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2012
W. Chen, Liu, X., Huang, Y., Jiang, Y., Zou, Q., and Lin, C., Improved method for predicting protein fold patterns with ensemble classifiers, vol. 11, pp. 174-181, 2012.
Boisvert S, Marchand M, Laviolette F and Corbeil J (2008). HIV-1 coreceptor usage prediction without multiple alignments: an application of string kernels. Retrovirology 5: 110. http://dx.doi.org/10.1186/1742-4690-5-110 PMid:19055831    PMCid:2637298 Breimin L (2001). Random forests. Machine Learn. 45: 5-32. http://dx.doi.org/10.1023/A:1010933404324 Cai CZ, Han LY, Ji ZL, Chen X, et al. (2003). SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence. Nucleic Acids Res. 31: 3692-3697. http://dx.doi.org/10.1093/nar/gkg600 PMid:12824396    PMCid:169006 Call ME, Schnell JR, Xu C, Lutz RA, et al. (2006). The structure of the zetazeta transmembrane dimer reveals features essential for its assembly with the T cell receptor. Cell 127: 355-368. http://dx.doi.org/10.1016/j.cell.2006.08.044 PMid:17055436 Chen K and Kurgan L (2007). PFRES: protein fold classification by using evolutionary information and predicted secondary structure. Bioinformatics 23: 2843-2850. http://dx.doi.org/10.1093/bioinformatics/btm475 PMid:17942446 Chou KC (2004). Structural bioinformatics and its impact to biomedical science. Curr. Med. Chem. 11: 2105-2134. PMid:15279552 Ding CHQ and Dubchak I (2001). Multi-class protein fold recognition using support vector machines and neural networks. Bioinformatics 17: 349-358. http://dx.doi.org/10.1093/bioinformatics/17.4.349 PMid:11301304 Douglas SM, Chou JJ and Shih WM (2007). DNA-nanotube-induced alignment of membrane proteins for NMR structure determination. Proc. Natl. Acad. Sci. U. S. A. 104: 6644-6648. http://dx.doi.org/10.1073/pnas.0700930104 PMid:17404217    PMCid:1871839 Gao WN, Wei DQ, Li Y, Gao H, et al. (2007). Agaritine and its derivatives are potential inhibitors against HIV proteases. Med. Chem. 3: 221-226. http://dx.doi.org/10.2174/157340607780620644 PMid:17504192 Honda M, Kawai H, Shirota Y, Yamashita T, et al. (2005). cDNA microarray analysis of autoimmune hepatitis, primary biliary cirrhosis and consecutive disease manifestation. J. Autoimmun. 25: 133-140. http://dx.doi.org/10.1016/j.jaut.2005.03.009 PMid:16150573 Li Y, Wei DQ, Gao WN, Gao H, et al. (2007). Computational approach to drug design for oxazolidinones as antibacterial agents. Med. Chem. 3: 576-582. http://dx.doi.org/10.2174/157340607782360362 PMid:18045208 Murzin AG, Brenner SE, Hubbard T and Chothia C (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247: 536-540. http://dx.doi.org/10.1016/S0022-2836(05)80134-2 Nanni L (2006). A novel ensemble of classifiers for protein fold recognition. Neurocomputing 69: 2434-2437. http://dx.doi.org/10.1016/j.neucom.2006.01.026 Niels L, Mark H and Eibe F (2005). Logistic model trees. Machine Learn 95: 161-205. Pu X, Guo J, Leung H and Lin Y (2007). Prediction of membrane protein types from sequences and position-specific scoring matrices. J. Theor. Biol. 247: 259-265. http://dx.doi.org/10.1016/j.jtbi.2007.01.016 PMid:17433369 Schaffer AA, Aravind L, Madden TL, Shavirin S, et al. (2001). Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res. 29: 2994-3005. http://dx.doi.org/10.1093/nar/29.14.2994 PMid:11452024    PMCid:55814 Schnell JR and Chou JJ (2008). Structure and mechanism of the M2 proton channel of influenza A virus. Nature 451: 591-595. http://dx.doi.org/10.1038/nature06531 PMid:18235503    PMCid:3108054 Shen HB and Chou KC (2006). Ensemble classifier for protein fold pattern recognition. Bioinformatics 22: 1717-1722. http://dx.doi.org/10.1093/bioinformatics/btl170 PMid:16672258 Shen HB and Chou KC (2009). Predicting protein fold pattern with functional domain and sequential evolution information. J. Theor. Biol. 256: 441-446. http://dx.doi.org/10.1016/j.jtbi.2008.10.007 PMid:18996396 Sumner M, Frank E and Hall MA (2005). Speeding up Logistic Model Tree Induction. In: Proceedings of 9th European Conference on Principles and Practice of Knowledge Discovery in Databases, Porto, Portugal (Jorge A, ed.). Springer, Germany, 675-683. Vendruscolo M and Dobson CM (2005). A glimpse at the organization of the protein universe. PNAS 102: 5641-5642. http://dx.doi.org/10.1073/pnas.0500274102 PMid:15827120    PMCid:556289
2011
Q. Zou, Lin, C., Liu, X. - Y., Han, Y. - P., Li, W. - B., and Guo, M. - Z., Novel representation of RNA secondary structure used to improve prediction algorithms, vol. 10, pp. 1986-1998, 2011.
