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Volumn 8, Issue , 2007, Pages

Ab initio identification of human microRNAs based on structure motifs

Author keywords

[No Author keywords available]

Indexed keywords

AB INITIO PREDICTION; ENERGY DISTRIBUTIONS; LINEAR GENETIC PROGRAMMING; MACHINE LEARNING TECHNIQUES; POST-TRANSCRIPTIONAL REGULATIONS; SECONDARY STRUCTURES; SEQUENCE INFORMATIONS; STRUCTURE INFORMATION;

EID: 39049169222     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-478     Document Type: Article
Times cited : (50)

References (38)
  • 1
    • 0347444723 scopus 로고    scopus 로고
    • MicroRNAs: Genomics, biogenesis, mechanism, and function
    • 10.1016/S0092-8674(04)00045-5 14744438
    • Bartel D MicroRNAs: Genomics, biogenesis, mechanism, and function Cell 2004, 116(2):281-297. 10.1016/S0092-8674(04)00045-5 14744438
    • (2004) Cell , vol.116 , Issue.2 , pp. 281-297
    • Bartel, D.1
  • 2
    • 4644309196 scopus 로고    scopus 로고
    • The functions of animal microRNAs
    • 10.1038/nature02871 15372042
    • Ambros V The functions of animal microRNAs Nature 2004, 431:350-355. 10.1038/nature02871 15372042
    • (2004) Nature , vol.431 , pp. 350-355
    • Ambros, V.1
  • 3
    • 3042767202 scopus 로고    scopus 로고
    • MicroRNAs: Small RNAs with a big role in gene regulation
    • 10.1038/nrg1379 15211354
    • He L Hannon G MicroRNAs: Small RNAs with a big role in gene regulation Nat Rev Genet 2004, 5(7):522-531. 10.1038/nrg1379 15211354
    • (2004) Nat Rev Genet , vol.5 , Issue.7 , pp. 522-531
    • He, L.1    Hannon, G.2
  • 4
    • 11444251652 scopus 로고    scopus 로고
    • New human and mouse microRNA genes found by homology search
    • 10.1111/j.1432-1033.2004.04389.x 15634332
    • Weber M New human and mouse microRNA genes found by homology search FEBS J 2005, 272:59-73. 10.1111/j.1432-1033.2004.04389.x 15634332
    • (2005) FEBS J , vol.272 , pp. 59-73
    • Weber, M.1
  • 5
    • 16344366331 scopus 로고    scopus 로고
    • Profile-based detection of microRNA precursors in animal genomes
    • 10.1093/bioinformatics/bti073 15509608
    • Legendre M Lambert A Gautheret D Profile-based detection of microRNA precursors in animal genomes Bioinformatics 2005, 21(7):841-845. 10.1093/ bioinformatics/bti073 15509608
    • (2005) Bioinformatics , vol.21 , Issue.7 , pp. 841-845
    • Legendre, M.1    Lambert, A.2    Gautheret, D.3
  • 6
    • 0037423845 scopus 로고    scopus 로고
    • Vertebrate microRNA genes
    • 10.1126/science.1080372 12624257
    • Lim L Glasner M Yekta S Burge C Bartel D Vertebrate microRNA genes Science 2003, 299:5612-1540. 10.1126/science.1080372 12624257
    • (2003) Science , vol.299 , pp. 1540
    • Lim, L.1    Glasner, M.2    Yekta, S.3    Burge, C.4    Bartel, D.5
  • 8
    • 0038825783 scopus 로고    scopus 로고
    • Computational identification of Drosophila microRNA genes
    • 10.1186/gb-2003-4-7-r42
    • Lai E Tomancak P Williams R Rubin G Computational identification of Drosophila microRNA genes Genome Biol 2003, 4:7-42. 10.1186/ gb-2003-4-7-r42
    • (2003) Genome Biol , vol.4 , pp. 42
    • Lai, E.1    Tomancak, P.2    Williams, R.3    Rubin, G.4
  • 9
    • 0038054470 scopus 로고    scopus 로고
    • Computational and experimental identification of C. elegans microRNAs
