Publications
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“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