Publications

Found 2 results
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2012
J. Wang, Guo, M. - Z., and Xing, L. L., FastJoin, an improved neighbor-joining algorithm, vol. 11. pp. 1909-1922, 2012.
Elias I and Lagergren J (2005). Fast Neighbor Joining. In: Proceedings of the 32nd International Colloquium: 11-15 July 2005 (L Caires, GF Italiano, L Monteiro, C Palamidessi, et al., eds.). Springer Berlin Heidelberg, Lisbon, 1263-1274.   Elias I and Lagergren J (2009). Fast neighbor joining. Theor. Comput. 410: 1993-2000. http://dx.doi.org/10.1016/j.tcs.2008.12.040   Evans J, Sheneman L and Foster J (2006). Relaxed neighbor joining: a fast distance-based phylogenetic tree construction method. J. Mol. Evol. 62: 785-792. http://dx.doi.org/10.1007/s00239-005-0176-2 PMid:16752216   Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, et al. (2006). Pfam: clans, web tools and services. Nucleic Acids Res. 34: D247-D251. http://dx.doi.org/10.1093/nar/gkj149 PMid:16381856 PMCid:1347511   Howe K, Bateman A and Durbin R (2002). QuickTree: building huge neighbor-joining trees of protein sequences. Bioinformatics 18: 1546-1547. http://dx.doi.org/10.1093/bioinformatics/18.11.1546 PMid:12424131   Mailund T and Pedersen CNS (2004). QuickJoin - fast neighbor-joining tree reconstruction. Bioinformatics 20: 3261- 3262. http://dx.doi.org/10.1093/bioinformatics/bth359 PMid:15201185   Mailund T, Brodal GS, Fagerberg R, Pedersen CNS, et al. (2006). Recrafting the neighbor-joining method. BMC Bioinformatics 7: 29. http://dx.doi.org/10.1186/1471-2105-7-29 PMid:16423304 PMCid:3271233   Nakhleh L, Moret BME, Roshan U and John KS (2002). The Accuracy of Fast Phylogenetic Methods for Large Datasets. In: Proceedings of the Seventh Pacific Symposium on Biocomputing: 2001 (Altman RB, Dunker AK, Hunter L, Lauderdale K, et al., eds.). World Scientific, Singapore, 211-222. PMid:11928477   Price MN, Dehal PS and Arkin AP (2009). FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol. Biol. Evol. 26: 1641-1650. http://dx.doi.org/10.1093/molbev/msp077 PMid:19377059 PMCid:2693737   Price MN, Dehal PS and Arkin AP (2010). FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One 5: e9490. http://dx.doi.org/10.1371/journal.pone.0009490 PMid:20224823 PMCid:2835736   Saitou N and Nei M (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425. PMid:3447015   Sheneman L, Evans J and Foster JA (2006). Clearcut: a fast implementation of relaxed neighbor joining. Bioinformatics 22: 2823-2824. http://dx.doi.org/10.1093/bioinformatics/btl478 PMid:16982706   Simonsen M, Mailund T and Pedersen CNS (2008). Rapid Neighbor-Joining. In: Proceedings of the Eighth International Workshop on Algorithms in Bioinformatics: 15-19 September 2008 (Crandall KA and Lagergren J, eds.). Springer Berlin Heidelberg, Karlsruhe, 113-122. http://dx.doi.org/10.1007/978-3-540-87361-7_10   Simonsen M, Mailund T and Pedersen CNS (2011). Inference of Large Phylogenies Using Neighbor-Joining. In: Proceedings of the Third International Joint Conference: 20-23 January 2010 (Fred A, Filipe J and Gamboa H, eds.). Springer Berlin Heidelberg, Valencia, 334-344. PMCid:3224425   Studier JA and Keppler KJ (1988). A note on the neighbor-joining algorithm of Saitou and Nei. Mol. Biol. Evol. 5: 729- 731. PMid:3221794   Wheeler TJ (2009). Large-Scale Neighbor-Joining with NINJA. In: Proceedings of the Ninth International Workshop on Algorithms in Bioinformatics: 12-13 September 2009 (Salzberg SL and Warnow T, eds.). Springer Berlin Heidelberg, Philadelphia, 375-389.   Zaslavsky L and Tatusova T (2008). Accelerating the Neighbor-Joining Algorithm Using the Adaptive Bucket Data Structure. In: Proceedings of the Fourth International Symposium: 6-9 May 2008 (Mandoiu I, Sunderraman R and Zelikovsky A, eds.). Springer Berlin Heidelberg, Atlanta, 122-133.
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