TY - JOUR AU - He, L. AU - Hannon, G. J. PY - 2004 DA - 2004// TI - MicroRNAs: small RNAs with a big role in gene regulation JO - Nat Rev Genet VL - 7 UR - https://doi.org/10.1038/nrg1379 DO - 10.1038/nrg1379 ID - He2004 ER - TY - JOUR AU - Julia, S. R. AU - Jacek, K. AU - Edyta, K. AU - Piotr, K. PY - 2010 DA - 2010// TI - Structural basis of microRNA length variety JO - Nucleic Acids Reaearch VL - 39 ID - Julia2010 ER - TY - JOUR AU - Chatterjee, S. AU - Grobhans, H. PY - 2009 DA - 2009// TI - Active turnover modulates mature microRNA activity in caenorhabditis elegans JO - Nature VL - 461 UR - https://doi.org/10.1038/nature08349 DO - 10.1038/nature08349 ID - Chatterjee2009 ER - TY - JOUR AU - Baek, D. AU - Villen, J. AU - Shin, C. AU - Camargo, F. D. AU - Gygi, S. P. AU - Bartel, D. P. PY - 2008 DA - 2008// TI - The impact of microRNAs on protein output JO - Nature VL - 7209 UR - https://doi.org/10.1038/nature07242 DO - 10.1038/nature07242 ID - Baek2008 ER - TY - JOUR AU - Brennecke, J. AU - Hipfner, D. R. AU - Stark, A. AU - Russell, R. B. AU - Cohen, S. M. PY - 2003 DA - 2003// TI - Bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila JO - Cell VL - 113 UR - https://doi.org/10.1016/S0092-8674(03)00231-9 DO - 10.1016/S0092-8674(03)00231-9 ID - Brennecke2003 ER - TY - JOUR AU - Xu, P. Z. AU - Vernooy, S. Y. AU - Guo, M. AU - Hay, B. A. PY - 2003 DA - 2003// TI - The Drosophila microRNA Mir-14suppresses cell death and is required for normal fat metabolism JO - Curr Biol VL - 13 UR - https://doi.org/10.1016/S0960-9822(03)00250-1 DO - 10.1016/S0960-9822(03)00250-1 ID - Xu2003 ER - TY - JOUR AU - Shusei, S. AU - Michael, E. AU - Robert, B. AU - Li, C. B. PY - 2012 DA - 2012// TI - The tomato genome sequence provides insights into fleshy fruit evolution JO - Nature VL - 485 UR - https://doi.org/10.1038/nature11119 DO - 10.1038/nature11119 ID - Shusei2012 ER - TY - JOUR AU - Mendes, N. D. AU - Freitas, A. T. AU - Sagot, M. F. PY - 2009 DA - 2009// TI - Current tools for the identification of miRNA genes and their targets JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkp145 DO - 10.1093/nar/gkp145 ID - Mendes2009 ER - TY - JOUR AU - Lim, L. P. AU - Lau, N. C. AU - Weinstein, E. G. PY - 2003 DA - 2003// TI - The microRNAs of Caenorhabditis elegans JO - Genes Dev VL - 17 UR - https://doi.org/10.1101/gad.1074403 DO - 10.1101/gad.1074403 ID - Lim2003 ER - TY - STD TI - Lai EC, Tomancak P, Williams RW: Computational identification of Drosophila microRNA genes. Genome Biol 2003, 7(4):R42., ID - ref10 ER - TY - STD TI - Huang TH, Fan B, Rothschild MF: MiRFinder: an improved approach and software implementation for genome-wide fast microRNA precursor scans. BMC Bioinformatics 2007, 8:341., ID - ref11 ER - TY - JOUR AU - Bartel, D. P. PY - 2004 DA - 2004// TI - MicroRNAs: genomics, biogenesis, mechanism, and function JO - Cell VL - 116 UR - https://doi.org/10.1016/S0092-8674(04)00045-5 DO - 10.1016/S0092-8674(04)00045-5 ID - Bartel2004 ER - TY - JOUR AU - Xue, C. H. AU - Li, F. AU - He, T. PY - 2005 DA - 2005// TI - Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine JO - BMC Bioinformatics VL - 6 UR - https://doi.org/10.1186/1471-2105-6-310 DO - 10.1186/1471-2105-6-310 ID - Xue2005 ER - TY - JOUR AU - Yousef, M. AU - Nebozhyn, M. AU - Shatkay, H. PY - 2006 DA - 2006// TI - Combining multi-species genomic data for microRNA identification using a Naïve Bayes classifier JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl094 DO - 10.1093/bioinformatics/btl094 ID - Yousef2006 ER - TY - JOUR AU - Jiang, P. AU - Wu, H. AU - Wang, W. PY - 2007 DA - 2007// TI - MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features JO - Nucleic Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkm368 DO - 10.1093/nar/gkm368 ID - Jiang2007 ER - TY - JOUR AU - Gordon, L. AU - Chervonenkis, A. Y. AU - Gammerman, A. J. AU - Shahmuradov, I. A. AU - Solovyev, V. V. PY - 2003 DA - 2003// TI - Sequence alignment kernel for recognition ofpromoter regions JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg265 DO - 10.1093/bioinformatics/btg265 ID - Gordon2003 ER - TY - JOUR AU - Lim, L. P. AU - Lau, N. C. AU - Weinstein, E. G. PY - 2003 DA - 2003// TI - The microRNAs of Caenorhabditis elegans JO - Genes Dev VL - 17 UR - https://doi.org/10.1101/gad.1074403 DO - 10.1101/gad.1074403 ID - Lim2003 ER - TY - STD TI - Meng J, Shi L, Luan YS: Plant microRNA-target interaction identification model based on the integration of prediction tools and support vector machine. Plos One 2014, 9(7):e103181., ID - ref18 ER - TY - STD TI - Lai EC, Tomancak P, Williams RW: Computational identification of Drosophila microRNA genes. Genome Biol 2003, 7(4):R42., ID - ref19 ER - TY - JOUR AU - Jones-Rhoades, M. W. AU - Bartel, D. P. PY - 2004 DA - 2004// TI - Computational identification of plant microRNAs and their targets including a stress-induced miRNA JO - Mol Cell VL - 14 UR - https://doi.org/10.1016/j.molcel.2004.05.027 DO - 10.1016/j.molcel.2004.05.027 ID - Jones-Rhoades2004 ER - TY - JOUR AU - Schultes, E. A. AU - Hraber, P. T. AU - LaBean, T. H. PY - 1999 DA - 1999// TI - Estimating the contributions of selection and self-organization in RNA secondary structure JO - J Mol Evol VL - 49 UR - https://doi.org/10.1007/PL00006536 DO - 10.1007/PL00006536 ID - Schultes1999 ER - TY - JOUR AU - Wojciechowski, P. AU - Formanowicz, P. AU - Blazewicz, J. PY - 2014 DA - 2014// TI - Reference Alignment Based Methods for Quality Evaluation of Multiple Sequence Alignment-A Survey JO - Current Bioinformatics VL - 9 UR - https://doi.org/10.2174/15748936113080990005 DO - 10.2174/15748936113080990005 ID - Wojciechowski2014 ER - TY - JOUR AU - Maji, S. AU - Garg, D. PY - 2014 DA - 2014// TI - Hybrid Approach Using SVM and MM2 in Splice Site Junction Identification JO - Current Bioinformatics VL - 9 UR - https://doi.org/10.2174/1574893608999140109121721 DO - 10.2174/1574893608999140109121721 ID - Maji2014 ER - TY - JOUR AU - Moorthy, K. AU - Saberi, M. AU - Deris, S. PY - 2014 DA - 2014// TI - A review on missing value imputation algorithms for microarray gene expression data JO - Current Bioinformatics VL - 9 UR - https://doi.org/10.2174/1574893608999140109120957 DO - 10.2174/1574893608999140109120957 ID - Moorthy2014 ER - TY - JOUR AU - Zhang, B. H. AU - Pan, X. P. AU - Cox, S. B. PY - 2006 DA - 2006// TI - Evidence that miRNAs are different from other RNAs JO - Cell Mol Life Sci VL - 63 UR - https://doi.org/10.1007/s00018-005-5467-7 DO - 10.1007/s00018-005-5467-7 ID - Zhang2006 ER - TY - JOUR AU - Batuwita, R. AU - Palade, V. PY - 2009 DA - 2009// TI - microPred: effective classification of pre-miRNAs for human miRNA gene prediction JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp107 DO - 10.1093/bioinformatics/btp107 ID - Batuwita2009 ER - TY - JOUR AU - Xuan, P. AU - Guo, M. AU - Liu, X. PY - 2011 DA - 2011// TI - PlantMiRNAPred: efficient classification of real and pseudo plant pre-miRNAs JO - Bioinformatics VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr153 DO - 10.1093/bioinformatics/btr153 ID - Xuan2011 ER - TY - STD TI - Chih-Chung C, Chih-Jen L: LIBSVM: A Library for Support Vector Machines. ACM Trans Intell Syst Technol 2011, 2(3):27 (27 pp.)