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	1. 3866 Accesses	Software Mojo Hand, a TALEN design tool for genome editing applications Kevin L Neff, David P Argue, Alvin C Ma, Han B Lee, Karl J Clark, Stephen C Ekker BMC Bioinformatics 2013, 14:1 (16 January 2013) Abstract \| Full text \| PDF \| PubMed
	2. 2957 Accesses	Software WGCNA: an R package for weighted correlation network analysis Peter Langfelder, Steve Horvath BMC Bioinformatics 2008, 9:559 (29 December 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology
	3. 2859 Accesses	Software HTQC: a fast quality control toolkit for Illumina sequencing data Xi Yang, Di Liu, Fei Liu, Jun Wu, Jing Zou, Xue Xiao, Fangqing Zhao, Baoli Zhu BMC Bioinformatics 2013, 14:33 (31 January 2013) Abstract \| Full text \| PDF \| PubMed
	4. 2577 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
	5. 2403 Accesses	Software FANTOM: Functional and taxonomic analysis of metagenomes Kemal Sanli, Fredrik H Karlsson, Intawat Nookaew, Jens Nielsen BMC Bioinformatics 2013, 14:38 (1 February 2013) Abstract \| Full text \| PDF \| PubMed
	6. 2353 Accesses	Software Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction Jian Ye, George Coulouris, Irena Zaretskaya, Ioana Cutcutache, Steve Rozen, Thomas L Madden BMC Bioinformatics 2012, 13:134 (18 June 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	7. 2204 Accesses	Software UniFrac – An online tool for comparing microbial community diversity in a phylogenetic context Catherine Lozupone, Micah Hamady, Rob Knight BMC Bioinformatics 2006, 7:371 (7 August 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A new online open-access tool, Unifrac, provides multivariate analysis techniques for comparing microbial communities in a phylogenetic context and contributes to our understanding of many microbial interactions and processes.
	8. 2128 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
	9. 2044 Accesses	Software Efficient analysis and extraction of MS/MS result data from Mascot™ result files Florian Grosse-Coosmann, Andreas M Boehm, Albert Sickmann BMC Bioinformatics 2005, 6:290 (7 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	10. 1729 Accesses	Methodology article A new unsupervised gene clustering algorithm based on the integration of biological knowledge into expression data Marie Verbanck, Sébastien Lê, Jérôme Pagès BMC Bioinformatics 2013, 14:42 (7 February 2013) Abstract \| Provisional PDF \| PubMed
	11. 1725 Accesses	Software VANTED: A system for advanced data analysis and visualization in the context of biological networks Björn H Junker, Christian Klukas, Falk Schreiber BMC Bioinformatics 2006, 7:109 (6 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	12. 1658 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
	13. 1655 Accesses	Methodology article Predicting drug side-effect profiles: a chemical fragment-based approach Edouard Pauwels, Véronique Stoven, Yoshihiro Yamanishi BMC Bioinformatics 2011, 12:169 (18 May 2011) Abstract \| Full text \| PDF \| PubMed
	14. 1604 Accesses	Methodology article A new measure for functional similarity of gene products based on Gene Ontology Andreas Schlicker, Francisco S Domingues, Jörg Rahnenführer, Thomas Lengauer BMC Bioinformatics 2006, 7:302 (15 June 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	15. 1585 Accesses	Methodology article STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation Tobias Wittkop, Emily TerAvest, Uday S Evani, K Mathew Fleisch, Ari E Berman, Corey Powell, Nigam H Shah, Sean D Mooney BMC Bioinformatics 2013, 14:53 (14 February 2013) Abstract \| Provisional PDF \| PubMed
	16. 1558 Accesses	Proceedings Investigating drug repositioning opportunities in FDA drug labels through topic modeling Halil Bisgin, Zhichao Liu, Reagan Kelly, Hong Fang, Xiaowei Xu, Weida Tong BMC Bioinformatics 2012, 13(Suppl 15):S6 (11 September 2012) Abstract \| Full text \| PDF \| PubMed
	17. 1532 Accesses	Methodology article Estimation of data-specific constitutive exons with RNA-Seq data Ellis Patrick, Michael Buckley, Yee Hwa Yang BMC Bioinformatics 2013, 14:31 (29 January 2013) Abstract \| Provisional PDF \| PubMed
	18. 1548 Accesses	Methodology article Improving accuracy for cancer classification with a new algorithm for genes selection Hongyan Zhang, Haiyan Wang, Zhijun Dai, Ming-shun Chen, Zheming Yuan BMC Bioinformatics 2012, 13:298 (13 November 2012) Abstract \| Full text \| PDF \| PubMed
	19. 1548 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
	20. 1528 Accesses	Proceedings Building the process-drug–side effect network to discover the relationship between biological Processes and side effects Sejoon Lee, Kwang H Lee, Min Song, Doheon Lee BMC Bioinformatics 2011, 12(Suppl 2):S2 (29 March 2011) Abstract \| Full text \| PDF \| PubMed
	21. 1524 Accesses	Software The Gaggle: An open-source software system for integrating bioinformatics software and data sources Paul T Shannon, David J Reiss, Richard Bonneau, Nitin S Baliga BMC Bioinformatics 2006, 7:176 (28 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	22. 1504 Accesses	Software Automics: an integrated platform for NMR-based metabonomics spectral processing and data analysis Tao Wang, Kang Shao, Qinying Chu, Yanfei Ren, Yiming Mu, Lijia Qu, Jie He, Changwen Jin, Bin Xia BMC Bioinformatics 2009, 10:83 (16 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary 'Automics' is a new open-source software package for integrated spectral processing and analysis of nuclear magnetic resonance-based metabonomic datasets, which would otherwise require the use of several separate programs.
	23. 1496 Accesses	Research Prediction of novel miRNAs and associated target genes in Glycine max Trupti Joshi, Zhe Yan, Marc Libault, Dong-Hoon Jeong, Sunhee Park, Pamela J Green, D Janine Sherrier, Andrew Farmer, Greg May, Blake C Meyers, Dong Xu, Gary Stacey BMC Bioinformatics 2010, 11(Suppl 1):S14 (18 January 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	24. 1483 Accesses	Research article Walk-weighted subsequence kernels for protein-protein interaction extraction Seonho Kim, Juntae Yoon, Jihoon Yang, Seog Park BMC Bioinformatics 2010, 11:107 (25 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	25. 1458 Accesses	Research article Discovery of novel biomarkers and phenotypes by semantic technologies Carlo A Trugenberger, Christoph Wälti, David Peregrim, Mark E Sharp, Svetlana Bureeva BMC Bioinformatics 2013, 14:51 (13 February 2013) Abstract \| Provisional PDF \| PubMed