Bioinformatics: Most-Read Full-Text Articles
http://bioinformatics.oxfordjournals.org/
Most-read rankings are recalculated at the beginning of the month based on usage of full-text and PDF views for the previous month.2009-11-15<![CDATA[Upcoming challenges for multiple sequence alignment methods in the high-throughput era]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/19/2455?rss=1&ssource=mfc
Oct 1, 2009; 25:2455-2465 SEQUENCE ANALYSIS]]>Carsten Kemena, Cedric Notredame2009-10-01Oxford University Press<![CDATA[The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/20/2730?rss=1&ssource=mfc
Oct 15, 2009; 25:2730-2731 GENOME ANALYSIS]]>John W. Nicol, Gregg A. Helt, Steven G. Blanchard Jr., Archana Raja, Ann E. Loraine2009-10-15Oxford 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. Higgins2007-11-01Oxford 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. Daly2005-01-15Oxford University Press<![CDATA[TopHat: discovering splice junctions with RNA-Seq]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/9/1105?rss=1&ssource=mfc
May 1, 2009; 25:1105-1111 SEQUENCE ANALYSIS]]>Cole Trapnell, Lior Pachter, Steven L. Salzberg2009-05-01Oxford University Press<![CDATA[Lost in translation: an assessment and perspective for computational microRNA target identification.]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/btp565v1?rss=1&ssource=mfc
Sep 29, 2009; 0:5651-565 ]]>Panagiotis Alexiou, Manolis Maragkakis, Giorgos L Papadopoulos, Martin Reczko, Artemis G Hatzigeorgiou2009-09-29Oxford University Press<![CDATA[TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/20/2625?rss=1&ssource=mfc
Oct 15, 2009; 25:2625-2631 GENOME ANALYSIS]]>Sanghamitra Bandyopadhyay, Ramkrishna Mitra2009-10-15Oxford University Press<![CDATA[Statistical methods for gene set co-expression analysis]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/21/2780?rss=1&ssource=mfc
Nov 1, 2009; 25:2780-2786 GENE EXPRESSION]]>YounJeong Choi, Christina Kendziorski2009-11-01Oxford University Press<![CDATA[A review of feature selection techniques in bioinformatics]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/23/19/2507?rss=1&ssource=mfc
Oct 1, 2007; 23:2507-2517 GENE EXPRESSION]]>Yvan Saeys, Inaki Inza, Pedro Larranaga2007-10-01Oxford University Press<![CDATA[Fast and accurate short read alignment with Burrows-Wheeler transform]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/14/1754?rss=1&ssource=mfc
Jul 15, 2009; 25:1754-1760 SEQUENCE ANALYSIS]]>Heng Li, Richard Durbin2009-07-15Oxford University Press<![CDATA[Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/21/18/3674?rss=1&ssource=mfc
Sep 15, 2005; 21:3674-3676 SEQUENCE ANALYSIS]]>Ana Conesa, Stefan Gotz, Juan Miguel Garcia-Gomez, Javier Terol, Manuel Talon, Montserrat Robles2005-09-15Oxford University Press<![CDATA[SOAP: short oligonucleotide alignment program]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/24/5/713?rss=1&ssource=mfc
Mar 1, 2008; 24:713-714 SEQUENCE ANALYSIS]]>Ruiqiang Li, Yingrui Li, Karsten Kristiansen, Jun Wang2008-03-01Oxford University Press<![CDATA[Efficiently finding genome-wide three-way gene interactions from transcript- and genotype-data]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/21/2735?rss=1&ssource=mfc
Nov 1, 2009; 25:2735-2743 GENOME ANALYSIS]]>Mitsunori Kayano, Ichigaku Takigawa, Motoki Shiga, Koji Tsuda, Hiroshi Mamitsuka2009-11-01Oxford University Press<![CDATA[TagDust--a program to eliminate artifacts from next generation sequencing data]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/21/2839?rss=1&ssource=mfc
Nov 1, 2009; 25:2839-2840 GENOME ANALYSIS]]>Timo Lassmann, Yoshihide Hayashizaki, Carsten O. Daub2009-11-01Oxford University Press<![CDATA[The Sequence Alignment/Map format and SAMtools]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/16/2078?rss=1&ssource=mfc
Aug 15, 2009; 25:2078-2079 SEQUENCE ANALYSIS]]>Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup2009-08-15Oxford University Press<![CDATA[An optimization model for metabolic pathways]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/20/2723?rss=1&ssource=mfc
Oct 15, 2009; 25:2723-2729 SYSTEMS BIOLOGY]]>F. J. Planes, J. E. Beasley2009-10-15Oxford University Press<![CDATA[False discovery rate, sensitivity and sample size for microarray studies]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/21/13/3017?rss=1&ssource=mfc
