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	1. 27396 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
	2. 21626 Accesses	Software Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community Konstantinos Krampis, Tim Booth, Brad Chapman, Bela Tiwari, Mesude Bicak, Dawn Field, Karen E Nelson BMC Bioinformatics 2012, 13:42 (19 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Cloud BioLinux includes over 135 pre-configured bioinformatics tools for sequence alignment, clustering, assembly, display and phylogeny, aimed at reducing costs to researchers of maintaining and configuring hardware, and encouraging sharing of codebase.
	3. 17176 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
	4. 13537 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
	5. 12176 Accesses	Software VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R Hanbo Chen, Paul C Boutros BMC Bioinformatics 2011, 12:35 (26 January 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	6. 11810 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
	7. 9314 Accesses	Software GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction Yao Yu, Kang Tu, Siyuan Zheng, Yun Li, Guohui Ding, Jie Ping, Pei Hao, Yixue Li BMC Bioinformatics 2009, 10:264 (25 August 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	8. 9203 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
	9. 8311 Accesses	Software BioWord: A sequence manipulation suite for Microsoft Word Laura J Anzaldi, Daniel Muñoz-Fernández, Ivan Erill BMC Bioinformatics 2012, 13:124 (7 June 2012) Abstract \| Full text \| PDF \| PubMed
	10. 8182 Accesses	Proceedings An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics Ronald C Taylor BMC Bioinformatics 2010, 11(Suppl 12):S1 (21 December 2010) Abstract \| Full text \| PDF \| PubMed
	11. 8037 Accesses	Research article The development and validation of the Virtual Tissue Matrix, a software application that facilitates the review of tissue microarrays on line Catherine M Conway, Deirdre O'Shea, Sallyann O'Brien, Darragh K Lawler, Graham D Dodrill, Anthony O'Grady, Helen Barrett, Christian Gulmann, Lorraine O'Driscoll, William M Gallagher, Elaine W Kay, Daniel G O'Shea BMC Bioinformatics 2006, 7:256 (17 May 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	12. 7923 Accesses	Research article Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer Pierre Peterlongo, Rayan Chikhi BMC Bioinformatics 2012, 13:48 (23 March 2012) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary Mapsembler, a sequence assembly tool for desktop computers, uses NGS reads from newly sequenced, non-assembled genomes or transcriptomes to provide targeted assemblies and has retrieved known gene fusions in human cancer and discovered new ones
	13. 7716 Accesses	Software An integrative variant analysis suite for whole exome next-generation sequencing data Danny Challis, Jin Yu, Uday S Evani, Andrew R Jackson, Sameer Paithankar, Cristian Coarfa, Aleksandar Milosavljevic, Richard A Gibbs, Fuli Yu BMC Bioinformatics 2012, 13:8 (12 January 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Atlas2 is an analysis suite for variant calling in whole exome sequencing that combines regression models and user-adjustable cutoffs in order to separate true SNPs and INDELs from sequencing and mapping errors, with high sensitivity
	14. 7700 Accesses	Methodology article Statistical significance of quantitative PCR Yann Karlen, Alan McNair, Sébastien Perseguers, Christian Mazza, Nicolas Mermod BMC Bioinformatics 2007, 8:131 (20 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	15. 7679 Accesses	Proceedings Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study Qiong-Yi Zhao, Yi Wang, Yi-Meng Kong, Da Luo, Xuan Li, Pei Hao BMC Bioinformatics 2011, 12(Suppl 14):S2 (14 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	16. 7036 Accesses	Software The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes F Meyer, D Paarmann, M D'Souza, R Olson, EM Glass, M Kubal, T Paczian, A Rodriguez, R Stevens, A Wilke, J Wilkening, RA Edwards BMC Bioinformatics 2008, 9:386 (19 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology
	17. 6939 Accesses	Software BioWarehouse: a bioinformatics database warehouse toolkit Thomas J Lee, Yannick Pouliot, Valerie Wagner, Priyanka Gupta, David WJ Stringer-Calvert, Jessica D Tenenbaum, Peter D Karp BMC Bioinformatics 2006, 7:170 (23 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	18. 6580 Accesses	Research article GC-Content Normalization for RNA-Seq Data Davide Risso, Katja Schwartz, Gavin Sherlock, Sandrine Dudoit BMC Bioinformatics 2011, 12:480 (17 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The combination of three different strategies for GC-content normalization of RNA-seq data leads to more accurate estimations of gene expression levels and fold-changes, making statistical inference of differential expression less prone to false discoveries.
	19. 6567 Accesses	Software Tavaxy: Integrating Taverna and Galaxy workflows with cloud computing support Mohamed Abouelhoda, Shadi Issa, Moustafa Ghanem BMC Bioinformatics 2012, 13:77 (4 May 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	20. 6448 Accesses	Editorial Cancer bioinformatics: A new approach to systems clinical medicine Duojiao Wu, Catherine M Rice, Xiangdong Wang BMC Bioinformatics 2012, 13:71 (1 May 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	21. 6445 Accesses	Software The MULTICOM toolbox for protein structure prediction Jianlin Cheng, Jilong Li, Zheng Wang, Jesse Eickholt, Xin Deng BMC Bioinformatics 2012, 13:65 (30 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary MULTICOM Toolbox contains an array of extensively tested and high performance tools aimed at reducing the growing gap between derived protein sequences and structural determination, that includes both secondary and tertiary structure predictors
	22. 6431 Accesses	Software MPprimer: a program for reliable multiplex PCR primer design Zhiyong Shen, Wubin Qu, Wen Wang, Yiming Lu, Yonghong Wu, Zhifeng Li, Xingyi Hang, Xiaolei Wang, Dongsheng Zhao, Chenggang Zhang BMC Bioinformatics 2010, 11:143 (18 March 2010) Abstract \| Full text \| PDF \| PubMed
	23. 6299 Accesses	Software pROC: an open-source package for R and S+ to analyze and compare ROC curves Xavier Robin, Natacha Turck, Alexandre Hainard, Natalia Tiberti, Frédérique Lisacek, Jean-Charles Sanchez, Markus Müller BMC Bioinformatics 2011, 12:77 (17 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	24. 6069 Accesses	Software MUSCLE: a multiple sequence alignment method with reduced time and space complexity Robert C Edgar BMC Bioinformatics 2004, 5:113 (19 August 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	25. 6017 Accesses	Software UniFrac – An online tool for comparing microbial community diversity in a phylogenetic context Catherine Lozupone, Micah Hamady, Rob Knight BMC Bioinformatics 2006, 7:371 (7 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A new online open-access tool, Unifrac, provides multivariate analysis techniques for comparing microbial communities in a phylogenetic context and contributes to our understanding of many microbial interactions and processes.