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Top Articles

1WGCNA: an R package for weighted correlation network analysisBMC Bioinformatics200817,294
2RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genomeBMC Bioinformatics201116,042
3BLAST+: architecture and applicationsBMC Bioinformatics200914,935
4pROC: an open-source package for R and S+ to analyze and compare ROC curvesBMC Bioinformatics20118,498
5Prodigal: prokaryotic gene recognition and translation initiation site identificationBMC Bioinformatics20108,237
6GSVA: gene set variation analysis for microarray and RNA-Seq dataBMC Bioinformatics20137,876
7MUSCLE: a multiple sequence alignment method with reduced time and space complexityBMC Bioinformatics20047,508
8Enrichr: interactive and collaborative HTML5 gene list enrichment analysis toolBMC Bioinformatics20135,305
9Genome sequence-based species delimitation with confidence intervals and improved distance functionsBMC Bioinformatics20135,139
10An automated method for finding molecular complexes in large protein interaction networksBMC Bioinformatics20034,773
11ImageJ2: ImageJ for the next generation of scientific image dataBMC Bioinformatics20174,464
12Primer-BLAST: A tool to design target-specific primers for polymerase chain reactionBMC Bioinformatics20124,446
13I-TASSER server for protein 3D structure predictionBMC Bioinformatics20084,415
14The COG database: an updated version includes eukaryotesBMC Bioinformatics20033,913
15The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomesBMC Bioinformatics20083,200
16GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene listsBMC Bioinformatics20093,032
17MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile dataBMC Bioinformatics20103,031
18DNA methylation arrays as surrogate measures of cell mixture distributionBMC Bioinformatics20122,563
19Gene finding in novel genomesBMC Bioinformatics20042,443
20Bias in random forest variable importance measures: Illustrations, sources and a solutionBMC Bioinformatics20072,328
21Automated generation of heuristics for biological sequence comparisonBMC Bioinformatics20052,294
22ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular ContextBMC Bioinformatics20062,218
23Conditional variable importance for random forestsBMC Bioinformatics20082,129
24Gene selection and classification of microarray data using random forestBMC Bioinformatics20062,081
25BIGSdb: Scalable analysis of bacterial genome variation at the population levelBMC Bioinformatics20102,074
26VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in RBMC Bioinformatics20112,018
27ANGSD: Analysis of Next Generation Sequencing DataBMC Bioinformatics20141,935
28Molecular ecological network analysesBMC Bioinformatics20121,917
29PANDAseq: paired-end assembler for illumina sequencesBMC Bioinformatics20121,906
30VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccinesBMC Bioinformatics20071,740
31MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projectsBMC Bioinformatics20111,654
32Statistical analysis of real-time PCR dataBMC Bioinformatics20061,651
33Interactive metagenomic visualization in a Web browserBMC Bioinformatics20111,617
34InteractiVenn: a web-based tool for the analysis of sets through Venn diagramsBMC Bioinformatics20151,609
35Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysisBMC Bioinformatics20101,597
36RNAstructure: software for RNA secondary structure prediction and analysisBMC Bioinformatics20101,568
37jvenn: an interactive Venn diagram viewerBMC Bioinformatics20141,528
38ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene treesBMC Bioinformatics20181,451
39Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experimentsBMC Bioinformatics20101,421
40UniFrac--an online tool for comparing microbial community diversity in a phylogenetic contextBMC Bioinformatics20061,321
41Removing Noise From Pyrosequenced AmpliconsBMC Bioinformatics20111,320
42STEM: a tool for the analysis of short time series gene expression dataBMC Bioinformatics20061,309
43The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAsBMC Bioinformatics20021,278
44SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing dataBMC Bioinformatics20101,268
45TreeGraph 2: Combining and visualizing evidence from different phylogenetic analysesBMC Bioinformatics20101,246
46Bias in error estimation when using cross-validation for model selectionBMC Bioinformatics20061,174
47Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end readsBMC Bioinformatics20141,134
48GAGE: generally applicable gene set enrichment for pathway analysisBMC Bioinformatics20091,132
49Dendroscope: An interactive viewer for large phylogenetic treesBMC Bioinformatics20071,127
50LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposonsBMC Bioinformatics20081,110