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Volumn 6, Issue 1, 2011, Pages 129-143

An overview of computational approaches for prediction of miRNA genes and their targets

Author keywords

Gene expression regulation; MicroRNA; MicroRNA prediction; MicroRNA target prediction; MiRNA; RNA interference

Indexed keywords

CELLULARS; COMPUTATIONAL APPROACH; EXPRESSION REGULATION; GENES EXPRESSION; MICRORNA; MICRORNA PREDICTION; MICRORNA TARGET PREDICTIONS; MIRNA; PROTEIN EXPRESSIONS; RNA INTERFERENCE;

EID: 79953871724     PISSN: 15748936     EISSN: None     Source Type: Journal    
DOI: 10.2174/157489311795222365     Document Type: Article
Times cited : (9)

References (116)
  • 1
    • 0027751663 scopus 로고
    • The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
    • Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993; 75: 843-54.
    • (1993) Cell , vol.75 , pp. 843-854
    • Lee, R.C.1    Feinbaum, R.L.2    Ambros, V.3
  • 2
    • 78649646228 scopus 로고    scopus 로고
    • Existence of snoRNA, microRNA, piRNA characteristics in a novel non-coding RNA: X-ncRNA and its biological implication in Homo sapiens
    • Meenakshisundaram K, Carmen L, Michela B, Diego DB, Rosaria V, Gabriella M. Existence of snoRNA, microRNA, piRNA characteristics in a novel non-coding RNA: x-ncRNA and its biological implication in Homo sapiens. J Bioinform Sequ Anal 2009; 1(2): 031-040.
    • (2009) J Bioinform Sequ Anal , vol.1 , Issue.2 , pp. 031-040
    • Meenakshisundaram, K.1    Carmen, L.2    Michela, B.3    Diego, D.B.4    Rosaria, V.5    Gabriella, M.6
  • 3
    • 77953169004 scopus 로고    scopus 로고
    • The role of small non-coding RNAs in genome stability and chromatin organization
    • Wolfswinkel JC, Ketting RF. The role of small non-coding RNAs in genome stability and chromatin organization. J Cell Sci 2010; 123: 1825-39.
    • (2010) J Cell Sci , vol.123 , pp. 1825-1839
    • Wolfswinkel, J.C.1    Ketting, R.F.2
  • 4
    • 33845242919 scopus 로고    scopus 로고
    • MicroRNAs: Regulators of gene expression and cell differentiation
    • Shivdasani RA. MicroRNAs: regulators of gene expression and cell differentiation. Blood 2006; 108(12): 3646-53.
    • (2006) Blood , vol.108 , Issue.12 , pp. 3646-3653
    • Shivdasani, R.A.1
  • 5
    • 0347444723 scopus 로고    scopus 로고
    • MicroRNAs: Genomics, biogenesis, mechanism, and function
    • Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004; 116: 281-97.
    • (2004) Cell , vol.116 , pp. 281-297
    • Bartel, D.P.1
  • 7
    • 33645294070 scopus 로고    scopus 로고
    • Oncomirs [mdash] microRNAs with a role in cancer
    • Esquela-Kerscher A, Slack FJ. Oncomirs [mdash] microRNAs with a role in cancer. Nat Rev Cancer 2006; 6: 259-69.
    • (2006) Nat Rev Cancer , vol.6 , pp. 259-269
    • Esquela-Kerscher, A.1    Slack, F.J.2
  • 8
    • 18144365478 scopus 로고    scopus 로고
    • MicroRNA biogenesis and cancer
    • Gregory RI, Shiekhattar R. MicroRNA biogenesis and cancer. Cancer Res 2005; 65: 3509-12.
    • (2005) Cancer Res , vol.65 , pp. 3509-3512
    • Gregory, R.I.1    Shiekhattar, R.2
  • 9
    • 28044471565 scopus 로고    scopus 로고
    • MicroRNA functions in animal development and human disease
    • Varez-Garcia, Miska EA. MicroRNA functions in animal development and human disease. Development 2005; 132: 4653-62.
    • (2005) Development , vol.132 , pp. 4653-4662
    • Varez-Garcia Miska, E.A.1
  • 10
    • 33644659734 scopus 로고    scopus 로고
    • Mammalian microRNAs: A small world for fine-tuning gene expression
    • Sevignani C, Calin G, Siracusa L, Croce C. Mammalian microRNAs: a small world for fine-tuning gene expression. Mamm Genome 2006; 17:189-202.
    • (2006) Mamm Genome , vol.17 , pp. 189-202
    • Sevignani, C.1    Calin, G.2    Siracusa, L.3    Croce, C.4
  • 11
    • 33644772270 scopus 로고    scopus 로고
    • The expansion of the metazoan microRNA repertoire
    • Hertel J, Lindemeyer M, Missal K, et al. The expansion of the metazoan microRNA repertoire. BMC Genomics 2006; 7: 25.
    • (2006) BMC Genomics , vol.7 , pp. 25
    • Hertel, J.1    Lindemeyer, M.2    Missal, K.3
  • 12
    • 0037009364 scopus 로고    scopus 로고
    • MicroRNA maturation: Stepwise processing and subcellular localization
    • Yoontae L, Kipyoung J, Jun-tae L, Sunyoung K, Narry KV. MicroRNA maturation: Stepwise processing and subcellular localization. EMBO J 2002; 21(17): 4663-70.
