Publications

Chen J, Tang B, Chen H, Yao Q, et al. (2010). Different functions of the insect soluble and membrane-bound trehalase genes in chitin biosynthesis revealed by RNA interference. PLoS One 5: e10133. http://dx.doi.org/10.1371/journal.pone.0010133 PMid:20405036 PMCid:2853572   Crowe JH, Crowe LM and Chapman D (1984). Preservation of membranes in anhydrobiotic organisms: the role of trehalose. Science 223: 701-703. http://dx.doi.org/10.1126/science.223.4637.701 PMid:17841031   Davidson P and Sun WQ (2001). Effect of sucrose/raffinose mass ratios on the stability of co-lyophilized protein during storage above the Tg. Pharm. Res. 18: 474-479. http://dx.doi.org/10.1023/A:1011002326825 PMid:11451034   de Almeida FM, Bonini BM, Beton D, Jorge JA, et al. (2009). Heterologous expression in Escherichia coli of Neurospora crassa neutral trehalase as an active enzyme. Protein Expr. Purif. 65: 185-189. http://dx.doi.org/10.1016/j.pep.2008.11.010 PMid:19073263   Elbein AD, Pan YT, Pastuszak I and Carroll D (2003). New insights on trehalose: a multifunctional molecule. Glycobiology 13: 17R-27R. http://dx.doi.org/10.1093/glycob/cwg047 PMid:12626396   Eleutherio EC, Araujo PS and Panek AD (1993). Role of the trehalose carrier in dehydration resistance of Saccharomyces cerevisiae. Biochim. Biophys. Acta 1156: 263-266. http://dx.doi.org/10.1016/0304-4165(93)90040-F   Frison M, Parrou JL, Guillaumot D, Masquelier D, et al. (2007). The Arabidopsis thaliana trehalase is a plasma membrane-bound enzyme with extracellular activity. FEBS Lett. 581: 4010-4016. http://dx.doi.org/10.1016/j.febslet.2007.07.036 PMid:17673210   Kamimura M, Takahashi M, Tomita S, Fujiwara H, et al. (1999). Expression of ecdysone receptor isoforms and trehalase in the anterior silk gland of Bombyx mori during an extra larval molt and precocious pupation induced by 20-hydroxyecdysone administration. Arch. Insect Biochem. Physiol. 41: 79-88. http://dx.doi.org/10.1002/(SICI)1520-6327(1999)41:2<79::AID-ARCH4>3.0.CO;2-7   Lee JH, Tsuji M, Nakamura M, Nishimoto M, et al. (2001). Purification and identification of the essential ionizable groups of honeybee, Apis mellifera L., trehalase. Biosci. Biotechnol. Biochem. 65: 2657-2665. http://dx.doi.org/10.1271/bbb.65.2657 PMid:11826961   Lee JH, Saito S, Mori H, Nishimoto M, et al. (2007). Molecular cloning of cDNA for trehalase from the European honeybee, Apis mellifera L., and its heterologous expression in Pichia pastoris. Biosci. Biotechnol. Biochem. 71: 2256-2265. http://dx.doi.org/10.1271/bbb.70239 PMid:17827701   Mariano AC, Santos R, Gonzalez MS, Feder D, et al. (2009). Synthesis and mobilization of glycogen and trehalose in adult male Rhodnius prolixus. Arch. Insect Biochem. Physiol. 72: 1-15. http://dx.doi.org/10.1002/arch.20319 PMid:19514081   Mitsumasu K, Azuma M, Niimi T, Yamashita O, et al. (2005). Membrane-penetrating trehalase from silkworm Bombyx mori. Molecular cloning and localization in larval midgut. Insect Mol. Biol. 14: 501-508. http://dx.doi.org/10.1111/j.1365-2583.2005.00581.x PMid:16164606   Mitsumasu K, Azuma M, Niimi T, Yamashita O, et al. (2008). Changes in the expression of soluble and integral-membrane trehalases in the midgut during metamorphosis in Bombyx mori. Zoolog. Sci. 25: 693-698. http://dx.doi.org/10.2108/zsj.25.693 PMid:18828655   Parkinson NM, Conyers CM, Keen JN, MacNicoll AD, et al. (2003). cDNAs encoding large venom proteins from the parasitoid wasp Pimpla hypochondriaca identified by random sequence analysis. Comp. Biochem. Physiol. C. Toxicol. Pharmacol. 