Most cited papers in Gene expression and cancer classification
What are the most cited papers in Gene expression and cancer classification?
The most cited paper in Gene expression and cancer classification is "Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method" (Kenneth J. Livak, Thomas D. Schmittgen, 2001), with 184,956 citations. Next come "Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles" (58,060) and "edgeR : a Bioconductor package for differential expression analysis of digital gene expression data" (45,449).
Showing 50 of 100 papers. Every paper with more than 4,994 citations is listed.
| # | Paper | ||
|---|---|---|---|
| 1 | Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method Kenneth J. Livak, Thomas D. Schmittgen · Methods | Dec 2001 | 184,956 |
| 2 | 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 |
| 3 | edgeR : a Bioconductor package for differential expression analysis of digital gene expression data Mark D. Robinson, Davis James McCarthy, Gordon K. Smyth · Bioinformatics | 11 Nov 2009 | 45,449 |
| 4 | limma powers differential expression analyses for RNA-sequencing and microarray studies Matthew E. Ritchie, Belinda Phipson, Di Wu et al. · Nucleic Acids Research | 20 Jan 2015 | 44,530 |
| 5 | 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 |
| 6 | 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 |
| 7 | A new mathematical model for relative quantification in real-time RT-PCR Michael Walter Pfaffl · Nucleic Acids Research | May 2001 | 35,329 |
| 8 | BEDTools: a flexible suite of utilities for comparing genomic features Aaron R. Quinlan, Ira M. Hall · Bioinformatics | 28 Jan 2010 | 31,302 |
| 9 | The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data Aaron McKenna, Matthew G. Hanna, Eric Banks et al. · Genome Research | 19 Jul 2010 | 30,696 |
| 10 | featureCounts: an efficient general purpose program for assigning sequence reads to genomic features Yang Liao, Gordon K. Smyth, Wei Shi · Bioinformatics | 13 Nov 2013 | 30,361 |
| 11 | WGCNA: an R package for weighted correlation network analysis Peter Langfelder, Steve Horvath · BMC Bioinformatics | Dec 2008 | 30,149 |
| 12 | Analyzing real-time PCR data by the comparative CT method Thomas D. Schmittgen, Kenneth J. Livak · Nature Protocols | Jun 2008 | 27,138 |
| 13 | Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 Evan K Bolyen et al. · Nature Biotechnology | 24 Jul 2019 | 25,165 |
| 14 | Regularization and Variable Selection Via the Elastic Net Hui Jun Zou, Trevor Hastie · Journal of the Royal Statistical Society Series B (Statistical Methodology) | 9 Mar 2005 | 21,757 |
| 15 | Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes Jo Vandesompele, Katleen De Preter, Filip Pattyn et al. · Genome biology | 18 Jun 2002 | 20,347 |
| 16 | Metagenomic biomarker discovery and explanation Nicola Segata, Jacques Izard, Levi D. Waldron et al. · Genome biology | 24 Jun 2011 | 17,136 |
| 17 | Twelve years of SAMtools and BCFtools Petr Danecek, James Bonfield, Jennifer Liddle et al. · GigaScience | 29 Jan 2021 | 17,094 |
| 18 | GSVA: gene set variation analysis for microarray and RNA-Seq data Sonja Hänzelmann, Robert Castelo, Justin Guinney · BMC Bioinformatics | 16 Jan 2013 | 17,089 |
| 19 | Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows Laurent Excoffier, Heidi E. L. Lischer · Molecular Ecology Resources | Mar 2010 | 16,765 |
| 20 | Differential expression analysis for sequence count data Simon Anders, Wolfgang K. Huber · Genome biology | Oct 2010 | 16,645 |
| 21 | The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments Stephen Andrew Bustin, Vladimı́r Beneš, Jeremy A. Garson et al. · Clinical Chemistry | 26 Feb 2009 | 16,583 |
| 22 | Molecular portraits of human breast tumours Charles M. Perou, Thérese Sørlie, Michael B. Eisen et al. · Nature | 17 Aug 2000 | 16,552 |
