Most cited papers in Microbial Community Ecology and Physiology
What are the most cited papers in Microbial Community Ecology and Physiology?
The most cited paper in Microbial Community Ecology and Physiology is "MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets" (Sudhir Kumar, Glen Stecher, Koichiro Tamura, 2016), with 46,273 citations. Next come "QIIME allows analysis of high-throughput community sequencing data" (36,341) and "The SILVA ribosomal RNA gene database project: improved data processing and web-based tools" (35,094).
Showing 50 of 99 papers. Every paper with more than 3,096 citations is listed.
| # | Paper | ||
|---|---|---|---|
| 1 | MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets Sudhir Kumar, Glen Stecher, Koichiro Tamura · Molecular Biology and Evolution | 22 Mar 2016 | 46,273 |
| 2 | QIIME allows analysis of high-throughput community sequencing data J. Gregory Caporaso et al. · Nature Methods | 11 Apr 2010 | 36,341 |
| 3 | The SILVA ribosomal RNA gene database project: improved data processing and web-based tools Christian Quast, Elmar Pruesse, Pelin Yilmaz et al. · Nucleic Acids Research | 27 Nov 2012 | 35,094 |
| 4 | SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing Anton Bankevich, Sergey Nurk, Dmitry Antipov et al. · Journal of Computational Biology | 16 Apr 2012 | 27,967 |
| 5 | Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities Patrick D. Schloss, Sarah L. Westcott, Thomas Ryabin et al. · Applied and Environmental Microbiology | 3 Oct 2009 | 22,073 |
| 6 | Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy Qiong Wang, George M Garrity, James M. Tiedje et al. · Applied and Environmental Microbiology | 22 Jun 2007 | 20,801 |
| 7 | UPARSE: highly accurate OTU sequences from microbial amplicon reads R. C. Edgar · Nature Methods | 18 Aug 2013 | 17,573 |
| 8 | UCHIME improves sensitivity and speed of chimera detection R. C. Edgar, Brian J. Haas, José Carlos Clemente et al. · Bioinformatics | 23 Jun 2011 | 15,726 |
| 9 | trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses Salvador Capella-Gutiérrez, José M. Silla-Martínez, Toni Gabaldón · Bioinformatics | 8 Jun 2009 | 14,201 |
| 10 | CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes Donovan H. Parks, Michael Imelfort, Connor T. Skennerton et al. · Genome Research | 14 May 2015 | 13,397 |
| 11 | Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA Gerard Muyzer, Ellen C. de Waal, André Gerardus Uitterlinden · Applied and Environmental Microbiology | Mar 1993 | 11,519 |
| 12 | Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB Todd Z. DeSantis, Philip Hugenholtz, Nis Elbrønd Larsen et al. · Applied and Environmental Microbiology | Jul 2006 | 11,348 |
| 13 | 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 |
| 14 | Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample J. Gregory Caporaso, Christian L. Lauber, William A. Walters et al. · Proceedings of the National Academy of Sciences | 3 Jun 2010 | 10,238 |
| 15 | The biofilm matrix Hans‐Curt Flemming, Jost Wingender · Nature Reviews Microbiology | 2 Aug 2010 | 10,070 |
| 16 | Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences Morgan G. I. Langille, Jesse Zaneveld, J. Gregory Caporaso et al. · Nature Biotechnology | 25 Aug 2013 | 9,519 |
| 17 | De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis Brian J. Haas et al. · Nature Protocols | 11 Jul 2013 | 9,312 |
| 18 | Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms J. Gregory Caporaso, Christian L. Lauber, William Anton Walters et al. · The ISME Journal | 8 Mar 2012 | 9,285 |
| 19 | Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies Anna Klindworth, Elmar Pruesse, Timmy Schweer et al. · Nucleic Acids Research | 28 Aug 2012 | 9,235 |
| 20 | UniFrac: a New Phylogenetic Method for Comparing Microbial Communities Catherine Lozupone, Rob Knight · Applied and Environmental Microbiology | Dec 2005 | 8,691 |
| 21 | Phylogenetic identification and in situ detection of individual microbial cells without cultivation Rudolf Amann, Wolfgang Ludwig, Karl‐Heinz Schleifer · Microbiological Reviews | Mar 1995 | 8,374 |
| 22 | Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies Seok-Hwan Yoon, Sung Min Ha, Soon‐Jae Kwon et al. · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY | 22 Dec 2016 | 7,916 |
| 23 | Generic Assignments, Strain Histories and Properties of Pure Cultures of Cyanobacteria Rosmarie Rippka, Roger Y. Stanier, Josette Deruelles et al. · Microbiology | Mar 1979 | 7,814 |
| 24 | Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform James J. Kozich, Sarah L. Westcott, Nielson T. Baxter et al. · Applied and Environmental Microbiology | 21 Jun 2013 | 7,674 |
