| # | Title | Journal | Year | Citations |
|---|
| 1 | Gapped BLAST and PSI-BLAST: a new generation of protein database search programs | Nucleic Acids Research | 1997 | 64,420 |
| 2 | CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice | Nucleic Acids Research | 1994 | 59,168 |
| 3 | MUSCLE: multiple sequence alignment with high accuracy and high throughput | Nucleic Acids Research | 2004 | 36,947 |
| 4 | The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools | Nucleic Acids Research | 1997 | 34,934 |
| 5 | The Protein Data Bank | Nucleic Acids Research | 2000 | 31,087 |
| 6 | A new mathematical model for relative quantification in real-time RT-PCR | Nucleic Acids Research | 2001 | 28,594 |
| 7 | limma powers differential expression analyses for RNA-sequencing and microarray studies | Nucleic Acids Research | 2015 | 26,032 |
| 8 | KEGG: Kyoto Encyclopedia of Genes and Genomes | Nucleic Acids Research | 2000 | 25,375 |
| 9 | The SILVA ribosomal RNA gene database project: improved data processing and web-based tools | Nucleic Acids Research | 2012 | 21,425 |
| 10 | A simple salting out procedure for extracting DNA from human nucleated cells | Nucleic Acids Research | 1988 | 17,239 |
| 11 | A comprehensive set of sequence analysis programs for the VAX | Nucleic Acids Research | 1984 | 15,665 |
| 12 | A rapid alkaline extraction procedure for screening recombinant plasmid DNA | Nucleic Acids Research | 1979 | 15,424 |
| 13 | KEGG: Kyoto Encyclopedia of Genes and Genomes | Nucleic Acids Research | 1999 | 13,711 |
| 14 | Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists | Nucleic Acids Research | 2009 | 13,313 |
| 15 | MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform | Nucleic Acids Research | 2002 | 12,537 |
| 16 | STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets | Nucleic Acids Research | 2019 | 12,237 |
| 17 | Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei | Nucleic Acids Research | 1983 | 12,076 |
| 18 | Mfold web server for nucleic acid folding and hybridization prediction | Nucleic Acids Research | 2003 | 11,479 |
| 19 | ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data | Nucleic Acids Research | 2010 | 10,960 |
| 20 | Gene Expression Omnibus: NCBI gene expression and hybridization array data repository | Nucleic Acids Research | 2002 | 10,953 |
| 21 | DNA polymorphisms amplified by arbitrary primers are useful as genetic markers | Nucleic Acids Research | 1990 | 10,873 |
| 22 | AFLP: a new technique for DNA fingerprinting | Nucleic Acids Research | 1995 | 10,873 |
| 23 | Rapid isolation of high molecular weight plant DNA | Nucleic Acids Research | 1980 | 10,345 |
| 24 | tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence | Nucleic Acids Research | 1997 | 9,417 |
| 25 | STRING v10: protein–protein interaction networks, integrated over the tree of life | Nucleic Acids Research | 2015 | 9,029 |
| 26 | SWISS-MODEL: homology modelling of protein structures and complexes | Nucleic Acids Research | 2018 | 8,474 |
| 27 | MEME SUITE: tools for motif discovery and searching | Nucleic Acids Research | 2009 | 8,180 |
| 28 | Primer3—new capabilities and interfaces | Nucleic Acids Research | 2012 | 7,501 |
| 29 | Enrichr: a comprehensive gene set enrichment analysis web server 2016 update | Nucleic Acids Research | 2016 | 7,240 |
| 30 | Efficientin vitrosynthesis of biologically active RNA and RNA hybridization probes from plasmids containing a bacteriophage SP6 promoter | Nucleic Acids Research | 1984 | 7,199 |
| 31 | NCBI GEO: archive for functional genomics data sets—update | Nucleic Acids Research | 2012 | 7,174 |
| 32 | GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses | Nucleic Acids Research | 2017 | 7,114 |
| 33 | Tandem repeats finder: a program to analyze DNA sequences | Nucleic Acids Research | 1999 | 6,803 |
| 34 | KEGG: new perspectives on genomes, pathways, diseases and drugs | Nucleic Acids Research | 2017 | 6,666 |
| 35 | Loop-mediated isothermal amplification of DNA | Nucleic Acids Research | 2000 | 6,647 |
| 36 | The PRIDE database and related tools and resources in 2019: improving support for quantification data | Nucleic Acids Research | 2019 | 6,449 |
| 37 | Relative expression software tool (REST(C)) for group-wise comparison and statistical analysis of relative expression results in real-time PCR | Nucleic Acids Research | 2002 | 6,443 |
| 38 | The Pfam protein families database | Nucleic Acids Research | 2007 | 6,372 |
| 39 | The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible | Nucleic Acids Research | 2017 | 6,303 |
| 40 | Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies | Nucleic Acids Research | 2013 | 6,268 |
| 41 | The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata | Nucleic Acids Research | 2010 | 6,188 |
| 42 | UniProt: a worldwide hub of protein knowledge | Nucleic Acids Research | 2019 | 6,185 |
| 43 | dbSNP: the NCBI database of genetic variation | Nucleic Acids Research | 2001 | 6,103 |
| 44 | ARB: a software environment for sequence data | Nucleic Acids Research | 2004 | 5,816 |
| 45 | SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB | Nucleic Acids Research | 2007 | 5,788 |
| 46 | KEGG for linking genomes to life and the environment | Nucleic Acids Research | 2007 | 5,451 |
| 47 | The carbohydrate-active enzymes database (CAZy) in 2013 | Nucleic Acids Research | 2014 | 5,443 |
| 48 | KEGG as a reference resource for gene and protein annotation | Nucleic Acids Research | 2016 | 5,435 |
| 49 | DrugBank 5.0: a major update to the DrugBank database for 2018 | Nucleic Acids Research | 2018 | 5,428 |
| 50 | Pfam: the protein families database | Nucleic Acids Research | 2014 | 5,425 |
