Bioinformatics: Most-Cited Full-Text Articles http://bioinformatics.oxfordjournals.org/ Most-cited rankings are recalculated at the beginning of the month and are based on citations to articles on this journal site from articles in other HighWire-hosted journals. 2009-11-15 <![CDATA[MODELTEST: testing the model of DNA substitution]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/14/9/817?rss=1&ssource=mfc Oct 1, 1998; 14:817-818
ARTICLES]]> D Posada, KA Crandall 1998-10-01 10.1093/bioinformatics/14.9.817 Oxford University Press <![CDATA[Tree View: An application to display phylogenetic trees on personal computers]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/12/4/357?rss=1&ssource=mfc Aug 1, 1996; 12:357-358
]]> Roderic D.M. Page 1996-08-01 10.1093/bioinformatics/12.4.357 Oxford University Press <![CDATA[MEGA2: molecular evolutionary genetics analysis software]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/17/12/1244?rss=1&ssource=mfc Dec 1, 2001; 17:1244-1245
APPLICATIONS NOTES]]> Sudhir Kumar, Koichiro Tamura, Ingrid B. Jakobsen, Masatoshi Nei 2001-12-01 10.1093/bioinformatics/17.12.1244 Oxford University Press <![CDATA[MRBAYES: Bayesian inference of phylogenetic trees]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/17/8/754?rss=1&ssource=mfc Aug 1, 2001; 17:754-755
APPLICATIONS NOTES]]> John P. Huelsenbeck, Fredrik Ronquist 2001-08-01 10.1093/bioinformatics/17.8.754 Oxford University Press <![CDATA[MrBayes 3: Bayesian phylogenetic inference under mixed models]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/19/12/1572?rss=1&ssource=mfc Aug 12, 2003; 19:1572-1574
APPLICATIONS NOTES]]> Fredrik Ronquist, John P. Huelsenbeck 2003-08-12 10.1093/bioinformatics/btg180 Oxford University Press <![CDATA[PAML: a program package for phylogenetic analysis by maximum likelihood]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/13/5/555?rss=1&ssource=mfc Oct 1, 1997; 13:555-556
APPLICATIONS NOTES]]> Ziheng Yang 1997-10-01 10.1093/bioinformatics/13.5.555 Oxford University Press <![CDATA[Haploview: analysis and visualization of LD and haplotype maps]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/21/2/263?rss=1&ssource=mfc Jan 15, 2005; 21:263-265
GENETICS AND POPULATION ANALYSIS]]> J. C. Barrett, B. Fry, J. Maller, M. J. Daly 2005-01-15 Oxford University Press <![CDATA[DnaSP, DNA polymorphism analyses by the coalescent and other methods]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/19/18/2496?rss=1&ssource=mfc Dec 12, 2003; 19:2496-2497
APPLICATIONS NOTES]]> Julio Rozas, Juan C. Sanchez-DelBarrio, Xavier Messeguer, Ricardo Rozas 2003-12-12 10.1093/bioinformatics/btg359 Oxford University Press <![CDATA[A comparison of normalization methods for high density oligonucleotide array data based on variance and bias]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/19/2/185?rss=1&ssource=mfc Jan 22, 2003; 19:185-193
ORIGINAL PAPERS]]> B.M. Bolstad, R.A Irizarry, M. Astrand, T.P. Speed 2003-01-22 10.1093/bioinformatics/19.2.185 Oxford University Press <![CDATA[Profile hidden Markov models]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/14/9/755?rss=1&ssource=mfc Oct 1, 1998; 14:755-763
ARTICLES]]> SR Eddy 1998-10-01 10.1093/bioinformatics/14.9.755 Oxford University Press <![CDATA[DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/15/2/174?rss=1&ssource=mfc Feb 1, 1999; 15:174-175
ARTICLES]]> J Rozas, R Rozas 1999-02-01 10.1093/bioinformatics/15.2.174 Oxford University Press <![CDATA[The rapid generation of mutation data matrices from protein sequences]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/8/3/275?rss=1&ssource=mfc Jun 1, 1992; 8:275-282
ORIGINAL PAPERS]]> David T. Jones, William R. Taylor, Janet M. Thornton 1992-06-01 10.1093/bioinformatics/8.3.275 Oxford University Press <![CDATA[TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/10/5/569?rss=1&ssource=mfc Sep 1, 1994; 10:569-570