    • (2002) EMBO J , vol.21 , Issue.17 , pp. 4663-4670
    • Yoontae, L.1    Kipyoung, J.2    Jun-Tae, L.3    Sunyoung, K.4    Narry, K.V.5
  • 13
    • 50549095181 scopus 로고    scopus 로고
    • Let-microRNAs in development, stem cells and cancer
    • doi: 10.1016/j.molmed.2008.07.001
    • Büssing I, Slack FJ, Grosshans H. let-microRNAs in development, stem cells and cancer. Trends Mol Med 2008; doi: 10.1016/j.molmed.2008.07.001.
    • (2008) Trends Mol Med
    • Büssing, I.1    Slack, F.J.2    Grosshans, H.3
  • 14
    • 33746844362 scopus 로고    scopus 로고
    • Bioinformatic discovery of microRNA precursors from human ESTs and introns
    • Sung-Chou L, Chao-Yu P, Wen-chang L. Bioinformatic discovery of microRNA precursors from human ESTs and introns. BMC Genomics 2006; 7: 164.
    • (2006) BMC Genomics , vol.7 , pp. 164
    • Sung-Chou, L.1    Chao-Yu, P.2    Wen-Chang, L.3
  • 16
    • 9344235449 scopus 로고    scopus 로고
    • Human micro-RNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs
    • Cai X, Hagedorn CH, Cullen BR. Human micro-RNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA 2004; 10: 1957-66.
    • (2004) RNA , vol.10 , pp. 1957-1966
    • Cai, X.1    Hagedorn, C.H.2    Cullen, B.R.3
  • 17
    • 8144225486 scopus 로고    scopus 로고
    • MicroRNA genes are transcribed by RNA polymerase II
    • Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH. MicroRNA genes are transcribed by RNA polymerase II. EMBO J 2004; 23: 4051-60.
    • (2004) EMBO J , vol.23 , pp. 4051-4060
    • Lee, Y.1    Kim, M.2    Han, J.3    Yeom, K.H.4    Lee, S.5    Baek, S.H.6
  • 20
    • 0347361541 scopus 로고    scopus 로고
    • Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs
    • Yi R, Qin Y, Macara IG, Cullen BR. Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev 2003; 17: 3011-6.
    • (2003) Genes Dev , vol.17 , pp. 3011-3016
    • Yi, R.1    Qin, Y.2    Macara, I.G.3    Cullen, B.R.4
  • 21
    • 0141843656 scopus 로고    scopus 로고
    • The nuclear RNase III Drosha initiates microRNA processing
    • Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J. The nuclear RNase III Drosha initiates microRNA processing. Nature 2003; 425: 415-9.
    • (2003) Nature , vol.425 , pp. 415-419
    • Lee, Y.1    Ahn, C.2    Han, J.3    Choi, H.4    Kim, J.5    Yim, J.6
  • 22
    • 27744537851 scopus 로고    scopus 로고
    • Human RISC couples microRNA biogenesis and posttranscriptional gene silencing
    • Gregory RI, Chendrimada TP, Cooch N, Shiekhattar R. Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell 2005; 123: 631-40.
    • (2005) Cell , vol.123 , pp. 631-640
    • Gregory, R.I.1    Chendrimada, T.P.2    Cooch, N.3    Shiekhattar, R.4
  • 23
    • 18144365478 scopus 로고    scopus 로고
    • MicroRNA Biogenesis and Cancer
    • Gregory RI, Shiekhattar R. MicroRNA Biogenesis and Cancer. Cancer Res 2005; 65: 3509.
    • (2005) Cancer Res , vol.65 , pp. 3509
    • Gregory, R.I.1    Shiekhattar, R.2
  • 24
    • 10644234841 scopus 로고    scopus 로고
    • The Drosha-DGCR8 complex in primary microRNA processing
    • Han J, Lee Y, Yeom KH, Kim YK, Jin H, Kim VN. The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev 2004; 18: 3016-27.
    • (2004) Genes Dev , vol.18 , pp. 3016-3027
    • Han, J.1    Lee, Y.2    Yeom, K.H.3    Kim, Y.K.4    Jin, H.5    Kim, V.N.6
  • 25
    • 10344248903 scopus 로고    scopus 로고
    • The human DiGeorge syndrome critical region gene 8 and its D. melanogaster homolog are required for miRNA biogenesis
    • Landthaler M, Yalcin A, Tuschl T. The human DiGeorge syndrome critical region gene 8 and its D. melanogaster homolog are required for miRNA biogenesis. Curr Biol 2004; 14: 2162-7.
    • (2004) Curr Biol , vol.14 , pp. 2162-2167
    • Landthaler, M.1    Yalcin, A.2    Tuschl, T.3
  • 26
    • 27144475302 scopus 로고    scopus 로고
    • Micro-RNA regulation of the mammalian lin-28 gene during neuronal differentiation of embryonal carcinoma cells
    • Wu L, Belasco JG. Micro-RNA regulation of the mammalian lin-28 gene during neuronal differentiation of embryonal carcinoma cells. Mol Cell Biol 2005; 25(21): p. 9198-208.
