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Volumn 3, Issue OCT, 2012, Pages

Computational methods for ab initio detection of microRNAs

Author keywords

Ab initio; Mature miRNA; Prediction accuracy; Prediction of miRNAs

Indexed keywords


EID: 84876136646     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2012.00209     Document Type: Article
Times cited : (32)

References (52)
  • 4
    • 64549116289 scopus 로고    scopus 로고
    • MicroPred: effective classification of pre-miRNAs for human miRNA gene prediction
    • Batuwita, R., and Palade, V. (2009). MicroPred: effective classification of pre-miRNAs for human miRNA gene prediction. Bioinformatics 25, 989-995.
    • (2009) Bioinformatics , vol.25 , pp. 989-995
    • Batuwita, R.1    Palade, V.2
  • 6
    • 22844440427 scopus 로고    scopus 로고
    • Identification of hundreds of conserved and nonconserved human microRNAs
    • Bentwich, I., Avniel, A., Karov, Y., Aharonov, R., Gilad, S., Barad, O., et al. (2005). Identification of hundreds of conserved and nonconserved human microRNAs. Nat. genet. 37, 766-770.
    • (2005) Nat. genet , vol.37 , pp. 766-770
    • Bentwich, I.1    Avniel, A.2    Karov, Y.3    Aharonov, R.4    Gilad, S.5    Barad, O.6
  • 7
    • 11844262661 scopus 로고    scopus 로고
    • Phylogenetic shadowing and computational identification of human microRNA genes
    • Berezikov, E., Guryev, V., van de Belt, J., Wienholds, E., Plasterk, R. H. A., and Cuppen, E. (2005). Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120, 21-24.
    • (2005) Cell , vol.120 , pp. 21-24
    • Berezikov, E.1    Guryev, V.2    van de Belt, J.3    Wienholds, E.4    Plasterk, R.H.A.5    Cuppen, E.6
  • 8
    • 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 Van de Peer, Y. (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    Van de Peer, Y.4
  • 10
    • 77953126039 scopus 로고    scopus 로고
    • Small noncod-ing RNAs: biogenesis, function, and emerging significance in toxicology
    • Choudhuri, S. (2010). Small noncod-ing RNAs: biogenesis, function, and emerging significance in toxicology. Mol. Toxicol. 24, 195-216.
    • (2010) Mol. Toxicol. , vol.24 , pp. 195-216
    • Choudhuri, S.1
  • 11
    • 77958050722 scopus 로고    scopus 로고
    • Mechanisms of control of microRNA biogenesis
    • Davis-Dusenbery, B. N., and Hata, A. (2010). Mechanisms of control of microRNA biogenesis. J. Biochem. 148,381-392.
    • (2010) J. Biochem. , vol.148 , pp. 381-392
    • Davis-Dusenbery, B.N.1    Hata, A.2
  • 12
    • 78650816392 scopus 로고    scopus 로고
    • MiRenSVM: towards better prediction of microRNA precursors using an ensemble SVM classifier with multi-loop features
    • doi: 10.1186/1471-2105-11-S11-S11
    • Ding, J., Zhou, S., and Guan, J. (2010). MiRenSVM: towards better prediction of microRNA precursors using an ensemble SVM classifier with multi-loop features. BMC Bioinformatics 11(Suppl. 1), S11. doi: 10.1186/1471-2105-11-S11-S11
    • (2010) BMC Bioinformatics , vol.11 , Issue.SUPPL. 1
    • Ding, J.1    Zhou, S.2    Guan, J.3
  • 13
    • 80655149142 scopus 로고    scopus 로고
    • Drosha processing controls the specificity and efficiency of global microRNA expression
    • Feng, Y., Zhang, X., Song, Q., Li, T., and Zeng, Y. (2011). Drosha processing controls the specificity and efficiency of global microRNA expression. Biochim. Biophys. Acta 1809, 700-707.
    • (2011) Biochim. Biophys. Acta , vol.1809 , pp. 700-707
    • Feng, Y.1    Zhang, X.2    Song, Q.3    Li, T.4    Zeng, Y.5
  • 14
    • 60149095444 scopus 로고    scopus 로고
    • Most mammalian mRNAs are conserved targets of microRNAs
    • Friedman, R. C., Farh, K. K.-H., Burge, C. B., and Bartel, D. P. (2009). Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 19,92-105.
    • (2009) Genome Res , vol.19 , pp. 92-105
    • Friedman, R.C.1    Farh, K.-H.2    Burge, C.B.3    Bartel, D.P.4
  • 15
    • 77957818081 scopus 로고    scopus 로고
    • MatureBayes: a probabilistic algorithm for identifying the mature miRNA within novel precursors
    • doi: 10.1371/journal.pone.0011843