| 23 | 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 |
| 24 | Tissue-based map of the human proteome Mathias Uhlén et al. · Science | 22 Jan 2015 | 16,343 |
| 25 | 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 |
| 26 | 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 |
| 27 | The Molecular Signatures Database Hallmark Gene Set Collection Arthur Liberzon, Chet Birger, Helga Thorvaldsdóttir et al. · Cell Systems | Dec 2015 | 15,167 |
| 28 | ggplot2: Elegant Graphics for Data Analysis Cedric E. Ginestet · Journal of the Royal Statistical Society Series A (Statistics in Society) | 2011 | 14,905 |
| 29 | 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 |
| 30 | Robust enumeration of cell subsets from tissue expression profiles Aaron M. Newman, Chih Long Liu, Michael Richard Green et al. · Nature Methods | 30 Mar 2015 | 14,493 |
| 31 | Mapping and quantifying mammalian transcriptomes by RNA-Seq Ali Mortazavi, Brian A. Williams, Kenneth McCue et al. · Nature Methods | 30 May 2008 | 14,472 |
| 32 | Gene Expression Omnibus: NCBI gene expression and hybridization array data repository Ron Edgar · Nucleic Acids Research | 2002 | 14,110 |
| 33 | Comprehensive molecular portraits of human breast tumours The Cancer Genome Atlas Network · Nature | 21 Sep 2012 | 12,624 |
| 34 | CD-HIT: accelerated for clustering the next-generation sequencing data LiMin Fu, Beifang Niu, Zhengwei Zhu et al. · Bioinformatics | 11 Oct 2012 | 12,256 |
| 35 | Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments Gordon K. Smyth · Statistical Applications in Genetics and Molecular Biology | 12 Jan 2004 | 12,191 |
| 36 | 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 |
| 37 | 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 |
| 38 | MEME SUITE: tools for motif discovery and searching Timothy L. Bailey, Mikael Bodén, Fabian A. Buske et al. · Nucleic Acids Research | 20 May 2009 | 11,719 |
| 39 | Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring Todd R. Golub, Donna K. Slonim, Pablo Tamayo et al. · Science | 15 Oct 1999 | 11,660 |
| 40 | Creating the CIPRES Science Gateway for inference of large phylogenetic trees Mark A. Miller, Wayne Pfeiffer, Terri Schwartz | Nov 2010 | 11,502 |
| 41 | Complex heatmaps reveal patterns and correlations in multidimensional genomic data Zuguang Gu, Roland Eils, Matthias Schlesner · Bioinformatics | 20 May 2016 | 11,317 |
| 42 | MultiQC: summarize analysis results for multiple tools and samples in a single report Philip Ewels, Måns Magnusson, Sverker Lundin et al. · Bioinformatics | 16 Jun 2016 | 11,105 |
| 43 | Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications Thérese Sørlie, Charles M. Perou, Robert John Tibshirani et al. · Proceedings of the National Academy of Sciences | 11 Sep 2001 | 11,073 |
| 44 | 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 |
| 45 | Exploration, normalization, and summaries of high density oligonucleotide array probe level data Rafael A. Irizarry · Biostatistics | Apr 2003 | 10,831 |
| 46 | 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 |
| 47 | Significance analysis of microarrays applied to the ionizing radiation response Virginia Goss Tusher, Robert John Tibshirani, Gilbert Chu · Proceedings of the National Academy of Sciences | 17 Apr 2001 | 10,744 |
| 48 | 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 |
| 49 | Feature selection based on mutual information criteria of max-dependency, max-relevance, and min-redundancy Hanchuan Peng, Fuhui Long, Chen Ding · IEEE Transactions on Pattern Analysis and Machine Intelligence | 22 Jun 2005 | 10,690 |
| 50 | MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph Dinghua Li, Chi-Man Liu, Ruibang Luo et al. · Bioinformatics | 20 Jan 2015 | 10,529 |
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.