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Top Articles

1Ultrafast and memory-efficient alignment of short DNA sequences to the human genomeGenome Biology200919,212
2Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genesGenome Biology200216,304
3Model-based Analysis of ChIP-Seq (MACS)Genome Biology200813,517
4TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusionsGenome Biology201311,713
5Metagenomic biomarker discovery and explanationGenome Biology201111,192
6Bioconductor: open software development for computational biology and bioinformaticsGenome Biology200410,796
7A scaling normalization method for differential expression analysis of RNA-seq dataGenome Biology20106,234
8Gene ontology analysis for RNA-seq: accounting for selection biasGenome Biology20105,824
9Versatile and open software for comparing large genomesGenome Biology20044,989
10voom: precision weights unlock linear model analysis tools for RNA-seq read countsGenome Biology20144,603
11DNA methylation age of human tissues and cell typesGenome Biology20134,566
12CellProfiler: image analysis software for identifying and quantifying cell phenotypesGenome Biology20064,287
13qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR dataGenome Biology20073,580
14Kraken: ultrafast metagenomic sequence classification using exact alignmentsGenome Biology20143,540
15Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciencesGenome Biology20103,082
16MicroRNA targets in DrosophilaGenome Biology20033,023
17Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced AlignmentsGenome Biology20082,484
18Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatmentGenome Biology20122,258
19The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene listsGenome Biology20072,105
20Quantifying similarity between motifsGenome Biology20071,579
21Fibroblast growth factorsGenome Biology20011,562
22methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profilesGenome Biology20121,541
23Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in ArabidopsisGenome Biology20141,501
24Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sitesGenome Biology20101,478
25Comparing protein abundance and mRNA expression levels on a genomic scaleGenome Biology20031,453
26Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiationGenome Biology20041,396
27LUMPY: a probabilistic framework for structural variant discoveryGenome Biology20141,199
28Improving RNA-Seq expression estimates by correcting for fragment biasGenome Biology20111,164
29Cyclin-dependent kinasesGenome Biology20141,103
30Accuracy and quality of massively parallel DNA pyrosequencingGenome Biology20071,060
31GoMiner: a resource for biological interpretation of genomic and proteomic dataGenome Biology20031,038
32Toward almost closed genomes with GapFillerGenome Biology20121,031
33Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumorsGenome Biology20071,009
34A whole-genome assembly of the domestic cow, Bos taurusGenome Biology20091,005
35The integrinsGenome Biology2007995
36Analyzing and minimizing PCR amplification bias in Illumina sequencing librariesGenome Biology2011943
37Moving pictures of the human microbiomeGenome Biology2011934
38Effectiveness of specific RNA-mediated interference through ingested double-stranded RNA in Caenorhabditis elegansGenome Biology2000918
39An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)Genome Biology2003880
40Accounting for cellular heterogeneity is critical in epigenome-wide association studiesGenome Biology2014880
41A novel and universal method for microRNA RT-qPCR data normalizationGenome Biology2009849
42MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtypeGenome Biology2007828
43Sp1- and Krüppel-like transcription factorsGenome Biology2003820
44A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomesGenome Biology2004814
45Plant NBS-LRR proteins: adaptable guardsGenome Biology2006804
46Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samplesGenome Biology2012797
47GeneMANIA: a real-time multiple association network integration algorithm for predicting gene functionGenome Biology2008795
48Untranslated regions of mRNAsGenome Biology2002779
49MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray dataGenome Biology2003776
50Automatic annotation of eukaryotic genes, pseudogenes and promotersGenome Biology2006749