6 , pp. 637-641
    • Conne, B.1    Stutz, A.2    Vassalli, J.D.3
  • 102
    • 1642374097 scopus 로고    scopus 로고
    • Specificity of microRNA target selection in translational repression
    • Doench,J.G. and Sharp,P.A. (2004) Specificity of microRNA target selection in translational repression. Genes Dev., 18, 504-511.
    • (2004) Genes Dev , vol.18 , pp. 504-511
    • Doench, J.G.1    Sharp, P.A.2
  • 104
    • 33745248430 scopus 로고    scopus 로고
    • microRNA target predictions in animals
    • Rajewsky,N. (2006) microRNA target predictions in animals. Nat. Genet., 38(Suppl.), S8-S13.
    • (2006) Nat. Genet , vol.38 , Issue.SUPPL.
    • Rajewsky, N.1
  • 105
  • 109
    • 11844278458 scopus 로고    scopus 로고
    • Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
    • Lewis,B.P., Burge,C.B. and Bartel,D.P. (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell, 120, 15-20.
    • (2005) Cell , vol.120 , pp. 15-20
    • Lewis, B.P.1    Burge, C.B.2    Bartel, D.P.3
  • 110
    • 1542297345 scopus 로고    scopus 로고
    • Computational identification of microRNA targets
    • Rajewsky,N. and Socci,N.D. (2004) Computational identification of microRNA targets. Dev. Biol., 267, 529-535.
    • (2004) Dev. Biol , vol.267 , pp. 529-535
    • Rajewsky, N.1    Socci, N.D.2
  • 112
    • 4644237189 scopus 로고    scopus 로고
    • Fast and effective prediction of microRNA/target duplexes
    • Rehmsmeier,M., Steffen,P., Hochsmann,M. and Giegerich,R. (2004) Fast and effective prediction of microRNA/target duplexes. RNA, 10, 1507-1517.
    • (2004) RNA , vol.10 , pp. 1507-1517
    • Rehmsmeier, M.1    Steffen, P.2    Hochsmann, M.3    Giegerich, R.4
  • 114
    • 25444461163 scopus 로고    scopus 로고
    • Prediction and verification of microRNA targets by MovingTargets, a highly adaptable prediction method
    • Burgler,C. and Macdonald,P.M. (2005) Prediction and verification of microRNA targets by MovingTargets, a highly adaptable prediction method. BMC Genomics, 6, 88.
    • (2005) BMC Genomics , vol.6 , pp. 88
    • Burgler, C.1    Macdonald, P.M.2
  • 115
    • 55449121696 scopus 로고    scopus 로고
    • Revealing post-transcriptional regulatory elements through network-level conservation
    • Chan,C.S., Elemento,O. and Tavazoie,S. (2005) Revealing post-transcriptional regulatory elements through network-level conservation. PLoS Comput. Biol., 1, e69.
    • (2005) PLoS Comput. Biol , vol.1
    • Chan, C.S.1    Elemento, O.2    Tavazoie, S.3
  • 116
    • 34347398567 scopus 로고    scopus 로고
    • Inference of miRNA targets using evolutionary conservation and pathway analysis
    • Gaidatzis,D., vanNimwegen,E., Hausser,J. and Zavolan,M. (2007) Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC Bioinformatics, 8, 69.
    • (2007) BMC Bioinformatics , vol.8 , pp. 69
    • Gaidatzis, D.1    vanNimwegen, E.2    Hausser, J.3    Zavolan, M.4
  • 117
    • 22244447130 scopus 로고    scopus 로고
    • Weighted sequence motifs as an improved seeding step in microRNA target prediction algorithms
    • Saetrom,O., Snøve,O. and Saetrom,P. (2005) Weighted sequence motifs as an improved seeding step in microRNA target prediction algorithms. RNA, 11, 995-1003.
    • (2005) RNA , vol.11 , pp. 995-1003
    • Saetrom, O.1    Snøve, O.2    Saetrom, P.3
  • 118
  • 119
    • 28944439309 scopus 로고    scopus 로고
    • Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3′UTR evolution
    • Stark,A., Brennecke,J., Bushati,N., Russell,R.B. and Cohen,S.M. (2005) Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3′UTR evolution. Cell, 123, 1133-1146.
    • (2005) Cell , vol.123 , pp. 1133-1146
    • Stark, A.1    Brennecke, J.2    Bushati, N.3    Russell, R.B.4    Cohen, S.M.5
  • 120
    • 38849145861 scopus 로고    scopus 로고
    • Prediction of both conserved and nonconserved microRNA targets in animals
    • Wang,X. and Naqa,I.M.E. (2008) Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics, 24 325-332.
    • (2008) Bioinformatics , vol.24 , pp. 325-332
    • Wang, X.1    Naqa, I.M.E.2
  • 121
    • 40549138450 scopus 로고    scopus 로고
    • Comparing sequence and expression for predicting microRNA targets using GenMiR3
    • Huang,J.C., Frey,B.J. and Morris,Q.D. (2008) Comparing sequence and expression for predicting microRNA targets using GenMiR3. Pac. Symp. on Biocomput., 52-63
    • (2008) Pac. Symp. on Biocomput , pp. 52-63
    • Huang, J.C.1    Frey, B.J.2    Morris, Q.D.3
  • 122
    • 44349128983 scopus 로고    scopus 로고
    • Cheng,C. and Li,L.M. (2008) Inferring microRNA activities by combining gene expression with microRNA target prediction. PLoS ONE, 3 e1989.