]]> Yves Van de Peer, Rupert De Wachter 1994-09-01 10.1093/bioinformatics/10.5.569 Oxford University Press <![CDATA[SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/12/6/543?rss=1&ssource=mfc Dec 1, 1996; 12:543-548
ORIGINAL PAPERS]]> N. Galtier, M. Gouy, C. Gautier 1996-12-01 10.1093/bioinformatics/12.6.543 Oxford University Press <![CDATA[SOSUI: classification and secondary structure prediction system for membrane proteins]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/14/4/378?rss=1&ssource=mfc May 1, 1998; 14:378-379
ARTICLES]]> T Hirokawa, S Boon-Chieng, S Mitaku 1998-05-01 10.1093/bioinformatics/14.4.378 Oxford University Press <![CDATA[The Jalview Java alignment editor]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/20/3/426?rss=1&ssource=mfc Feb 12, 2004; 20:426-427
APPLICATIONS NOTES]]> Michele Clamp, James Cuff, Stephen M. Searle, Geoffrey J. Barton 2004-02-12 Oxford University Press <![CDATA[CLUSTAL V: improved software for multiple sequence alignment]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/8/2/189?rss=1&ssource=mfc Apr 1, 1992; 8:189-191
ORIGINAL PAPERS]]> Desmond G. Higgins, Alan J. Bleasby, Rainer Fuchs 1992-04-01 10.1093/bioinformatics/8.2.189 Oxford University Press <![CDATA[ESPript: analysis of multiple sequence alignments in PostScript]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/15/4/305?rss=1&ssource=mfc Apr 1, 1999; 15:305-308
ARTICLES]]> P Gouet, E Courcelle, DI Stuart, F Metoz 1999-04-01 10.1093/bioinformatics/15.4.305 Oxford University Press <![CDATA[Clustal W and Clustal X version 2.0]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/23/21/2947?rss=1&ssource=mfc Nov 1, 2007; 23:2947-2948
SEQUENCE ANALYSIS]]> M.A. Larkin, G. Blackshields, N.P. Brown, R. Chenna, P.A. McGettigan, H. McWilliam, F. Valentin, I.M. Wallace, A. Wilm, R. Lopez, J.D. Thompson, T.J. Gibson, D.G. Higgins 2007-11-01 Oxford University Press <![CDATA[TopPred II: an improved software for membrane protein structure predictions]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/10/6/685?rss=1&ssource=mfc Dec 1, 1994; 10:685-686
APPLICATIONS NOTES]]> Manuel G. Claros, Gunnar von Heijne 1994-12-01 10.1093/bioinformatics/10.6.685 Oxford University Press <![CDATA[Artemis: sequence visualization and annotation]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/16/10/944?rss=1&ssource=mfc Oct 1, 2000; 16:944-945
APPLICATIONS NOTES]]> Kim Rutherford, Julian Parkhill, James Crook, Terry Horsnell, Peter Rice, Marie-Adele Rajandream, Bart Barrell 2000-10-01 10.1093/bioinformatics/16.10.944 Oxford University Press <![CDATA[JPred: a consensus secondary structure prediction server]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/14/10/892?rss=1&ssource=mfc Nov 1, 1998; 14:892-893
ARTICLES]]> JA Cuff, ME Clamp, AS Siddiqui, M Finlay, GJ Barton 1998-11-01 10.1093/bioinformatics/14.10.892 Oxford University Press <![CDATA[The HMMTOP transmembrane topology prediction server]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/17/9/849?rss=1&ssource=mfc Sep 1, 2001; 17:849-850
APPLICATIONS NOTES]]> Gabor E. Tusnady, Istvan Simon 2001-09-01 10.1093/bioinformatics/17.9.849 Oxford University Press <![CDATA[Fast and sensitive multiple sequence alignments on a microcomputer]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/5/2/151?rss=1&ssource=mfc Apr 1, 1989; 5:151-153
COMMUNICATIONS]]> Desmond G. Higgins, Paul M. Sharp 1989-04-01 10.1093/bioinformatics/5.2.151 Oxford University Press <![CDATA[Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/13/3/235?rss=1&ssource=mfc Jun 1, 1997; 13:235-238
ORIGINAL PAPERS]]> Andrew Rambaut, Nicholas C. Grass 1997-06-01 10.1093/bioinformatics/13.3.235 Oxford University Press <![CDATA[Identifying DNA and protein patterns with statistically significant alignments of multiple sequences]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/15/7/563?rss=1&ssource=mfc Jul 1, 1999; 15:563-577