    • (2005) Mol Cell Biol , vol.25 , Issue.21 , pp. 9198-9208
    • Wu, L.1    Belasco, J.G.2
  • 27
    • 0037418839 scopus 로고    scopus 로고
    • Bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila
    • Brennecke J, Hipfner DR, Stark A, Russell RB, Cohen SM. Bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell 2003; 113: 25-36.
    • (2003) Cell , vol.113 , pp. 25-36
    • Brennecke, J.1    Hipfner, D.R.2    Stark, A.3    Russell, R.B.4    Cohen, S.M.5
  • 28
    • 0027751663 scopus 로고
    • The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
    • Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993; 75: 843-54.
    • (1993) Cell , vol.75 , pp. 843-854
    • Lee, R.C.1    Feinbaum, R.L.2    Ambros, V.3
  • 29
    • 0027730383 scopus 로고
    • Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans
    • 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 1993; 75: 855-62.
    • (1993) Cell , vol.75 , pp. 855-862
    • Wightman, B.1    Ha, I.2    Ruvkun, G.3
  • 30
    • 26244440240 scopus 로고    scopus 로고
    • Intrinsic and extrinsic regulators of developmental timing: From miRNAs to nutritional cues
    • doi:10.1242/dev.01972
    • Rougvie AE. Intrinsic and extrinsic regulators of developmental timing: from miRNAs to nutritional cues. Development 2005; doi:10.1242/dev.01972.
    • (2005) Development
    • Rougvie, A.E.1
  • 31
    • 24144494563 scopus 로고    scopus 로고
    • The let-7 MicroRNA family members mir-48, mir-84 and mir-241 function together to regulate developmental timing in caenorhabditis elegans
    • Abbott AL, Alvarez-Saavedra E, Miska EA, et al. The let-7 MicroRNA family members mir-48, mir-84 and mir-241 function together to regulate developmental timing in caenorhabditis elegans. Devel Cell 2005; 9: 403-14.
    • (2005) Devel Cell , vol.9 , pp. 403-414
    • Abbott, A.L.1    Alvarez-Saavedra, E.2    Miska, E.A.3
  • 32
    • 0035955361 scopus 로고    scopus 로고
    • An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans
    • Lau NC, Lim LP, Weinstein EG, Bartel DP. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 2001; 294: 858-62.
    • (2001) Science , vol.294 , pp. 858-862
    • Lau, N.C.1    Lim, L.P.2    Weinstein, E.G.3    Bartel, D.P.4
  • 33
    • 24144467823 scopus 로고    scopus 로고
    • Regulatory mutations upstream of mir-48, a C. elegans let-7 family microRNA cause developmental timing defects
    • Lin M, Jones-Rhoades MW, Lau NC, Bartel DP, Rougvie AE. Regulatory mutations upstream of mir-48, a C. elegans let-7 family microRNA cause developmental timing defects. Devel Cell 2005; 9: 415-22.
    • (2005) Devel Cell , vol.9 , pp. 415-422
    • Lin, M.1    Jones-Rhoades, M.W.2    Lau, N.C.3    Bartel, D.P.4    Rougvie, A.E.5
  • 34
    • 0034708122 scopus 로고    scopus 로고
    • The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans
    • Reinhart BJ, Slack FJ, Basson M, et al. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 2000; 403: 901-6.
    • (2000) Nature , vol.403 , pp. 901-906
    • Reinhart, B.J.1    Slack, F.J.2    Basson, M.3
  • 35
    • 0036670695 scopus 로고    scopus 로고
    • The bantam gene regulates Drosophila growth
    • Hipfner DR, Weigmann K, Cohen SM. The bantam gene regulates Drosophila growth. Genetic 2002; 161: 1527-37.
    • (2002) Genetic , vol.161 , pp. 1527-1537
    • Hipfner, D.R.1    Weigmann, K.2    Cohen, S.M.3
  • 37
    • 23344439006 scopus 로고    scopus 로고
    • The RNaseIII enzyme Dicer is required for morphogenesis but not patterning of the vertebrate limb
    • Harfe BD, McManus MT, Mansfield JH, Hornstein E, Tabin CJ. The RNaseIII enzyme Dicer is required for morphogenesis but not patterning of the vertebrate limb. Proc Natl Acad Sci USA 2005; 102: 10898-903.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 10898-10903
    • Harfe, B.D.1    McManus, M.T.2    Mansfield, J.H.3    Hornstein, E.4    Tabin, C.J.5
  • 38
    • 0037694970 scopus 로고    scopus 로고
    • The drosophila microRNA mir-14 suppresses cell death and is required for normal fat metabolism
    • Xu P, Vernooy SY, Guo M, Hay BA. The drosophila microRNA mir-14 suppresses cell death and is required for normal fat metabolism. Curr Biol 2003; 13: 790-5.
    • (2003) Curr Biol , vol.13 , pp. 790-795
    • Xu, P.1    Vernooy, S.Y.2    Guo, M.3    Hay, B.A.4
  • 39
    • 9144225636 scopus 로고    scopus 로고
    • The Microprocessor complex mediates the genesis of microRNAs
    • Gregory RI, Yan KP, Amuthan G, et al. The Microprocessor complex mediates the genesis of microRNAs. Nature 2004; 432: 235-40.
