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	1. 3566 Accesses	Correspondence Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics Barry R Zeeberg, Joseph Riss, David W Kane, Kimberly J Bussey, Edward Uchio, W Marston Linehan, J Carl Barrett, John N Weinstein BMC Bioinformatics 2004, 5:80 (23 June 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 7 comments
	2. 3521 Accesses	Research article A comparison of methods for differential expression analysis of RNA-seq data Charlotte Soneson, Mauro Delorenzi BMC Bioinformatics 2013, 14:91 (9 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
	3. 2280 Accesses	Methodology article Statistical analysis of real-time PCR data Joshua S Yuan, Ann Reed, Feng Chen, C Neal Stewart BMC Bioinformatics 2006, 7:85 (22 February 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	4. 2264 Accesses	Software An automated graphics tool for comparative genomics: the Coulson plot generator Helen I Field, Richard MR Coulson, Mark C Field BMC Bioinformatics 2013, 14:141 (27 April 2013) Abstract \| Provisional PDF \| PubMed
	5. 2093 Accesses	Software Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient Arlin Stoltzfus, Hilmar Lapp, Naim Matasci, Helena Deus, Brian Sidlauskas, Christian M Zmasek, Gaurav Vaidya, Enrico Pontelli, Karen Cranston, Rutger Vos, Campbell O Webb, Luke J Harmon, Megan Pirrung, Brian O'Meara, Matthew W Pennell, Siavash Mirarab, Michael S Rosenberg, James P Balhoff, Holly M Bik, Tracy A Heath, Peter E Midford, Joseph W Brown, Emily Jane McTavish, Jeet Sukumaran, Mark Westneat, Michael E Alfaro, Aaron Steele, Greg Jordan BMC Bioinformatics 2013, 14:158 (13 May 2013) Abstract \| Provisional PDF \| PubMed
	6. 1647 Accesses	Software RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome Bo Li, Colin N Dewey BMC Bioinformatics 2011, 12:323 (4 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary RSEM is a new user-friendly software tool for quantifying transcript abundance from RNA-seq data that does not rely on a reference genome and is particularly useful for quantification with de novo transcriptome assemblies
	7. 1571 Accesses	Methodology article CNV-TV: A robust method to discover copy number variation from short sequencing reads Junbo Duan, Ji-Gang Zhang, Hong-Wen Deng, Yu-Ping Wang BMC Bioinformatics 2013, 14:150 (2 May 2013) Abstract \| Provisional PDF \| PubMed
	8. 1460 Accesses	Research article Real-time interactive data mining for chemical imaging information: application to automated histopathology David Mayerich, Michael Walsh, Matthew Schulmerich, Rohit Bhargava BMC Bioinformatics 2013, 14:156 (8 May 2013) Abstract \| Full text \| PDF \| PubMed
	9. 1431 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
	10. 1305 Accesses	Research article Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments James H Bullard, Elizabeth Purdom, Kasper D Hansen, Sandrine Dudoit BMC Bioinformatics 2010, 11:94 (18 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	11. 1298 Accesses	Methodology article Analysis of multiple phenotypes in genome-wide genetic mapping studies Chen Suo, Timothea Toulopoulou, Elvira Bramon, Muriel Walshe, Marco Picchioni, Robin Murray, Jurg Ott BMC Bioinformatics 2013, 14:151 (2 May 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
	12. 1262 Accesses	Methodology article Copy number variation genotyping using family information Jen-hwa Chu, Angela Rogers, Iuliana Ionita-Laza, Katayoon Darvishi, Ryan E Mills, Charles Lee, Benjamin A Raby BMC Bioinformatics 2013, 14:157 (9 May 2013) Abstract \| Provisional PDF \| PubMed
	13. 1202 Accesses	Software Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction Jian Ye, George Coulouris, Irena Zaretskaya, Ioana Cutcutache, Steve Rozen, Thomas L Madden BMC Bioinformatics 2012, 13:134 (18 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	14. 1173 Accesses	Research article Compression-based distance (CBD): a simple, rapid, and accurate method for microbiota composition comparison Fang Yang, Nicholas Chia, Bryan A White, Lawrence B Schook BMC Bioinformatics 2013, 14:136 (23 April 2013) Abstract \| Full text \| PDF \| PubMed
	15. 1148 Accesses	Methodology article Iterative rank-order normalization of gene expression microarray data Eric A Welsh, Steven A Eschrich, Anders E Berglund, David A Fenstermacher BMC Bioinformatics 2013, 14:153 (7 May 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
	16. 1108 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
	17. 1096 Accesses	Methodology article How cyanobacteria pose new problems to old methods: challenges in microarray time series analysis Robert Lehmann, Rainer Machné, Jens Georg, Manuela Benary, Ilka Axmann, Ralf Steuer BMC Bioinformatics 2013, 14:133 (21 April 2013) Abstract \| Provisional PDF \| PubMed
	18. 1078 Accesses	Research article Disk-based k-mer counting on a PC Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Szymon Grabowski BMC Bioinformatics 2013, 14:160 (16 May 2013) Abstract \| Provisional PDF \| PubMed
	19. 1066 Accesses	Research article Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces Andrew J Bordner, Andrey A Gorin BMC Bioinformatics 2008, 9:234 (12 May 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	20. 1014 Accesses	Methodology article Ensemble-based prediction of RNA secondary structures Nima Aghaeepour, Holger H Hoos BMC Bioinformatics 2013, 14:139 (24 April 2013) Abstract \| Provisional PDF \| PubMed
	21. 1007 Accesses	Research article Steiner tree methods for optimal sub-network identification: an empirical study Afshin Sadeghi, Holger Fröhlich BMC Bioinformatics 2013, 14:144 (30 April 2013) Abstract \| Provisional PDF \| PubMed
	22. 987 Accesses	Research article Investigating the concordance of Gene Ontology terms reveals the intra- and inter-platform reproducibility of enrichment analysis Lifang Zhang, Juan Zhang, Gang Yang, Di Wu, Lina Jiang, Zhining Wen, Menglong Li BMC Bioinformatics 2013, 14:143 (29 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
	23. 986 Accesses	Methodology article Comparison study on statistical features of predicted secondary structures for protein structural class prediction: From content to position Qi Dai, Yan Li, Xiaoqing Liu, Yuhua Yao, Yunjie Cao, Pingan He BMC Bioinformatics 2013, 14:152 (4 May 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
	24. 969 Accesses	Software WGCNA: an R package for weighted correlation network analysis Peter Langfelder, Steve Horvath BMC Bioinformatics 2008, 9:559 (29 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology
	25. 966 Accesses	Methodology article Incorporating phylogenetic-based covarying mutations into RNAalifold for RNA consensus structure prediction Ping Ge, Shaojie Zhang BMC Bioinformatics 2013, 14:142 (27 April 2013) Abstract \| Provisional PDF \| PubMed