ARTICLES]]> GZ Hertz, GD Stormo 1999-07-01 10.1093/bioinformatics/15.7.563 Oxford University Press <![CDATA[MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/10/2/189?rss=1&ssource=mfc Apr 2, 1994; 10:189-191
ORIGINAL PAPERS]]> Sudhir Kumar, Koichiro Tamura, Masatoshi Nei 1994-04-02 10.1093/bioinformatics/10.2.189 Oxford University Press <![CDATA[FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/20/4/578?rss=1&ssource=mfc Mar 1, 2004; 20:578-580
APPLICATIONS NOTES]]> Fatima Al-Shahrour, Ramon Diaz-Uriarte, Joaquin Dopazo 2004-03-01 Oxford University Press <![CDATA[fastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/10/1/41?rss=1&ssource=mfc Feb 1, 1994; 10:41-48
ORIGINAL PAPERS]]> Gary J. Olsen, Hideo Matsuda, Ray Hagstrom, Ross Overbeek 1994-02-01 10.1093/bioinformatics/10.1.41 Oxford University Press <![CDATA[SplitsTree: analyzing and visualizing evolutionary data]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/14/1/68?rss=1&ssource=mfc Feb 1, 1998; 14:68-73
ARTICLES]]> DH Huson 1998-02-01 10.1093/bioinformatics/14.1.68 Oxford University Press <![CDATA[Identifying differentially expressed genes using false discovery rate controlling procedures]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/19/3/368?rss=1&ssource=mfc Feb 12, 2003; 19:368-375
ORIGINAL PAPERS]]> Anat Reiner, Daniel Yekutieli, Yoav Benjamini 2003-02-12 10.1093/bioinformatics/btf877 Oxford University Press <![CDATA[A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/17/6/509?rss=1&ssource=mfc Jun 1, 2001; 17:509-519
ORIGINAL PAPERS]]> Pierre Baldi, Anthony D. Long 2001-06-01 10.1093/bioinformatics/17.6.509 Oxford University Press <![CDATA[VISTA : visualizing global DNA sequence alignments of arbitrary length]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/16/11/1046?rss=1&ssource=mfc Nov 1, 2000; 16:1046-1047
APPLICATIONS NOTES]]> Chris Mayor, Michael Brudno, Jody R. Schwartz, Alexander Poliakov, Edward M. Rubin, Kelly A. Frazer, Lior S. Pachter, Inna Dubchak 2000-11-01 10.1093/bioinformatics/16.11.1046 Oxford University Press <![CDATA[affy--analysis of Affymetrix GeneChip data at the probe level]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/20/3/307?rss=1&ssource=mfc Feb 12, 2004; 20:307-315
ORIGINAL PAPERS]]> Laurent Gautier, Leslie Cope, Benjamin M. Bolstad, Rafael A. Irizarry 2004-02-12 10.1093/bioinformatics/btg405 Oxford University Press <![CDATA[The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/19/4/524?rss=1&ssource=mfc Mar 1, 2003; 19:524-531
ORIGINAL PAPERS]]> M. Hucka, A. Finney, H. M. Sauro, H. Bolouri, J. C. Doyle, H. Kitano, and the rest of the SBML Forum:, A. P. Arkin, B. J. Bornstein, D. Bray, A. Cornish-Bowden, A. A. Cuellar, S. Dronov, E. D. Gilles, M. Ginkel, V. Gor, I. I. Goryanin, W. J. Hedley, T. C. Hodgman, J.-H. Hofmeyr, P. J. Hunter, N. S. Juty, J. L. Kasberger, A. Kremling, U. Kummer, N. Le Novere, L. M. Loew, D. Lucio, P. Mendes, E. Minch, E. D. Mjolsness, Y. Nakayama, M. R. Nelson, P. F. Nielsen, T. Sakurada, J. C. Schaff, B. E. Shapiro, T. S. Shimizu, H. D. Spence, J. Stelling, K. Takahashi, M. Tomita, J. Wagner, J. Wang 2003-03-01 10.1093/bioinformatics/btg015 Oxford University Press <![CDATA[MatInspector and beyond: promoter analysis based on transcription factor binding sites]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/21/13/2933?rss=1&ssource=mfc Jul 1, 2005; 21:2933-2942
SEQUENCE ANALYSIS]]> K. Cartharius, K. Frech, K. Grote, B. Klocke, M. Haltmeier, A. Klingenhoff, M. Frisch, M. Bayerlein, T. Werner 2005-07-01 Oxford University Press <![CDATA[DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/15/3/211?rss=1&ssource=mfc Mar 1, 1999; 15:211-218
ARTICLES]]> B Morgenstern 1999-03-01 10.1093/bioinformatics/15.3.211 Oxford University Press <![CDATA[Hidden Markov models for detecting remote protein homologies]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/14/10/846?rss=1&ssource=mfc Nov 1, 1998; 14:846-856