    • (2004) Nature , vol.432 , pp. 235-240
    • Gregory, R.I.1    Yan, K.P.2    Amuthan, G.3
  • 40
    • 10644234841 scopus 로고    scopus 로고
    • The Drosha DGCR8 complex in primary microRNA processing
    • Han J, Lee Y, Yeom KH, Kim YK, Jin H, Kim VN. The Drosha DGCR8 complex in primary microRNA processing. Genes Dev 2004; 18: 3016-27.
    • (2004) Genes Dev , vol.18 , pp. 3016-3027
    • Han, J.1    Lee, Y.2    Yeom, K.H.3    Kim, Y.K.4    Jin, H.5    Kim, V.N.6
  • 42
    • 17644363376 scopus 로고    scopus 로고
    • A cellular microRNA mediates antiviral defense in human cells
    • Lecellier CH, Dunoyer P, Arar K, et al. A cellular microRNA mediates antiviral defense in human cells. Science 2005; 308: 557-60.
    • (2005) Science , vol.308 , pp. 557-560
    • Lecellier, C.H.1    Dunoyer, P.2    Arar, K.3
  • 45
    • 14344260087 scopus 로고    scopus 로고
    • HIV-1 encoded candidate micro-RNAs and their cellular targets
    • Bennasser Y, Le SY, Yeung ML, Jeang KT. HIV-1 encoded candidate micro-RNAs and their cellular targets. Retrovirology 2004; 1: 43.
    • (2004) Retrovirology , vol.1 , pp. 43
    • Bennasser, Y.1    Le, S.Y.2    Yeung, M.L.3    Jeang, K.T.4
  • 46
    • 18744396337 scopus 로고    scopus 로고
    • Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia
    • Calin GA, Dumitru CD, Shimizu M, Bichi R, Zupo S, Noch E. Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci USA 2002; 99: 15524-9.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 15524-15529
    • Calin, G.A.1    Dumitru, C.D.2    Shimizu, M.3    Bichi, R.4    Zupo, S.5    Noch, E.6
  • 48
    • 9144225636 scopus 로고    scopus 로고
    • The Microprocessor complex mediates the genesis of microRNAs
    • Gregory RI, Yan KP, Amuthan G, et al. The Microprocessor complex mediates the genesis of microRNAs. Nature 2004; 432: 235-40.
    • (2004) Nature , vol.432 , pp. 235-240
    • Gregory, R.I.1    Yan, K.P.2    Amuthan, G.3
  • 50
    • 6044248871 scopus 로고    scopus 로고
    • Therapeutic potential of RNA interference
    • Stevenson M. Therapeutic potential of RNA interference. N Engl J Med 2004; 351: 17727.
    • (2004) N Engl J Med , vol.351 , pp. 17727
    • Stevenson, M.1
  • 51
    • 12144290519 scopus 로고    scopus 로고
    • Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers
    • Calin GA, Sevignani C, Dumitru CD, Hyslop T, Noch E, Yendamuri S. Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc Natl Acad Sci USA 2004; 101: 2999-3004.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 2999-3004
    • Calin, G.A.1    Sevignani, C.2    Dumitru, C.D.3    Hyslop, T.4    Noch, E.5    Yendamuri, S.6
  • 52
    • 33646715590 scopus 로고    scopus 로고
    • Improved targeting of miRNA with antisense oligonucleotides
    • Davis S, Lollo B, Freier S, Esau C. Improved targeting of miRNA with antisense oligonucleotides. Nucleic Acids Res 2006; 34: 2294-304.
    • (2006) Nucleic Acids Res , vol.34 , pp. 2294-2304
    • Davis, S.1    Lollo, B.2    Freier, S.3    Esau, C.4
  • 53
    • 33947309774 scopus 로고    scopus 로고
    • Evolution of plant microRNA gene families
    • Li A, Mao L. Evolution of plant microRNA gene families. Cell Res 2007; 17: 212-8.
    • (2007) Cell Res , vol.17 , pp. 212-218
    • Li, A.1    Mao, L.2
  • 54
    • 35348847214 scopus 로고    scopus 로고
    • Prediction and validation of microRNA targets in animal genomes
    • Martin G, Schouest K, Kovvuru P, Spillane C. Prediction and validation of microRNA targets in animal genomes. J Biosci 2007; 32: 1049-52.
    • (2007) J Biosci , vol.32 , pp. 1049-1052
    • Martin, G.1    Schouest, K.2    Kovvuru, P.3    Spillane, C.4
  • 56
    • 0037447334 scopus 로고    scopus 로고
    • The microRNAs of Caenorhabditis elegans
    • Lim LP, Lau NC, Weinstein EG, et al. The microRNAs of Caenorhabditis elegans. Genes Dev 2003; 17: 991-1008.
    • (2003) Genes Dev , vol.17 , pp. 991-1008
    • Lim, L.P.1    Lau, N.C.2    Weinstein, E.G.3
  • 57
    • 0842278323 scopus 로고    scopus 로고
    • Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification
    • Ohler U, Yekta S, Lim LP, Bartel DP, Burge CB. Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification. RNA 2004; 10: 1309-22.