    • 10.1016/S1097-2765(03)00153-9 12769849
    • Grad Y Aach J Hayes G Reinhart B Church G Ruvkun G Kim J Computational and experimental identification of C. elegans microRNAs Mol Cell 2003, 11:1253-1263. 10.1016/S1097-2765(03)00153-9 12769849
    • (2003) Mol Cell , vol.11 , pp. 1253-1263
    • Grad, Y.1    Aach, J.2    Hayes, G.3    Reinhart, B.4    Church, G.5    Ruvkun, G.6    Kim, J.7
  • 10
    • 24644476482 scopus 로고    scopus 로고
    • MicroRNA identification based on sequence and structure alignment
    • 10.1093/bioinformatics/bti562 15994192
    • Wang X Zhang J Li F Gu G He T Zhang X Li Y MicroRNA identification based on sequence and structure alignment Bioinformatics 2005, 21(18):3610-3614. 10.1093/bioinformatics/bti562 15994192
    • (2005) Bioinformatics , vol.21 , Issue.18 , pp. 3610-3614
    • Wang, X.1    Zhang, J.2    Li, F.3    Gu, G.4    He, T.5    Zhang, X.6    Li, Y.7
  • 11
    • 0842278323 scopus 로고    scopus 로고
    • Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification
    • 1370619 15317971 10.1261/rna.5206304
    • Ohler U Yekta S Lim L Bartel D Burge C Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification RNA 2004, 10:1309-1322. 1370619 15317971 10.1261/ rna.5206304
    • (2004) RNA , vol.10 , pp. 1309-1322
    • Ohler, U.1    Yekta, S.2    Lim, L.3    Bartel, D.4    Burge, C.5
  • 13
    • 11844262661 scopus 로고    scopus 로고
    • Phylogenetic shadowing and computational identification of human microRNA genes
    • 10.1016/j.cell.2004.12.031 15652478
    • Berezikov E Guryev V van de Belt J Wienholds E Plasterk R Cuppen E Phylogenetic shadowing and computational identification of human microRNA genes Cell 2005, 120(1):21-24. 10.1016/j.cell.2004.12.031 15652478
    • (2005) Cell , vol.120 , Issue.1 , pp. 21-24
    • Berezikov, E.1    Guryev, V.2    van de Belt, J.3    Wienholds, E.4    Plasterk, R.5    Cuppen, E.6
  • 15
    • 30344447264 scopus 로고    scopus 로고
    • Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine
    • 1360673 16381612 10.1186/1471-2105-6-310
    • Xue C Li F He T Liu G Li Y Zhang X Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine BMC Bioinformatics 2005, 6:310. 1360673 16381612 10.1186/ 1471-2105-6-310
    • (2005) BMC Bioinformatics , vol.6 , pp. 310
    • Xue, C.1    Li, F.2    He, T.3    Liu, G.4    Li, Y.5    Zhang, X.6
  • 17
    • 21844477027 scopus 로고    scopus 로고
    • Human microRNA prediction through a probabilistic co-learning model of sequence and structure
    • 1159118 15987789 10.1093/nar/gki668
    • Nam J Shin K Han J Lee Y Kim V Zhang B Human microRNA prediction through a probabilistic co-learning model of sequence and structure Nucleic Acids Res 2005, 33:3570-3581. 1159118 15987789 10.1093/nar/gki668
    • (2005) Nucleic Acids Res , vol.33 , pp. 3570-3581
    • Nam, J.1    Shin, K.2    Han, J.3    Lee, Y.4    Kim, V.5    Zhang, B.6
  • 18
    • 33846650507 scopus 로고    scopus 로고
    • Reliable prediction of Drosha processing sites improves microRNA gene prediction
    • 10.1093/bioinformatics/btl570 17105718
    • Helvik S Snove O Saetrom P Reliable prediction of Drosha processing sites improves microRNA gene prediction Bioinformatics 2007, 23(2):142-149. 10.1093/bioinformatics/btl570 17105718