Brown JW (1999). The ribonuclease P database. Nucleic Acids Res. 27: 314. http://dx.doi.org/10.1093/nar/27.1.314 PMid:9847214    PMCid:148169 Byun Y and Han K (2006). PseudoViewer: web application and web service for visualizing RNA pseudoknots and secondary structures. Nucleic Acids Res. 34: W416-W422. http://dx.doi.org/10.1093/nar/gkl210 PMid:16845039    PMCid:1538805 Chan PP and Lowe TM (2009). GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res. 37: D93-D97. http://dx.doi.org/10.1093/nar/gkn787 PMid:18984615    PMCid:2686519 Ding Y, Chan CY and Lawrence CE (2004). Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res. 32: W135-W141. http://dx.doi.org/10.1093/nar/gkh449 PMid:15215366    PMCid:441587 Gardner PP and Giegerich R (2004). A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics 5: 140. http://dx.doi.org/10.1186/1471-2105-5-140 PMid:15458580    PMCid:526219 Griffiths-Jones S, Moxon S, Marshall M, Khanna A, et al. (2005). Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res. 33: D121-D124. http://dx.doi.org/10.1093/nar/gki081 PMid:15608160    PMCid:540035 Hertel J, Hofacker IL and Stadler PF (2008). SnoReport: computational identification of snoRNAs with unknown targets. Bioinformatics 24: 158-164. http://dx.doi.org/10.1093/bioinformatics/btm464 PMid:17895272 Hofacker IL (2003). Vienna RNA secondary structure server. Nucleic Acids Res. 31: 3429-3431. http://dx.doi.org/10.1093/nar/gkg599 PMid:12824340    PMCid:169005 Knudsen B and Hein J (1999). RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. Bioinformatics 15: 446-454. http://dx.doi.org/10.1093/bioinformatics/15.6.446 PMid:10383470 Lambert A, Fontaine JF, Legendre M, Leclerc F, et al. (2004). The ERPIN server: an interface to profile-based RNA motif identification. Nucleic Acids Res. 32: W160-W165. http://dx.doi.org/10.1093/nar/gkh418 PMid:15215371    PMCid:441556 Larkin MA, Blackshields G, Brown NP, Chenna R, et al. (2007). Clustal W and clustal X version 2.0. Bioinformatics 23: 2947-2948. http://dx.doi.org/10.1093/bioinformatics/btm404 PMid:17846036 Leland W (1999). Dot Plots. Am. Statistician 53: 276-281. http://dx.doi.org/10.2307/2686111 Lowe TM and Eddy SR (1997). tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955-964. http://dx.doi.org/10.1093/nar/25.5.955 PMid:9023104    PMCid:146525 Rounsevell R, Forman JR and Clarke J (2004). Atomic force microscopy: mechanical unfolding of proteins. Methods 34: 100-111. http://dx.doi.org/10.1016/j.ymeth.2004.03.007 PMid:15283919 Siebert S and Backofen R (2005). Marna: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons. Bioinformatics 21: 3352-3359. http://dx.doi.org/10.1093/bioinformatics/bti550 PMid:15972285 Touzet H and Perriquet O (2004). Carnac: folding families of related RNAs. Nucleic Acids Res. 32: W142-W145. http://dx.doi.org/10.1093/nar/gkh415 PMid:15215367    PMCid:441553 Witwer C, Hofacker IL and Stadler PF (2004). Prediction of consensus RNA secondary structures including pseudoknots. IEEE/ACM Trans. Comput. Biol. Bioinform. 1: 66-77. http://dx.doi.org/10.1109/TCBB.2004.22 PMid:17048382 Zhang TT, Guo M and Zou Q (2007). RNA Secondary Structure Prediction Based on Forest Representation and Genetic Algorithm. Proceedings of the Third International Conference on Natural Computation, IEE Computer Society, Washington, 370-374. Zou Q, Guo MZ, Liu Y and Xing ZA (2008). A Novel Comparative Sequence Analysis Method for ncRNA Secondary Structure Prediction Without Multiple Sequence Alignment. Proceedings of the Fourth International Conference on Natural Computation. IEE Computer Society, Washington, 29-33. Zou Q, Guo MZ, Wang CY and Han YP (2009a). Novel H/ACA Box snoRNA Mining and Secondary Structure Prediction Algorithms. Proceedings of the Rough Sets and Knowledge Technology, Gold Coast, 538-546. Zou Q, Zhao T, Liu Y and Guo M (2009b). Predicting RNA secondary structure based on the class information and hopfield network. Comput. Biol. Med. 39: 206-214. http://dx.doi.org/10.1016/j.compbiomed.2008.12.010 PMid:19215914 Zou Q, Guo M, Liu Y and Xuan P (2010). DuplexFinder: predicting the miRNA-miRNA* duplex from the animal precursors. Int. J. Bioinform. Res. Appl. 6: 69-81. http://dx.doi.org/10.1504/IJBRA.2010.031293 PMid:20110210 Zuker M (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31: 3406-3415. http://dx.doi.org/10.1093/nar/gkg595 PMid:12824337    PMCid:169194