    • (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
  • 58
    • 33646745146 scopus 로고    scopus 로고
    • Prediction and Identification of Herpes Simplex Virus 1-Encoded MicroRNAs
    • Cui C, Griffiths A, Li G, et al. Prediction and Identification of Herpes Simplex Virus 1-Encoded MicroRNAs. J Virol 2006; 5499-508.
    • (2006) J Virol , pp. 5499-5508
    • Cui, C.1    Griffiths, A.2    Li, G.3
  • 59
    • 20444446357 scopus 로고    scopus 로고
    • SV40-encoded microRNAs regulate viral gene expression and reduce susceptibility to cytotoxic T cells
    • Sullivan CS, Grundhoff AT, Tevethia S, Pipas JM, Ganem D. SV40-encoded microRNAs regulate viral gene expression and reduce susceptibility to cytotoxic T cells. Nature 2005; 435: 682-6.
    • (2005) Nature , vol.435 , pp. 682-686
    • Sullivan, C.S.1    Grundhoff, A.T.2    Tevethia, S.3    Pipas, J.M.4    Ganem, D.5
  • 61
    • 33646168051 scopus 로고    scopus 로고
    • A combined computational and microarray-based approach identifies novel microRNAs encoded by human gamma-herpesviruses
    • Grundhoff A, Sullivan CS, Ganem D. A combined computational and microarray-based approach identifies novel microRNAs encoded by human gamma-herpesviruses. RNA 2006; 12(5): 733-50.
    • (2006) RNA , vol.12 , Issue.5 , pp. 733-750
    • Grundhoff, A.1    Sullivan, C.S.2    Ganem, D.3
  • 62
    • 24644484014 scopus 로고    scopus 로고
    • Identification and Characterization of Human Cytomegalovirus-Encoded Micro-RNAs
    • Grey F, Antoniewicz A, Allen E, et al. Identification and Characterization of Human Cytomegalovirus-Encoded Micro-RNAs. J Virol 2005; 79: 12095-9.
    • (2005) J Virol , vol.79 , pp. 12095-12099
    • Grey, F.1    Antoniewicz, A.2    Allen, E.3
  • 63
    • 20844463414 scopus 로고    scopus 로고
    • Identification of microRNAs of the herpesvirus family
    • Pfeffer S, Sewer A, Lagos-Quintana M, et al. Identification of microRNAs of the herpesvirus family. Nat Methods 2005; 2(4): 269-76.
    • (2005) Nat Methods , vol.2 , Issue.4 , pp. 269-276
    • Pfeffer, S.1    Sewer, A.2    Lagos-Quintana, M.3
  • 65
    • 11444251652 scopus 로고    scopus 로고
    • New human and mouse microRNA genes found by homology search
    • Weber MJ. New human and mouse microRNA genes found by homology search. FEBS J 2005; 272 (1): 59-73.
    • (2005) FEBS J , vol.272 , Issue.1 , pp. 59-73
    • Weber, M.J.1
  • 66
    • 0038054470 scopus 로고    scopus 로고
    • Computational and Experimental Identification of C. elegans microRNAs
    • Grad Y, Aach J, Hayes GD, et al. Computational and Experimental Identification of C. elegans microRNAs. Mol Cell 2003; 11(5): 1253-63.
    • (2003) Mol Cell , vol.11 , Issue.5 , pp. 1253-1263
    • Grad, Y.1    Aach, J.2    Hayes, G.D.3
  • 67
    • 11844262661 scopus 로고    scopus 로고
    • Phylogenetic shadowing and computational identification of human microrna genes
    • Berezikov E, Guryev V, Belt JVD, et al. Phylogenetic shadowing and computational identification of human microrna genes. Cell 2005; 120(1): 21-4.
    • (2005) Cell , vol.120 , Issue.1 , pp. 21-24
    • Berezikov, E.1    Guryev, V.2    Belt, J.V.D.3
  • 68
    • 0242418246 scopus 로고    scopus 로고
    • Phylogenetic shadowing of primate sequences to find functional regions of the human genome
    • Boffelli D, McAuliffe J, Ovcharenko D, et al. Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 2003; 299: 1391-4.
    • (2003) Science , vol.299 , pp. 1391-1394
    • Boffelli, D.1    McAuliffe, J.2    Ovcharenko, D.3
  • 69
    • 77956508095 scopus 로고    scopus 로고
    • MIReNA: Finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data
    • doi:10.1093/bioinformatics/ btq329
    • Mathelier A, Carbone A. MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data. Bioinformatics 2010; doi:10.1093/bioinformatics/ btq329.
    • (2010) Bioinformatics
    • Mathelier, A.1    Carbone, A.2
  • 70
    • 77950547534 scopus 로고    scopus 로고
    • miRTRAP. A computational method for the systematic identification of miRNAs from high throughput sequencing data
    • Hendrix D, Levine M, Shi W. miRTRAP. A computational method for the systematic identification of miRNAs from high throughput sequencing data. Genome Biol 2010; 11: R39.
    • (2010) Genome Biol , vol.11
    • Hendrix, D.1    Levine, M.2    Shi, W.3
  • 71
    • 22944464084 scopus 로고    scopus 로고
    • Computational methods for identification of human microrna precursors
    • Nam JW, Lee WJ, Zhang B. Computational methods for identification of human microrna precursors. Pricai 2004; 3157: 732-41.
