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	1. 2641 Accesses	Methodology article Readjoiner: a fast and memory efficient string graph-based sequence assembler Giorgio Gonnella, Stefan Kurtz BMC Bioinformatics 2012, 13:82 (6 May 2012) Abstract \| Provisional PDF \| PubMed
	2. 2504 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. 2434 Accesses	Software Tavaxy: Integrating Taverna and Galaxy workflows with cloud computing support Mohamed Abouelhoda, Shadi A Issa, Moustafa Ghanem BMC Bioinformatics 2012, 13:77 (4 May 2012) Abstract \| Provisional PDF \| PubMed
	4. 2336 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 \| Provisional PDF \| PubMed
	5. 2101 Accesses	Research article A comparative evaluation of sequence classification programs Adam L Bazinet, Michael P Cummings BMC Bioinformatics 2012, 13:92 (10 May 2012) Abstract \| Provisional PDF \| PubMed
	6. 2096 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 Nelson BMC Bioinformatics 2012, 13:42 (19 March 2012) Abstract \| Provisional PDF \| PubMed \| 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.
	7. 1630 Accesses	Methodology article Inferring high-confidence human protein-protein interactions Xueping Yu, Anders Wallqvist, Jaques Reifman BMC Bioinformatics 2012, 13:79 (4 May 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A novel unsupervised statistical approach for ranking protein-protein interactions called interaction detection based on shuffling reduces inherent experiment-dependent noise and increases the likelihood of detecting high confidence protein interactions.
	8. 1440 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
	9. 1372 Accesses	Software PHYLOViZ: Phylogenetic Inference and Data Visualization for Sequence Based Typing Methods Alexandre P Francisco, Cátia Vaz, Pedro T Monteiro, José Melo-Cristino, Mário Ramirez, João André Carriço BMC Bioinformatics 2012, 13:87 (8 May 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Phyloviz is an exciting free software for visualizing genotype datasets, isolating populations for epidemiological analysis, vizualising potential evolutionary relationships between bacteria and providing access to publicly available data plus potential to export high resolution images.
	10. 1304 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 \| Provisional PDF \| PubMed
	11. 1299 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
	12. 1259 Accesses	Research article Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art Rasna R Walia, Cornelia Caragea, Benjamin A Lewis, Fadi G Towfic, Michael Terribilini, Yasser El-Manzalawy, Drena Dobbs, Vasant Honavar BMC Bioinformatics 2012, 13:89 (10 May 2012) Abstract \| Provisional PDF \| PubMed
	13. 1238 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
	14. 1205 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 \| Provisional 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
	15. 1166 Accesses	Software SparSNP: Fast and memory-efficient analysis of all SNPs for phenotype prediction Gad Abraham, Adam Kowalczyk, Justin Zobel, Michael Inouye BMC Bioinformatics 2012, 13:88 (10 May 2012) Abstract \| Provisional PDF \| PubMed
	16. 1097 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 \| Provisional PDF \| PubMed
	17. 1081 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 \| Provisional 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
	18. 1052 Accesses	Methodology article Integrating biological knowledge into variable selection: an empirical Bayes approach with an application in cancer biology Steven M Hill, Richard M Neve, Nora Bayani, Wen-Lin Kuo, Safiyyah Ziyad, Paul T Spellman, Joe W Gray, Sach Mukherjee BMC Bioinformatics 2012, 13:94 (11 May 2012) Abstract \| Provisional PDF \| PubMed
	19. 1020 Accesses	Methodology article Handling the data management needs of high-throughput sequencing data: SpeedGene, a compression algorithm for the efficient storage of genetic data Dandi Qiao, Wai-Ki Yip, Christoph Lange BMC Bioinformatics 2012, 13:100 (16 May 2012) Abstract \| Provisional PDF \| PubMed
	20. 997 Accesses	Research article SIS: a program to generate draft genome sequence scaffolds for prokaryotes Zanoni Dias, Ulisses Dias, Joao C Setubal BMC Bioinformatics 2012, 13:96 (14 May 2012) Abstract \| Provisional PDF \| PubMed
	21. 985 Accesses	Software TreeSnatcher plus: capturing phylogenetic trees from images Thomas Laubach, Arndt von Haeseler, Martin J. Lercher BMC Bioinformatics 2012, 13:110 (24 May 2012) Abstract \| Provisional PDF \| PubMed
	22. 926 Accesses	Software DIPSBC - Data Integration Platform for Systems Biology Collaborations Felix Dreher, Thomas Kreitler, Christopher Hardt, Atanas Kamburov, Reha Yildirimman, Karl Schellander, Hans Lehrach, Bodo M.H. Lange, Ralf Herwig BMC Bioinformatics 2012, 13:85 (8 May 2012) Abstract \| Provisional PDF \| PubMed
	23. 878 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
	24. 863 Accesses	Research article A unified computational model for revealing and predicting subtle subtypes of cancers Xianwen Ren, Yong Wang, Jiguang Wang, Xiang-Sun Zhang BMC Bioinformatics 2012, 13:70 (1 May 2012) Abstract \| Provisional PDF \| PubMed
	25. 845 Accesses	Methodology article A Bayesian variable selection procedure to rank overlapping gene sets Axel Skarman, Mohammad Shariati, Luc Janss, Li Jiang, Peter Sørensen BMC Bioinformatics 2012, 13:73 (3 May 2012) Abstract \| Provisional PDF \| PubMed