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	1. 27740 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
	2. 13131 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
	3. 12777 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
	4. 10967 Accesses	Software CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing Samuel V Angiuoli, Malcolm Matalka, Aaron Gussman, Kevin Galens, Mahesh Vangala, David R Riley, Cesar Arze, James R White, Owen White, W Florian Fricke BMC Bioinformatics 2011, 12:356 (30 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary Cloud Virtual Resource (CloVR) is a new desktop application for large-scale sequence analysis using remote computing resources that provides several automated pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis.
	5. 9879 Accesses	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 Nelson BMC Bioinformatics 2012, 13:42 (19 March 2012) Abstract \| Provisional PDF \| PubMed \| 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.
	6. 8969 Accesses	Software VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R Hanbo Chen, Paul C Boutros BMC Bioinformatics 2011, 12:35 (26 January 2011) Abstract \| Full text \| PDF \| PubMed
	7. 8915 Accesses	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
	8. 8824 Accesses	Software GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction Yao Yu, Kang Tu, Siyuan Zheng, Yun Li, Guohui Ding, Jie Ping, Pei Hao, Yixue Li BMC Bioinformatics 2009, 10:264 (25 August 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	9. 8674 Accesses	Database UbiProt: a database of ubiquitylated proteins Alexander L Chernorudskiy, Alejandro Garcia, Eugene V Eremin, Anastasia S Shorina, Ekaterina V Kondratieva, Murat R Gainullin BMC Bioinformatics 2007, 8:126 (18 April 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	10. 7762 Accesses	Research article GC-Content Normalization for RNA-Seq Data Davide Risso, Katja Schwartz, Gavin Sherlock, Sandrine Dudoit BMC Bioinformatics 2011, 12:480 (17 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The combination of three different strategies for GC-content normalization of RNA-seq data leads to more accurate estimations of gene expression levels and fold-changes, making statistical inference of differential expression less prone to false discoveries.
	11. 7685 Accesses	Software An integrative variant analysis suite for whole exome next-generation sequencing data Danny Challis, Jin Yu, Uday S Evani, Andrew R Jackson, Sameer Paithankar, Cristian Coarfa, Aleksandar Milosavljevic, Richard A Gibbs, Fuli Yu BMC Bioinformatics 2012, 13:8 (12 January 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The Atlas2 is an analysis suite for variant calling in whole exome sequencing that combines regression models and user-adjustable cutoffs in order to separate true SNPs and INDELs from sequencing and mapping errors, with high sensitivity
	12. 7679 Accesses	Proceedings An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics Ronald C Taylor BMC Bioinformatics 2010, 11(Suppl 12):S1 (21 December 2010) Abstract \| Full text \| PDF \| PubMed
	13. 7519 Accesses	Software SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data Xutao Deng BMC Bioinformatics 2011, 12:267 (29 June 2011) Abstract \| Full text \| PDF \| PubMed
	14. 6518 Accesses	Research article Estimation of allele frequency and association mapping using next-generation sequencing data Su Kim, Kirk E Lohmueller, Anders Albrechtsen, Yingrui Li, Thorfinn Korneliussen, Geng Tian, Niels Grarup, Tao Jiang, Gitte Andersen, Daniel Witte, Torben Jorgensen, Torben Hansen, Oluf Pedersen, Jun Wang, Rasmus Nielsen BMC Bioinformatics 2011, 12:231 (11 June 2011) Abstract \| Full text \| PDF \| PubMed
	15. 6516 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
	16. 6377 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
	17. 6342 Accesses	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
	18. 6329 Accesses	Software BioWarehouse: a bioinformatics database warehouse toolkit Thomas J Lee, Yannick Pouliot, Valerie Wagner, Priyanka Gupta, David WJ Stringer-Calvert, Jessica D Tenenbaum, Peter D Karp BMC Bioinformatics 2006, 7:170 (23 March 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	19. 6169 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
	20. 5855 Accesses	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
	21. 5735 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
	22. 5712 Accesses	Research article Bias detection and correction in RNA-Sequencing data Wei Zheng, Lisa M Chung, Hongyu Zhao BMC Bioinformatics 2011, 12:290 (19 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	23. 5703 Accesses	Methodology article Information extraction from full text scientific articles: Where are the keywords? Parantu K Shah, Carolina Perez-Iratxeta, Peer Bork, Miguel A Andrade BMC Bioinformatics 2003, 4:20 (29 May 2003) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	24. 5646 Accesses	Correspondence Implementing a genomic data management system using iRODS in the Wellcome Trust Sanger Institute Gen-Tao Chiang, Peter Clapham, Guoying Qi, Kevin Sale, Guy Coates BMC Bioinformatics 2011, 12:361 (9 September 2011) Abstract \| Full text \| PDF \| PubMed
	25. 5431 Accesses	Correspondence Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics Barry R Zeeberg, Joseph Riss, David W Kane, Kimberly J Bussey, Edward Uchio, W Marston Linehan, J Carl Barrett, John N Weinstein BMC Bioinformatics 2004, 5:80 (23 June 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 7 comments