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2012
L. L. Hu, Huang, Y., Wang, Q. C., Zou, Q., and Jiang, Y., Benchmark comparison of ab initio microRNA identification methods and software, vol. 11, pp. 4525-4538, 2012.
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Computational identification and characteristics of novel microRNAs from the silkworm (Bombyx mori L.). Mol. Biol. Rep. 37: 3171-3176. http://dx.doi.org/10.1007/s11033-009-9897-4 PMid:19823945   Huang Y, Shen XJ, Zou Q, Wang SP, et al. (2011a). Biological functions of microRNAs: a review. J. Physiol. Biochem. 67: 129-139. http://dx.doi.org/10.1007/s13105-010-0050-6 PMid:20981514   Huang Y, Zou Q, Wang SP, Tang SM, et al. (2011b). The discovery approaches and detection methods of microRNAs. Mol. Biol. Rep. 38: 4125-4135. http://dx.doi.org/10.1007/s11033-010-0532-1 PMid:21107708   Jiang P, Wu H, Wang W, Ma W, et al. (2007). MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Nucleic Acids Res. 35: W339-W344. http://dx.doi.org/10.1093/nar/gkm368 PMid:17553836 PMCid:1933124   Kumar S, Ansari FA and Scaria V (2009). Prediction of viral microRNA precursors based on human microRNA precursor sequence and structural features. Virol. J. 6: 129. http://dx.doi.org/10.1186/1743-422X-6-129 PMid:19691855 PMCid:2743665   Lee Y, Ahn C, Han J, Choi H, et al. (2003). The nuclear RNase III Drosha initiates microRNA processing. Nature 425: 415-419. http://dx.doi.org/10.1038/nature01957 PMid:14508493   Li PW, Lu XY, Li CZ, Fang J, et al. (2007). Advances in the study of plant microRNAs. Yi Chuan 29: 283-288. http://dx.doi.org/10.1360/yc-007-0283 PMid:17369147   Lim LP, Lau NC, Weinstein EG, Abdelhakim A, et al. (2003). The microRNAs of Caenorhabditis elegans. Genes Dev. http://dx.doi.org/10.1101/gad.1074403   Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, et al. (2000). The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403: 901-906. http://dx.doi.org/10.1038/35002607 PMid:10706289   Ruby JG, Jan C, Player C, Axtell MJ, et al. (2006). Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127: 1193-1207. http://dx.doi.org/10.1016/j.cell.2006.10.040 PMid:17174894   Sankoff D, Kruskal JB, Mainville S and Cedergren RJ (1983). Fast Algorithms to Determine RNA Secondary Structures Containing Multiple Loops. In: Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison (Sankoff D and Kruskal JB, eds.). Chapter 3. Addison-Wesley, Reading, 93-120.   Sewer A, Paul N, Landgraf P, Aravin A, et al. (2005). Identification of clustered microRNAs using an ab initio prediction method. BMC Bioinformatics 6: 267. http://dx.doi.org/10.1186/1471-2105-6-267 PMid:16274478 PMCid:1315341   Wang X, Zhang J, Li F, Gu J, et al. (2005). MicroRNA identification based on sequence and structure alignment. Bioinformatics 21: 3610-3614. http://dx.doi.org/10.1093/bioinformatics/bti562 PMid:15994192   Wu Y, Wei B, Liu H, Li T, et al. (2011). MiRPara: a SVM-based software tool for prediction of most probable microRNA   Genetics and Molecular Research 11 (4): 4525-4538 (2012) ©FUNPEC-RP www.funpecrp.com.br   L.L. Hu et al. 4538 coding regions in genome scale sequences. BMC Bioinformatics 12: 107.   Xue C, Li F, He T, Liu GP, et al. (2005). Classification of real and pseudo microRNA precursors using local structuresequence features and support vector machine. BMC Bioinformatics 6: 310. http://dx.doi.org/10.1186/1471-2105-6-310 PMid:16381612 PMCid:1360673   Yousef M, Nebozhyn M, Shatkay H, Kanterakis S, et al. (2006). Combining multi-species genomic data for microRNA identification using a Naive Bayes classifier. Bioinformatics 22: 1325-1334. http://dx.doi.org/10.1093/bioinformatics/btl094 PMid:16543277   Zeng Y, Yi R and Cullen BR (2005). Recognition and cleavage of primary microRNA precursors by the nuclear processing enzyme Drosha. 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Y. Jiang, Fan, S. L., Song, M. Z., Yu, J. N., and Yu, S. X., Identification of RNA editing sites in cotton (Gossypium hirsutum) chloroplasts and editing events that affect secondary and three-dimensional protein structures, vol. 11, pp. 987-1001, 2012.
