| # | Title | Journal | Year | Citations |
|---|
| 1 | The Genome Sequence of Drosophila melanogaster | Science | 2000 | 5,566 |
| 2 | The Ensembl Variant Effect Predictor | Genome Biology | 2016 | 5,181 |
| 3 | Twelve years of SAMtools and BCFtools | GigaScience | 2021 | 4,546 |
| 4 | AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models | Nucleic Acids Research | 2022 | 3,692 |
| 5 | A Draft Sequence of the Neandertal Genome | Science | 2010 | 3,588 |
| 6 | A SARS-CoV-2 protein interaction map reveals targets for drug repurposing | Nature | 2020 | 3,542 |
| 7 | The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019 | Nucleic Acids Research | 2019 | 3,179 |
| 8 | The CCPN data model for NMR spectroscopy: Development of a software pipeline | Proteins: Structure, Function and Bioinformatics | 2005 | 2,805 |
| 9 | Ensembl 2018 | Nucleic Acids Research | 2018 | 2,710 |
| 10 | InterProScan - an integration platform for the signature-recognition methods in InterPro | Bioinformatics | 2001 | 2,580 |
| 11 | GENCODE reference annotation for the human and mouse genomes | Nucleic Acids Research | 2019 | 2,350 |
| 12 | An atlas of active enhancers across human cell types and tissues | Nature | 2014 | 2,269 |
| 13 | Synaptic, transcriptional and chromatin genes disrupted in autism | Nature | 2014 | 2,254 |
| 14 | Systematic identification of genomic markers of drug sensitivity in cancer cells | Nature | 2012 | 2,173 |
| 15 | Errors in protein structures | Nature | 1996 | 1,987 |
| 16 | The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog) | Nucleic Acids Research | 2017 | 1,932 |
| 17 | The Proteomics Identifications (PRIDE) database and associated tools: status in 2013 | Nucleic Acids Research | 2012 | 1,858 |
| 18 | Highly accurate protein structure prediction for the human proteome | Nature | 2021 | 1,773 |
| 19 | Landscape of somatic mutations in 560 breast cancer whole-genome sequences | Nature | 2016 | 1,760 |
| 20 | The ChEMBL database in 2017 | Nucleic Acids Research | 2017 | 1,718 |
| 21 | The IPD and IMGT/HLA database: allele variant databases | Nucleic Acids Research | 2015 | 1,712 |
| 22 | Prospective Derivation of a Living Organoid Biobank of Colorectal Cancer Patients | Cell | 2015 | 1,710 |
| 23 | On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database | Biochimica Et Biophysica Acta - General Subjects | 1999 | 1,601 |
| 24 | Comparative Genomics of the Eukaryotes | Science | 2000 | 1,573 |
| 25 | Control of Treg and TH17 cell differentiation by the aryl hydrocarbon receptor | Nature | 2008 | 1,544 |
| 26 | A Landscape of Pharmacogenomic Interactions in Cancer | Cell | 2016 | 1,518 |
| 27 | Targeting CXCL12 from FAP-expressing carcinoma-associated fibroblasts synergizes with anti–PD-L1 immunotherapy in pancreatic cancer | Proceedings of the National Academy of Sciences of the United States of America | 2013 | 1,482 |
| 28 | Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics | Proceedings of the National Academy of Sciences of the United States of America | 2013 | 1,471 |
| 29 | [22] Using CLUSTAL for multiple sequence alignments | Methods in Enzymology | 1996 | 1,456 |
| 30 | A comparative encyclopedia of DNA elements in the mouse genome | Nature | 2014 | 1,444 |
| 31 | HMMER web server: 2018 update | Nucleic Acids Research | 2018 | 1,432 |
| 32 | Ensembl 2016 | Nucleic Acids Research | 2016 | 1,372 |
| 33 | Applications of machine learning in drug discovery and development | Nature Reviews Drug Discovery | 2019 | 1,358 |
| 34 | Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R | Bioinformatics | 2017 | 1,283 |
| 35 | IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets | Nucleic Acids Research | 2017 | 1,251 |
| 36 | Ensembl 2021 | Nucleic Acids Research | 2021 | 1,231 |
| 37 | ChEMBL: towards direct deposition of bioassay data | Nucleic Acids Research | 2019 | 1,212 |
| 38 | Ensembl 2015 | Nucleic Acids Research | 2015 | 1,145 |
| 39 | Towards complete and error-free genome assemblies of all vertebrate species | Nature | 2021 | 1,139 |
| 40 | Ensembl 2022 | Nucleic Acids Research | 2022 | 1,103 |
| 41 | Ensembl 2020 | Nucleic Acids Research | 2020 | 1,076 |
| 42 | Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells | Nature Biotechnology | 2015 | 1,068 |
| 43 | Deep learning for computational biology | Molecular Systems Biology | 2016 | 1,059 |
| 44 | EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates | Genome Research | 2009 | 1,058 |
| 45 | The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease | Cell | 2016 | 1,052 |
| 46 | iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution | Nature Structural and Molecular Biology | 2010 | 1,026 |
| 47 | A high-resolution map of human evolutionary constraint using 29 mammals | Nature | 2011 | 1,016 |
| 48 | Function of alternative splicing | Gene | 2005 | 1,004 |
| 49 | High-throughput discovery of novel developmental phenotypes | Nature | 2016 | 1,001 |
| 50 | Diffusion pseudotime robustly reconstructs lineage branching | Nature Methods | 2016 | 982 |
