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Volumn 1107, Issue , 2014, Pages 177-187

Machine learning methods for microRNA gene prediction

Author keywords

Classification; Examples; Machine learning; miRNA gene detection; miRNA gene prediction; Test data

Indexed keywords

MICRORNA;

EID: 84934444923     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-748-8_10     Document Type: Article
Times cited : (33)

References (38)
  • 1
    • 22844440427 scopus 로고    scopus 로고
    • Identifi cation of hundreds of conserved and nonconserved human microRNAs
    • Bentwich I, Avniel A, Karov Y, et al. (2005) Identifi cation 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
  • 2
    • 34447309058 scopus 로고    scopus 로고
    • De novo SVM classifi cation of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures
    • Ng KLS, Mishra SK. (2007) De novo SVM classifi cation 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
  • 3
    • 66149167564 scopus 로고    scopus 로고
    • In silico miRNA prediction in metazoan genomes: Balancing between sensitivity and specifi city
    • van der Burgt A, Fiers MWJE, Nap J-P, et al. (2009) In silico miRNA prediction in metazoan genomes: Balancing between sensitivity and specifi city. BMC Genomics 10:204
    • (2009) BMC Genomics , vol.10 , pp. 204
    • Van Der Burgt, A.1    Fiers, M.W.J.E.2    Nap, J.-P.3
  • 4
    • 80155214025 scopus 로고    scopus 로고
    • Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction
    • Janssen S, Schudoma C, Steger G, et al. (2011) Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction. BMC Bioinformatics 12:429
    • (2011) BMC Bioinformatics , vol.12 , pp. 429
    • Janssen, S.1    Schudoma, C.2    Steger, G.3
  • 5
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA secondary structure server
    • Hofacker IL. (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31: 3429-3431
    • (2003) Nucleic Acids Res , vol.31 , pp. 3429-3431
    • Hofacker, I.L.1
  • 6
    • 34249003938 scopus 로고    scopus 로고
    • Principles and limitations of computational microRNA gene and target fi nding
    • Lindow M, Gorodkin J. (2007) Principles and limitations of computational microRNA gene and target fi nding. DNA Cell Biol 26:339-351
    • (2007) DNA Cell Biol , vol.26 , pp. 339-351
    • Lindow, M.1    Gorodkin, J.2
  • 7
    • 29444457713 scopus 로고    scopus 로고
    • Rapid evolution of noncoding RNAs: Lack of conservation does not mean lack of function
    • Pang KC, Frith MC, Mattick JS. (2006) Rapid evolution of noncoding RNAs: Lack of conservation does not mean lack of function. Trends Genet 22:1-5
    • (2006) Trends Genet , vol.22 , pp. 1-5
    • Pang, K.C.1    Frith, M.C.2    Mattick, J.S.3
  • 9
    • 0034597777 scopus 로고    scopus 로고
    • Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA
    • Pasquinelli AE, Reinhart BJ, Slack F, et al. (2000) Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408:86-89
    • (2000) Nature , vol.408 , pp. 86-89
    • Pasquinelli, A.E.1    Reinhart, B.J.2    Slack, F.3
  • 10
    • 3242876311 scopus 로고    scopus 로고
    • BLAST: At the core of a powerful and diverse set of sequence analysis tools
    • McGinnis S, Madden TL. (2004) BLAST: At the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res 32: W20-W25
    • (2004) Nucleic Acids Res , vol.32
    • McGinnis, S.1    Madden, T.L.2
  • 11
    • 66249117657 scopus 로고    scopus 로고
    • Lowly expressed human microRNA genes evolve rapidly
    • Liang H, 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
  • 12
    • 11844262661 scopus 로고    scopus 로고
    • Phylogenetic shadowing and computational identifi cation of human microRNA genes
    • Berezikov E, Guryev V, van de Belt J, et al. (2005) Phylogenetic shadowing and computational identifi cation 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
