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	51. 683 Accesses	Methodology article Base calling for high-throughput short-read sequencing: dynamic programming solutions Shreepriya Das, Haris Vikalo BMC Bioinformatics 2013, 14:129 (15 April 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
	52. 681 Accesses	Research article Mining prokaryotic genomes for unknown amino acids: a stop-codon-based approach Masashi Fujita, Hisaaki Mihara, Susumu Goto, Nobuyoshi Esaki, Minoru Kanehisa BMC Bioinformatics 2007, 8:225 (28 June 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary As two rare amino acids are stop codon-encoded, a 23rd undiscovered amino acid might also be, but a systematic search for 'readthrough proteins’ in prokaryotes showed no trace of an additional stop codon-encoded amino acid.
	53. 680 Accesses	Software D-Light on promoters: A client-server system for the analysis and visualization of cis-regulatory elements Josef Laimer, Clemens J Zuzan, Tobias Ehrenberger, Monika Freudenberger, Simone Gschwandtner, Carina Lebherz, Peter Lackner BMC Bioinformatics 2013, 14:140 (24 April 2013) Abstract \| Provisional PDF \| PubMed
	54. 674 Accesses	Software MUSCLE: a multiple sequence alignment method with reduced time and space complexity Robert C Edgar BMC Bioinformatics 2004, 5:113 (19 August 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	55. 663 Accesses	Research article Mobilomics in Saccharomyces cerevisiae strains Giulia Menconi, Giovanni Battaglia, Roberto Grossi, Nadia Pisanti, Roberto Marangoni BMC Bioinformatics 2013, 14:102 (20 March 2013) Abstract \| Provisional PDF \| PubMed
	56. 653 Accesses	Research article Quantifying variances in comparative RNA secondary structure prediction James WJ Anderson, Ádám Novák, Zsuzsanna Sükösd, Michael Golden, Preeti Arunapuram, Ingolfur Edvardsson, Jotun Hein BMC Bioinformatics 2013, 14:149 (1 May 2013) Abstract \| Provisional PDF \| PubMed
	57. 646 Accesses	Methodology article Gene selection and classification of microarray data using random forest Ramón Díaz-Uriarte, Sara Alvarez de Andrés BMC Bioinformatics 2006, 7:3 (6 January 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	58. 650 Accesses	Software MIMO: an efficient tool for molecular interaction maps overlap Pietro Di Lena, Gang Wu, Pier Luigi Martelli, Rita Casadio, Christine Nardini BMC Bioinformatics 2013, 14:159 (15 May 2013) Abstract \| Provisional PDF \| PubMed
	59. 645 Accesses	Software PubFocus: semantic MEDLINE/PubMed citations analytics through integration of controlled biomedical dictionaries and ranking algorithm Maksim V Plikus, Zina Zhang, Cheng-Ming Chuong BMC Bioinformatics 2006, 7:424 (2 October 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	60. 619 Accesses	Research article The COG database: an updated version includes eukaryotes Roman L Tatusov, Natalie D Fedorova, John D Jackson, Aviva R Jacobs, Boris Kiryutin, Eugene V Koonin, Dmitri M Krylov, Raja Mazumder, Sergei L Mekhedov, Anastasia N Nikolskaya, B Sridhar Rao, Sergei Smirnov, Alexander V Sverdlov, Sona Vasudevan, Yuri I Wolf, Jodie J Yin, Darren A Natale BMC Bioinformatics 2003, 4:41 (11 September 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology
	61. 618 Accesses	Methodology article Bacterial cell identification in differential interference contrast microscopy images Boguslaw Obara, Mark Roberts, Judith Armitage, Vicente Grau BMC Bioinformatics 2013, 14:134 (23 April 2013) Abstract \| Provisional PDF \| PubMed
	62. 614 Accesses	Methodology article HMM Logos for visualization of protein families Benjamin Schuster-Böckler, Jörg Schultz, Sven Rahmann BMC Bioinformatics 2004, 5:7 (21 January 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A new method of visualizing profile Hidden Markov Models as a sequence logo, applied here to the GTPases Ras and Rab by way of example, makes it easy to compare protein families visually.
