| 1 | A comprehensive map of molecular drug targets | Nature Reviews Drug Discovery | 2016 | 2,134 |
| 2 | PDBsum: Structural summaries of PDB entries | Protein Science | 2018 | 1,498 |
| 3 | An atlas of genetic influences on human blood metabolites | Nature Genetics | 2014 | 1,453 |
| 4 | ClassyFire: automated chemical classification with a comprehensive, computable taxonomy | Journal of Cheminformatics | 2016 | 1,255 |
| 5 | ChEBI in 2016: Improved services and an expanding collection of metabolites | Nucleic Acids Research | 2016 | 982 |
| 6 | Benchmark and integration of resources for the estimation of human transcription factor activities | Genome Research | 2019 | 912 |
| 7 | scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation | Genome Biology | 2020 | 671 |
| 8 | Protein–RNA interactions: new genomic technologies and perspectives | Nature Reviews Genetics | 2012 | 517 |
| 9 | Mendelian Randomization | Cold Spring Harbor Perspectives in Medicine | 0 | 404 |
| 10 | Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking | Nature Genetics | 2016 | 380 |
| 11 | Evolution and functional cross‐talk of protein post‐translational modifications | Molecular Systems Biology | 2013 | 356 |
| 12 | Efficient storage of high throughput DNA sequencing data using reference-based compression | Genome Research | 2011 | 355 |
| 13 | Comprehensive characterization of the Published Kinase Inhibitor Set | Nature Biotechnology | 2016 | 318 |
| 14 | Whole-genome fingerprint of the DNA methylome during human B cell differentiation | Nature Genetics | 2015 | 317 |
| 15 | Exome sequencing identifies NBEAL2 as the causative gene for gray platelet syndrome | Nature Genetics | 2011 | 264 |
| 16 | Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond | PLoS Pathogens | 2016 | 262 |
| 17 | Selenoprotein Gene Nomenclature | Journal of Biological Chemistry | 2016 | 251 |
| 18 | Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression | Nature Communications | 2015 | 250 |
| 19 | SBMLLevel 3: an extensible format for the exchange and reuse of biological models | Molecular Systems Biology | 2020 | 240 |
| 20 | Making proteomics data accessible and reusable: Current state of proteomics databases and repositories | Proteomics | 2015 | 202 |
| 21 | Impact of Alternative Splicing on the Human Proteome | Cell Reports | 2017 | 175 |
| 22 | Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing | Nature Methods | 2015 | 166 |
| 23 | AlphaFold heralds a data-driven revolution in biology and medicine | Nature Medicine | 2021 | 161 |
| 24 | Open and closed states of Candida antarctica lipase B: protonation and the mechanism of interfacial activation | Journal of Lipid Research | 2015 | 159 |
| 25 | Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment | Proteins: Structure, Function and Bioinformatics | 2016 | 154 |
| 26 | Crowdsourcing biomedical research: leveraging communities as innovation engines | Nature Reviews Genetics | 2016 | 154 |
| 27 | The Olfactory Transcriptomes of Mice | PLoS Genetics | 2014 | 152 |
| 28 | The impact of AlphaFold2 one year on | Nature Methods | 2022 | 149 |
| 29 | KNIME-CDK: Workflow-driven cheminformatics | BMC Bioinformatics | 2013 | 137 |
| 30 | Causal integration of multi‐omics data with prior knowledge to generate mechanistic hypotheses | Molecular Systems Biology | 2021 | 135 |
| 31 | Long-range enhancers regulating Myc expression are required for normal facial morphogenesis | Nature Genetics | 2014 | 133 |
| 32 | Modeling protein‐protein, protein‐peptide, and protein‐oligosaccharide complexes: CAPRI 7th edition | Proteins: Structure, Function and Bioinformatics | 2020 | 130 |
| 33 | EC-BLAST: a tool to automatically search and compare enzyme reactions | Nature Methods | 2014 | 125 |
| 34 | The eNanoMapper database for nanomaterial safety information | Beilstein Journal of Nanotechnology | 2015 | 124 |
| 35 | Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment | Proteins: Structure, Function and Bioinformatics | 2019 | 124 |
| 36 | Genome-wide Bisulfite Sequencing in Zygotes Identifies Demethylation Targets and Maps the Contribution of TET3 Oxidation | Cell Reports | 2014 | 123 |
| 37 | Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment | Proteins: Structure, Function and Bioinformatics | 2021 | 118 |
| 38 | PubChemRDF: towards the semantic annotation of PubChem compound and substance databases | Journal of Cheminformatics | 2015 | 117 |
| 39 | An atlas of human kinase regulation | Molecular Systems Biology | 2016 | 115 |
| 40 | VarSite: Disease variants and protein structure | Protein Science | 2020 | 109 |
| 41 | Reproducibility in systems biology modelling | Molecular Systems Biology | 2021 | 108 |
| 42 | The European Genome-phenome Archive in 2021 | Nucleic Acids Research | 2022 | 105 |
| 43 | The challenge of modeling protein assemblies: the CASP12‐CAPRI experiment | Proteins: Structure, Function and Bioinformatics | 2018 | 96 |
| 44 | Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5′ splice site strength | Genome Biology | 2015 | 93 |
| 45 | PDBsum extras: SARS‐CoV‐2 and AlphaFold models | Protein Science | 2022 | 92 |
| 46 | Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data | Nature Communications | 2015 | 89 |
| 47 | eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment | Journal of Biomedical Semantics | 2015 | 81 |
| 48 | Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets | Journal of Cheminformatics | 2013 | 80 |
| 49 | Exploring the potential of public proteomics data | Proteomics | 2016 | 80 |
| 50 | Solid Tumors of Childhood Display Specific Serum microRNA Profiles | Cancer Epidemiology Biomarkers and Prevention | 2015 | 78 |
