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	51. 5155 Accesses	Proceedings Fold change and p-value cutoffs significantly alter microarray interpretations Mark R Dalman, Anthony Deeter, Gayathri Nimishakavi, Zhong-Hui Duan BMC Bioinformatics 2012, 13(Suppl 2):S11 (13 March 2012) Abstract \| Full text \| PDF \| PubMed
	52. 5135 Accesses	Methodology article Improving accuracy for cancer classification with a new algorithm for genes selection Hongyan Zhang, Haiyan Wang, Zhijun Dai, Ming-shun Chen, Zheming Yuan BMC Bioinformatics 2012, 13:298 (13 November 2012) Abstract \| Full text \| PDF \| PubMed
	53. 4995 Accesses	Methodology article Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory Mark J Chaisson, Glenn Tesler BMC Bioinformatics 2012, 13:238 (19 September 2012) Abstract \| Full text \| PDF \| PubMed
	54. 4979 Accesses	Research article The COG database: an updated version includes eukaryotes Roman L Tatusov, Natalie D Fedorova, John D Jackson, Aviva R Jacobs, Boris Kiryutin, Eugene V Koonin, Dmitri M Krylov, Raja Mazumder, Sergei L Mekhedov, Anastasia N Nikolskaya, B Sridhar Rao, Sergei Smirnov, Alexander V Sverdlov, Sona Vasudevan, Yuri I Wolf, Jodie J Yin, Darren A Natale BMC Bioinformatics 2003, 4:41 (11 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology
	55. 4967 Accesses	Software High-throughput sequence alignment using Graphics Processing Units Michael C Schatz, Cole Trapnell, Arthur L Delcher, Amitabh Varshney BMC Bioinformatics 2007, 8:474 (10 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	56. 4884 Accesses	Methodology article A new measure for functional similarity of gene products based on Gene Ontology Andreas Schlicker, Francisco S Domingues, Jörg Rahnenführer, Thomas Lengauer BMC Bioinformatics 2006, 7:302 (15 June 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	57. 4871 Accesses	Methodology article Conditional variable importance for random forests Carolin Strobl, Anne-Laure Boulesteix, Thomas Kneib, Thomas Augustin, Achim Zeileis BMC Bioinformatics 2008, 9:307 (11 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	58. 4816 Accesses	Proceedings A survey of DNA motif finding algorithms Modan K Das, Ho-Kwok Dai BMC Bioinformatics 2007, 8(Suppl 7):S21 (1 November 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	59. 4766 Accesses	Methodology article Detecting outliers when fitting data with nonlinear regression – a new method based on robust nonlinear regression and the false discovery rate Harvey J Motulsky, Ronald E Brown BMC Bioinformatics 2006, 7:123 (9 March 2006) Abstract \| Full text \| PDF \| PubMed \| 1 comment
	60. 4734 Accesses	Software Efficient analysis and extraction of MS/MS result data from Mascot™ result files Florian Grosse-Coosmann, Andreas M Boehm, Albert Sickmann BMC Bioinformatics 2005, 6:290 (7 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	61. 4715 Accesses	Research article Protein-protein binding site identification by enumerating the configurations Fei Guo, Shuai Li, Lusheng Wang, Daming Zhu BMC Bioinformatics 2012, 13:158 (6 July 2012) Abstract \| Full text \| PDF \| PubMed
	62. 4636 Accesses	Software A flexible R package for nonnegative matrix factorization Renaud Gaujoux, Cathal Seoighe BMC Bioinformatics 2010, 11:367 (2 July 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	63. 4553 Accesses	Research article DNA methylation arrays as surrogate measures of cell mixture distribution Eugene Houseman, William P Accomando, Devin C Koestler, Brock C Christensen, Carmen J Marsit, Heather H Nelson, John K Wiencke, Karl T Kelsey BMC Bioinformatics 2012, 13:86 (8 May 2012) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology
	64. 4526 Accesses	Proceedings ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context Adam A Margolin, Ilya Nemenman, Katia Basso, Chris Wiggins, Gustavo Stolovitzky, Riccardo Favera, Andrea Califano BMC Bioinformatics 2006, 7(Suppl 1):S7 (20 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology
	65. 4516 Accesses	Methodology article Bias in random forest variable importance measures: Illustrations, sources and a solution Carolin Strobl, Anne-Laure Boulesteix, Achim Zeileis, Torsten Hothorn BMC Bioinformatics 2007, 8:25 (25 January 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Random forest algorithms classify biological data, and can be biased when variables of different types are used such as sequence data and folding energy, but if the weighting of the importance of the variables is calculated differently this bias is corrected.
	66. 4467 Accesses	Software CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing Samuel V Angiuoli, Malcolm Matalka, Aaron Gussman, Kevin Galens, Mahesh Vangala, David R Riley, Cesar Arze, James R White, Owen White, W Florian Fricke BMC Bioinformatics 2011, 12:356 (30 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary Cloud Virtual Resource (CloVR) is a new desktop application for large-scale sequence analysis using remote computing resources that provides several automated pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis.