    • (2007) Bioinformatics , vol.23 , Issue.2 , pp. 142-149
    • Helvik, S.1    Snove, O.2    Saetrom, P.3
  • 20
    • 84886758582 scopus 로고    scopus 로고
    • miRBase http://microrna.sanger.ac.uk/sequences
    • MiRBase
  • 21
    • 33644750115 scopus 로고    scopus 로고
    • miRBase: Microrna sequences, targets and gene nomenclature
    • (Database Issue) 1347474 16381832 10.1093/nar/gkj112
    • Griffiths-Jones S Grocock R van Dongen S Bateman A Enright A miRBase: microRNA sequences, targets and gene nomenclature Nucleic Acids Res 2006, 34: (Database Issue) D140-4. 1347474 16381832 10.1093/nar/gkj112
    • (2006) Nucleic Acids Res , vol.34
    • Griffiths-Jones, S.1    Grocock, R.2    van Dongen, S.3    Bateman, A.4    Enright, A.5
  • 22
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA secondary structure server
    • 169005 12824340 10.1093/nar/gkg599
    • Hofacker I Vienna RNA secondary structure server Nucleic Acids Res 2003, 31:3429-3431. 169005 12824340 10.1093/nar/gkg599
    • (2003) Nucleic Acids Res , vol.31 , pp. 3429-3431
    • Hofacker, I.1
  • 23
    • 1042304206 scopus 로고    scopus 로고
    • Prediction of locally stable RNA secondary structures for genome-wide surveys
    • 10.1093/bioinformatics/btg388
    • Hofacker I Priwitzer B Stadler P Prediction of locally stable RNA secondary structures for genome-wide surveys Bioinformatics 2004, 20(2):186-190. 10.1093/bioinformatics/btg388 14734309
    • (2004) Bioinformatics , vol.20 , Issue.2 , pp. 186-190
    • Hofacker, I.1    Priwitzer, B.2    Stadler, P.3
  • 24
    • 23044502585 scopus 로고    scopus 로고
    • Efficient processing of primary microRNA hairpins by Drosha requires flanking non-structured RNA sequences
    • 10.1074/jbc.M504714200 15932881
    • Zeng Y Cullen B Efficient processing of primary microRNA hairpins by Drosha requires flanking non-structured RNA sequences J Biol Chem 2005, 280(30):27595-27603. 10.1074/jbc.M504714200 15932881
    • (2005) J Biol Chem , vol.280 , pp. 27595-27603
    • Zeng, Y.1    Cullen, B.2
  • 25
    • 33744520104 scopus 로고    scopus 로고
    • Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex
    • 10.1016/j.cell.2006.03.043 16751099
    • Han J Lee Y Yeom K Nam J Heo I Rhee J Sohn S Cho Y Zhang B Kim V Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex Cell 2006, 125(5):887-901. 10.1016/ j.cell.2006.03.043 16751099
    • (2006) Cell , vol.125 , pp. 887-901
    • Han, J.1    Lee, Y.2    Yeom, K.3    Nam, J.4    Heo, I.5    Rhee, J.6    Sohn, S.7    Cho, Y.8    Zhang, B.9    Kim, V.10
  • 27
    • 34447309058 scopus 로고    scopus 로고
    • De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures
    • 10.1093/bioinformatics/btm026 17267435
    • Kwang Loong S Mishra S De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures Bioinformatics 2007, 23(11):1321-1330. 10.1093/bioinformatics/btm026 17267435
    • (2007) Bioinformatics , vol.23 , Issue.11 , pp. 1321-1330
    • Kwang Loong, S.1    Mishra, S.2
  • 28
    • 34547596338 scopus 로고    scopus 로고
    • MiPred: Classification of real and pseudo microRNA precursors using random forest prediction model with combined features
    • 1933124 17553836 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: Web Server issue W339-W344. 1933124 17553836 10.1093/nar/gkm368
