[1]
|
V. Ambros. (2004) The functions of animal microRNAs. Nature, 431, 350–355.
|
[2]
|
D. P. Bartel. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116, 281–297.
|
[3]
|
I. Bentwich. (2005) Prediction and validation of microRNAs and their targets. FEBS Lett, 579, 5904–5910.
|
[4]
|
E. Berezikov, E. Cuppen, and R. H. Plasterk. (2006) Approaches to
|
[5]
|
C. J. Burges. (1998) A tutorial on support vector machines for pattern recognition. J. Data Mining and Knowledge Discovery, 2, 121-167.
|
[6]
|
M. T. Bohnsack, K. Czaplinski and D. Grlich. (2004) Exportin 5 is
|
[7]
|
J. Brown, P. Sanseau. (2005) A computational view of microRNAs and their targets. Drug discovery today: biosilico, 10(8), 595–601.
|
[8]
|
C. -C. Chang, and C. -J. Lin. (2001) LIBSVM: a library for support vector machines.
|
[9]
|
Y. Chen, X. Zhou, and T. S. Huang. (2001) One-class SVM for learning in image retrieval. Proc. IEEE Int’l Conf. on Image Processing, Thes-saloniki, Greece.
|
[10]
|
M. A. Denli, B. J. Tops, H. A. Plasterk, R. F. Ketting, and G. J.Hannon. (2004) Processing of primary microRNAs by the Microprocessor complex. Nature, 432, 231–235.
|
[11]
|
Y. Grad, J. Aach, G. D. Hayes, B. J. Reinhart, G. M. Church, G. Ruvkun, and J. Kim. (2003) Computational and experimental identifica-tion of C. elegans microRNAs. Mol Cell, 11,1253–1263.
|
[12]
|
R. I. Gregory, K. P. Yan, G. Amuthan, T. Chendrimada, B. Doratotaj, N. Cooch, and R. Shiekhattar. (2004) The microprocessor complex medi-ates the genesis of microRNAs. Nature, 423, 235–240.
|
[13]
|
S. Griffiths-Jones, R. J. Grocock, S. Dongen, A. Bateman, A. J. Enright. (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res., 34, D140–D144.
|
[14]
|
S. Griffiths-Jones. (2004) The microRNA Registry, Nucleic Acids Res., 32, D109–D111.
|
[15]
|
S. A. Helvik, O. S. Jr, and P. Strom. (2007) Reliable prediction of Drosha processing sites improves microRNA gene prediction. Bioin-formatics, 23(2), 142-149.
|
[16]
|
I. L. Hofacker, S. Fontana, W. Stadler, S. Bonhoeffer, M. Tacker, and P. Schuster. (1994) Fast folding and comparison of RNA secondary struc-tures, Monatshefte f. Chemie, 125, 167-188.
|
[17]
|
I. L. Hofacker. (2003) Vienna RNA secondary structure server. Nucleic Acids Res, 31, 3429–3431.
|
[18]
|
M. Kiriakidou, P. T. Nelson, A. Kouranov, P. Fitziev, C. Bouyioukos, Z. Mourelatos, and A. Hatzigeorgiou. (2004) A combined computational experimental approach predicts human microRNA targets. Genes Dev, 18, 1165–1178.
|
[19]
|
A. Kowalczyk, and B. Raskutti. (2002) One-class svm for yeast regu-lation prediction. Proc. SIGKDD Explorations Workshop, 99–100.
|
[20]
|
R. Kohavi. (1995) A study of cross-validation and bootstrap for accuracy estimation and model selection. Proc. 14th IJCAI, San Fran-cisco, CA, Morgan Kaufmann Pubshers, 1137–1143,.
|
[21]
|
Y. Kong, J.-H. Han. (2005) MicroRNA: Biological and computational perspective. Geno. Prot. Bioinfo., 3(2), 62–72.
|
[22]
|
J. Krol, K. Sobczak, U. Wilcztnska, M. Drath, A. Jasinska, D.
|
[23]
|
M. Lagos-Quintana, R. Rauhut, W. Lendeckel, and T. Tuschl. (2001) Identification of novel gene coding for small expressed RNAs. Science, 294, 853–858.
|
[24]
|
E. C. Lai, P. Tomancak, R. W. Williams, and G. M. Rubin. (2003) Computational identification of Drosophila microRNA genes. Genome Biol, 4, R42.
