Most cited papers in Chromosomal and Genetic Variations
What are the most cited papers in Chromosomal and Genetic Variations?
The most cited paper in Chromosomal and Genetic Variations is "MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0" (Koichiro Tamura, Joel T. Dudley, M Nei et al., 2007), with 28,894 citations. Next come "IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies" (28,418) and "RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome" (24,027).
Showing 50 of 100 papers. Every paper with more than 2,373 citations is listed.
| # | Paper | ||
|---|---|---|---|
| 1 | MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0 Koichiro Tamura, Joel T. Dudley, M Nei et al. · Molecular Biology and Evolution | 18 Apr 2007 | 28,894 |
| 2 | IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies Lam-Tung Nguyen, Heiko A. Schmidt, Arndt von Haeseler et al. · Molecular Biology and Evolution | 3 Nov 2014 | 28,418 |
| 3 | RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome Bo Li, Colin N. Dewey · BMC Bioinformatics | 4 Aug 2011 | 24,027 |
| 4 | A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood Stéphane Guindon, Olivier Gascuel · Systematic Biology | Oct 2003 | 17,109 |
| 5 | Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype Daehwan Kim, Joseph M. Paggi, Chanhee Park et al. · Nature Biotechnology | Aug 2019 | 16,558 |
| 6 | GENEPOP (Version 1.2): Population Genetics Software for Exact Tests and Ecumenicism Michel Raymond, François Rousset · Journal of Heredity | May 1995 | 15,620 |
| 7 | TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions Daehwan Kim, Geo M. Pertea, Cole Trapnell et al. · Genome biology | 25 Apr 2013 | 13,857 |
| 8 | DNA polymorphisms amplified by arbitrary primers are useful as genetic markers John Garnett Williams, Anne R. Kubelik, Kenneth J. Livak et al. · Nucleic Acids Research | 1990 | 13,158 |
| 9 | Rapid isolation of high molecular weight plant DNA Michael G. Murray, William F. Thompson · Nucleic Acids Research | 1980 | 12,462 |
| 10 | Circos: An information aesthetic for comparative genomics Martin I. Krzywinski, Jacqueline E. Schein, İnanç Birol et al. · Genome Research | 18 Jun 2009 | 12,144 |
| 11 | Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets Benjamin P. Lewis, Christopher B. Burge, David P. Bartel · Cell | 2005 | 12,048 |
| 12 | QUAST: quality assessment tool for genome assemblies Alexey A. Gurevich, Vladislav Saveliev, Nikolay Vyahhi et al. · Bioinformatics | 19 Feb 2013 | 11,980 |
| 13 | The Human Genome Browser at UCSC W. James Kent, Charles W. Sugnet, Terrence S. Furey et al. · Genome Research | 16 May 2002 | 10,998 |
| 14 | Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome Erez Lieberman-Aiden, Nynke L. van Berkum, Louise Williams et al. · Science | 8 Oct 2009 | 9,848 |
| 15 | Velvet: Algorithms for de novo short read assembly using de Bruijn graphs Daniel R. Zerbino, Ewan Birney · Genome Research | 18 Mar 2008 | 9,816 |
| 16 | Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray Mark Schena, Dari Shalon, Ronald W. Davis et al. · Science | 20 Oct 1995 | 9,654 |
| 17 | Analysis of Gene Diversity in Subdivided Populations Masatoshi Nei · Proceedings of the National Academy of Sciences | Dec 1973 | 9,028 |
| 18 | MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity Yupeng Wang, Haibao Tang, Jeremy D. DeBarry et al. · Nucleic Acids Research | 4 Jan 2012 | 8,668 |
| 19 | OrthoFinder: phylogenetic orthology inference for comparative genomics David Emms, Steven L. Kelly · Genome biology | 14 Nov 2019 | 8,364 |
| 20 | The Protein Kinase Complement of the Human Genome Gerard Manning, D B Whyte, Robert A. Martinez et al. · Science | 5 Dec 2002 | 8,252 |
| 21 | DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets Julio Rozas, Albert Ferrer-Mata, Juan Carlos Sánchez-DelBarrio et al. · Molecular Biology and Evolution | 18 Sep 2017 | 8,112 |
| 22 | Topological domains in mammalian genomes identified by analysis of chromatin interactions Jesse R. Dixon, Siddarth Selvaraj, Feng Yue et al. · Nature | 10 Apr 2012 | 7,584 |
| 23 | A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species Robert J. Elshire, Jeffrey C. Glaubitz, Qi Sun et al. · PLoS ONE | 4 May 2011 | 6,896 |
