| # | Title | Journal | Year | Citations |
|---|
|
| 1 | Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks | Genome Research | 2003 | 39,475 |
| 2 | Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 | Nature Biotechnology | 2019 | 12,956 |
| 3 | Circulating microRNAs as stable blood-based markers for cancer detection | Proceedings of the National Academy of Sciences of the United States of America | 2008 | 7,173 |
| 4 | The Cancer Genome Atlas Pan-Cancer analysis project | Nature Genetics | 2013 | 6,646 |
| 5 | Mass spectrometry-based proteomics | Nature | 2003 | 6,359 |
| 6 | Empirical Statistical Model To Estimate the Accuracy of Peptide Identifications Made by MS/MS and Database Search | Analytical Chemistry | 2002 | 4,564 |
| 7 | A Statistical Model for Identifying Proteins by Tandem Mass Spectrometry | Analytical Chemistry | 2003 | 4,377 |
| 8 | The Somatic Genomic Landscape of Glioblastoma | Cell | 2013 | 4,133 |
| 9 | The Immune Landscape of Cancer | Immunity | 2018 | 4,015 |
| 10 | A distinct lineage of CD4 T cells regulates tissue inflammation by producing interleukin 17 | Nature Immunology | 2005 | 3,927 |
| 11 | The innate immune response to bacterial flagellin is mediated by Toll-like receptor 5 | Nature | 2001 | 3,219 |
| 12 | A cross-platform toolkit for mass spectrometry and proteomics | Nature Biotechnology | 2012 | 3,018 |
| 13 | ProteomeXchange provides globally coordinated proteomics data submission and dissemination | Nature Biotechnology | 2014 | 2,572 |
| 14 | An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics | Cell | 2018 | 2,498 |
| 15 | The MicroRNA Spectrum in 12 Body Fluids | Clinical Chemistry | 2010 | 2,404 |
| 16 | Oncogenic Signaling Pathways in The Cancer Genome Atlas | Cell | 2018 | 2,287 |
| 17 | Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Metabolic Network | Science | 2001 | 1,927 |
| 18 | RepeatModeler2 for automated genomic discovery of transposable element families | Proceedings of the National Academy of Sciences of the United States of America | 2020 | 1,835 |
| 19 | Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer | Cell | 2018 | 1,834 |
| 20 | A Landscape of Pharmacogenomic Interactions in Cancer | Cell | 2016 | 1,620 |
| 21 | Lipocalin 2 mediates an innate immune response to bacterial infection by sequestrating iron | Nature | 2004 | 1,571 |
| 22 | The complete sequence of a human genome | Science | 2022 | 1,565 |
| 23 | The Phaeodactylum genome reveals the evolutionary history of diatom genomes | Nature | 2008 | 1,501 |
| 24 | T Helper 17 Lineage Differentiation Is Programmed by Orphan Nuclear Receptors RORα and RORγ | Immunity | 2008 | 1,488 |
| 25 | A NEWAPPROACH TODECODINGLIFE: Systems Biology | Annual Review of Genomics and Human Genetics | 2001 | 1,474 |
| 26 | Collaborative Induction of Inflammatory Responses by Dectin-1 and Toll-like Receptor 2 | Journal of Experimental Medicine | 2003 | 1,462 |
| 27 | A Genomic Regulatory Network for Development | Science | 2002 | 1,411 |
| 28 | Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry | Nature Biotechnology | 2003 | 1,383 |
| 29 | Essential autocrine regulation by IL-21 in the generation of inflammatory T cells | Nature | 2007 | 1,350 |
| 30 | A network of protein–protein interactions in yeast | Nature Biotechnology | 2000 | 1,292 |
| 31 | Comet: An open‐source MS/MS sequence database search tool | Proteomics | 2013 | 1,267 |
| 32 | Selected reaction monitoring for quantitative proteomics: a tutorial | Molecular Systems Biology | 2008 | 1,235 |
| 33 | Mass Spectrometry in Proteomics | Chemical Reviews | 2001 | 1,155 |
| 34 | Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancy | Nature Genetics | 2013 | 1,139 |
| 35 | Caspase-1-induced pyroptosis is an innate immune effector mechanism against intracellular bacteria | Nature Immunology | 2010 | 1,113 |
| 36 | Discovering regulatory and signalling circuits in molecular interaction networks | Bioinformatics | 2002 | 1,111 |
| 37 | Circulating microRNAs, potential biomarkers for drug-induced liver injury | Proceedings of the National Academy of Sciences of the United States of America | 2009 | 1,101 |
| 38 | Generation of T Follicular Helper Cells Is Mediated by Interleukin-21 but Independent of T Helper 1, 2, or 17 Cell Lineages | Immunity | 2008 | 1,082 |
| 39 | Critical Regulation of Early Th17 Cell Differentiation by Interleukin-1 Signaling | Immunity | 2009 | 1,067 |
| 40 | Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans | Nature Immunology | 2009 | 1,042 |
| 41 | Cytoplasmic flagellin activates caspase-1 and secretion of interleukin 1β via Ipaf | Nature Immunology | 2006 | 1,038 |
| 42 | The evolution of vertebrate Toll-like receptors | Proceedings of the National Academy of Sciences of the United States of America | 2005 | 1,034 |
| 43 | Phagocytosis of Microbes: Complexity in Action | Annual Review of Immunology | 2002 | 966 |
| 44 | Exosomes: proteomic insights and diagnostic potential | Expert Review of Proteomics | 2009 | 961 |
| 45 | A community-driven global reconstruction of human metabolism | Nature Biotechnology | 2013 | 936 |
| 46 | Export of microRNAs and microRNA-protective protein by mammalian cells | Nucleic Acids Research | 2010 | 920 |
| 47 | Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry | Nature Biotechnology | 2001 | 917 |
| 48 | Interpretation of Shotgun Proteomic Data | Molecular and Cellular Proteomics | 2005 | 916 |
| 49 | Variable host-pathogen compatibility in Mycobacterium tuberculosis | Proceedings of the National Academy of Sciences of the United States of America | 2006 | 914 |
| 50 | The UCSC Genome Browser database: 2015 update | Nucleic Acids Research | 2015 | 905 |
