Publications
Found 2 results
Filters: Author is M.-Z. Guo [Clear All Filters]
“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.
“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