    • (2007) Nucleic Acids Res , vol.35
    • Jiang, P.1    Wu, H.2    Wang, W.3    Ma, W.4    Sun, X.5    Lu, Z.6
  • 30
    • 31544436362 scopus 로고    scopus 로고
    • Current perspectives in intronic microRNAs (miRNAs)
    • 10.1007/s11373-005-9036-8 16228283
    • Ying S Lin S Current perspectives in intronic microRNAs (miRNAs) J Biomed Sci 2006, 13(5):15. 10.1007/s11373-005-9036-8 16228283
    • (2006) J Biomed Sci , vol.13 , Issue.5 , pp. 5-15
    • Ying, S.1    Lin, S.2
  • 31
    • 6344281172 scopus 로고    scopus 로고
    • Identification of mammalian microRNA host genes and transcription units
    • 524413 15364901 10.1101/gr.2722704
    • Rodriguez A Griffiths-Jones S Ashurst J Bradley A Identification of mammalian microRNA host genes and transcription units Genome Res 2004, 14(10):1902-1910. 524413 15364901 10.1101/gr.2722704
    • (2004) Genome Res , vol.14 , Issue.10 , pp. 1902-1910
    • Rodriguez, A.1    Griffiths-Jones, S.2    Ashurst, J.3    Bradley, A.4
  • 32
    • 13944260434 scopus 로고    scopus 로고
    • Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes
    • 1370713 15701730 10.1261/rna.7240905
    • Baskerville S Bartel D Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes RNA 2005, 11(3):241-247. 1370713 15701730 10.1261/rna.7240905
    • (2005) RNA , vol.11 , Issue.3 , pp. 241-247
    • Baskerville, S.1    Bartel, D.2
  • 33
    • 10244243802 scopus 로고    scopus 로고
    • Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences
    • 10.1093/bioinformatics/bth374 15217813
    • Bonnet E Wuyts J Rouze P van de Peer Y Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences Bioinformatics 2004, 20(17):2911-2917. 10.1093/bioinformatics/bth374 15217813
    • (2004) Bioinformatics , vol.20 , Issue.17 , pp. 2911-2917
    • Bonnet, E.1    Wuyts, J.2    Rouze, P.3    van de Peer, Y.4
  • 34
    • 34250308428 scopus 로고    scopus 로고
    • Origin of phenotypes: Genes and transcripts
    • 10.1101/gr.6525007 17567989
    • Gingeras T Origin of phenotypes: Genes and transcripts Genome Res 2007, 17:682-690. 10.1101/gr.6525007 17567989
    • (2007) Genome Res , vol.17 , pp. 682-690
    • Gingeras, T.1
  • 37
    • 33947728394 scopus 로고    scopus 로고
    • RNA stem loops: To be or not to be cleaved by RNAse III
    • 1831864 17299129 10.1261/rna.366507
    • Ritchie W Legendre M Gautheret D RNA stem loops: To be or not to be cleaved by RNAse III RNA 2007, 13(4):457-462. 1831864 17299129 10.1261/ rna.366507
    • (2007) RNA , vol.13 , Issue.4 , pp. 457-462
    • Ritchie, W.1    Legendre, M.2    Gautheret, D.3
  • 38
    • 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
    • 10.1074/jbc.M404931200 15292246
    • Krol J Sobczak K Wilczynska U Drath M Jasinska A Kaczynska D Krzyzosiak W Structural features of microRNA (miRNA) precursors and their relevance to miRNA biogenesis and small interfering RNA/short hairpin RNA design J Biol Chem 2004, 279(40):42230-42239. 10.1074/jbc.M404931200 15292246
    • (2004) J Biol Chem , vol.279 , Issue.40 , pp. 42230-42239
    • Krol, J.1    Sobczak, K.2    Wilczynska, U.3    Drath, M.4    Jasinska, A.5    Kaczynska, D.6    Krzyzosiak, W.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.