| # | Title | Journal | Year | Citations |
|---|
| 1 | Fast and accurate short read alignment with Burrows–Wheeler transform | Bioinformatics | 2009 | 43,062 |
| 2 | The variant call format and VCFtools | Bioinformatics | 2011 | 11,326 |
| 3 | Mutations of the BRAF gene in human cancer | Nature | 2002 | 9,374 |
| 4 | Velvet: Algorithms for de novo short read assembly using de Bruijn graphs | Genome Research | 2008 | 8,699 |
| 5 | The FAIR Guiding Principles for scientific data management and stewardship | Scientific Data | 2016 | 8,670 |
| 6 | EMBOSS: The European Molecular Biology Open Software Suite | Trends in Genetics | 2000 | 8,136 |
| 7 | Signatures of mutational processes in human cancer | Nature | 2013 | 8,060 |
| 8 | Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence | Nature | 1998 | 7,357 |
| 9 | The PRIDE database and related tools and resources in 2019: improving support for quantification data | Nucleic Acids Research | 2019 | 6,449 |
| 10 | The Pfam protein families database | Nucleic Acids Research | 2007 | 6,372 |
| 11 | The mutational constraint spectrum quantified from variation in 141,456 humans | Nature | 2020 | 6,140 |
| 12 | The Genome Sequence of Drosophila melanogaster | Science | 2000 | 5,566 |
| 13 | The Pfam protein families database: towards a more sustainable future | Nucleic Acids Research | 2016 | 5,391 |
| 14 | The Ensembl Variant Effect Predictor | Genome Biology | 2016 | 5,181 |
| 15 | Twelve years of SAMtools and BCFtools | GigaScience | 2021 | 4,546 |
| 16 | Landscape of transcription in human cells | Nature | 2012 | 4,484 |
| 17 | The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression | Genome Research | 2012 | 4,428 |
| 18 | miRBase: microRNA sequences, targets and gene nomenclature | Nucleic Acids Research | 2006 | 4,192 |
| 19 | LigPlot+: Multiple Ligand–Protein Interaction Diagrams for Drug Discovery | Journal of Chemical Information and Modeling | 2011 | 4,148 |
| 20 | Roary: rapid large-scale prokaryote pan genome analysis | Bioinformatics | 2015 | 4,099 |
| 21 | Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease | Nature | 2012 | 4,038 |
| 22 | The Pfam protein families database in 2019 | Nucleic Acids Research | 2019 | 3,937 |
| 23 | Global variation in copy number in the human genome | Nature | 2006 | 3,831 |
| 24 | The EMBL-EBI search and sequence analysis tools APIs in 2019 | Nucleic Acids Research | 2019 | 3,820 |
| 25 | Minimum information about a microarray experiment (MIAME)—toward standards for microarray data | Nature Genetics | 2001 | 3,750 |
| 26 | The zebrafish reference genome sequence and its relationship to the human genome | Nature | 2013 | 3,708 |
| 27 | A Draft Sequence of the Neandertal Genome | Science | 2010 | 3,588 |
| 28 | 2016 update of the PRIDE database and its related tools | Nucleic Acids Research | 2016 | 3,451 |
| 29 | Systematic functional analysis of the Caenorhabditis elegans genome using RNAi | Nature | 2003 | 3,343 |
| 30 | The Reactome pathway Knowledgebase | Nucleic Acids Research | 2016 | 3,319 |
| 31 | The Pfam protein families database | Nucleic Acids Research | 2012 | 3,306 |
| 32 | COSMIC: the Catalogue Of Somatic Mutations In Cancer | Nucleic Acids Research | 2019 | 3,196 |
| 33 | The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019 | Nucleic Acids Research | 2019 | 3,179 |
| 34 | Accurate whole human genome sequencing using reversible terminator chemistry | Nature | 2008 | 3,118 |
| 35 | The Pfam protein families database | Nucleic Acids Research | 2004 | 3,084 |
| 36 | Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt | Nature Protocols | 2009 | 3,084 |
| 37 | ChEMBL: a large-scale bioactivity database for drug discovery | Nucleic Acids Research | 2012 | 3,028 |
| 38 | UniProt: the Universal Protein knowledgebase | Nucleic Acids Research | 2004 | 2,994 |
| 39 | Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2) | Nature | 2002 | 2,940 |
| 40 | Artemis: sequence visualization and annotation | Bioinformatics | 2000 | 2,912 |
| 41 | A census of human cancer genes | Nature Reviews Cancer | 2004 | 2,868 |
| 42 | Patterns of somatic mutation in human cancer genomes | Nature | 2007 | 2,802 |
| 43 | The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences | Nucleic Acids Research | 2022 | 2,766 |
| 44 | Ensembl 2018 | Nucleic Acids Research | 2018 | 2,710 |
| 45 | Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease | Nature Genetics | 2009 | 2,697 |
| 46 | The Pfam protein families database | Nucleic Acids Research | 2010 | 2,693 |
| 47 | Discovery and refinement of loci associated with lipid levels | Nature Genetics | 2013 | 2,641 |
| 48 | InterProScan - an integration platform for the signature-recognition methods in InterPro | Bioinformatics | 2001 | 2,580 |
| 49 | InterProScan: protein domains identifier | Nucleic Acids Research | 2005 | 2,556 |
| 50 | ProteomeXchange provides globally coordinated proteomics data submission and dissemination | Nature Biotechnology | 2014 | 2,505 |
