| # | Title | Journal | Year | Citations |
|---|
| 1 | WGCNA: an R package for weighted correlation network analysis | BMC Bioinformatics | 2008 | 17,294 |
| 2 | RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome | BMC Bioinformatics | 2011 | 16,042 |
| 3 | BLAST+: architecture and applications | BMC Bioinformatics | 2009 | 14,935 |
| 4 | pROC: an open-source package for R and S+ to analyze and compare ROC curves | BMC Bioinformatics | 2011 | 8,498 |
| 5 | Prodigal: prokaryotic gene recognition and translation initiation site identification | BMC Bioinformatics | 2010 | 8,237 |
| 6 | GSVA: gene set variation analysis for microarray and RNA-Seq data | BMC Bioinformatics | 2013 | 7,876 |
| 7 | MUSCLE: a multiple sequence alignment method with reduced time and space complexity | BMC Bioinformatics | 2004 | 7,508 |
| 8 | Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool | BMC Bioinformatics | 2013 | 5,305 |
| 9 | Genome sequence-based species delimitation with confidence intervals and improved distance functions | BMC Bioinformatics | 2013 | 5,139 |
| 10 | An automated method for finding molecular complexes in large protein interaction networks | BMC Bioinformatics | 2003 | 4,773 |
| 11 | ImageJ2: ImageJ for the next generation of scientific image data | BMC Bioinformatics | 2017 | 4,464 |
| 12 | Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction | BMC Bioinformatics | 2012 | 4,446 |
| 13 | I-TASSER server for protein 3D structure prediction | BMC Bioinformatics | 2008 | 4,415 |
| 14 | The COG database: an updated version includes eukaryotes | BMC Bioinformatics | 2003 | 3,913 |
| 15 | The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes | BMC Bioinformatics | 2008 | 3,200 |
| 16 | GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists | BMC Bioinformatics | 2009 | 3,032 |
| 17 | MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data | BMC Bioinformatics | 2010 | 3,031 |
| 18 | DNA methylation arrays as surrogate measures of cell mixture distribution | BMC Bioinformatics | 2012 | 2,563 |
| 19 | Gene finding in novel genomes | BMC Bioinformatics | 2004 | 2,443 |
| 20 | Bias in random forest variable importance measures: Illustrations, sources and a solution | BMC Bioinformatics | 2007 | 2,328 |
| 21 | Automated generation of heuristics for biological sequence comparison | BMC Bioinformatics | 2005 | 2,294 |
| 22 | ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context | BMC Bioinformatics | 2006 | 2,218 |
| 23 | Conditional variable importance for random forests | BMC Bioinformatics | 2008 | 2,129 |
| 24 | Gene selection and classification of microarray data using random forest | BMC Bioinformatics | 2006 | 2,081 |
| 25 | BIGSdb: Scalable analysis of bacterial genome variation at the population level | BMC Bioinformatics | 2010 | 2,074 |
| 26 | VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R | BMC Bioinformatics | 2011 | 2,018 |
| 27 | ANGSD: Analysis of Next Generation Sequencing Data | BMC Bioinformatics | 2014 | 1,935 |
| 28 | Molecular ecological network analyses | BMC Bioinformatics | 2012 | 1,917 |
| 29 | PANDAseq: paired-end assembler for illumina sequences | BMC Bioinformatics | 2012 | 1,906 |
| 30 | VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines | BMC Bioinformatics | 2007 | 1,740 |
| 31 | MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects | BMC Bioinformatics | 2011 | 1,654 |
| 32 | Statistical analysis of real-time PCR data | BMC Bioinformatics | 2006 | 1,651 |
| 33 | Interactive metagenomic visualization in a Web browser | BMC Bioinformatics | 2011 | 1,617 |
| 34 | InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams | BMC Bioinformatics | 2015 | 1,609 |
| 35 | Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis | BMC Bioinformatics | 2010 | 1,597 |
| 36 | RNAstructure: software for RNA secondary structure prediction and analysis | BMC Bioinformatics | 2010 | 1,568 |
| 37 | jvenn: an interactive Venn diagram viewer | BMC Bioinformatics | 2014 | 1,528 |
| 38 | ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees | BMC Bioinformatics | 2018 | 1,451 |
| 39 | Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments | BMC Bioinformatics | 2010 | 1,421 |
| 40 | UniFrac--an online tool for comparing microbial community diversity in a phylogenetic context | BMC Bioinformatics | 2006 | 1,321 |
| 41 | Removing Noise From Pyrosequenced Amplicons | BMC Bioinformatics | 2011 | 1,320 |
| 42 | STEM: a tool for the analysis of short time series gene expression data | BMC Bioinformatics | 2006 | 1,309 |
| 43 | The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs | BMC Bioinformatics | 2002 | 1,278 |
| 44 | SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data | BMC Bioinformatics | 2010 | 1,268 |
| 45 | TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses | BMC Bioinformatics | 2010 | 1,246 |
| 46 | Bias in error estimation when using cross-validation for model selection | BMC Bioinformatics | 2006 | 1,174 |
| 47 | Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads | BMC Bioinformatics | 2014 | 1,134 |
| 48 | GAGE: generally applicable gene set enrichment for pathway analysis | BMC Bioinformatics | 2009 | 1,132 |
| 49 | Dendroscope: An interactive viewer for large phylogenetic trees | BMC Bioinformatics | 2007 | 1,127 |
| 50 | LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons | BMC Bioinformatics | 2008 | 1,110 |