    • Gkirtzou, K., Tsamardinos, I., Tsakalides, P., and Poirazi, P. (2010). MatureBayes: a probabilistic algorithm for identifying the mature miRNA within novel precursors. PLoS ONE 5, e11843. doi: 10.1371/journal.pone.0011843
    • (2010) PLoS ONE , vol.5
    • Gkirtzou, K.1    Tsamardinos, I.2    Tsakalides, P.3    Poirazi, P.4
  • 16
    • 77949621355 scopus 로고    scopus 로고
    • miRBase: microRNA sequences and annotation
    • Chapter 12, Unit 12.9.1-12.9.10
    • Griffiths-Jones, S. (2010). miRBase: microRNA sequences and annotation. Curr. Protoc. Bioinformatics Chapter 12, Unit 12.9.1-12.9.10.
    • Curr. Protoc. Bioinformatics
    • Griffiths-Jones, S.1
  • 18
    • 79960070453 scopus 로고    scopus 로고
    • Computational prediction of viral miRNAs
    • Grundhoff, A. (2011). Computational prediction of viral miRNAs. Methods Mol. Biol. 721, 143-152.
    • (2011) Methods Mol. Biol. , vol.721 , pp. 143-152
    • Grundhoff, A.1
  • 19
    • 35348977190 scopus 로고    scopus 로고
    • Stressful splicing
    • Guil, S., and Cáceres, J. F. (2007). Stressful splicing. Mol. Cell 28, 180-181.
    • (2007) Mol. Cell , vol.28 , pp. 180-181
    • Guil, S.1    Cáceres, J.F.2
  • 20
    • 33744520104 scopus 로고    scopus 로고
    • Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex
    • Han, J., Lee, Y., Yeom, K.-H., Nam, J.-W., Heo, I., Rhee, J.-K., et al. (2006). Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 125, 887-901.
    • (2006) Cell , vol.125 , pp. 887-901
    • Han, J.1    Lee, Y.2    Yeom, K.-H.3    Nam, J.-W.4    Heo, I.5    Rhee, J.-K.6
  • 21
    • 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, 197-202.
    • (2006) Bioinformatics , vol.22 , pp. 197-202
    • Hertel, J.1    Stadler, P.F.2
  • 22
    • 80155214025 scopus 로고    scopus 로고
    • Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction
    • doi: 10.1186/1471-2105-12-429
    • Janssen, S., Schudoma, C., Steger, G., and Giegerich, R. (2011). Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction. BMC Bioinformatics 12, 429. doi: 10.1186/1471-2105-12-429
    • (2011) BMC Bioinformatics , vol.12 , pp. 429
    • Janssen, S.1    Schudoma, C.2    Steger, G.3    Giegerich, R.4
  • 23
    • 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
  • 24
    • 0038825783 scopus 로고    scopus 로고
    • Computational identification of Drosophila microRNA genes
    • Lai, E. C., Tomancak, P., Williams, R. W., and Rubin, G. M. (2003). Computational identification of Drosophila microRNA genes. Genome Biol. 4, R42.
    • (2003) Genome Biol , vol.4
    • Lai, E.C.1    Tomancak, P.2    Williams, R.W.3    Rubin, G.M.4
  • 25
    • 0027751663 scopus 로고
    • The C. elegans hete-rochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
    • Lee, R. C., Feinbaum, R. L., and Ambros, V. (1993). The C. elegans hete-rochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843-854.
    • (1993) Cell , vol.75 , pp. 843-854
    • Lee, R.C.1    Feinbaum, R.L.2    Ambros, V.3
  • 26
    • 66249117657 scopus 로고    scopus 로고
    • Lowly expressed human microRNA genes evolve rapidly
    • Liang, H., and Li, W.-H. (2009). Lowly expressed human microRNA genes evolve rapidly. Mol. Biol. Evol. 26, 1195-1198.
    • (2009) Mol. Biol. Evol. , vol.26 , pp. 1195-1198
    • Liang, H.1    Li, W.-H.2
  • 28
    • 39749083331 scopus 로고    scopus 로고
    • The birth and death of microRNA genes in Drosophila
    • Lu, J., Shen, Y., Wu, Q., Kumar, S., He, B., Shi, S., et al. (2008). The birth and death of microRNA genes in Drosophila. Nat. Genet. 40, 351-355.
    • (2008) Nat. Genet. , vol.40 , pp. 351-355
    • Lu, J.1    Shen, Y.2    Wu, Q.3    Kumar, S.4    He, B.5    Shi, S.6
  • 29
    • 30844438338 scopus 로고    scopus 로고
    • Structural basis for double-stranded RNA processing by dicer
    • MacRae, I. J., Zhou, K., Li, F., Repic, A., Brooks, A. N., Cande, W. Z., et al. (2006). Structural basis for double-stranded RNA processing by dicer. Science 311,195-198.
    • (2006) Science , vol.311 , pp. 195-198
    • MacRae, I.J.1    Zhou, K.2    Li, F.3    Repic, A.4    Brooks, A.N.5    Cande, W.Z.6
  • 31
