A novel pre-MiRNA classification approach for the prediction of microRNA genes

Proceedings of the IEEE/EMBS Region 8 International Conference on Information Technology Applications in Biomedicine, ITAB

Volumn , Issue , 2010, Pages

  Theofilatos, Konstantinos A ^a   Kleftogiannis, Dimitrios A ^a   Rapsomaniki, Maria Anna V ^a   Haidinis, Vasileios A ^a   Likothanassis, Spiridon D ^a   Tsakalidis, Athanasios K ^a   Mavroudi, Seferina P ^a  

^a UNIVERSITY OF PATRAS   (Greece)

Author keywords

[No Author keywords available]

Indexed keywords

CLASSIFICATION APPROACH; CLASSIFICATION METHODS; CLASSIFICATION PERFORMANCE; FEATURE SELECTION; FEATURE SETS; GENE REGULATIONS; MICRORNAS; MINIMUM SUBSETS; NON-CODING RNAS; PARAMETERS OPTIMIZATION;

BIOINFORMATICS; GENES; INFORMATION TECHNOLOGY;

FEATURE EXTRACTION;

EID: 79951626199     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ITAB.2010.5687799     Document Type: Conference Paper

References (35)

1. D.P. Bartel, "MicroRNAs: genomics, biogenesis, mechanism, and function," Cell, vol. 116, Jan. 2004, pp. 281-297.
2. L. He and GJ. Hannon, "MicroRNAs: small RNAs with a big role in gene regulation," Nature Reviews. Genetics, vol. 5, Jul. 2004, pp. 522-531. (Pubitemid 38868508)
3. P. Nelson, M. Kiriakidou, A Sharma, E. Maniataki, and Z. Mourelatos, "The microRNA world: small is mighty," Trends in Biochemical Sciences, vol. 28, Oct. 2003, pp. 534-540. (Pubitemid 38366279)
4. S. Vasudevan, Y. Tong, and J.A. Steitz, "Cell-cycle control of microRNA-mediated translation regulation," Cell Cycle (Georgetown, Tex.), vol. 7, Jun. 2008, pp. 1545-1549. (Pubitemid 351881318)
5. S. Subramanian and C.J. Steer, "MicroRNAs as gatekeepers of apoptosis," Journal of Cellular Physiology, vol. 223, May. 2010, pp. 289-298.
6. L. He, J.M. Thomson, M.T. Hemann, E. Hernando-Monge, D. Mu, S. Goodson, S. Powers, C. Cordon-Cardo, S.W. Lowe, G.J. Hannon, and S.M. Hammond, "A microRNA polycistron as a potential human oncogene," Nature, vol. 435, Jun. 2005, pp. 828-833. (Pubitemid 40839734)
7. H.M. Heneghan, N. Miller, AJ. Lowery, K.J. Sweeney, and M.J. Kerin, "MicroRNAs as Novel Biomarkers for Breast Cancer," Journal of Oncology, vol. 2009,2009, p. 950201.
8. Y. Zhao, J.F. Ransom, A Li, V. Vedantham, M. von Drehle, AN. Muth, T. Tsuchihashi, M.T. McManus, R.I. Schwartz, and D. Srivastava, "Dysregulation of cardiogenesis, cardiac conduction, and cell cycle in mice lacking miRNA-I-2," Cell, vol. 129, Apr. 2007, pp. 303-317. (Pubitemid 46574975)
9. O.C. Maes, H.M. Chertkow, E. Wang, and H.M. Schipper, "MicroRNA: Implications for Alzheimer Disease and other Human CNS Disorders," Current Genomics, vol. 10, May. 2009, pp. 154-168.
10. V.N. Kim and J. Nam, "Genomics of microRNA," Trends in Genetics: TIG, vol. 22, Mar. 2006, pp. 165-173. (Pubitemid 43290020)
11. M. Lagos-Quintana, R Rauhut, J. Meyer, A Borkhardt, and T. Tuschl, "New microRNAs from mouse and human," RNA (New York, N. Y.), vol. 9, Feb. 2003, pp. 175-179. (Pubitemid 36206285)
12. L.P. Lim, M.E. Glasner, S. Yekta, C.B. Burge, and D.P. Bartel, "Vertebrate microRNA genes," Science (New York, N.Y.), vol. 299, Mar. 2003, p. 1540. (Pubitemid 36297696)
13. J. Hertel and P.F. Stadler, "Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data," Bioinformatics (Oxford, England), vol. 22, Jul. 2006, pp. e197-202. (Pubitemid 44288287)
14. E.C. Lai, P. Tomancak, RW. Williams, and G.M. Rubin, "Computational identification of Drosophila microRNA genes," Genome Biology, vol. 4, 2003, p. R42.
15. E. Berezikov, V. Guryev, J. van de Belt, E. Wienholds, RH.A. Plasterk, and E. Cuppen, "Phylogenetic shadowing and computational identification of human microRNA genes," Cell, vol. 120, Jan. 2005, pp. 21-24. (Pubitemid 40094599)