134: 513-520. http://dx.doi.org/10.1016/S1532-0456(03)00041-3   Sato K, Komoto M, Sato T, Enei H, et al. (1997). Baculovirus-mediated expression of a gene for trehalase of the Mealworm Beetle, Tenebrio molitor, in insect cells, SF-9, and larvae of the cabbage armyworm, Mamestra brassicae. Insect Biochem. Mol. Biol. 27: 1007-1016. http://dx.doi.org/10.1016/S0965-1748(97)00059-3   Silva MC, Terra WR and Ferreira C (2010). The catalytic and other residues essential for the activity of the midgut trehalase from Spodoptera frugiperda. Insect Biochem. Mol. Biol. 40: 733-741. http://dx.doi.org/10.1016/j.ibmb.2010.07.006 PMid:20691783   Su ZH, Sato Y and Yamashita O (1993). Purification, cDNA cloning and northern blot analysis of trehalase of pupal midgut of the silkworm, Bombyx mori. Biochim. Biophys. Acta 1173: 217-224. http://dx.doi.org/10.1016/0167-4781(93)90184-F   Su ZH, Ikeda M, Sato Y, Saito H, et al. (1994). Molecular characterization of ovary trehalase of the silkworm, Bombyx mori and its transcriptional activation by diapause hormone. Biochim. Biophys. Acta 1218: 366-374. http://dx.doi.org/10.1016/0167-4781(94)90190-2   Sumida M and Yamashita O (1977). Trehalase transformation in silkworm midgut during metamorphosis. J. Comp. Physiol. 115: 241-253.   Sumida M and Yamashita O (1983). Purification and some properties of soluble trehalase from midgut of pharate adult of the silkworm, Bombyx mori. Insect Biochem. 13: 257-265. http://dx.doi.org/10.1016/0020-1790(83)90047-1   Sun WQ and Davidson P (1998). Protein inactivation in amorphous sucrose and trehalose matrices: effects of phase separation and crystallization. Biochim. Biophys. Acta 1425: 235-244. http://dx.doi.org/10.1016/S0304-4165(98)00076-2   Takiguchi M, Niimi T, Su ZH and Yaginuma T (1992). Trehalase from male accessory gland of an insect, Tenebrio molitor. cDNA sequencing and developmental profile of the gene expression. Biochem. J. 288: 19-22. PMid:1445264 PMCid:1132073   Tang B, Chen X, Liu Y, Tian H, et al. (2008). Characterization and expression patterns of a membrane-bound trehalase from Spodoptera exigua. BMC Mol. Biol. 9: 51. http://dx.doi.org/10.1186/1471-2199-9-51 PMid:18492231 PMCid:2424068   Tatun N, Singtripop T, Tungjitwitayakul J and Sakurai S (2008). Regulation of soluble and membrane-bound trehalase activity and expression of the enzyme in the larval midgut of the bamboo borer Omphisa fuscidentalis. Insect Biochem. Mol. Biol. 38: 788-795. http://dx.doi.org/10.1016/j.ibmb.2008.05.003 PMid:18625402   Ujita M, Yamanaka M, Maeno Y, Yoshida K, et al. (2011). Expression of active and inactive recombinant soluble trehalase using baculovirus-silkworm expression system and their glycan structures. J. Biosci. Bioeng. 111: 22-25. http://dx.doi.org/10.1016/j.jbiosc.2010.08.020 PMid:20870456   Wegener G, Tschiedel V, Schloder P and Ando O (2003). The toxic and lethal effects of the trehalase inhibitor trehazolin in locusts are caused by hypoglycaemia. J. Exp. Biol. 206: 1233-1240. http://dx.doi.org/10.1242/jeb.00217 PMid:12604583   Wyatt GR (1967). The biochemistry of sugars and polysaccharides in insects. Adv. Insect Physiol. 4: 287-360. http://dx.doi.org/10.1016/S0065-2806(08)60210-6   Yamashita O, Sumida M and Hasegawa K (1974). Developmental changes in midgut trehalase activity and its localization in the silkworm, Bombyx mori. J. Insect Physiol. 20: 1079-1085. http://dx.doi.org/10.1016/0022-1910(74)90149-8   Yamoah E, Jones EE, Weld RJ, Suckling DM, et al. (2008). Microbial population and diversity on the exoskeletons of 4 insect species associated with gorse (Ulex europaeus L.). Aust. J. Entomol. 47: 370-379. http://dx.doi.org/10.1111/j.1440-6055.2008.00655.x