    • (2004) Pricai , vol.3157 , pp. 732-741
    • Nam, J.W.1    Lee, W.J.2    Zhang, B.3
  • 72
    • 21844477027 scopus 로고    scopus 로고
    • Human microRNA prediction through a probabilistic co-learning model of sequence and structure
    • Nam JW, Shin KR, Han J, Lee Y, Kim VN, Zhang BT. Human microRNA prediction through a probabilistic co-learning model of sequence and structure. Nucleic Acids Res 2005; 33(11): 3570-81.
    • (2005) Nucleic Acids Res , vol.33 , Issue.11 , 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
  • 73
    • 33747871855 scopus 로고    scopus 로고
    • Hairpins in a Haystack: Recognizing microRNA precursors in comparative genomics data
    • Hertel J, Stadler PF. Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data. Bioinformatics 2006; 22: e197-e202.
    • (2006) Bioinformatics , vol.22
    • Hertel, J.1    Stadler, P.F.2
  • 74
    • 34249003938 scopus 로고    scopus 로고
    • Principles and limitations of computational microrna gene and target finding
    • Doi: 10.1089/dna.2006.0551
    • Lindow M, Gorodkin J. Principles and limitations of computational microrna gene and target finding. DNA Cell Biol 2007; Doi: 10.1089/dna.2006.0551.
    • (2007) DNA Cell Biol
    • Lindow, M.1    Gorodkin, J.2
  • 75
    • 30344447264 scopus 로고    scopus 로고
    • Classification of real and pseudo microRNA precursors using local sructure-sequence features and support vector machine
    • Chenghai X, Fei L, Tao H, Guo-Ping L, Yanda L, Xuegong Z. Classification of real and pseudo microRNA precursors using local sructure-sequence features and support vector machine. BMC Bioinformatics 2005; 6: 310.
    • (2005) BMC Bioinformatics , vol.6 , pp. 310
    • Chenghai, X.1    Fei, L.2    Tao, H.3    Guo-Ping, L.4    Yanda, L.5    Xuegong, Z.6
  • 76
    • 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, Rouze P, Peer YV. Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics 2004; 20: 2911-7.
    • (2004) Bioinformatics , vol.20 , pp. 2911-2917
    • Bonnet, E.1    Wuyts, J.2    Rouze, P.3    Peer, Y.V.4
  • 77
    • 34547596338 scopus 로고    scopus 로고
    • MiPred: Classification of real and pseudo microRNA precursors using random forest prediction model with combined features
    • doi:10.1093/nar/gkm368
    • Jiang P, Wu H, Wang W, Ma W, Sun X, Lu Z. MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Nucleic Acids Res 2007; 35: 1-6 doi:10.1093/nar/gkm368.
    • (2007) Nucleic Acids Res , vol.35 , pp. 1-6
    • Jiang, P.1    Wu, H.2    Wang, W.3    Ma, W.4    Sun, X.5    Lu, Z.6
  • 79
    • 85200524936 scopus 로고    scopus 로고
    • Prediction and analysis of human microRNA regulatory modules, engineering in medicine and biology
    • China September 1-4
    • Yoon S, Micheli GD. Prediction and analysis of human microRNA regulatory modules, engineering in medicine and biology. 27th Annual Conference Shanghai, China September 1-4 2005.
    • (2005) 27th Annual Conference Shanghai
    • Yoon, S.1    Micheli, G.D.2
  • 80
    • 75149197426 scopus 로고    scopus 로고
    • Prediction of novel precursor miRNAs using a context-sensitive hidden Markov model (CSHMM)
    • Agarwal S, Vaz C, Bhattacharya A, Srinivasan A. Prediction of novel precursor miRNAs using a context-sensitive hidden Markov model (CSHMM). BMC Bioinformatics 2010; 11(Suppl 1): S29.
    • (2010) BMC Bioinformatics , vol.11 , Issue.SUPPL. 1
    • Agarwal, S.1    Vaz, C.2    Bhattacharya, A.3    Srinivasan, A.4
  • 82
    • 1642374097 scopus 로고    scopus 로고
    • Specificity of microRNA target selection in translational repression
    • Doench JG, Sharp PA. Specificity of microRNA target selection in translational repression. Genes Dev 2004; 18: 504-11.
    • (2004) Genes Dev , vol.18 , pp. 504-511
    • Doench, J.G.1    Sharp, P.A.2
  • 83
    • 10644253787 scopus 로고    scopus 로고
    • Architecture of a validated microRNA:Target interaction
    • Vella MC, Reinert K, Slack FJ. Architecture of a validated microRNA:target interaction. Chem Biol 2004; 11: 1619-23.
    • (2004) Chem Biol , vol.11 , pp. 1619-1623
    • Vella, M.C.1    Reinert, K.2    Slack, F.J.3
  • 86
    • 12744262431 scopus 로고    scopus 로고
    • Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets
    • Wang XJ, Reyes JL, Chua NH, Gaasterland T. Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biol 2004; 5: R65.