ARTICLES]]> K Karplus, C Barrett, R Hughey 1998-11-01 10.1093/bioinformatics/14.10.846 Oxford University Press <![CDATA[Variance stabilization applied to microarray data calibration and to the quantification of differential expression]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/18/suppl_1/S96?rss=1&ssource=mfc Jul 1, 2002; 18:96-104
ORIGINAL PAPERS]]> Wolfgang Huber, Anja von Heydebreck, Holger Sultmann, Annemarie Poustka, Martin Vingron 2002-07-01 10.1093/bioinformatics/18.suppl_1.S96 Oxford University Press <![CDATA[Combining evidence using p-values: application to sequence homology searches]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/14/1/48?rss=1&ssource=mfc Feb 1, 1998; 14:48-54
ARTICLES]]> TL Bailey, M Gribskov 1998-02-01 10.1093/bioinformatics/14.1.48 Oxford University Press <![CDATA[R/qtl: QTL mapping in experimental crosses]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/19/7/889?rss=1&ssource=mfc May 1, 2003; 19:889-890
APPLICATIONS NOTES]]> Karl W. Broman, Hao Wu, Saunak Sen, Gary A. Churchill 2003-05-01 10.1093/bioinformatics/btg112 Oxford University Press <![CDATA[Genetic Power Calculator: design of linkage and association genetic mapping studies of complex traits]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/19/1/149?rss=1&ssource=mfc Jan 1, 2003; 19:149-150
APPLICATIONS NOTES]]> S. Purcell, S. S. Cherny, P. C. Sham 2003-01-01 10.1093/bioinformatics/19.1.149 Oxford University Press <![CDATA[GOstat: find statistically overrepresented Gene Ontologies within a group of genes]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/20/9/1464?rss=1&ssource=mfc Jun 12, 2004; 20:1464-1465
APPLICATIONS NOTES]]> Tim Beissbarth, Terence P. Speed 2004-06-12 Oxford University Press <![CDATA[InterProScan - an integration platform for the signature-recognition methods in InterPro]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/17/9/847?rss=1&ssource=mfc Sep 1, 2001; 17:847-848
APPLICATIONS NOTES]]> Evgeni M. Zdobnov, Rolf Apweiler 2001-09-01 10.1093/bioinformatics/17.9.847 Oxford University Press <![CDATA[Missing value estimation methods for DNA microarrays]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/17/6/520?rss=1&ssource=mfc Jun 1, 2001; 17:520-525
ORIGINAL PAPERS]]> Olga Troyanskaya, Michael Cantor, Gavin Sherlock, Pat Brown, Trevor Hastie, Robert Tibshirani, David Botstein, Russ B. Altman 2001-06-01 10.1093/bioinformatics/17.6.520 Oxford University Press <![CDATA[CONSEL: for assessing the confidence of phylogenetic tree selection]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/17/12/1246?rss=1&ssource=mfc Dec 1, 2001; 17:1246-1247
APPLICATIONS NOTES]]> Hidetoshi Shimodaira, Masami Hasegawa 2001-12-01 10.1093/bioinformatics/17.12.1246 Oxford University Press <![CDATA[RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/22/21/2688?rss=1&ssource=mfc Nov 1, 2006; 22:2688-2690
PHYLOGENETICS]]> Alexandros Stamatakis 2006-11-01 Oxford University Press <![CDATA[PHD-an automatic mail server for protein secondary structure prediction]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/10/1/53?rss=1&ssource=mfc Feb 1, 1994; 10:53-60
ORIGINAL PAPERS]]> Burkhard Rost, Chris Sander, Reinhard Schneider 1994-02-01 10.1093/bioinformatics/10.1.53 Oxford University Press <![CDATA[Optimal alignments in linear space]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/4/1/11?rss=1&ssource=mfc Mar 1, 1988; 4:11-17
ORIGINAL PAPERS]]> Eugene W. Myers, Webb Miller 1988-03-01 10.1093/bioinformatics/4.1.11 Oxford University Press <![CDATA[r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock]]> http://bioinformatics.oxfordjournals.org/cgi/content/short/19/2/301?rss=1&ssource=mfc Jan 22, 2003; 19:301-302
APPLICATIONS NOTES]]> Michael J. Sanderson 2003-01-22 10.1093/bioinformatics/19.2.301 Oxford University Press