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	1. 2936 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. 2186 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 \| Provisional PDF \| PubMed \| 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
	3. 1904 Accesses	Research article Independent Principal Component Analysis for biologically meaningful dimension reduction of large biological data sets Fangzhou Yao, Jeff Coquery, Kim-Anh DR Le Cao BMC Bioinformatics 2012, 13:24 (3 February 2012) Abstract \| Provisional PDF \| PubMed
	4. 1659 Accesses	Software graphite - a Bioconductor package to convert pathway topology to gene network Gabriele Sales, Enrica Calura, Duccio Cavalieri, Chiara Romualdi BMC Bioinformatics 2012, 13:20 (31 January 2012) Abstract \| Provisional PDF \| PubMed
	5. 1627 Accesses	Software TranscriptomeBrowser 3.0 : introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks Cyrille Lepoivre, Aurelie Bergon, Fabrice Lopez, Narayanan B Perumal, Catherine Nguyen, Jean Imbert, Denis Puthier BMC Bioinformatics 2012, 13:19 (31 January 2012) Abstract \| Provisional PDF \| PubMed
	6. 1501 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
	7. 1398 Accesses	Software PANDAseq: PAired-eND Assembler for Illumina sequences Andre P Masella, Andrea K Bartram, Jakub M Truszkowski, Daniel G Brown, Josh D Neufeld BMC Bioinformatics 2012, 13:31 (14 February 2012) Abstract \| Provisional PDF
	8. 1349 Accesses	Methodology article Markov Chain Ontology Analysis (MCOA) H ROBERT Frost, Alexa T McCray BMC Bioinformatics 2012, 13:23 (3 February 2012) Abstract \| Provisional PDF \| PubMed
	9. 1323 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 \| Provisional 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.
	10. 1194 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
	11. 1063 Accesses	Software The EnzymeTracker: an open-source laboratory information management system for sample tracking Thomas Triplet, Gregory Butler BMC Bioinformatics 2012, 13:15 (26 January 2012) Abstract \| Provisional PDF \| PubMed
	12. 1017 Accesses	Research article Protein docking prediction using predicted protein-protein interface Bin Li, Daisuke Kihara BMC Bioinformatics 2012, 13:7 (10 January 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A novel pairwise protein docking algorithm, PI-LZerD, is an important development applicable to multiple protein docking and valuable for providing pictures of interactions in network analyses, that performs better than alternatives in benchmark experiment.
	13. 1005 Accesses	Research article Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs Hani Z Girgis, Ivan Ovcharenko BMC Bioinformatics 2012, 13:25 (7 February 2012) Abstract \| Provisional PDF \| PubMed
	14. 1002 Accesses	Software Developing a Powerful In Silico Tool for the Discovery of Novel Caspase-3 Substrates: A Preliminary Screening of the Human Proteome Muneef Ayyash, Hashem Tamimi, Yaqoub Ashhab BMC Bioinformatics 2012, 13:14 (23 January 2012) Abstract \| Provisional PDF \| PubMed
	15. 970 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
	16. 911 Accesses	Methodology article Automatic categorization of diverse experimental information in the bioscience literature Ruihua Fang, Gary Schindelman, Kimberly Van Auken, Jolene Fernandes, Wen Chen, Xiaodong Wang, Paul Davis, Mary Ann Tuli, Steven Marygold, Gillian Millburn, Beverley Matthews, Haiyan Zhang, Nick Brown, William M Gelbart, Paul W Sternberg BMC Bioinformatics 2012, 13:16 (26 January 2012) Abstract \| Provisional PDF \| PubMed \| Cited on BioMed Central
	17. 891 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. 881 Accesses	Methodology article Assessing statistical significance in causal graphs Leonid Chindelevitch, Po-Ru Loh, Ahmed Enayetallah, Bonnie Berger, Daniel Ziemek BMC Bioinformatics 2012, 13:35 (20 February 2012) Abstract \| Provisional PDF
	19. 876 Accesses	Methodology article Propagating semantic information in biochemical network models Marvin Schulz, Edda Klipp, Wolfram Liebermeister BMC Bioinformatics 2012, 13:18 (30 January 2012) Abstract \| Provisional PDF \| PubMed
	20. 872 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
	21. 826 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 \| 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
	22. 825 Accesses	Methodology article Analysis of Energy-based Algorithms for RNA Secondary Structure Prediction Monir Hajiaghayi, Anne Condon, Holger H. Hoos BMC Bioinformatics 2012, 13:22 (1 February 2012) Abstract \| Provisional PDF \| PubMed
	23. 818 Accesses	Software ICGE: an R package for detecting relevant clusters and atypical units in gene expression Itziar Irigoien, Basilio Sierra, Concepcion Arenas BMC Bioinformatics 2012, 13:30 (13 February 2012) Abstract \| Provisional PDF
	24. 809 Accesses	Research article Core module biomarker identification with network exploration for breast cancer metastasis Ruoting Yang, Bernie J Daigle, Linda R Petzold, Francis J Doyle BMC Bioinformatics 2012, 13:12 (18 January 2012) Abstract \| Provisional PDF \| PubMed
	25. 806 Accesses	Methodology article BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins Matti Kankainen, Teija Ojala, Liisa Holm BMC Bioinformatics 2012, 13:33 (15 February 2012) Abstract \| Provisional PDF \| Editor’s summary BLANNOTATOR, an automated, accurate method for bacterial genome annotation, applicable to metagenomics research as it does not require pre-existing sequence clustering, has outperformed five tested methods even in the absence of highly similar sequence hits.