    • (2004) Genome Biol , vol.5
    • Wang, X.J.1    Reyes, J.L.2    Chua, N.H.3    Gaasterland, T.4
  • 87
    • 33645472191 scopus 로고    scopus 로고
    • Systematic identification of microRNA functions by combining target prediction and expression profiling
    • Wang X, Wang X. Systematic identification of microRNA functions by combining target prediction and expression profiling. Nucleic Acids Res 2006; 34(5): 1646-52.
    • (2006) Nucleic Acids Res , vol.34 , Issue.5 , pp. 1646-1652
    • Wang, X.1    Wang, X.2
  • 88
    • 25444461163 scopus 로고    scopus 로고
    • Prediction and verification of microRNA targets by moving targets, a highly adaptable prediction method
    • Burgler C, Macdonald PM. Prediction and verification of microRNA targets by moving targets, a highly adaptable prediction method. BMC Genomics 2005; 6: 88.
    • (2005) BMC Genomics , vol.6 , pp. 88
    • Burgler, C.1    Macdonald, P.M.2
  • 91
    • 2442672918 scopus 로고    scopus 로고
    • A combined computational-experimental approach predicts human micro-RNA targets
    • Kiriakidou M, Nelson PT, Kouranov A, et al. A combined computational-experimental approach predicts human micro-RNA targets. Genes Dev 2004; 18(10): 1165-78.
    • (2004) Genes Dev , vol.18 , Issue.10 , pp. 1165-1178
    • Kiriakidou, M.1    Nelson, P.T.2    Kouranov, A.3
  • 93
    • 85200522915 scopus 로고    scopus 로고
    • Computational prediction of drosophila MicroRNA targets and analysis of their negative feedback control
    • Poster
    • Watanabe Y, Yachie N, Tomita M, Kanai A. Computational prediction of drosophila MicroRNA targets and analysis of their negative feedback control. GIW 2006; Poster.
    • (2006) GIW
    • Watanabe, Y.1    Yachie, N.2    Tomita, M.3    Kanai, A.4
  • 95
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003; 31 (13): 3406-15.
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3406-3415
    • Zuker, M.1
  • 96
    • 33748346026 scopus 로고    scopus 로고
    • Perfect seed pairing is not a generally reliable predictor for miRNA-target interactions
    • Didiano D, Hobert O. Perfect seed pairing is not a generally reliable predictor for miRNA-target interactions. Nat Struct Mol Biol 2006; 13: 849-51.
    • (2006) Nat Struct Mol Biol , vol.13 , pp. 849-851
    • Didiano, D.1    Hobert, O.2
  • 97
    • 33344477448 scopus 로고    scopus 로고
    • Genomics of microRNA
    • Kim VN, Nam JW. Genomics of microRNA. Trends Genet 2006; 22: 165-73.
    • (2006) Trends Genet , vol.22 , pp. 165-173
    • Kim, V.N.1    Nam, J.W.2
  • 98
    • 31044444975 scopus 로고    scopus 로고
    • TarBase: A comprehensive database of experimentally supported animal micro-RNA targets
    • Sethupathy P, Corda B, Hatzigeorgiou AG. TarBase: a comprehensive database of experimentally supported animal micro-RNA targets. RNA 2006; 12: 192-7.
    • (2006) RNA , vol.12 , pp. 192-197
    • Sethupathy, P.1    Corda, B.2    Hatzigeorgiou, A.G.3
  • 99
    • 4644237189 scopus 로고    scopus 로고
    • Fast and effective prediction of microRNA/target duplexes
    • Rehmsmeier M, Steffen P, Höchsmann M, Giegerich R. Fast and effective prediction of microRNA/target duplexes. RNA 2004; 10: 1507-17.
    • (2004) RNA , vol.10 , pp. 1507-1517
    • Rehmsmeier, M.1    Steffen, P.2    Höchsmann, M.3    Giegerich, R.4
  • 100
    • 15244354492 scopus 로고    scopus 로고
    • Incorporating structure to predict microRNA targets
    • Robins H, Li Y, Padgett RW. Incorporating structure to predict microRNA targets. Proc Natl Acad Sci USA 2005; 102: 4006-9.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 4006-4009
    • Robins, H.1    Li, Y.2    Padgett, R.W.3
  • 101
    • 33947424813 scopus 로고    scopus 로고
    • MicroTar: Predicting microRNA targets from RNA duplexes
    • doi: 10.1186/1471-2105-7-S5-S20
    • Thadani R, Tammi MT. MicroTar: predicting microRNA targets from RNA duplexes. BMC Bioinformatics 2006; doi: 10.1186/1471-2105-7-S5-S20.
    • (2006) BMC Bioinformatics
    • Thadani, R.1    Tammi, M.T.2
  • 102
    • 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 EJ, et al. Systematic discovery of regulatory motifs in human promoters and 3'UTRs by comparison of several mammals. Nature 2005; 434: 338-45.