Jul 1, 2005; 21:3017-3024 GENE EXPRESSION]]>Yudi Pawitan, Stefan Michiels, Serge Koscielny, Arief Gusnanto, Alexander Ploner2005-07-01Oxford University Press<![CDATA[Network analyses in systems pharmacology]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/19/2466?rss=1&ssource=mfc
Oct 1, 2009; 25:2466-2472 SYSTEMS BIOLOGY]]>Seth I. Berger, Ravi Iyengar2009-10-01Oxford University Press<![CDATA[A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/21/2787?rss=1&ssource=mfc
Nov 1, 2009; 25:2787-2794 GENE EXPRESSION]]>Andreas Keller, Christina Backes, Andreas Gerasch, Michael Kaufmann, Oliver Kohlbacher, Eckart Meese, Hans-Peter Lenhof2009-11-01Oxford University Press<![CDATA[Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/btp579v1?rss=1&ssource=mfc
Oct 6, 2009; 0:5791-579 ]]>Jacob F. Degner, John C. Marioni, Athma A. Pai, Joseph K. Pickrell, Everlyne Nkadori, Yoav Gilad, Jonathan K. Pritchard2009-10-06Oxford University Press<![CDATA[Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/20/2677?rss=1&ssource=mfc
Oct 15, 2009; 25:2677-2684 GENE EXPRESSION]]>Kengo Kinoshita, Takeshi Obayashi2009-10-15Oxford University Press<![CDATA[The SNP ratio test: pathway analysis of genome-wide association datasets]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/20/2762?rss=1&ssource=mfc
Oct 15, 2009; 25:2762-2763 SYSTEMS BIOLOGY]]>Colm O''Dushlaine, Elaine Kenny, Elizabeth A. Heron, Ricardo Segurado, Michael Gill, Derek W. Morris, Aiden Corvin2009-10-15Oxford University Press<![CDATA[A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG)]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/21/2863?rss=1&ssource=mfc
Nov 1, 2009; 25:2863-2864 REPORT]]>Michael Brudno, Paul Medvedev, Jens Stoye, Francisco M. De La Vega2009-11-01Oxford University Press<![CDATA[Caleydo: connecting pathways and gene expression]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/20/2760?rss=1&ssource=mfc
Oct 15, 2009; 25:2760-2761 SYSTEMS BIOLOGY]]>Marc Streit, Alexander Lex, Michael Kalkusch, Kurt Zatloukal, Dieter Schmalstieg2009-10-15Oxford University Press<![CDATA[ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/19/2607?rss=1&ssource=mfc
Oct 1, 2009; 25:2607-2608 SEQUENCE ANALYSIS]]>Martin Morgan, Simon Anders, Michael Lawrence, Patrick Aboyoun, Herve Pages, Robert Gentleman2009-10-01Oxford University Press<![CDATA[Gene ranking and biomarker discovery under correlation]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/20/2700?rss=1&ssource=mfc
Oct 15, 2009; 25:2700-2707 GENE EXPRESSION]]>Verena Zuber, Korbinian Strimmer2009-10-15Oxford 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. Speed2003-01-2210.1093/bioinformatics/19.2.185Oxford University Press<![CDATA[Editorial]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/4/429?rss=1&ssource=mfc
Feb 15, 2009; 25:429-429 ]]>Alex Bateman, John Quackenbush2009-02-15Oxford University Press<![CDATA[VarScan: variant detection in massively parallel sequencing of individual and pooled samples]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/17/2283?rss=1&ssource=mfc
Sep 1, 2009; 25:2283-2285 SEQUENCE ANALYSIS]]>Daniel C. Koboldt, Ken Chen, Todd Wylie, David E. Larson, Michael D. McLellan, Elaine R. Mardis, George M. Weinstock, Richard K. Wilson, Li Ding2009-09-01Oxford University Press<![CDATA[Computational epigenetics]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/24/1/1?rss=1&ssource=mfc
Jan 1, 2008; 24:1-10 GENOME ANALYSIS]]>Christoph Bock, Thomas Lengauer2008-01-01Oxford University Press<![CDATA[Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/24/23/2776?rss=1&ssource=mfc
Dec 1, 2008; 24:2776-2777 SEQUENCE ANALYSIS]]>Brian D. Ondov, Anjana Varadarajan, Karla D. Passalacqua, Nicholas H. Bergman2008-12-01Oxford University Press<![CDATA[PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/19/2514?rss=1&ssource=mfc
Oct 1, 2009; 25:2514-2521 SEQUENCE ANALYSIS]]>Yangho Chen, Tade Souaiaia, Ting Chen2009-10-01Oxford University Press<![CDATA[A clustering approach for identification of enriched domains from histone modification ChIP-Seq data]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/15/1952?rss=1&ssource=mfc
Aug 1, 2009; 25:1952-1958 DATA AND TEXT MINING]]>Chongzhi Zang, Dustin E. Schones, Chen Zeng, Kairong Cui, Keji Zhao, Weiqun Peng2009-08-01Oxford University Press<![CDATA[HTqPCR: High-throughput analysis and visualization of quantitative real-time PCR data in R]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/btp578v1?rss=1&ssource=mfc
