Topic · RNA Research and Splicing
Most cited papers in RNA Research and Splicing
What are the most cited papers in RNA Research and Splicing?
The most cited paper in RNA Research and Splicing 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 "Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2" (104,335) and "STAR: ultrafast universal RNA-seq aligner" (58,026).
Showing 50 of 100 papers. Every paper with more than 3,299 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 | Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Michael I. Love, Wolfgang K. Huber, Simon Anders · Genome biology | 5 Dec 2014 | 104,335 |
| 3 | STAR: ultrafast universal RNA-seq aligner Alexander Yu. Dobin, Carrie Davis, Felix Schlesinger et al. · Bioinformatics | 25 Oct 2012 | 58,026 |
| 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 | Analyzing real-time PCR data by the comparative CT method Thomas D. Schmittgen, Kenneth J. Livak · Nature Protocols | Jun 2008 | 27,138 |
| 6 | Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Cole Trapnell, Brian A. Williams, Geo M. Pertea et al. · Nature Biotechnology | May 2010 | 16,702 |
| 7 | Differential expression analysis for sequence count data Simon Anders, Wolfgang K. Huber · Genome biology | Oct 2010 | 16,645 |
| 8 | Mapping and quantifying mammalian transcriptomes by RNA-Seq Ali Mortazavi, Brian A. Williams, Kenneth McCue et al. · Nature Methods | 30 May 2008 | 14,472 |
| 9 | Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks Cole Trapnell, Adam Roberts, Loyal A. Goff et al. · Nature Protocols | Mar 2012 | 13,036 |
| 10 | TopHat: discovering splice junctions with RNA-Seq Cole Trapnell, Lior S. Pachter, Steven L. Salzberg · Bioinformatics | 16 Mar 2009 | 12,264 |
| 11 | Exploration, normalization, and summaries of high density oligonucleotide array probe level data Rafael A. Irizarry · Biostatistics | Apr 2003 | 10,831 |
| 12 | A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping Suhas S.P. Rao, Miriam H. Huntley, Neva C. Durand et al. · Cell | Dec 2014 | 10,225 |
| 13 | In vitro selection of RNA molecules that bind specific ligands Andrew D. Ellington, Jack W. Szostak · Nature | Aug 1990 | 9,885 |
| 14 | Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells Sayda M. Elbashir, Jens Harborth, Winfried Lendeckel et al. · Nature | May 2001 | 9,461 |
| 15 | A scaling normalization method for differential expression analysis of RNA-seq data Mark D. Robinson, Alicia Oshlack · Genome biology | 2 Mar 2010 | 8,712 |
| 16 | Most mammalian mRNAs are conserved targets of microRNAs Robin C. Friedman, Kyle Kai‐How Farh, Christopher B. Burge et al. · Genome Research | 27 Oct 2008 | 8,671 |
| 17 | The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells Cole Trapnell, Davide Cacchiarelli, Jonna Grimsby et al. · Nature Biotechnology | 23 Mar 2014 | 8,179 |
| 18 | Gene ontology analysis for RNA-seq: accounting for selection bias Matthew D. Young, Matthew J. Wakefield, Gordon K. Smyth et al. · Genome biology | 4 Feb 2010 | 7,920 |
| 19 | Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1 Roel G.W. Verhaak et al. · Cancer Cell | 2010 | 7,880 |
| 20 | Predicting effective microRNA target sites in mammalian mRNAs Vikram Agarwal, George W. Bell, Jin‐Wu Nam et al. · eLife | 12 Aug 2015 | 7,826 |
| 21 | Relative expression software tool (REST(C)) for group-wise comparison and statistical analysis of relative expression results in real-time PCR Michael Walter Pfaffl · Nucleic Acids Research | May 2002 | 7,466 |
| 22 | Normalization of Real-Time Quantitative Reverse Transcription-PCR Data: A Model-Based Variance Estimation Approach to Identify Genes Suited for Normalization, Applied to Bladder and Colon Cancer Data Sets Claus L. Andersen, Jens Ledet Jensen, Torben Falck Orntoft · Cancer Research | Aug 2004 | 7,281 |
| 23 | U1 snRNP regulates cancer cell migration and invasion in vitro Jung‐Min Oh, Christopher C. Venters, Chao Di et al. · Nature Communications | 7 Jan 2020 | 7,252 |