., ID - ref28 ER - TY - JOUR AU - Guyon, I. AU - Weston, J. AU - Barnhill, S. PY - 2002 DA - 2002// TI - Gene selection for cancer classification using support vector machines JO - Machine learning VL - 46 UR - https://doi.org/10.1023/A:1012487302797 DO - 10.1023/A:1012487302797 ID - Guyon2002 ER - TY - JOUR AU - Guyon, I. AU - Elisseeff, A. PY - 2003 DA - 2003// TI - An introduction to variable and feature selection JO - The J Mach Learn Res VL - 3 ID - Guyon2003 ER - TY - JOUR AU - Kent, J. T. PY - 1983 DA - 1983// TI - Information gain and a general measure of correlation JO - Biometrika VL - 70 UR - https://doi.org/10.1093/biomet/70.1.163 DO - 10.1093/biomet/70.1.163 ID - Kent1983 ER - TY - JOUR AU - Chawla, N. V. AU - Bowyer, K. W. AU - Hall, L. O. PY - 2011 DA - 2011// TI - SMOTE: synthetic minority over-sampling technique JO - arXiv preprint VL - 11 ID - Chawla2011 ER - TY - BOOK AU - Hall, M. A. PY - 1999 DA - 1999// TI - Correlation-based feature selection for machine learning PB - The University of Waikato CY - Hamilton ID - Hall1999 ER - TY - STD TI - John GH, Langley P: Estimating continuous distributions in Bayesian classifiers. In: Proceedings of the Eleventh conference on Uncertainty in artificial intelligence. San Francisco: Morgan Kaufmann Publishers Inc., 1995: 338–345. ID - ref34 ER - TY - JOUR AU - Breiman, L. PY - 2001 DA - 2001// TI - Random Forests JO - Machine Learning VL - 45 UR - https://doi.org/10.1023/A:1010933404324 DO - 10.1023/A:1010933404324 ID - Breiman2001 ER - TY - JOUR AU - Xuan, P. AU - Guo, M. AU - Liu, X. AU - Huang, Y. AU - Li, W. AU - Huang, Y. PY - 2011 DA - 2011// TI - PlantMiRNAPred: efficient classification of real and pseudo plant pre-miRNAs JO - Bioinformatics VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr153 DO - 10.1093/bioinformatics/btr153 ID - Xuan2011 ER - TY - JOUR AU - Bonnet, E. AU - Wuyts, J. AU - Rouzé, P. AU - Van de Peer, Y. PY - 2004 DA - 2004// TI - Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/bth374 DO - 10.1093/bioinformatics/bth374 ID - Bonnet2004 ER - TY - JOUR AU - Umesono, K. AU - Evans, R. M. PY - 1989 DA - 1989// TI - Determinants of target gene specificity for steroid/thyroid hormone receptors JO - Cell VL - 57 UR - https://doi.org/10.1016/0092-8674(89)90051-2 DO - 10.1016/0092-8674(89)90051-2 ID - Umesono1989 ER - TY - JOUR AU - Lund, E. AU - Sheets, M. D. AU - Imboden, S. B. PY - 2011 DA - 2011// TI - Limiting Ago protein restricts RNAi and microRNA biogenesis during early development in Xenopus laevis JO - Genes Dev VL - 25 UR - https://doi.org/10.1101/gad.2038811 DO - 10.1101/gad.2038811 ID - Lund2011 ER - TY - STD TI - Regnier M: Knuth-Morris-Pratt algorithm: an analysis. In: Mathematical Foundations of Computer Science 1989. New York: Springer, 1989: 431–444. ID - ref40 ER - TY - JOUR AU - Ohler, U. AU - Yekta, S. AU - Lim, L. P. PY - 2004 DA - 2004// TI - Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification JO - RNA VL - 10 UR - https://doi.org/10.1261/rna.5206304 DO - 10.1261/rna.5206304 ID - Ohler2004 ER -