| 25 | Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics L G Wayne, William E. Moore, Erko Stackebrandt et al. · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY | Oct 1987 | 7,348 |
| 26 | Bacterial biofilms: from the Natural environment to infectious diseases Luanne Hall‐Stoodley, John William Costerton, Paul Stoodley · Nature Reviews Microbiology | 14 Jan 2004 | 7,252 |
| 27 | Taxonomic Note: A Place for DNA-DNA Reassociation and 16S rRNA Sequence Analysis in the Present Species Definition in Bacteriology Erko Stackebrandt, Brett M. Goebel · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY | Oct 1994 | 7,129 |
| 28 | SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB Elmar Pruesse, Christian Quast, Katrin Knittel et al. · Nucleic Acids Research | 18 Oct 2007 | 6,958 |
| 29 | Spreading Dead Zones and Consequences for Marine Ecosystems Robert J. Díaz, Rutger Rosenberg · Science | 14 Aug 2008 | 6,753 |
| 30 | Fluorescence Excitation−Emission Matrix Regional Integration to Quantify Spectra for Dissolved Organic Matter Wen Chen, Paul K. Westerhoff, Jerry A. Leenheer et al. · Environmental Science & Technology | 15 Nov 2003 | 6,382 |
| 31 | Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. C R Woese, O. Kandler, Mark L. Wheelis · Proceedings of the National Academy of Sciences | Jun 1990 | 6,136 |
| 32 | Biofilms: an emergent form of bacterial life Hans‐Curt Flemming, Jost Wingender, Ulrich Szewzyk et al. · Nature Reviews Microbiology | 11 Aug 2016 | 6,029 |
| 33 | The diversity and biogeography of soil bacterial communities Noah Fierer, Robert B. Jackson · Proceedings of the National Academy of Sciences | 9 Jan 2006 | 5,830 |
| 34 | An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea Daniel T. McDonald, Morgan N. Price, Julia K. Goodrich et al. · The ISME Journal | Dec 2011 | 5,371 |
| 35 | Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species Ok-Sun Kim, Yong‐Joon Cho, Kihyun Lee et al. · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY | 25 Nov 2011 | 5,292 |
| 36 | Quorum Sensing in Bacteria Melissa B. Miller, Bonnie L. Bassler · Annual Review of Microbiology | Oct 2001 | 5,167 |
| 37 | TOWARD AN ECOLOGICAL CLASSIFICATION OF SOIL BACTERIA Noah Fierer, Mark A. Bradford, Robert B. Jackson · Ecology | Jun 2007 | 5,143 |
| 38 | The use of DAPI for identifying and counting aquatic microflora1 Karen Glaus Porter, Yvette S. Feig · Limnology and Oceanography | Sep 1980 | 5,103 |
| 39 | metaSPAdes: a new versatile metagenomic assembler Sergey Nurk, Dmitry Meleshko, Anton Korobeynikov et al. · Genome Research | 15 Mar 2017 | 5,016 |
| 40 | Kraken: ultrafast metagenomic sequence classification using exact alignments Derrick E. Wood, Steven L. Salzberg · Genome biology | 3 Mar 2014 | 4,992 |
| 41 | DNA–DNA hybridization values and their relationship to whole-genome sequence similarities Johan Goris, Konstantinos T. Konstantinidis, Joel A. Klappenbach et al. · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY | 2007 | 4,922 |
| 42 | Prokaryotes: The unseen majority William B. Whitman, David C. Coleman, W. J. Wiebe · Proceedings of the National Academy of Sciences | 9 Jun 1998 | 4,917 |
| 43 | The Ribosomal Database Project: improved alignments and new tools for rRNA analysis James R. Cole, Qi Wang, Erick Cardenas et al. · Nucleic Acids Research | 12 Nov 2008 | 4,882 |
| 44 | Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking Mingxun Wang et al. · Nature Biotechnology | Aug 2016 | 4,812 |
| 45 | The EMBL-EBI search and sequence analysis tools APIs in 2019 Fábio Madeira, Young Mi Park, Joon Lee et al. · Nucleic Acids Research | 3 Apr 2019 | 4,708 |
| 46 | Ribosomal Database Project: data and tools for high throughput rRNA analysis James R. Cole, Qiong Wang, Jordan A. Fish et al. · Nucleic Acids Research | 27 Nov 2013 | 4,655 |
| 47 | The microbial nitrogen-cycling network Marcel M. M. Kuypers, Hannah K. Marchant, Boran Kartal · Nature Reviews Microbiology | 5 Feb 2018 | 4,604 |
| 48 | Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing Nicholas A. Bokulich, Sathish Subramanian, Jeremiah J. Faith et al. · Nature Methods | 2 Dec 2012 | 4,559 |
| 49 | MICROBIAL BIOFILMS J. W. Costerton, Zbigniew Lewandowski, Douglas E. Caldwell et al. · Annual Review of Microbiology | Oct 1995 | 4,555 |
| 50 | BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences Minoru I. Kanehisa, Yoko Sato, Kanae Morishima · Journal of Molecular Biology | 14 Nov 2015 | 4,447 |
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.