    • (2005) Nature , vol.434 , pp. 338-345
    • Xie, X.1    Lu, J.2    Kulbokas, E.J.3
  • 103
    • 60649111889 scopus 로고    scopus 로고
    • HuMiTar: A sequence-based method for prediction of human microRNA targets
    • doi:10.1186/1748-7188-3-16
    • Ruan J, Chen H, Kurgan L, Chen K, Kang C, Pu P. HuMiTar: a sequence-based method for prediction of human microRNA targets. Algorithms Mol Biol 2008; doi:10.1186/1748-7188-3-16
    • (2008) Algorithms Mol Biol
    • Ruan, J.1    Chen, H.2    Kurgan, L.3    Chen, K.4    Kang, C.5    Pu, P.6
  • 104
    • 85200523684 scopus 로고    scopus 로고
    • Combining structure-based Features and conserved data for microRNA target Prediction by the neural network method
    • Chao SY, Chiang JH. Combining structure-based Features and conserved data for microRNA target Prediction by the neural network method. ICS 2006.
    • (2006) ICS
    • Chao, S.Y.1    Chiang, J.H.2
  • 106
    • 22244447130 scopus 로고    scopus 로고
    • Weighted sequence motifs as an improved seeding step in microRNA target prediction algorithms
    • Saetrom O, Snove O, Saetrom P. Weighted sequence motifs as an improved seeding step in microRNA target prediction algorithms. RNA 2005; 11: 995-1003.
    • (2005) RNA , vol.11 , pp. 995-1003
    • Saetrom, O.1    Snove, O.2    Saetrom, P.3
  • 107
    • 75149129669 scopus 로고    scopus 로고
    • MTar: A computational microRNA target prediction architecture for human transcriptome
    • doi: 10.1186/1471-2105-11-S1-S2
    • Chandra V, Girijadevi R, Nair AS, Pillai SS, Pillai RM. MTar: a computational microRNA target prediction architecture for human transcriptome. BMC Bioinformatics 2010; doi: 10.1186/1471-2105-11-S1-S2.
    • (2010) BMC Bioinformatics
    • Chandra, V.1    Girijadevi, R.2    Nair, A.S.3    Pillai, S.S.4    Pillai, R.M.5
  • 108
    • 77952671774 scopus 로고    scopus 로고
    • TargetSpy: A supervised machine learning approach for microRNA target prediction
    • Sturm M, Hackenberg M, Langenberger D, Frishman D. TargetSpy: a supervised machine learning approach for microRNA target prediction. BMC Bioinformatics 2010; 11: 292.
    • (2010) BMC Bioinformatics , vol.11 , pp. 292
    • Sturm, M.1    Hackenberg, M.2    Langenberger, D.3    Frishman, D.4
  • 109
    • 63049136932 scopus 로고    scopus 로고
    • A study of microRNAs in silico and in vivo: Bioinformatics approaches to microRNA discovery and target identification
    • Yousef M, Showe L, Showe M. A study of microRNAs in silico and in vivo: bioinformatics approaches to microRNA discovery and target identification. FEBS J 2009; 276: 2150-6.
    • (2009) FEBS J , vol.276 , pp. 2150-2156
    • Yousef, M.1    Showe, L.2    Showe, M.3
  • 110
    • 0038054470 scopus 로고    scopus 로고
    • Computational and experimental identification of C. elegans microRNAs
    • Grad Y, Aach J, Hayes GD, et al. Computational and experimental identification of C. elegans microRNAs. Mol Cell 2003; 11: 1253-63.
    • (2003) Mol Cell , vol.11 , pp. 1253-1263
    • Grad, Y.1    Aach, J.2    Hayes, G.D.3
  • 112
    • 66149167564 scopus 로고    scopus 로고
    • In silico miRNA prediction in metazoan genomes: Balancing between sensitivity and specificity
    • Burgt A, Fiers MW, Nap JP, Ham RC. In silico miRNA prediction in metazoan genomes: balancing between sensitivity and specificity. BMC Genomics 2009; 10: 204.
    • (2009) BMC Genomics , vol.10 , pp. 204
    • Burgt, A.1    Fiers, M.W.2    Nap, J.P.3    Ham, R.C.4
  • 113
    • 67349123973 scopus 로고    scopus 로고
    • Redefining MicroRNA Targets
    • doi 10.10-16/j.cub.03.059
    • Seitz H. Redefining MicroRNA Targets. Curr Biol 2009; doi 10.10-16/j.cub.03.059.
    • (2009) Curr Biol
    • Seitz, H.1
  • 114
    • 0033634943 scopus 로고    scopus 로고
    • The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor
    • Slack FJ, Basson M, Liu Z, Ambros V, Horvitz HR, Ruvkun G. The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor. Mol Cell 2000; 5, 659-69.
    • (2000) Mol Cell , vol.5 , pp. 659-669
    • Slack, F.J.1    Basson, M.2    Liu, Z.3    Ambros, V.4    Horvitz, H.R.5    Ruvkun, G.6
  • 115
    • 0024963695 scopus 로고
    • A hierarchy of regulatory genes controls a larva-toadult developmental switch in C. elegans
    • Ambros V. A hierarchy of regulatory genes controls a larva-toadult developmental switch in C. elegans. Cell 1989; 57: 49-57.
    • (1989) Cell , vol.57 , pp. 49-57
    • Ambros, V.1
  • 116
    • 34249076321 scopus 로고    scopus 로고
    • The regulation of genes and genomes by small RNAs
    • Ambros V, Chen X. The regulation of genes and genomes by small RNAs. Development 2007; 134: 1635-41.
    • (2007) Development , vol.134 , pp. 1635-1641
    • Ambros, V.1    Chen, X.2


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