| 24 | Assembly of long, error-prone reads using repeat graphs Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin et al. · Nature Biotechnology | Apr 2019 | 6,680 |
| 25 | The Genome Sequence of Drosophila melanogaster Mark D. Adams et al. · Science | 24 Mar 2000 | 6,049 |
| 26 | High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries Chirag Jain, Luis Miguel Rodriguez-R, Adam M. Phillippy et al. · Nature Communications | 26 Nov 2018 | 6,041 |
| 27 | FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix Morgan N. Price, Paramvir Dehal, Adam P. Arkin · Molecular Biology and Evolution | 17 Apr 2009 | 6,025 |
| 28 | Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments Gerard Talavera, José Castresana · Systematic Biology | 26 Jul 2007 | 5,974 |
| 29 | Versatile and open software for comparing large genomes Stefan Kurtz, Adam M. Phillippy, Arthur L. Delcher et al. · Genome biology | 30 Jan 2004 | 5,934 |
| 30 | Prospects for inferring very large phylogenies by using the neighbor-joining method Koichiro Tamura, Masatoshi Nei, Sudhir Kumar · Proceedings of the National Academy of Sciences | 16 Jul 2004 | 5,681 |
| 31 | Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements Aaron E. Darling, Bob Mau, Frederick R. Blattner et al. · Genome Research | Jul 2004 | 5,312 |
| 32 | Genome-Wide Insertional Mutagenesis of Arabidopsis thaliana José M. Alonso et al. · Science | 31 Jul 2003 | 5,137 |
| 33 | Role for a bidentate ribonuclease in the initiation step of RNA interference Emily Bernstein, Amy A. Caudy, Scott M. Hammond et al. · Nature | 2001 | 4,947 |
| 34 | Global variation in copy number in the human genome Richard Redon et al. · Nature | Nov 2006 | 4,397 |
| 35 | Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes Adam C. Siepel, Gill Bejerano, Jakob Skou Pedersen et al. · Genome Research | 15 Jul 2005 | 4,393 |
| 36 | A Draft Sequence of the Rice Genome ( Oryza sativa L. ssp. indica ) Jun Myoung Yu et al. · Science | 5 Apr 2002 | 4,279 |
| 37 | The B73 Maize Genome: Complexity, Diversity, and Dynamics Patrick S. Schnable et al. · Science | 20 Nov 2009 | 4,265 |
| 38 | RepeatModeler2 for automated genomic discovery of transposable element families Jullien M. Flynn, Robert M. Hubley, Clément Goubert et al. · Proceedings of the National Academy of Sciences | 16 Apr 2020 | 4,179 |
| 39 | progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement Aaron E. Darling, Bob Mau, Nicole T. Perna · PLoS ONE | 25 Jun 2010 | 4,152 |
| 40 | MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies Dongwan Don Kang, Feng Li, Edward Kirton et al. · PeerJ | 26 Jul 2019 | 4,119 |
| 41 | Gene Flow and the Geographic Structure of Natural Populations Montgomery Slatkin · Science | 15 May 1987 | 3,981 |
| 42 | A gene complex controlling segmentation in Drosophila E. B. Lewis · Nature | Dec 1978 | 3,889 |
| 43 | Accurate whole human genome sequencing using reversible terminator chemistry David Bentley et al. · Nature | Nov 2008 | 3,809 |
| 44 | Hypervariable ‘minisatellite’ regions in human DNA Alec J. Jeffreys, Victoria E. D. Wilson, Swee Lay Thein · Nature | Mar 1985 | 3,783 |
| 45 | GATEWAY™ vectors for Agrobacterium-mediated plant transformation Mansour Karimi, Dirk Inzé, Ann G. Depicker · Trends in Plant Science | May 2002 | 3,747 |
| 46 | ATAC‐seq: A Method for Assaying Chromatin Accessibility Genome‐Wide Jason Daniel Buenrostro, Beijing Wu, Howard Y. Chang et al. · Current Protocols in Molecular Biology | 2015 | 3,737 |
| 47 | A measure of population subdivision based on microsatellite allele frequencies. Montgomery Slatkin · Genetics | 1995 | 3,732 |
| 48 | Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences Maja Tarailo‐Graovac, Nansheng Chen · Current Protocols in Bioinformatics | Mar 2009 | 3,697 |
| 49 | Repbase Update, a database of eukaryotic repetitive elements Jerzy Jurka, Vladimir V. Kapitonov, Adam Pavlı́ček et al. · Cytogenetic and Genome Research | 2005 | 3,575 |
| 50 | The complete sequence of a human genome Sergey Nurk et al. · Science | 31 Mar 2022 | 3,475 |
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.