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	1.	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.	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
	3.	Software R/parallel – speeding up bioinformatics analysis with R Gonzalo Vera, Ritsert C Jansen, Remo L Suppi BMC Bioinformatics 2008, 9:390 (22 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	4.	Software CBESW: Sequence Alignment on the Playstation 3 Adrianto Wirawan, Chee Kwoh, Nim Hieu, Bertil Schmidt BMC Bioinformatics 2008, 9:377 (17 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment
	5.	Methodology article A comparison of common programming languages used in bioinformatics Mathieu Fourment, Michael R Gillings BMC Bioinformatics 2008, 9:82 (5 February 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 2 comments
	6.	Research article Alignment and clustering of phylogenetic markers - implications for microbial diversity studies James R White, Saket Navlakha, Niranjan Nagarajan, Mohammad-Reza Ghodsi, Carl Kingsford, Mihai Pop BMC Bioinformatics 2010, 11:152 (24 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An assessment of methodologies for clustering sequences into operational taxonomic units demonstrates that small changes in algorithm parameters can lead to inflated estimates of microbial diversity, but semi-supervised clustering can produce a more robust result.
	7.	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.
	8.	Methodology article NITPICK: peak identification for mass spectrometry data Bernhard Y Renard, Marc Kirchner, Hanno Steen, Judith AJ Steen, Fred A Hamprecht BMC Bioinformatics 2008, 9:355 (28 August 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	9.	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
	10.	Correspondence An introduction to scripting in Ruby for biologists Jan Aerts, Andy Law BMC Bioinformatics 2009, 10:221 (16 July 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment
	11.	Software High-throughput sequence alignment using Graphics Processing Units Michael C Schatz, Cole Trapnell, Arthur L Delcher, Amitabh Varshney BMC Bioinformatics 2007, 8:474 (10 December 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	12.	Software SPRINT: A new parallel framework for R Jon Hill, Matthew Hambley, Thorsten Forster, Muriel Mewissen, Terence M Sloan, Florian Scharinger, Arthur Trew, Peter Ghazal BMC Bioinformatics 2008, 9:558 (29 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new interface, SPRINT, allows statistical analyses written in the R programming language to be run on high performance computing systems without the need for specialist programming to exploit parallel processors.
	13.	Research article Identification and correction of systematic error in high-throughput sequence data Frazer Meacham, Dario Boffelli, Joseph Dhahbi, David IK Martin, Meromit Singer, Lior Pachter BMC Bioinformatics 2011, 12:451 (21 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	14.	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
	15.	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
	16.	Software BLAST+: architecture and applications Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden BMC Bioinformatics 2009, 10:421 (15 December 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary With the advent of more complete genomes BLAST has been re-written to include a new set of command line searches and a new modular structure, giving substantial speed improvements for long queries and an improved user interface.
	17.	Methodology article A unified approach to false discovery rate estimation Korbinian Strimmer BMC Bioinformatics 2008, 9:303 (9 July 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A generalized algorithm that simultaneously estimates both local false discovery rates and tail area-based FDR gives a common framework to apply a range of test statistics to high-dimensional data.
	18.	Software BisoGenet: a new tool for gene network building, visualization and analysis Alexander Martin, Maria E Ochagavia, Laya C Rabasa, Jamilet Miranda, Jorge Fernandez-de-Cossio, Ricardo Bringas BMC Bioinformatics 2010, 11:91 (17 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	19.	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
	20.	Methodology Advancing translational research with the Semantic Web Alan Ruttenberg, Tim Clark, William Bug, Matthias Samwald, Olivier Bodenreider, Helen Chen, Donald Doherty, Kerstin Forsberg, Yong Gao, Vipul Kashyap, June Kinoshita, Joanne Luciano, M Scott Marshall, Chimezie Ogbuji, Jonathan Rees, Susie Stephens, Gwendolyn T Wong, Elizabeth Wu, Davide Zaccagnini, Tonya Hongsermeier, Eric Neumann, Ivan Herman, Kei-Hoi Cheung BMC Bioinformatics 2007, 8(Suppl 3):S2 (9 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| F1000 Biology
	21.	Research article Identification and correction of abnormal, incomplete and mispredicted proteins in public databases Alinda Nagy, Hédi Hegyi, Krisztina Farkas, Hedvig Tordai, Evelin Kozma, László Bányai, László Patthy BMC Bioinformatics 2008, 9:353 (27 August 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The MisPred tool improves gene predictions within public databases by using five distinct approaches to detect incomplete or incorrect sequences, such as missing signal peptides or problems with domain integrity.
	22.	Software Next generation tools for genomic data generation, distribution, and visualization David A Nix, Tonya L Di Sera, Brian K Dalley, Brett A Milash, Robert M Cundick, Kevin S Quinn, Samir J Courdy BMC Bioinformatics 2010, 11:455 (9 September 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	23.	Software SeqAn An efficient, generic C++ library for sequence analysis Andreas Döring, David Weese, Tobias Rausch, Knut Reinert BMC Bioinformatics 2008, 9:11 (9 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	24.	Software SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data Murray P Cox, Daniel A Peterson, Patrick J Biggs BMC Bioinformatics 2010, 11:485 (27 September 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	25.	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