| 24 | Biomolecular condensates: organizers of cellular biochemistry Salman F. Banani, Hyun O. Lee, Anthony A. Hyman et al. · Nature Reviews Molecular Cell Biology | 22 Feb 2017 | 6,730 |
| 25 | The GTEx Consortium atlas of genetic regulatory effects across human tissues François Aguet et al. · Science | 10 Sep 2020 | 6,192 |
| 26 | starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data Jun-Hao Li, Shun Liu, Hui Zhou et al. · Nucleic Acids Research | Dec 2013 | 6,040 |
| 27 | Long non-coding RNAs: insights into functions Tim R. Mercer, Marcel E. Dinger, John S. Mattick · Nature Reviews Genetics | 3 Feb 2009 | 5,835 |
| 28 | An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex Ye Zhang, Kenian Chen, Steven A. Sloan et al. · Journal of Neuroscience | 3 Sep 2014 | 5,474 |
| 29 | Alternative isoform regulation in human tissue transcriptomes Eric T. Wang, Rickard Sandberg, Shujun J. Luo et al. · Nature | Nov 2008 | 5,451 |
| 30 | Landscape of transcription in human cells Sarah Djebali et al. · Nature | Sep 2012 | 5,447 |
| 31 | Overview of MicroRNA Biogenesis, Mechanisms of Actions, and Circulation Jacob Anderson O’Brien, Heyam Hayder, Yara Zayed et al. · Frontiers in Endocrinology | 3 Aug 2018 | 5,381 |
| 32 | Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis Rajnish A. Gupta, Nilay Shah, Ke Wang et al. · Nature | Apr 2010 | 5,341 |
| 33 | The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression Thomas Derrien et al. · Genome Research | Sep 2012 | 5,308 |
| 34 | Gene regulation by long non-coding RNAs and its biological functions Luisa Statello, Chunjie Guo, Ling‐Ling Chen et al. · Nature Reviews Molecular Cell Biology | 22 Dec 2020 | 5,304 |
| 35 | Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Witold Filipowicz, Suvendra N. Bhattacharyya, Nahum Sonenberg · Nature Reviews Genetics | 16 Jan 2008 | 5,265 |
| 36 | The zebrafish reference genome sequence and its relationship to the human genome Kerstin Howe et al. · Nature | 16 Apr 2013 | 5,261 |
| 37 | An analysis of 5'-noncoding sequences from 699 vertebrate messenger RNAs Marilyn Kozak · Nucleic Acids Research | 1987 | 5,192 |
| 38 | Evolution and Functions of Long Noncoding RNAs Chris Paul Ponting, Peter L. Oliver, Wolf Reik · Cell | Feb 2009 | 5,169 |
| 39 | Osteoprotegerin: A Novel Secreted Protein Involved in the Regulation of Bone Density W. Scott Simonet et al. · Cell | Apr 1997 | 5,161 |
| 40 | GENCODE: The reference human genome annotation for The ENCODE Project Jennifer Harrow et al. · Genome Research | Sep 2012 | 5,112 |
| 41 | Differential Display of Eukaryotic Messenger RNA by Means of the Polymerase Chain Reaction Peng Liang, Arthur B. Pardee · Science | 14 Aug 1992 | 5,040 |
| 42 | The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans Brenda J. Reinhart, Frank John Slack, Michael Basson et al. · Nature | Feb 2000 | 5,025 |
| 43 | Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes Audrey P. Gasch, Paul T. Spellman, Camilla M. Kao et al. · Molecular Biology of the Cell | Dec 2000 | 4,991 |
| 44 | Identification of Novel Genes Coding for Small Expressed RNAs Mariana Lagos‐Quintana, Reinhard Rauhut, Winfried Lendeckel et al. · Science | 26 Oct 2001 | 4,985 |
| 45 | The single-cell transcriptional landscape of mammalian organogenesis Junyue Cao, Malte Spielmann, Xiaojie Qiu et al. · Nature | 20 Feb 2019 | 4,970 |
| 46 | N6-methyladenosine-dependent regulation of messenger RNA stability Xiao Wang, Zhike Lu, Adrian Gomez-Nguyen et al. · Nature | 26 Nov 2013 | 4,938 |
| 47 | Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs Lee P. Lim, Nelson C. Lau, Philip W. Garrett-Engele et al. · Nature | 30 Jan 2005 | 4,816 |
| 48 | Genetic effects on gene expression across human tissues François Aguet et al. · Nature | 10 Oct 2017 | 4,762 |
| 49 | The widespread regulation of microRNA biogenesis, function and decay Jacek Król, Inga Loedige, Witold Filipowicz · Nature Reviews Genetics | 27 Jul 2010 | 4,754 |
| 50 | RNA velocity of single cells Gioele La Manno et al. · Nature | 7 Aug 2018 | 4,678 |
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.