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Plant Cell Physiol. 45: 1615-1622. http://dx.doi.org/10.1093/pcp/pch191 PMid:15574837 Jiang Y, Yu J, Yao Y, Song M, et al. (2010). Research progress of cotton chloroplast genome. Cotton Sci. 22: 495-500. Kahlau S, Aspinall S, Gray JC and Bock R (2006). Sequence of the tomato chloroplast DNA and evolutionary comparison of solanaceous plastid genomes. J. Mol. Evol. 63: 194-207. http://dx.doi.org/10.1007/s00239-005-0254-5 PMid:16830097 Kugita M, Yamamoto Y, Fujikawa T, Matsumoto T, et al. (2003). RNA editing in hornwort chloroplasts makes more than half the genes functional. Nucleic Acids Res. 31: 2417-2423. http://dx.doi.org/10.1093/nar/gkg327 PMid:12711687    PMCid:154213 Lee SB, Kaittanis C, Jansen RK, Hostetler JB, et al. (2006). The complete chloroplast genome sequence of Gossypium hirsutum: organization and phylogenetic relationships to other angiosperms. BMC Genomics 7: 61. http://dx.doi.org/10.1186/1471-2164-7-61 PMid:16553962    PMCid:1513215 Lutz KA and Maliga P (2001). Lack of conservation of editing sites in mRNAs that encode subunits of the NAD(P)H dehydrogenase complex in plastids and mitochondria of Arabidopsis thaliana. Curr. Genet. 40: 214-219. http://dx.doi.org/10.1007/s002940100242 PMid:11727998 Maier RM, Neckermann K, Igloi GL and Kössel H (1995). Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. J. Mol. Biol. 251: 614- 628. http://dx.doi.org/10.1006/jmbi.1995.0460 PMid:7666415 Miyata Y and Sugita M (2004). Tissue- and stage-specific RNA editing of rps 14 transcripts in moss (Physcomitrella patens) chloroplasts. J. Plant Physiol. 161: 113-115. http://dx.doi.org/10.1078/0176-1617-01220 PMid:15002671 Okuda K, Myouga F, Motohashi R, Shinozaki K, et al. (2007). Conserved domain structure of pentatricopeptide repeat proteins involved in chloroplast RNA editing. Proc. Natl. Acad. Sci. U. S. 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Identification of RNA editing sites in chloroplast transcripts from the maternal and paternal progenitors of tobacco (Nicotiana tabacum): comparative analysis shows the involvement of distinct trans-factors for ndhB editing. Mol. Biol. Evol. 20: 1028-1035. http://dx.doi.org/10.1093/molbev/msg098 PMid:12716996 Sasaki T, Yukawa Y, Wakasugi T, Yamada K, et al. (2006). A simple in vitro RNA editing assay for chloroplast transcripts using fluorescent dideoxynucleotides: distinct types of sequence elements required for editing of ndh transcripts. Plant J. 47: 802-810. http://dx.doi.org/10.1111/j.1365-313X.2006.02825.x PMid:16856984 Sasaki Y and Nagano Y (2004). Plant acetyl-CoA carboxylase: structure, biosynthesis, regulation, and gene manipulation for plant breeding. Biosci. Biotechnol. Biochem. 68: 1175-1184. http://dx.doi.org/10.1271/bbb.68.1175 PMid:15215578 Sasaki Y, Kozaki A, Ohmori A, Iguchi H, et al. (2001). Chloroplast RNA editing required for functional acetyl-CoA carboxylase in plants. J. Biol. Chem. 276: 3937-3940. http://dx.doi.org/10.1074/jbc.M008166200 PMid:11078738 Schmitz-Linneweber C, Regel R, Du TG, Hupfer H, et al. (2002). The plastid chromosome of Atropa belladonna and its comparison with that of Nicotiana tabacum: the role of RNA editing in generating divergence in the process of plant speciation. Mol. Biol. Evol. 19: 1602-1612. http://dx.doi.org/10.1093/oxfordjournals.molbev.a004222 PMid:12200487 Schmitz-Linneweber C, Kushnir S, Babiychuk E, Poltnigg P, et al. (2005). Pigment deficiency in nightshade/tobacco cybrids is caused by the failure to edit the plastid ATPase alpha-subunit mRNA. Plant Cell 17: 1815-1828. http://dx.doi.org/10.1105/tpc.105.032474 PMid:15894714    PMCid:1143079 Shikanai T (2006). RNA editing in plant organelles: machinery, physiological function and evolution. Cell Mol. 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Correlation between amino acid residues converted by RNA editing and functional residues in protein three-dimensional structures in plant organelles. BMC Plant Biol. 8: 79. http://dx.doi.org/10.1186/1471-2229-8-79 PMid:18631376    PMCid:2488346 Yura K, Sulaiman S, Hatta Y, Shionyu M, et al. (2009). RESOPS: A database for analyzing the correspondence of RNA editing sites to protein three-dimensional structures. Plant Cell Physiol. 50: 1865-1873. http://dx.doi.org/10.1093/pcp/pcp132 PMid:19808808    PMCid:2775959 Zeng WH, Liao SC and Chang CC (2007). Identification of RNA editing sites in chloroplast transcripts of Phalaenopsis aphrodite and comparative analysis with those of other seed plants. Plant Cell Physiol. 48: 362-368. http://dx.doi.org/10.1093/pcp/pcl058 PMid:17169923 Zhou W, Cheng Y, Yap A, Chateigner-Boutin AL, et al. (2009). 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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
Y. Jiang, Nie, L. W., Huang, Z. F., Jing, W. X., Wang, L., Liu, L., and Dai, X. T., Comparison of complete mitochondrial DNA control regions among five Asian freshwater turtle species and their phylogenetic relationships, vol. 10, pp. 1545-1557, 2011.
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