| # | Title | Journal | Year | Citations |
|---|
| 1 | Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks | Genome Research | 2003 | 37,062 |
| 2 | The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data | Genome Research | 2010 | 21,358 |
| 3 | WebLogo: A Sequence Logo Generator | Genome Research | 2004 | 10,751 |
| 4 | Circos: An information aesthetic for comparative genomics | Genome Research | 2009 | 9,003 |
| 5 | The Human Genome Browser at UCSC | Genome Research | 2002 | 8,776 |
| 6 | Velvet: Algorithms for de novo short read assembly using de Bruijn graphs | Genome Research | 2008 | 8,699 |
| 7 | CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes | Genome Research | 2015 | 7,539 |
| 8 | BLAT—The BLAST-Like Alignment Tool | Genome Research | 2002 | 7,227 |
| 9 | Most mammalian mRNAs are conserved targets of microRNAs | Genome Research | 2009 | 7,226 |
| 10 | Fast model-based estimation of ancestry in unrelated individuals | Genome Research | 2009 | 6,588 |
| 11 | Base-Calling of Automated Sequencer Traces UsingPhred. I. Accuracy Assessment | Genome Research | 1998 | 5,939 |
| 12 | Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation | Genome Research | 2017 | 5,620 |
| 13 | OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes | Genome Research | 2003 | 5,497 |
| 14 | Real time quantitative PCR. | Genome Research | 1996 | 4,991 |
| 15 | Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities | Genome Research | 1998 | 4,991 |
| 16 | CAP3: A DNA Sequence Assembly Program | Genome Research | 1999 | 4,533 |
| 17 | The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression | Genome Research | 2012 | 4,428 |
| 18 | GENCODE: The reference human genome annotation for The ENCODE Project | Genome Research | 2012 | 4,217 |
| 19 | VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing | Genome Research | 2012 | 4,086 |
| 20 | Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements | Genome Research | 2004 | 4,085 |
| 21 | Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes | Genome Research | 2005 | 3,517 |
| 22 | ABySS: A parallel assembler for short read sequence data | Genome Research | 2009 | 3,134 |
| 23 | Consed: A Graphical Tool for Sequence Finishing | Genome Research | 1998 | 3,116 |
| 24 | Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons | Genome Research | 2011 | 3,015 |
| 25 | metaSPAdes: a new versatile metagenomic assembler | Genome Research | 2017 | 2,779 |
| 26 | MEGAN analysis of metagenomic data | Genome Research | 2007 | 2,764 |
| 27 | PANTHER: A Library of Protein Families and Subfamilies Indexed by Function | Genome Research | 2003 | 2,703 |
| 28 | The Significance of Digital Gene Expression Profiles | Genome Research | 1997 | 2,665 |
| 29 | Base-calling of automated sequencer traces using phred. II. Error probabilities | Genome Research | 1998 | 2,632 |
| 30 | Maftools: efficient and comprehensive analysis of somatic variants in cancer | Genome Research | 2018 | 2,614 |
| 31 | De novo assembly of human genomes with massively parallel short read sequencing | Genome Research | 2010 | 2,516 |
| 32 | RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays | Genome Research | 2008 | 2,393 |
| 33 | Annotation of functional variation in personal genomes using RegulomeDB | Genome Research | 2012 | 2,335 |
| 34 | Mapping short DNA sequencing reads and calling variants using mapping quality scores | Genome Research | 2008 | 2,275 |
| 35 | Predicting Deleterious Amino Acid Substitutions | Genome Research | 2001 | 2,186 |
| 36 | GeneWise and Genomewise | Genome Research | 2004 | 2,128 |
| 37 | Fast and accurate de novo genome assembly from long uncorrected reads | Genome Research | 2017 | 2,071 |
| 38 | Detection of nonneutral substitution rates on mammalian phylogenies | Genome Research | 2010 | 1,878 |
| 39 | Galaxy: A platform for interactive large-scale genome analysis | Genome Research | 2005 | 1,795 |
| 40 | A novel method for real time quantitative RT-PCR. | Genome Research | 1996 | 1,765 |
| 41 | ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia | Genome Research | 2012 | 1,708 |
| 42 | Identification of Mammalian microRNA Host Genes and Transcription Units | Genome Research | 2004 | 1,704 |
| 43 | The NIH Human Microbiome Project | Genome Research | 2009 | 1,700 |
| 44 | Genomic analysis identifies association of Fusobacterium with colorectal carcinoma | Genome Research | 2012 | 1,587 |
| 45 | PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data | Genome Research | 2007 | 1,586 |
| 46 | Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma | Genome Research | 2012 | 1,582 |
| 47 | MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes | Genome Research | 2008 | 1,564 |
| 48 | AAA+: A Class of Chaperone-Like ATPases Associated with the Assembly, Operation, and Disassembly of Protein Complexes | Genome Research | 1999 | 1,549 |
| 49 | The Human Genome Browser at UCSC | Genome Research | 2002 | 1,472 |
| 50 | Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins | Genome Research | 2014 | 1,470 |