|
[25]
|
Y. Lee, C. Ahn, J. Han, H. Choi, J. Yim, P. Provost, O. Radmark, S. Kim, and V. N. Kim. (2003) The nuclear RNase III Drosha initiates microRNA processing. Nature, 424, 415–419.
|
[26]
|
Y. Lee, M. Kim, J. Han, K. Yeom, S. H. Lee, S. H. Baek, and V. N. Kim. (2004) MicroRNA genes are transcribed by RNA polymerase II. EmboJ, 23,4051–4060.
|
[27]
|
L. P. Lim, M. E. Glasner, S. Yekta, C. B. Burge, and D. P. Bartel. (2003) Vertebrate microRNA genes. Science, 299, 1540.
|
[28]
|
L. P. Lim, N. C. Lau, E. G. Weinstein, A. Abdelhakim, S. Yekta, M. W. Rhoades, C. B. Burge, and D. P. Bartel. (2003) The microRNAs of Caenorhabditis elegans. Genes Dev, 17, 991-1008.
|
[29]
|
E. Lund, S. Guttinger, A. Calado, J. E. Dahlberg, and U. Kutay. (2004) Nuclear export of microRNA precursors. Science, 303, 95–98.
|
[30]
|
L. M. Manevitz, and M. Yousef. (2001) One-class SVMs for document classification. Journal of Machine Learning, 2, 139–154.
|
[31]
|
J. W. Nam, K. R. Shin, Y. V. Lee, N. Kim, and B. T. Zhang. (2005) Human microRNA prediction through a probabilistic co-learning model of sequence and structure. Nucleic Acids Res., 33, 3570–3581.
|
[32]
|
U. Ohler, S. Yekta, L. P. Lim, D. P. Bartel, and C. B. Burge. (2004) Patterns of flanking sequence conservation and a characteristic up-stream motif for microRNA gene identification. RNA, 10, 1309–1322.
|
[33]
|
B. Scholkopf, J. C. Platt, J. Shawe-Taylor, A. J. Smola, and R. C. Williamson. (2001) Estimating the support of a high-dimensional distri-bution. Neural Comput, 13, 1443–1471.
|
[34]
|
P. Strom, O. S. Jr, M. Nedland, T. B. Grnfeld, Y. Lin, M. B.Bass, J. Canon. (2006) Conserved microRNA characteristics in mammals. Oli-gonucleotides, 16, 115–144.
|
[35]
|
K. Szafranski, M. Megraw, M. Reczko, G. H. Hatzigeorgiou. (2006) Support vector machine for predicting microRNA hairpins. Proc. The 2006 International Conference on Bioinformatics and Computational Biology, 270–276.
|
[36]
|
A. Tsirigos, and I. Rigoutsos. (2005) A sensitive, support-vector-machine method for the detection of horizontal gene transfers in viral, archaeal and bacterial genomes. Nucleic Acids Research, 33(12):3699–3707.
|
[37]
|
D. H. Tran, T. H. Pham, K. Satou, and T. B. Ho. (2008) Prediction of microRNA hairpins using one-class support vector machine. Proc. The 2nd international conference on bioinformatics and biomedical engineering (iCBBE), Sanghai, China, May 16-18.
|
[38]
|
V. Vapnik. Statistical learning theory, Wiley, Chichester, United Kingdom, 1998.
|
[39]
|
X. Xie, J. Lu, E. J. Kulbokas, T. R. Golub, V. Mootha, K. Lindblad-Toh, E. S. Lander, and M. Kellis. (2005) Systematic discovery of regulatory motifs in human promoters and 3’ UTRs by comparison of several mammals. Nature, 434, 338–346.
|
[40]
|
C. Xue, F. Li, T. He, G. P. Liu, Y. Li, and X. Zhang. (2005) Classi-fication of real and pseudo microRNA precursors using local structure-sequence features and support vector machine. BMC Bioinformatics, 6, 310.
|
[41]
|
L. H. Yang, W. Hsu, M. L. Lee, and L. Wong. (2006) Identification
|
[42]
|
Y. Zeng, R. Yi, and B. R. Cullen. (2005) Recognition and cleavage of primary microRNA precursors by the nuclear processing enzyme Drosha. Embo J, 24,138–148.
|
[43]
|
http://www.csie.ntu.edu.tw/ cjlin/libsvm/
|
[44]
|
http://microrna.sanger.ac.uk/sequences/index.shtml
|
[45]
|
http://www.tbi.univie.ac.at/RNA/
|