    • Cheng,C. and Li,L.M. (2008) Inferring microRNA activities by combining gene expression with microRNA target prediction. PLoS ONE, 3 e1989.
  • 123
    • 15244354492 scopus 로고    scopus 로고
    • Incorporating structure to predict microRNA targets
    • Robins,H., Li,Y. and Padgett,R.W. (2005) Incorporating structure to predict microRNA targets. Proc. Natl Acad. Sci. USA, 102, 4006-4009.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 4006-4009
    • Robins, H.1    Li, Y.2    Padgett, R.W.3
  • 124
    • 33947424813 scopus 로고    scopus 로고
    • MicroTar: Predicting microRNA targets from RNA duplexes
    • Thadani,R. and Tammi,M.T. (2006) MicroTar: Predicting microRNA targets from RNA duplexes. BMC Bioinformatics, 7(Suppl. 5), S20.
    • (2006) BMC Bioinformatics , vol.7 , Issue.SUPPL. 5
    • Thadani, R.1    Tammi, M.T.2
  • 125
    • 34748821761 scopus 로고    scopus 로고
    • The role of site accessibility in microRNA target recognition
    • Kertesz,M., Iovino,N., Unnerstall,U., Gaul,U. and Segal,E. (2007) The role of site accessibility in microRNA target recognition. Nat. Genet., 39, 1278-1284.
    • (2007) Nat. Genet , vol.39 , pp. 1278-1284
    • Kertesz, M.1    Iovino, N.2    Unnerstall, U.3    Gaul, U.4    Segal, E.5
  • 126
    • 50849141708 scopus 로고    scopus 로고
    • mirWIP: MicroRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts
    • doi:101038/nmeth.1247
    • Hammell,M., Long,D., Zhang,L., Lee,A., Carmack,C., Han,M., Ding,Y. and Ambros,V. (2008) mirWIP: MicroRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts. Nat. Methods, doi:101038/nmeth.1247.
    • (2008) Nat. Methods
    • Hammell, M.1    Long, D.2    Zhang, L.3    Lee, A.4    Carmack, C.5    Han, M.6    Ding, Y.7    Ambros, V.8
  • 127
    • 10244243802 scopus 로고    scopus 로고
    • Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences
    • Bonnet,E., Wuyts,J., Rouzé,P. and dePeer,Y.V. (2004) Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics, 20, 2911-2917.
    • (2004) Bioinformatics , vol.20 , pp. 2911-2917
    • Bonnet, E.1    Wuyts, J.2    Rouzé, P.3    dePeer, Y.V.4
  • 129
    • 33646240072 scopus 로고    scopus 로고
    • Direct evolution of genetic robustness in microRNA
    • Borenstein,E. and Ruppin,E. (2006) Direct evolution of genetic robustness in microRNA. Proc. Natl Acad. Sci. USA, 103, 6593-6598.
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 6593-6598
    • Borenstein, E.1    Ruppin, E.2
  • 130
    • 56249145105 scopus 로고    scopus 로고
    • Structure of the guide-strand-containing argonaute silencing complex
    • Wang,Y., Sheng,G., Juranek,S., Tuschl,T. and Patel,D.J. (2008) Structure of the guide-strand-containing argonaute silencing complex. Nature 456, 209-213.
    • (2008) Nature , vol.456 , pp. 209-213
    • Wang, Y.1    Sheng, G.2    Juranek, S.3    Tuschl, T.4    Patel, D.J.5
  • 131
    • 10644253787 scopus 로고    scopus 로고
    • Architecture of a validated microRNA::Target interaction
    • Vella,M.C., Reinert,K. and Slack,F.J. (2004) Architecture of a validated microRNA::Target interaction. Chem. Biol., 11, 1619-1623.
    • (2004) Chem. Biol , vol.11 , pp. 1619-1623
    • Vella, M.C.1    Reinert, K.2    Slack, F.J.3
  • 133
    • 34848865601 scopus 로고    scopus 로고
    • A-to-I editing challenger or ally to the microRNA process
    • Ohman,M. (2007) A-to-I editing challenger or ally to the microRNA process. Biochimie, 89, 1171-1176.
    • (2007) Biochimie , vol.89 , pp. 1171-1176
    • Ohman, M.1
  • 134
    • 27344448283 scopus 로고    scopus 로고
    • Human microRNAs target a functionally distinct population of genes with AT-rich 3′ UTRs
    • Robins,H. and Press,W.H. (2005) Human microRNAs target a functionally distinct population of genes with AT-rich 3′ UTRs. Proc. Natl Acad. Sci. USA, 102, 15557-15562.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 15557-15562
    • Robins, H.1    Press, W.H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.