Batuwita R and Palade V (2009). microPred: effective classification of pre-miRNAs for human miRNA gene prediction. Bioinformatics 25: 989-995. http://dx.doi.org/10.1093/bioinformatics/btp107 PMid:19233894   Bentwich I, Avniel A, Karov Y, Aharonov R, et al. (2005). Identification of hundreds of conserved and nonconserved human microRNAs. Nat. Genet. 37: 766-770. http://dx.doi.org/10.1038/ng1590 PMid:15965474   Borchert GM, Lanier W and Davidson BL (2006). RNA polymerase III transcribes human microRNAs. Nat. Struct. Mol. Biol. 13: 1097-1101. http://dx.doi.org/10.1038/nsmb1167 PMid:17099701   Brennecke J, Hipfner DR, Stark A, Russell RB, et al. (2003). bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell 113: 25-36. http://dx.doi.org/10.1016/S0092-8674(03)00231-9   Carrington JC and Ambros V (2003). Role of microRNAs in plant and animal development. Science 301: 336-338. http://dx.doi.org/10.1126/science.1085242 PMid:12869753   Friedlander MR, Chen W, Adamidi C, Maaskola J, et al. (2008). Discovering microRNAs from deep sequencing data using miRDeep. Nat. Biotechnol. 26: 407-415. http://dx.doi.org/10.1038/nbt1394 PMid:18392026   Hackenberg M, Sturm M, Langenberger D, Falcon-Perez JM, et al. (2009). miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res. 37: W68-W76. http://dx.doi.org/10.1093/nar/gkp347 PMid:19433510 PMCid:2703919   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   Huang JC, Babak T, Corson TW, Chua G, et al. (2007). Using expression profiling data to identify human microRNA targets. Nat. Methods 4: 1045-1049. http://dx.doi.org/10.1038/nmeth1130 PMid:18026111   Huang Y, Zou Q, Tang SM, Wang LG, et al. (2010). 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. EMBO J. 24: 138-148. http://dx.doi.org/10.1038/sj.emboj.7600491 PMid:15565168 PMCid:544904   Zou Q, Zhao T, Liu Y and Guo M (2009). 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, Lin C, Liu XY, Han YP, et al. (2011). Novel representation of RNA secondary structure used to improve prediction algorithms. Genet. Mol. Res. 10: 1986-1998. http://dx.doi.org/10.4238/vol10-3gmr1181 PMid:21948761   Zuker M (1989a). Computer prediction of RNA structure. Methods Enzymol. 180: 262-288. http://dx.doi.org/10.1016/0076-6879(89)80106-5   Zuker M (1989b). On finding all suboptimal foldings of an RNA molecule. Science 244: 48-52. http://dx.doi.org/10.1126/science.2468181 PMid:2468181   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   Zuker M and Stiegler P (1981). Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 9: 133-148. http://dx.doi.org/10.1093/nar/9.1.133 PMid:6163133 PMCid:326673

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

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