	67. 4453 Accesses	Methodology article Integrating gene expression and protein-protein interaction network to prioritize cancer-associated genes Chao Wu, Jun Zhu, Xuegong Zhang BMC Bioinformatics 2012, 13:182 (28 July 2012) Abstract \| Full text \| PDF \| PubMed
	68. 4450 Accesses	Database BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions Jan Schellenberger, Junyoung O Park, Tom M Conrad, Bernhard Ø Palsson BMC Bioinformatics 2010, 11:213 (29 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	69. 4395 Accesses	Correspondence The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics Paula de Matos, Jennifer A Cham, Hong Cao, Rafael Alcántara, Francis Rowland, Rodrigo Lopez, Christoph Steinbeck BMC Bioinformatics 2013, 14:103 (20 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed \| Editor’s summary The first ‘how to’ guide for applying User-Centred Design (UCD) to websites for bioinformatics involves biomedical researchers rather than developers to design better web experiences, for example The Enzyme Portal
	70. 4387 Accesses	Software The Gaggle: An open-source software system for integrating bioinformatics software and data sources Paul T Shannon, David J Reiss, Richard Bonneau, Nitin S Baliga BMC Bioinformatics 2006, 7:176 (28 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	71. 4370 Accesses	Methodology article BSMAP: whole genome bisulfite sequence MAPping program Yuanxin Xi, Wei Li BMC Bioinformatics 2009, 10:232 (27 July 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment
	72. 4362 Accesses	Research article Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms Berat Z Haznedaroglu, Darryl Reeves, Hamid Rismani-Yazdi, Jordan Peccia BMC Bioinformatics 2012, 13:170 (18 July 2012) Abstract \| Full text \| PDF \| PubMed
	73. 4356 Accesses	Software CellProfiler Analyst: data exploration and analysis software for complex image-based screens Thouis R Jones, In Kang, Douglas B Wheeler, Robert A Lindquist, Adam Papallo, David M Sabatini, Polina Golland, Anne E Carpenter BMC Bioinformatics 2008, 9:482 (15 November 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	74. 4342 Accesses	Methodology article A statistical approach to selecting and confirming validation targets in -omics experiments Jeffrey T Leek, Margaret A Taub, Jason L Rasgon BMC Bioinformatics 2012, 13:150 (27 June 2012) Abstract \| Full text \| PDF \| PubMed
	75. 4313 Accesses	Research article Prediction of antigenic epitopes on protein surfaces by consensus scoring Shide Liang, Dandan Zheng, Chi Zhang, Martin Zacharias BMC Bioinformatics 2009, 10:302 (22 September 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	76. 4302 Accesses	Methodology article A comparison of common programming languages used in bioinformatics Mathieu Fourment, Michael R Gillings BMC Bioinformatics 2008, 9:82 (5 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 2 comments
	77. 4282 Accesses	Methodology article Efficient counting of k -mers in DNA sequences using a bloom filter Páll Melsted, Jonathan K Pritchard BMC Bioinformatics 2011, 12:333 (10 August 2011) Abstract \| Full text \| PDF \| PubMed
	78. 4250 Accesses	Software Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython Eric Talevich, Brandon M Invergo, Peter JA Cock, Brad A Chapman BMC Bioinformatics 2012, 13:209 (21 August 2012) Abstract \| Full text \| PDF \| PubMed
	79. 4238 Accesses	Research article PubMed related articles: a probabilistic topic-based model for content similarity Jimmy Lin, W John Wilbur BMC Bioinformatics 2007, 8:423 (30 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	80. 4173 Accesses	Research Ortholog-based protein-protein interaction prediction and its application to inter-species interactions Sheng-An Lee, Cheng-hsiung Chan, Chi-Hung Tsai, Jin-Mei Lai, Feng-Sheng Wang, Cheng-Yan Kao, Chi-Ying F Huang BMC Bioinformatics 2008, 9(Suppl 12):S11 (12 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	81. 4143 Accesses	Software Prodigal: prokaryotic gene recognition and translation initiation site identification Doug Hyatt, Gwo-Liang Chen, Philip F LoCascio, Miriam L Land, Frank W Larimer, Loren J Hauser BMC Bioinformatics 2010, 11:119 (8 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	82. 4127 Accesses	Research article Comparison of co-expression measures: mutual information, correlation, and model based indices Lin Song, Peter Langfelder, Steve Horvath BMC Bioinformatics 2012, 13:328 (9 December 2012) Abstract \| Full text \| PDF \| PubMed
	83. 4125 Accesses	Software EXPANDER – an integrative program suite for microarray data analysis Ron Shamir, Adi Maron-Katz, Amos Tanay, Chaim Linhart, Israel Steinfeld, Roded Sharan, Yosef Shiloh, Ran Elkon BMC Bioinformatics 2005, 6:232 (21 September 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary EXPANDER 2.0 is an integrated gene expression analysis package which implements various data analysis algorithms including normalization and filtering, clustering and biclustering, and the analysis of functional enrichment and promoters.