	63. 613 Accesses	Software A metadata-aware application for remote scoring and exchange of tissue microarray images Lorna Morris, Andrew Tsui, Charles Crichton, Steve Harris, Peter H Maccallum, William J Howat, Jim Davies, James D Brenton, Carlos Caldas BMC Bioinformatics 2013, 14:147 (1 May 2013) Abstract \| Full text \| PDF \| PubMed
	64. 596 Accesses	Database The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats Ibtissem Grissa, Gilles Vergnaud, Christine Pourcel BMC Bioinformatics 2007, 8:172 (23 May 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	65. 593 Accesses	Research article A systematic comparison of the MetaCyc and KEGG pathway databases Tomer Altman, Michael Travers, Anamika Kothari, Ron Caspi, Peter D Karp BMC Bioinformatics 2013, 14:112 (27 March 2013) Abstract \| Provisional PDF \| PubMed
	66. 591 Accesses	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
	67. 567 Accesses	Software MPprimer: a program for reliable multiplex PCR primer design Zhiyong Shen, Wubin Qu, Wen Wang, Yiming Lu, Yonghong Wu, Zhifeng Li, Xingyi Hang, Xiaolei Wang, Dongsheng Zhao, Chenggang Zhang BMC Bioinformatics 2010, 11:143 (18 March 2010) Abstract \| Full text \| PDF \| PubMed
	68. 566 Accesses	Software I-TASSER server for protein 3D structure prediction Yang Zhang BMC Bioinformatics 2008, 9:40 (23 January 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The I-TASSER protein 3D-structure prediction algorithm - the best performer in the CASP7 experiment - is now available in an online version and also now provides a benchmarking score for assessment of the accuracy of its structure predictions.
	69. 562 Accesses	Methodology article Greedy feature selection for glycan chromatography data with the generalized Dirichlet distribution Marie C Galligan, Radka Saldova, Matthew P Campbell, Pauline M Rudd, Thomas B Murphy BMC Bioinformatics 2013, 14:155 (7 May 2013) Abstract \| Provisional PDF \| PubMed
	70. 559 Accesses	Methodology article CNV-seq, a new method to detect copy number variation using high-throughput sequencing Chao Xie, Martti T Tammi BMC Bioinformatics 2009, 10:80 (6 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	71. 557 Accesses	Database MIMAS 3.0 is a Multiomics Information Management and Annotation System Alexandre Gattiker, Leandro Hermida, Robin Liechti, Ioannis Xenarios, Olivier Collin, Jacques Rougemont, Michael Primig BMC Bioinformatics 2009, 10:151 (18 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An international collaboration of software developers, computer scientists, life scientists and research technicians has extended a database tool that manages microarray data from various sources to include data from the latest ultra-high throughput DNA sequencing technologies.
	72. 539 Accesses	Research article Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study Lei Sun, Zhihua Zhang, Timothy L Bailey, Andrew C Perkins, Michael R Tallack, Zhao Xu, Hui Liu BMC Bioinformatics 2012, 13:331 (13 December 2012) Abstract \| Full text \| PDF \| PubMed
	73. 533 Accesses	Research article DNA methylation arrays as surrogate measures of cell mixture distribution Eugene Houseman, William P Accomando, Devin C Koestler, Brock C Christensen, Carmen J Marsit, Heather H Nelson, John K Wiencke, Karl T Kelsey BMC Bioinformatics 2012, 13:86 (8 May 2012) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology
	74. 532 Accesses	Research article Gene regulatory network modeling via global optimization of high-order dynamic Bayesian network Nguyen Xuan, Madhu Chetty, Ross Coppel, Pramod P Wangikar BMC Bioinformatics 2012, 13:131 (13 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	75. 528 Accesses	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 \| Cited on BioMed Central