16. I. Bentwich, A Avniel, Y. Karov, R Aharonov, S. Gilad, O. Barad, A Barzilai, P. Einat, U. Einav, E. Meiri, E. Sharon, Y. Spector, and Z. Bentwich, "Identification of hundreds of conserved and nonconserved human microRNAs," Nature Genetics, vol. 37, Jul. 2005, pp. 766-770. (Pubitemid 41754896)
17. J. Nam, K. Shin, J. Han, Y. Lee, V.N. Kim, and B. Zhang, "Human microRNA prediction through a probabilistic co-learning model of sequence and structure," Nucl. Acids Res., vol. 33, Jun. 2005, pp. 3570-3581. (Pubitemid 41430579)
18. S. Agarwal, C. Vaz, A Bhattacharya, and A Srinivasan, "Prediction of novel precursor miRNAs using a context-sensitive hidden Markov model (CSHMM)," BMC Bioiriformatics, vol. 11,2010, p. S29.
19. Y. Xu, X. Zhou, and W. Zhang, "MicroRNA prediction with a novel ranking algorithm based on random walks," Bioiriformatics, vol. 24, Jul. 2008, pp. i50-58. (Pubitemid 351911657)
20. K.L.S. Ng and S.K. Mishra, "De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures," Bioiriformatics, vol. 23, Jun. 2007, pp. 1321-1330. (Pubitemid 47050513)
21. C. Xue, F. Li, T. He, G. Liu, Y. Li, and X. Zhang, "Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine," BMC Bioiriformatics, vol. 6, 2005, p. 310.
22. A Sewer, N. Paul, P. Landgraf, A Aravin, S. Pfeffer, M.J Brownstein, T. Tuschl, E. van Nimwegen, and M. Zavolan, "Identification of clustered microRNAs using an ab initio prediction method," BMC Bioinformatics, vol. 6,2005, p. 267.
23. R Batuwita and V. Palade, "microPred: effective classification of premiRNAs for human miRNA gene prediction," Bioinformatics, vol. 25, Apr. 2009, pp. 989-995.
24. K.D. Pruitt and D.R Maglott, "RefSeq and LocusLink: NCB! genecentered resources," Nucleic Acids Research, vol. 29, Jan. 2001, pp. 137-140. (Pubitemid 32054428)
25. V.N. Vapnik, The nature of statistical leaming theory, Springer, 2000.
26. C.J. Burges, "A Tutorial on Support Vector Machines for Pattern Recognition," Data Mining and Knowledge Discovery, vol. 2, Jun. 1998, pp. 121-167. (Pubitemid 128695475)
27. T.S. Furey, N. Cristianini, N. Duffy, D.W. Bednarski, M. Schummer, and D. Haussler, "Support vector machine classification and validation of cancer tissue samples using microarray expression data," Bioiriformatics, vol. 16, Oct. 2000, pp. 906-914.
28. H.W. Ressom, RS. Varghese, M. Abdel-Hamid, S.A. Eissa, D. Saba, L. Goldman, E.F. Petricoin, T.P. Conrads, T.D. Veenstra, C.A. Loffredo, and R Goldman, "Analysis of mass spectral serum profiles for biomarker selection," Bioinformatics, vol. 21, Nov. 2005, pp. 4039-4045. (Pubitemid 41631847)
29. S. Kerthi and C. J. Lin, "Asymptotic behaviors of support vector machines with Gaussian Kernel ", Neural Computation, vol. 15, Jul. 2003,pp. 1667-1689.
30. J. Holland, Adaptation in natural and artificial systems: an introductory analysis with applications to biology, control, and artificial intelligence, Cambridge: Mass ;MIT Press, 1995.
31. S. Papadimitriou and K. Terzidis, "Efficient and interpretable fuzzy classifiers from data with support vector learning", Intelligent Data Analysis, Vol. 9, Nov. 2005, p.p. 527-550.
32. S. Griffiths-Jones, RJ. Grocock, S. van Dongen, A Bateman, and AJ. Enright, "miRBase: microRNA sequences, targets and gene nomenclature," Nucl. Acids Res., vol. 34, Jan. 2006, pp. Dl40-144.
33. S. Mavroudi, P. Katsanos, S. Papadimitriou and S. Likothanassis, "Transparent Classification Process of Bioinformatics data With An Approximated Support Vector Fuzzy Inference System ", The International Special Topic Conference on Information Technology in Biomedicine (ITAB 2006), Ioannina -Epirus Greece, October 26-28, 2006.
34. Aïssani B, Bernardi G O. "CpG islands, genes and isochores in the genomes of vertebrates". Gene 106 (2): 185-95, October 1991.
35. Ng Kwang Loong, S., Mishra, S.K. "Unique folding of precursor microRNAs: Quantitative evidence and implications for de novo identification ". RNA 13:170-187,2007. (Pubitemid 46147894)