Oct 6, 2009; 0:5781-578 ]]>Heidi Dvinge, Paul Bertone2009-10-06Oxford University Press<![CDATA[SOAP2: an improved ultrafast tool for short read alignment]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/15/1966?rss=1&ssource=mfc
Aug 1, 2009; 25:1966-1967 SEQUENCE ANALYSIS]]>Ruiqiang Li, Chang Yu, Yingrui Li, Tak-Wah Lam, Siu-Ming Yiu, Karsten Kristiansen, Jun Wang2009-08-01Oxford University Press<![CDATA[Comparative study on ChIP-seq data: normalization and binding pattern characterization]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/18/2334?rss=1&ssource=mfc
Sep 15, 2009; 25:2334-2340 GENE EXPRESSION]]>Cenny Taslim, Jiejun Wu, Pearlly Yan, Greg Singer, Jeffrey Parvin, Tim Huang, Shili Lin, Kun Huang2009-09-15Oxford University Press<![CDATA[Eukaryotic transcription factor binding sites--modeling and integrative search methods]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/24/11/1325?rss=1&ssource=mfc
Jun 1, 2008; 24:1325-1331 GENE EXPRESSION]]>Sridhar Hannenhalli2008-06-01Oxford University Press<![CDATA[Statistical inferences for isoform expression in RNA-Seq]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/8/1026?rss=1&ssource=mfc
Apr 15, 2009; 25:1026-1032 GENE EXPRESSION]]>Hui Jiang, Wing Hung Wong2009-04-15Oxford University Press<![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 Crandall1998-10-0110.1093/bioinformatics/14.9.817Oxford University Press<![CDATA[The Sequence Alignment/Map format and SAMtools]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/btp352v1?rss=1&ssource=mfc
Aug 15, 2009; 25:2078-2079 SEQUENCE ANALYSIS]]>Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup2009-08-15Oxford University Press<![CDATA[Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/22/13/1658?rss=1&ssource=mfc
Jul 1, 2006; 22:1658-1659 SEQUENCE ANALYSIS]]>Weizhong Li, Adam Godzik2006-07-01Oxford University Press<![CDATA[CloudBurst: highly sensitive read mapping with MapReduce]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/11/1363?rss=1&ssource=mfc
Jun 1, 2009; 25:1363-1369 SEQUENCE ANALYSIS]]>Michael C. Schatz2009-06-01Oxford University Press<![CDATA[R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/19/2621?rss=1&ssource=mfc
Oct 1, 2009; 25:2621-2623 GENETICS AND POPULATION ANALYSIS]]>Matthew E. Ritchie, Benilton S. Carvalho, Kurt N. Hetrick, Simon Tavare, Rafael A. Irizarry2009-10-01Oxford University Press<![CDATA[Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/23/1/127?rss=1&ssource=mfc
Jan 1, 2007; 23:127-128 PHYLOGENETICS]]>Ivica Letunic, Peer Bork2007-01-01Oxford University Press<![CDATA[Predicting citation count of Bioinformatics papers within four years of publication]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/btp585v1?rss=1&ssource=mfc
Oct 9, 2009; 0:5851-585 ]]>Alfonso Ibanez, Pedro Larranaga, Concha Bielza2009-10-09Oxford University Press<![CDATA[Knowledge-guided inference of domain-domain interactions from incomplete protein-protein interaction networks]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/19/2492?rss=1&ssource=mfc
Oct 1, 2009; 25:2492-2499 GENOME ANALYSIS]]>Mei Liu, Xue-wen Chen, Raja Jothi2009-10-01Oxford University Press<![CDATA[lumi: a pipeline for processing Illumina microarray]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/24/13/1547?rss=1&ssource=mfc
Jul 1, 2008; 24:1547-1548 GENE EXPRESSION]]>Pan Du, Warren A. Kibbe, Simon M. Lin2008-07-01Oxford University Press<![CDATA[integrOmics: an R package to unravel relationships between two omics datasets]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/25/21/2855?rss=1&ssource=mfc
Nov 1, 2009; 25:2855-2856 SYSTEMS BIOLOGY]]>Kim-Anh Le Cao, Ignacio Gonzalez, Sebastien Dejean2009-11-01Oxford 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 Eddy1998-10-0110.1093/bioinformatics/14.9.755Oxford University Press<![CDATA[Protein solubility: sequence based prediction and experimental verification]]>
http://bioinformatics.oxfordjournals.org/cgi/content/short/23/19/2536?rss=1&ssource=mfc
Oct 1, 2007; 23:2536-2542 SEQUENCE ANALYSIS]]>Pawel Smialowski, Antonio J. Martin-Galiano, Aleksandra Mikolajka, Tobias Girschick, Tad A. Holak, Dmitrij Frishman2007-10-01Oxford University Press