Most cited papers in Bioinformatics and Genomic Networks
What are the most cited papers in Bioinformatics and Genomic Networks?
The most cited paper in Bioinformatics and Genomic Networks is "Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles" (Aravind N. Subramanian, Pablo Tamayo, Vamsi Krishna Mootha et al., 2005), with 58,060 citations. Next come "Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks" (55,788) and "Gene Ontology: tool for the unification of biology" (45,425).
Showing 50 of 100 papers. Every paper with more than 4,734 citations is listed.
| # | Paper | ||
|---|---|---|---|
| 1 | Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles Aravind N. Subramanian, Pablo Tamayo, Vamsi Krishna Mootha et al. · Proceedings of the National Academy of Sciences | 30 Sep 2005 | 58,060 |
| 2 | Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks Paul T. Shannon, Andrew Markiel, Owen W. Ozier et al. · Genome Research | Nov 2003 | 55,788 |
| 3 | Gene Ontology: tool for the unification of biology Michael Ashburner, Catherine A. Ball, Judith A. Blake et al. · Nature Genetics | May 2000 | 45,425 |
| 4 | The Protein Data Bank Helen Miriam Berman · Nucleic Acids Research | 2000 | 40,564 |
| 5 | KEGG: Kyoto Encyclopedia of Genes and Genomes Minoru I. Kanehisa · Nucleic Acids Research | 2000 | 40,289 |
| 6 | clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters Guangchuang Yu, Li-Gen Wang, Yanyan Han et al. · OMICS A Journal of Integrative Biology | 28 Mar 2012 | 39,704 |
| 7 | Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources Da Wei Huang, Brad T. Sherman, Richard A. Lempicki · Nature Protocols | 18 Dec 2008 | 37,929 |
| 8 | PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses Shaun Purcell, Benjamin M. Neale, Katherine EO Todd-Brown et al. · The American Journal of Human Genetics | 8 Aug 2007 | 36,890 |
| 9 | QIIME allows analysis of high-throughput community sequencing data J. Gregory Caporaso et al. · Nature Methods | 11 Apr 2010 | 36,341 |
| 10 | KEGG: Kyoto Encyclopedia of Genes and Genomes Hiroyuki Ogata, Susumu Goto, Kazushige Sato et al. · Nucleic Acids Research | 1999 | 32,529 |
| 11 | WGCNA: an R package for weighted correlation network analysis Peter Langfelder, Steve Horvath · BMC Bioinformatics | Dec 2008 | 30,149 |
| 12 | phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data Paul J. McMurdie, Susan Holmes · PLoS ONE | 22 Apr 2013 | 23,323 |
| 13 | Search and clustering orders of magnitude faster than BLAST R. C. Edgar · Bioinformatics | 12 Aug 2010 | 22,013 |
| 14 | STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets Damian Szklarczyk, Annika L. Gable, David B. Lyon et al. · Nucleic Acids Research | 16 Nov 2018 | 19,535 |
| 15 | New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0 Stéphane Guindon, Jean-François Dufayard, Vincent Lefort et al. · Systematic Biology | 29 Mar 2010 | 19,476 |
| 16 | The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data Ethan G Cerami, Jianjiong Gao, Uğur Doğrusöz et al. · Cancer Discovery | May 2012 | 18,789 |
| 17 | GSVA: gene set variation analysis for microarray and RNA-Seq data Sonja Hänzelmann, Robert Castelo, Justin Guinney · BMC Bioinformatics | 16 Jan 2013 | 17,089 |
| 18 | Cluster analysis and display of genome-wide expression patterns Michael B. Eisen, Paul T. Spellman, Patrick O. Brown et al. · Proceedings of the National Academy of Sciences | 8 Dec 1998 | 16,479 |
| 19 | Tissue-based map of the human proteome Mathias Uhlén et al. · Science | 22 Jan 2015 | 16,343 |
| 20 | Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal Jianjiong Gao, Bülent Arman Aksoy, Uğur Doğrusöz et al. · Science Signaling | 2 Apr 2013 | 16,184 |
| 21 | Metascape provides a biologist-oriented resource for the analysis of systems-level datasets Yingyao Zhou, Bin Zhou, Lars Pache et al. · Nature Communications | 3 Apr 2019 | 16,072 |
| 22 | Community structure in social and biological networks Michelle Girvan, Mark E. J. Newman · Proceedings of the National Academy of Sciences | 11 Jun 2002 | 15,819 |
| 23 | Fast and sensitive protein alignment using DIAMOND Benjamin Buchfink, Chao Xie, Daniel H. Huson · Nature Methods | 17 Nov 2014 | 15,753 |
| 24 | TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data Chengjie Chen, Hao Chen, Yi Zhang et al. · Molecular Plant | 23 Jun 2020 | 15,674 |
| 25 | The Molecular Signatures Database Hallmark Gene Set Collection Arthur Liberzon, Chet Birger, Helga Thorvaldsdóttir et al. · Cell Systems | Dec 2015 | 15,167 |