  • 13
    • 0242418246 scopus 로고    scopus 로고
    • Phylogenetic shadowing of primate sequences to fi nd functional regions of the human genome
    • Boffelli D, McAuliffe J, Ovcharenko D, et al. (2003) Phylogenetic shadowing of primate sequences to fi nd functional regions of the human genome. Science (New York, NY) 299: 1391-1394
    • (2003) Science (New York, NY , vol.299 , pp. 1391-1394
    • Boffelli, D.1    McAuliffe, J.2    Ovcharenko, D.3
  • 14
    • 0037447334 scopus 로고    scopus 로고
    • The microRNAs of Caenorhabditis elegans
    • Lim LP, Lau NC, Weinstein EG, et al. (2003) The microRNAs of Caenorhabditis elegans. Genes Dev 17:991-1008
    • (2003) Genes Dev , vol.17 , pp. 991-1008
    • Lim, L.P.1    Lau, N.C.2    Weinstein, E.G.3
  • 16
    • 39849111033 scopus 로고    scopus 로고
    • MiRNAminer: A tool for homologous microRNA gene search
    • Artzi S, Kiezun A, Shomron N. (2008) MiRNAminer: A tool for homologous microRNA gene search. BMC Bioinformatics 9:39
    • (2008) BMC Bioinformatics , vol.9 , pp. 39
    • Artzi, S.1    Kiezun, A.2    Shomron, N.3
  • 17
    • 33747814183 scopus 로고    scopus 로고
    • ProMiR II: A web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs
    • Nam J-W, Kim J, Kim S-K, et al. (2006) ProMiR II: A web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs. Nucleic Acids Res 34: W455-W458
    • (2006) Nucleic Acids Res , vol.34
    • Nam, J.-W.1    Kim, J.2    Kim, S.-K.3
  • 18
    • 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, et al. (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
  • 19
    • 38349097919 scopus 로고    scopus 로고
    • MiRFinder: An improved approach and software implementation for genome-wide fast microRNA precursor scans
    • Huang T-H, Fan B, Rothschild MF, et al. (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.-H.1    Fan, B.2    Rothschild, M.F.3
  • 20
    • 39049169222 scopus 로고    scopus 로고
    • Ab initio identifi cation of human microRNAs based on structure motifs
    • Brameier M, Wiuf C. (2007) Ab initio identifi cation of human microRNAs based on structure motifs. BMC Bioinformatics 8:478
    • (2007) BMC Bioinformatics , vol.8 , pp. 478
    • Brameier, M.1    Wiuf, C.2
  • 21
    • 84876136646 scopus 로고    scopus 로고
    • Computational methods for ab initio detection of microRNAs
    • Allmer J, Yousef M. (2012) Computational methods for ab initio detection of microRNAs. Front Genet 3:209
    • (2012) Front Genet , vol.3 , pp. 209
    • Allmer, J.1    Yousef, M.2
  • 22
    • 78650816392 scopus 로고    scopus 로고
    • MiRenSVM: Towards better prediction of microRNA precursors using an ensemble SVM classifi er with multi-loop features
    • Ding J, Zhou S, Guan J. (2010) MiRenSVM: Towards better prediction of microRNA precursors using an ensemble SVM classifi er with multi-loop features. BMC Bioinformatics 11(Suppl 1):S11
    • (2010) BMC Bioinformatics , vol.11 , Issue.SUPPL. 1
    • Ding, J.1    Zhou, S.2    Guan, J.3
  • 23
    • 40649118763 scopus 로고    scopus 로고
    • Identifying human microRNAs
    • Bentwich I. (2008) Identifying human microRNAs. Curr Top Microbiol Immunol 320: 257-269
    • (2008) Curr Top Microbiol Immunol , vol.320 , pp. 257-269
    • Bentwich, I.1
  • 24
    • 30344447264 scopus 로고    scopus 로고
    • Classifi cation of real and pseudo microRNA precursors using local structure-sequence features and support vector machine
    • Xue C, Li F, He T, et al. (2005) Classifi cation 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
  • 25
    • 34547596338 scopus 로고    scopus 로고
    • MiPred: Classifi cation of real and pseudo microRNA precursors using random forest prediction model with combined features