    • 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
  • 32
    • 77953032534 scopus 로고    scopus 로고
    • Emerging paradigms of regulated microRNA processing
    • Newman, M. A., and Hammond, S. M. (2010). Emerging paradigms of regulated microRNA processing. Genes Dev. 24, 1086-1092.
    • (2010) Genes Dev , vol.24 , pp. 1086-1092
    • Newman, M.A.1    Hammond, S.M.2
  • 33
    • 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., andMishra, 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
  • 34
    • 43449090367 scopus 로고    scopus 로고
    • MicroRNA-10a binds the 5'UTR of ribosomal protein mRNAs and enhances their translation
    • Ørom, U. A., Nielsen, F. C., and Lund, A. H. (2008). MicroRNA-10a binds the 5'UTR of ribosomal protein mRNAs and enhances their translation. Mol. Cell 30, 460-471.
    • (2008) Mol. Cell , vol.30 , pp. 460-471
    • Ørom, U.A.1    Nielsen, F.C.2    Lund, A.H.3
  • 35
    • 84860440134 scopus 로고    scopus 로고
    • Experimental verification of a predicted intronic microRNA in human NGFR gene with a potential pro-apoptotic function
    • doi: 10.1371/jour-nal.pone.0035561
    • Parsi, S., Soltani, B. M., Hosseini, E., Tousi, S. E., and Mowla, S. J. (2012). Experimental verification of a predicted intronic microRNA in human NGFR gene with a potential pro-apoptotic function. PloS ONE 7, e35561. doi: 10.1371/jour-nal.pone.0035561
    • (2012) PloS ONE , vol.7
    • Parsi, S.1    Soltani, B.M.2    Hosseini, E.3    Tousi, S.E.4    Mowla, S.J.5
  • 37
    • 84876119677 scopus 로고    scopus 로고
    • Ssa miRNAs DB: online repository of in silico predicted miRNAs in Salmo salar
    • Reyes, D., Cepeda, V., González, R., and Vidal, R. (2012). Ssa miRNAs DB: online repository of in silico predicted miRNAs in Salmo salar. Bioinformation 8, 284-286.
    • (2012) Bioinformation , vol.8 , pp. 284-286
    • Reyes, D.1    Cepeda, V.2    González, R.3    Vidal, R.4
  • 38
    • 84859743784 scopus 로고    scopus 로고
    • Defining and providing robust controls for microRNA prediction
    • Ritchie, W., Gao, D., and Rasko, J. E. J. (2012). Defining and providing robust controls for microRNA prediction. Bioinformatics 28, 1058-1061.
    • (2012) Bioinformatics , vol.28 , pp. 1058-1061
    • Ritchie, W.1    Gao, D.2    Rasko, J.E.J.3
  • 39
    • 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
  • 40
    • 77955196800 scopus 로고    scopus 로고
    • MiR-RACE, a new efficient approach to determine the precise sequences of computationally identified trifoliate orange (Poncirus trifoliata) microRNAs
    • doi: 10.1371/journal.pone.00 10861
    • Song, C., Fang, J., Wang, C., Guo, L., Nicholas, K. K., and Ma, Z. (2010). MiR-RACE, a new efficient approach to determine the precise sequences of computationally identified trifoliate orange (Poncirus trifoliata) microRNAs. PLoS ONE 5, e10861. doi: 10.1371/journal.pone.00 10861
    • (2010) PLoS ONE , vol.5
    • Song, C.1    Fang, J.2    Wang, C.3    Guo, L.4    Nicholas, K.K.5    Ma, Z.6
  • 41
    • 84876098623 scopus 로고    scopus 로고
    • Thermodynamic and structural consensus principle predicts mature miRNA location and structure, categorizes conserved interspecies miRNA subgroups, and hints new possible mechanisms of miRNA maturization
    • arXiv:0710.4181
    • Tao, M. (2007). Thermodynamic and structural consensus principle predicts mature miRNA location and structure, categorizes conserved interspecies miRNA subgroups, and hints new possible mechanisms of miRNA maturization. Quant. Biol. arXiv:0710.4181.
    • (2007) Quant. Biol
    • Tao, M.1
  • 42
    • 66149167564 scopus 로고    scopus 로고
    • In silico miRNA prediction in metazoan genomes: balancing between sensitivity and specificity
    • doi: 10.1186/1471-2164-10-204
    • van der Burgt, A., Fiers, M. W. J. E., Nap, J.-P., and van Ham, R. C. H. J. (2009). In silico miRNA prediction in metazoan genomes: balancing between sensitivity and specificity. BMC Genomics 10, 204. doi: 10.1186/1471-2164-10-204
    • (2009) BMC Genomics , vol.10 , pp. 204
    • van der Burgt, A.1    Fiers, M.W.J.E.2    Nap, J.-P.3    van Ham, R.C.H.J.4