Altschul SF, Madden TL, Schaffer AA, Zhang J, et al. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402. http://dx.doi.org/10.1093/nar/25.17.3389 PMid:9254694 PMCid:146917   Barker G, Batley J, O' Sullivan H, Edwards KJ, et al. (2003). Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP. Bioinformatics 19: 421-422. http://dx.doi.org/10.1093/bioinformatics/btf881 PMid:12584131   Batley J, Barker G, O'Sullivan H, Edwards KJ, et al. (2003). Mining for single nucleotide polymorphisms and insertions/ deletions in maize expressed sequence tag data. Plant Physiol. 132: 84-91. http://dx.doi.org/10.1104/pp.102.019422 PMid:12746514 PMCid:166954   Clifford R, Edmonson M, Hu Y, Nguyen C, et al. (2000). Expression-based genetic/physical maps of single-nucleotide polymorphisms identified by the cancer genome anatomy project. Genome Res. 10: 1259-1265. http://dx.doi.org/10.1101/gr.10.8.1259 PMid:10958644 PMCid:310932   Deutsch S, Iseli C, Bucher P, Antonarakis SE, et al. (2001). A cSNP map and database for human chromosome 21. Genome Res. 11: 300-307. PMid:11157793 PMCid:311032   Frank E and Witten IH (2005). Data Mining: Practical machine learning tools and techniques. 2nd edn. Morgan Kaufmann, San Francisco.   Frank E, Hall M, Trigg L, Holmes G, et al. (2004). Data mining in bioinformatics using Weka. Bioinformatics 20: 2479-2481. http://dx.doi.org/10.1093/bioinformatics/bth261 PMid:15073010   Holliday R and Grigg GW (1993). DNA methylation and mutation. Mutat. Res. 285: 61-67. http://dx.doi.org/10.1016/0027-5107(93)90052-H   Huang X and Madan A (1999). CAP3: A DNA sequence assembly program. Genome Res. 9: 868-877. http://dx.doi.org/10.1101/gr.9.9.868 PMid:10508846 PMCid:310812   Huntley D, Baldo A, Johri S and Sergot M (2006). SEAN: SNP prediction and display program utilizing EST sequence clusters. Bioinformatics 22: 495-496. http://dx.doi.org/10.1093/bioinformatics/btk006 PMid:16357032   Irizarry K, Kustanovich V, Li C, Brown N, et al. (2000). Genome-wide analysis of single-nucleotide polymorphisms in human expressed sequences. Nat. Genet. 26: 233-236. http://dx.doi.org/10.1038/79981 PMid:11017085   Krogh A and Vedelsby J (1995). Advances in Neural Information Processing Systems 7. In: Neural Network Ensembles, Cross Validation, and Active Learning (Krogh A and Vedelsby J, eds.). MIT Press, Cambridge, 231-238.   Marth GT, Korf I, Yandell MD, Yeh RT, et al. (1999). A general approach to single-nucleotide polymorphism discovery. Nat. Genet. 23: 452-456. http://dx.doi.org/10.1038/70570 PMid:10581034   Mullikin JC, Hunt SE, Cole CG, Mortimore BJ, et al. (2000). An SNP map of human chromosome 22. Nature 407: 516-520. http://dx.doi.org/10.1038/35035089 PMid:11029003   Ning Z, Caccamo M and Mullikin JC (2005). ssahaSNP-A polymorphism detection tool by genomic alignment. Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05), Stanford, 251-254.   Picoult-Newberg L, Ideker TE, Pohl MG, Taylor SL, et al. (1999). Mining SNPs from EST databases. Genome Res. 9: 167-174. PMid:10022981 PMCid:310719   Savage D, Batley J, Erwin T, Logan E, et al. (2005). SNPServer: a real-time SNP discovery tool. Nucleic Acids Res. 33: W493-W495. http://dx.doi.org/10.1093/nar/gki462 PMid:15980519 PMCid:1160223   Sherry ST, Ward MH, Kholodov M, Baker J, et al. (2001). dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29: 308-311. http://dx.doi.org/10.1093/nar/29.1.308 PMid:11125122 PMCid:29783   Taillon-Miller P, Gu Z, Li Q, Hillier LD, et al. (1998). Overlapping genomic sequences: a treasure trove of single-nucleotide polymorphisms. Genome Res. 748: 754.   Zhang J, Wheeler DA, Yakub I, Wei S, et al. (2005). SNPdetector: a software tool for sensitive and accurate SNP detection. PLoS. Comput. Biol. 1: e53. http://dx.doi.org/10.1371/journal.pcbi.0010053 PMid:16261194 PMCid:1274293