    • Jiang P, Wu H, Wang W, et al. (2007) MiPred: Classifi cation 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
  • 26
    • 79958033251 scopus 로고    scopus 로고
    • MiRPara: A SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences
    • Wu Y, Wei B, Liu H, et al. (2011) MiRPara: A SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences. BMC Bioinformatics 12:107
    • (2011) BMC Bioinformatics , vol.12 , pp. 107
    • Wu, Y.1    Wei, B.2    Liu, H.3
  • 27
    • 78651293534 scopus 로고    scopus 로고
    • Mirbase: Integrating microRNA annotation and deep-sequencing data
    • Kozomara A, Griffiths-Jones S. (2011) miRBase: Integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39: D152-D157
    • (2011) Nucleic Acids Res , vol.39
    • Kozomara, A.1    Griffiths-Jones, S.2
  • 28
    • 84859743784 scopus 로고    scopus 로고
    • Defi ning and providing robust controls for microRNA prediction
    • Ritchie W, Gao D, Rasko JEJ (2012) Defi ning and providing robust controls for microRNA prediction. Bioinformatics (Oxford, England) 28:1058-1061
    • (2012) Bioinformatics (Oxford, England , vol.28 , pp. 1058-1061
    • Ritchie, W.1    Gao, D.2    Rasko, J.E.J.3
  • 29
    • 84891760538 scopus 로고    scopus 로고
    • Can MiRBase provide positive data for machine learning for the detection of MiRNA hairpins?
    • Saçar MD, Hamzeiy H, Allmer J. (2013) Can MiRBase provide positive data for machine learning for the detection of MiRNA hairpins? J Integr Bioinform 10(2):215
    • (2013) J Integr Bioinform , vol.10 , Issue.2 , pp. 215
    • Saçar, M.D.1    Hamzeiy, H.2    Allmer, J.3
  • 30
    • 13444306641 scopus 로고    scopus 로고
    • NCBI reference sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins
    • Pruitt KD, Tatusova T, Maglott DR. (2005) NCBI reference sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 33: D501-D504
    • (2005) Nucleic Acids Res , vol.33
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 31
    • 33746747476 scopus 로고    scopus 로고
    • Machine learning in bioinformatics: A brief survey and recommendations for practitioners
    • Bhaskar H, Hoyle DC, Singh S. (2006) Machine learning in bioinformatics: A brief survey and recommendations for practitioners. Comput Biol Med 36:1104-1125
    • (2006) Comput Biol Med , vol.36 , pp. 1104-1125
    • Bhaskar, H.1    Hoyle, D.C.2    Singh, S.3
  • 34
    • 0002240319 scopus 로고
    • A k-sample slippage test for an extreme population
    • Mosteller F. (1948) A k-sample slippage test for an extreme population. Ann Math Stat 19:58-65
    • (1948) Ann Math Stat , vol.19 , pp. 58-65
    • Mosteller, F.1
  • 35
    • 77957818081 scopus 로고    scopus 로고
    • MatureBayes: A probabilistic algorithm for identifying the mature miRNA within novel precursors
    • Gkirtzou K, Tsamardinos I, Tsakalides P, et al. (2010) MatureBayes: A probabilistic algorithm for identifying the mature miRNA within novel precursors. PloS one 5:e11843
    • (2010) PloS one , vol.5
    • Gkirtzou, K.1    Tsamardinos, I.2    Tsakalides, P.3
  • 37
    • 43949125230 scopus 로고    scopus 로고
    • Learning from positive examples when the negative class is undetermined-microRNA gene identifi cation
    • Yousef M, Jung S, Showe LC, et al. (2008) Learning from positive examples when the negative class is undetermined-microRNA gene identifi cation. Algorithms Mol Biol 3:2
    • (2008) Algorithms Mol Biol , vol.3 , pp. 2
    • Yousef, M.1    Jung, S.2    Showe, L.C.3
  • 38
    • 26944498633 scopus 로고    scopus 로고
    • Prediction and validation of microRNAs and their targets
    • Bentwich I. (2005) Prediction and validation of microRNAs and their targets. FEBS Lett 579: 5904-5910
    • (2005) FEBS Lett , vol.579 , pp. 5904-5910
    • Bentwich, I.1


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