	84. 4119 Accesses	Methodology article Information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments Tianqing Liu, Nan Lin, Ningzhong Shi, Baoxue Zhang BMC Bioinformatics 2009, 10:146 (15 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	85. 4114 Accesses	Research Prediction of novel miRNAs and associated target genes in Glycine max Trupti Joshi, Zhe Yan, Marc Libault, Dong-Hoon Jeong, Sunhee Park, Pamela J Green, D Janine Sherrier, Andrew Farmer, Greg May, Blake C Meyers, Dong Xu, Gary Stacey BMC Bioinformatics 2010, 11(Suppl 1):S14 (18 January 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	86. 4105 Accesses	Methodology article HMM Logos for visualization of protein families Benjamin Schuster-Böckler, Jörg Schultz, Sven Rahmann BMC Bioinformatics 2004, 5:7 (21 January 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new method of visualizing profile Hidden Markov Models as a sequence logo, applied here to the GTPases Ras and Rab by way of example, makes it easy to compare protein families visually.
	87. 4100 Accesses	Methodology article Differential expression analysis for paired RNA-seq data Lisa M Chung, John P Ferguson, Wei Zheng, Feng Qian, Vincent Bruno, Ruth R Montgomery, Hongyu Zhao BMC Bioinformatics 2013, 14:110 (27 March 2013) Abstract \| Provisional PDF \| PubMed
	88. 4073 Accesses	Software ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data Lihua J Zhu, Claude Gazin, Nathan D Lawson, Hervé Pagès, Simon M Lin, David S Lapointe, Michael R Green BMC Bioinformatics 2010, 11:237 (11 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	89. 3966 Accesses	Methodology article Copy Number Variation detection from 1000 Genomes project exon capture sequencing data Jiantao Wu, Krzysztof R Grzeda, Chip Stewart, Fabian Grubert, Alexander E Urban, Michael P Snyder, Gabor T Marth BMC Bioinformatics 2012, 13:305 (17 November 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	90. 3959 Accesses	Research article Identification and correction of systematic error in high-throughput sequence data Frazer Meacham, Dario Boffelli, Joseph Dhahbi, David IK Martin, Meromit Singer, Lior Pachter BMC Bioinformatics 2011, 12:451 (21 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	91. 3950 Accesses	Software GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists Eran Eden, Roy Navon, Israel Steinfeld, Doron Lipson, Zohar Yakhini BMC Bioinformatics 2009, 10:48 (3 February 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	92. 3927 Accesses	Proceedings Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens Ying Wang, Noushin Ghaffari, Charles D Johnson, Ulisses M Braga-Neto, Hui Wang, Rui Chen, Huaijun Zhou BMC Bioinformatics 2011, 12(Suppl 10):S5 (18 October 2011) Abstract \| Full text \| PDF \| PubMed
	93. 3927 Accesses	Software Genes2FANs: connecting genes through functional association networks Ruth Dannenfelser, Neil R Clark, Avi Ma'ayan BMC Bioinformatics 2012, 13:156 (2 July 2012) Abstract \| Full text \| PDF \| PubMed
	94. 3923 Accesses	Methodology article SNP-based pathway enrichment analysis for genome-wide association studies Lingjie Weng, Fabio Macciardi, Aravind Subramanian, Guia Guffanti, Steven G Potkin, Zhaoxia Yu, Xiaohui Xie BMC Bioinformatics 2011, 12:99 (15 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	95. 3900 Accesses	Methodology article Estimation of sequencing error rates in short reads Xin Victoria Wang, Natalie Blades, Jie Ding, Razvan Sultana, Giovanni Parmigiani BMC Bioinformatics 2012, 13:185 (30 July 2012) Abstract \| Full text \| PDF \| PubMed
	96. 3891 Accesses	Research article Extracting semantically enriched events from biomedical literature Makoto Miwa, Paul Thompson, John McNaught, Douglas B Kell, Sophia Ananiadou BMC Bioinformatics 2012, 13:108 (23 May 2012) Abstract \| Full text \| PDF \| PubMed
	97. 3875 Accesses	Research article MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity Dinesh K Barupal, Pradeep K Haldiya, Gert Wohlgemuth, Tobias Kind, Shanker L Kothari, Kent E Pinkerton, Oliver Fiehn BMC Bioinformatics 2012, 13:99 (16 May 2012) Abstract \| Full text \| PDF \| PubMed
	98. 3871 Accesses	Research article Pre-processing Agilent microarray data Marianna Zahurak, Giovanni Parmigiani, Wayne Yu, Robert B Scharpf, David Berman, Edward Schaeffer, Shabana Shabbeer, Leslie Cope BMC Bioinformatics 2007, 8:142 (1 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	99. 3871 Accesses	Proceedings An evaluation of human protein-protein interaction data in the public domain Suresh Mathivanan, Balamurugan Periaswamy, TKB Gandhi, Kumaran Kandasamy, Shubha Suresh, Riaz Mohmood, YL Ramachandra, Akhilesh Pandey BMC Bioinformatics 2006, 7(Suppl 5):S19 (18 December 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	100. 3846 Accesses	Research CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment Svetlin A Manavski, Giorgio Valle BMC Bioinformatics 2008, 9(Suppl 2):S10 (26 March 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central