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	1. 3464 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
	2. 2889 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
	3. 1566 Accesses	Software PyElph - a software tool for gel images analysis and phylogenetics Ana Brandusa Pavel, Cristian Ioan Vasile BMC Bioinformatics 2012, 13:9 (13 January 2012) Abstract \| Provisional PDF \| PubMed
	4. 1487 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.
	5. 1459 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.
	6. 1346 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. 1237 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
	8. 1206 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
	9. 1188 Accesses	Research article Unintended consequences of existential quantifications in biomedical ontologies Martin Boeker, Ilinca Tudose, Janna Hastings, Daniel Schober, Stefan Schulz BMC Bioinformatics 2011, 12:456 (24 November 2011) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Almost a quarter of all existential restrictions in the Open Biomedical Ontologies (OBO) Foundry contain assertions that do not properly describe the underlying biological reality, suggesting that a restriction to fewer, well-defined, relation types is needed.
	10. 1185 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
	11. 1174 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
	12. 1123 Accesses	Database MetRxn: A Knowledgebase of Metabolites and Reactions Spanning Metabolic Models and Databases Akhil Kumar, Patrick F Suthers, Costas D Maranas BMC Bioinformatics 2012, 13:6 (10 January 2012) Abstract \| Provisional PDF \| PubMed
	13. 1084 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
	14. 1061 Accesses	Methodology article A new strategy for better genome assembly from very short reads Yan Ji, Yixiang Shi, Guohui Ding, Yixue Li BMC Bioinformatics 2011, 12:493 (30 December 2011) Abstract \| Full text \| PDF \| PubMed
	15. 1061 Accesses	Research article Convergent evolution in structural elements of proteins investigated using cross profile analysis Kentaro Tomii, Yoshito Sawada, Shinya Honda BMC Bioinformatics 2012, 13:11 (16 January 2012) Abstract \| Provisional PDF \| PubMed
	16. 1058 Accesses	Software ABrowse - a customizable next-generation genome browser framework Lei Kong, Jun Wang, Shuqi Zhao, Xiaocheng Gu, Jingchu Luo, Ge Gao BMC Bioinformatics 2012, 13:2 (5 January 2012) Abstract \| Full text \| PDF \| PubMed
	17. 974 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
	18. 923 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
	19. 906 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
	20. 884 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
	21. 885 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
	22. 867 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
	23. 842 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
	24. 838 Accesses	Software proTRAC - a software for probabilistic piRNA cluster detection, visualization and analysis David Rosenkranz, Hans Zischler BMC Bioinformatics 2012, 13:5 (10 January 2012) Abstract \| Provisional PDF \| PubMed
	25. 798 Accesses	Methodology article MIPHENO: Data normalization for high throughput metabolite analysis Shannon M Bell, Lyle D Burgoon, Robert L Last BMC Bioinformatics 2012, 13:10 (13 January 2012) Abstract \| Provisional PDF \| PubMed