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	1.	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.	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 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.
	4.	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
	5.	Research article The ancient history of the structure of ribonuclease P and the early origins of Archaea Feng-Jie Sun, Gustavo Caetano-Anollés BMC Bioinformatics 2010, 11:153 (24 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	6.	Research article Semi-automated screening of biomedical citations for systematic reviews Byron C Wallace, Thomas A Trikalinos, Joseph Lau, Carla Brodley, Christopher H Schmid BMC Bioinformatics 2010, 11:55 (26 January 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	7.	Research Reverse engineering gene regulatory network from microarray data using linear time-variant model Mitra Kabir, Nasimul Noman, Hitoshi Iba BMC Bioinformatics 2010, 11(Suppl 1):S56 (18 January 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	8.	Software rnaSeqMap: a Bioconductor package for RNA sequencing data exploration Anna Leśniewska, Michał J Okoniewski BMC Bioinformatics 2011, 12:200 (25 May 2011) Abstract \| Full text \| PDF \| PubMed
	9.	Methodology article Proportion statistics to detect differentially expressed genes: a comparison with log-ratio statistics Tracy L Bergemann, Jason Wilson BMC Bioinformatics 2011, 12:228 (7 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	10.	Research article Removing Noise From Pyrosequenced Amplicons Christopher Quince, Anders Lanzen, Russell J Davenport, Peter J Turnbaugh BMC Bioinformatics 2011, 12:38 (28 January 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary AmpliconNoise and Perseus are novel algorithms for the removal of noise and chimeras from pyrosequenced amplicons, reducing per-base error rates and allowing more accurate estimates of operational taxonomic units than alternative methods.
	11.	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
	12.	Research article SNPInterForest: A new method for detecting epistatic interactions Makiko Yoshida, Asako Koike BMC Bioinformatics 2011, 12:469 (12 December 2011) Abstract \| Full text \| PDF \| PubMed
	13.	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
	14.	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
	15.	Software PyMS: a Python toolkit for processing of gas chromatography--mass spectrometry (GC-MS) data. Application and comparative study of selected tools Sean O'Callaghan, David P DeSouza, Andrew Isaac, Qiao Wang, Luke Hodkinson, Moshe Olshansky, Tim Erwin, Bill Appelbe, Dedreia L Tull, Ute Roessner, Antony Bacic, Malcolm J McConville, Vladimir A Likic BMC Bioinformatics 2012, 13:115 (30 May 2012) Abstract \| Provisional PDF
	16.	Methodology article MergeAlign: improving multiple sequence alignment performance by dynamic reconstruction of consensus multiple sequence alignments. Peter W Collingridge, Steven Kelly BMC Bioinformatics 2012, 13:117 (30 May 2012) Abstract \| Provisional PDF
	17.	Methodology article Identification of polymorphic inversions from genotypes Alejandro Cáceres, Suzanne S Sindi, Benjamin J Raphael, Mario Cáceres, Juan R González BMC Bioinformatics 2012, 13:28 (9 February 2012) Abstract \| Full text \| PDF \| PubMed
	18.	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
	19.	Methodology article Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance Zhang Zhang, Jun Li, Peng Cui, Feng Ding, Ang Li, Jeffrey P Townsend, Jun Yu BMC Bioinformatics 2012, 13:43 (22 March 2012) Abstract \| Provisional PDF \| PubMed
	20.	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
	21.	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
	22.	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 \| Provisional PDF \| PubMed
	23.	Methodology article Ultrahigh-dimensional variable selection method for whole-genome gene-gene interaction analysis Masao Ueki, Gen Tamiya BMC Bioinformatics 2012, 13:72 (3 May 2012) Abstract \| Provisional PDF \| PubMed
	24.	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
	25.	Research article Quantitatively integrating molecular structure and bioactivity profile evidence into drug-target relationship analysis Tianlei Xu, Ruixin Zhu, Qi Liu, Zhiwei Cao BMC Bioinformatics 2012, 13:75 (4 May 2012) Abstract \| Provisional PDF \| PubMed