  • 43
    • 79952899503 scopus 로고    scopus 로고
    • Computational dissection of Arabidopsis smRNAome leads to discovery of novel microRNAs and short interfering RNAs associated with transcription start sites
    • Wang, X., Laurie, J. D., Liu, T., Wentz, J., and Liu, X. S. (2011). Computational dissection of Arabidopsis smRNAome leads to discovery of novel microRNAs and short interfering RNAs associated with transcription start sites. Genomics 97, 235-243.
    • (2011) Genomics , vol.97 , pp. 235-243
    • Wang, X.1    Laurie, J.D.2    Liu, T.3    Wentz, J.4    Liu, X.S.5
  • 44
    • 84871522891 scopus 로고    scopus 로고
    • Systematic Curation of miRBase Annotation Using Integrated Small RNA High-Throughput Sequencing Data for C. elegans and Drosophila
    • doi: 10.3389/fgene.2011.00025
    • Wang, X., and Liu, X.S. (2011). Systematic Curation of miRBase Annotation Using Integrated Small RNA High-Throughput Sequencing Data for C. elegans and Drosophila. Front. Genet. 2:25. doi: 10.3389/fgene.2011.00025
    • (2011) Front. Genet. , vol.2 , pp. 25
    • Wang, X.1    Liu, X.S.2
  • 45
    • 61849137222 scopus 로고    scopus 로고
    • Many roads to maturity: microRNA biogenesis pathways and their regulation
    • Winter, J., Jung, S., Keller, S., Gregory, R. I., and Diederichs, S. (2009). Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat. Cell Biol. 11, 228-234.
    • (2009) Nat. Cell Biol. , vol.11 , pp. 228-234
    • Winter, J.1    Jung, S.2    Keller, S.3    Gregory, R.I.4    Diederichs, S.5
  • 46
    • 79958033251 scopus 로고    scopus 로고
    • MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences
    • doi: 10.1186/1471-2105-12-107
    • Wu, Y., Wei, B., Liu, H., Li, T., and Rayner, S. (2011). MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences. BMC Bioinformatics 12, 107. doi: 10.1186/1471-2105-12-107
    • (2011) BMC Bioinformatics , vol.12 , pp. 107
    • Wu, Y.1    Wei, B.2    Liu, H.3    Li, T.4    Rayner, S.5
  • 47
    • 81155131543 scopus 로고    scopus 로고
    • MaturePred: efficient identification of microRNAs within novel plant pre-miRNAs
    • doi: 10.1371/journal.pone.0027422
    • Xuan, P., Guo, M., Huang, Y., Li, W., and Huang, Y. (2011). MaturePred: efficient identification of microRNAs within novel plant pre-miRNAs. PLoS ONE 6, e27422. doi: 10.1371/journal.pone.0027422
    • (2011) PLoS ONE , vol.6
    • Xuan, P.1    Guo, M.2    Huang, Y.3    Li, W.4    Huang, Y.5
  • 48
    • 30344447264 scopus 로고    scopus 로고
    • Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine
    • doi: 10.1186/1471-2105-6-310
    • 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. doi: 10.1186/1471-2105-6-310
    • (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
  • 49
    • 43949125230 scopus 로고    scopus 로고
    • Learning from positive examples when the negative class is undetermined - microRNA gene identification
    • Yousef, M., Jung, S., Showe, L. C., and Showe, M. K. (2008). Learning from positive examples when the negative class is undetermined - microRNA gene identification. Algorithms Mol. Biol. 3, 2.
    • (2008) Algorithms Mol. Biol. , vol.3 , pp. 2
    • Yousef, M.1    Jung, S.2    Showe, L.C.3    Showe, M.K.4
  • 50
    • 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
  • 51
    • 23044502585 scopus 로고    scopus 로고
    • Efficient processing of primary microRNA hairpins by Drosha requires flanking nonstructured RNA sequences
    • Zeng, Y., and Cullen, B. R. (2005). Efficient processing of primary microRNA hairpins by Drosha requires flanking nonstructured RNA sequences. J. Biol. Chem. 280, 27595-27603.
    • (2005) J. Biol. Chem. , vol.280 , pp. 27595-27603
    • Zeng, Y.1    Cullen, B.R.2
  • 52
    • 78649870594 scopus 로고    scopus 로고
    • The terminal loop region controls microRNA processing by Drosha and Dicer
    • Zhang, X. (2010). The terminal loop region controls microRNA processing by Drosha and Dicer. Nucleic Acids Res. 38, 7689-7697.
    • (2010) Nucleic Acids Res , vol.38 , pp. 7689-7697
    • Zhang, X.1


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