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	1.	Methodology article Cloud computing for comparative genomics Dennis P Wall, Parul Kudtarkar, Vincent A Fusaro, Rimma Pivovarov, Prasad Patil, Peter J Tonellato BMC Bioinformatics 2010, 11:259 (18 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	2.	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 \| Full text \| PDF \| PubMed
	3.	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.
	4.	Research article Merging microarray data from separate breast cancer studies provides a robust prognostic test Lei Xu, Aik Tan, Raimond L Winslow, Donald Geman BMC Bioinformatics 2008, 9:125 (27 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	5.	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 A Carriço BMC Bioinformatics 2012, 13:87 (8 May 2012) Abstract \| Full text \| 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.
	6.	Research article A comparative evaluation of sequence classification programs Adam L Bazinet, Michael P Cummings BMC Bioinformatics 2012, 13:92 (10 May 2012) Abstract \| Full text \| PDF \| PubMed
	7.	Research article BioCause: Annotating and analysing causality in the biomedical domain Claudiu Mihaila, Tomoko Ohta, Sampo Pyysalo, Sophia Ananiadou BMC Bioinformatics 2013, 14:2 (16 January 2013) Abstract \| Provisional PDF \| PubMed
	8.	Methodology article Identifying structural domains of proteins using clustering Howard J Feldman BMC Bioinformatics 2012, 13:286 (1 November 2012) Abstract \| Full text \| PDF \| PubMed
	9.	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
	10.	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
	11.	Research Scratchpads: a data-publishing framework to build, share and manage information on the diversity of life Vincent S Smith, Simon D Rycroft, Kehan T Harman, Ben Scott, David Roberts BMC Bioinformatics 2009, 10(Suppl 14):S6 (10 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Scratchpads, a new social networking tool for natural history researchers and enthusiasts, links information from disparate sources, encourages data sharing, and promotes the ultimate goal of describing and synthesising all facets of the diversity of life.
	12.	Research CMKb: a web-based prototype for integrating Australian Aboriginal customary medicinal plant knowledge Jitendra Gaikwad, Varun Khanna, Subramanyam Vemulpad, Joanne Jamie, Jim Kohen, Shoba Ranganathan BMC Bioinformatics 2008, 9(Suppl 12):S25 (12 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	13.	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.	Software PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity Bhakti Dwivedi, Robert Schmieder, Dawn B Goldsmith, Robert A Edwards, Mya Breitbart BMC Bioinformatics 2012, 13:37 (4 March 2012) Abstract \| Full text \| PDF \| PubMed
	15.	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 \| Full text \| PDF \| PubMed
	16.	Methodology article Surprising results on phylogenetic tree building methods based on molecular sequences Gaston H Gonnet BMC Bioinformatics 2012, 13:148 (27 June 2012) Abstract \| Full text \| PDF \| PubMed
	17.	Methodology article SNP-based pathway enrichment analysis for genome-wide association studies Lingjie Weng, Fabio Macciardi, Aravind Subramanian, Guia Guffanti, Steven G Potkin, Zhaoxia Yu, Xiaohui Xie BMC Bioinformatics 2011, 12:99 (15 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	18.	Methodology article Coupled mutation finder: A new entropy-based method quantifying phylogenetic noise for the detection of compensatory mutations Mehmet Gültas, Martin Haubrock, Nesrin Tüysüz, Stephan Waack BMC Bioinformatics 2012, 13:225 (11 September 2012) Abstract \| Full text \| PDF \| PubMed
	19.	Software Coral: an integrated suite of visualizations for comparing clusterings Darya Filippova, Aashish Gadani, Carl Kingsford BMC Bioinformatics 2012, 13:276 (29 October 2012) Abstract \| Full text \| PDF \| PubMed
	20.	Methodology article Arrow plot: a new graphical tool for selecting up and down regulated genes and genes differentially expressed on sample subgroups Carina Silva-Fortes, Maria Amaral Turkman, Lisete Sousa BMC Bioinformatics 2012, 13:147 (26 June 2012) Abstract \| Full text \| PDF \| PubMed
	21.	Database T3DB: an integrated database for bacterial type III secretion system Yejun Wang, He Huang, Ming’an Sun, Qing Zhang, Dianjing Guo BMC Bioinformatics 2012, 13:66 (30 April 2012) Abstract \| Full text \| PDF \| PubMed
	22.	Research article Phamerator: a bioinformatic tool for comparative bacteriophage genomics Steven G Cresawn, Matt Bogel, Nathan Day, Deborah Jacobs-Sera, Roger W Hendrix, Graham F Hatfull BMC Bioinformatics 2011, 12:395 (12 October 2011) Abstract \| Full text \| PDF \| PubMed
	23.	Methodology article A new real-time PCR method to overcome significant quantitative inaccuracy due to slight amplification inhibition Michele Guescini, Davide Sisti, Marco BL Rocchi, Laura Stocchi, Vilberto Stocchi BMC Bioinformatics 2008, 9:326 (30 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	24.	Research EVA: Exome Variation Analyzer, an efficient and versatile tool for filtering strategies in medical genomics Sophie Coutant, Chloé Cabot, Arnaud Lefebvre, Martine Léonard, Elise Prieur-Gaston, Dominique Campion, Thierry Lecroq, Hélène Dauchel BMC Bioinformatics 2012, 13(Suppl 14):S9 (7 September 2012) Abstract \| Full text \| PDF \| PubMed
	25.	Methodology article Molecular ecological network analyses Ye Deng, Yi-Huei Jiang, Yunfeng Yang, Zhili He, Feng Luo, Jizhong Zhou BMC Bioinformatics 2012, 13:113 (30 May 2012) Abstract \| Full text \| PDF \| PubMed