| 26 | BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs Felipe A. Simão, Robert Michael Waterhouse, Panagiotis Ioannidis et al. · Bioinformatics | 9 Jun 2015 | 14,906 |
| 27 | Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists Da Wei Huang, Brad T. Sherman, Richard A. Lempicki · Nucleic Acids Research | 25 Nov 2008 | 14,856 |
| 28 | SWISS-MODEL: homology modelling of protein structures and complexes Andrew Mark Waterhouse, Martino Bertoni, Stefan Bienert et al. · Nucleic Acids Research | 7 May 2018 | 14,049 |
| 29 | clusterProfiler 4.0: A universal enrichment tool for interpreting omics data Tianzhi Wu, Erqiang Hu, Shuangbin Xu et al. · The Innovation | Jul 2021 | 13,194 |
| 30 | A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff Pablo Cingolani, Adrian E. Platts, Le Lily Wang et al. · Fly | Apr 2012 | 12,997 |
| 31 | Modularity and community structure in networks Mark E. J. Newman · Proceedings of the National Academy of Sciences | 24 May 2006 | 12,522 |
| 32 | Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research Ana Conesa, Stefan Götz, Juan Miguel García-Gómez et al. · Bioinformatics | 4 Aug 2005 | 12,162 |
| 33 | Enrichr: a comprehensive gene set enrichment analysis web server 2016 update Maxim V. Kuleshov, Matthew R. Jones, Andrew D. Rouillard et al. · Nucleic Acids Research | 3 May 2016 | 12,102 |
| 34 | Community detection in graphs Santo Fortunato · Physics Reports | 18 Nov 2009 | 11,474 |
| 35 | STRING v10: protein–protein interaction networks, integrated over the tree of life Damian Szklarczyk, Andrea Franceschini, Stefan Wyder et al. · Nucleic Acids Research | 28 Oct 2014 | 11,220 |
| 36 | node2vec Aditya Grover, Jure Leskovec | 8 Aug 2016 | 11,121 |
| 37 | NCBI GEO: archive for functional genomics data sets—update Tanya Barrett, Stephen E. Wilhite, Pierre Ledoux et al. · Nucleic Acids Research | 26 Nov 2012 | 11,009 |
| 38 | In silico prediction of protein-protein interactions in human macrophages Oussema Souiai, Fatma Zahra Guerfali, Slimane Ben Miled et al. · BMC Research Notes | 2014 | 10,946 |
| 39 | PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes Vamsi Krishna Mootha et al. · Nature Genetics | 13 Jun 2003 | 10,808 |
| 40 | GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses Zefang Tang, Chenwei Li, Chenwei Li et al. · Nucleic Acids Research | 5 Apr 2017 | 10,731 |
| 41 | EMBOSS: The European Molecular Biology Open Software Suite Peter Rice, Ian Longden, Alan J. Bleasby · Trends in Genetics | Jun 2000 | 10,011 |
| 42 | The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest Damian Szklarczyk, Rebecca L. Kirsch, Mikaela Koutrouli et al. · Nucleic Acids Research | 19 Oct 2022 | 9,763 |
| 43 | KEGG: new perspectives on genomes, pathways, diseases and drugs Minoru I. Kanehisa, Miho Furumichi, Mao Tanabe et al. · Nucleic Acids Research | 26 Oct 2016 | 9,650 |
| 44 | DAVID: Database for Annotation, Visualization, and Integrated Discovery Glynn Dennis, Brad T. Sherman, Douglas A Hosack et al. · Genome biology | 3 Apr 2003 | 9,558 |
| 45 | Adjusting batch effects in microarray expression data using empirical Bayes methods William Evan Johnson, Cheng Li, Ariel Rabinovic · Biostatistics | 21 Apr 2006 | 9,409 |
| 46 | The Perseus computational platform for comprehensive analysis of (prote)omics data Stefka Tyanova, Tikira Temu, Pavel G. Sinitcyn et al. · Nature Methods | 27 Jun 2016 | 9,121 |
| 47 | The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets Damian Szklarczyk, Annika L Gable, Katerina C. Nastou et al. · Nucleic Acids Research | 23 Nov 2020 | 8,805 |
| 48 | Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool Edward Y. Chen, Christopher M. Tan, Yan Kou et al. · BMC Bioinformatics | 15 Apr 2013 | 8,650 |
| 49 | Cancer Genome Landscapes Bert Vogelstein, Nickolas Papadopoulos, Victor E. Velculescu et al. · Science | 28 Mar 2013 | 8,204 |
| 50 | Network biology: understanding the cell's functional organization Albert-Ĺaszló Barabási, Zoltán N. Oltvai · Nature Reviews Genetics | 21 Jan 2004 | 8,151 |
Citations are OpenAlex's own counts, from its 2026-09-23 snapshot, so the ranking can differ from Google Scholar or Web of Science. A paper is listed for a field when OpenAlex files it under one of the field's topics; retracted papers and papers whose citation count cannot be traced to citing works are left out, and a preprint and the article it became are shown once. Release dates are OpenAlex's: where a source gave only a month or a year, that is what is shown. How the lists are chosen.