Most cited papers in Environmental DNA in Biodiversity Studies
What are the most cited papers in Environmental DNA in Biodiversity Studies?
The most cited paper in Environmental DNA in Biodiversity Studies is "Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB" (Todd Z. DeSantis, Philip Hugenholtz, Nis Elbrønd Larsen et al., 2006), with 11,348 citations. Next come "Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample" (10,238) and "SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB" (6,958).
Showing 50 of 100 papers. Every paper with more than 1,157 citations is listed.
| # | Paper | ||
|---|---|---|---|
| 1 | 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 |
| 2 | 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 |
| 3 | 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 |
| 4 | bold : The Barcode of Life Data System (http://www.barcodinglife.org) Sujeevan Ratnasingham, Paul D. N. Hebert · Molecular Ecology Notes | 24 Jan 2007 | 6,485 |
| 5 | Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool Ivica Letunić, Peer Bork · Nucleic Acids Research | 2 Apr 2024 | 4,591 |
| 6 | Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species Paul D. N. Hebert, Sujeevan Ratnasingham, Jeremy R. de Waard · Proceedings of the Royal Society B Biological Sciences | 7 Aug 2003 | 4,521 |
| 7 | The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks Pelin Yilmaz, Laura Wegener Parfrey, Pablo Yarza et al. · Nucleic Acids Research | 28 Nov 2013 | 4,257 |
| 8 | TESTING SIGNIFICANCE OF INCONGRUENCE James S. Farris, Mari Källersjö, Arnold G. Kluge et al. · Cladistics | Sep 1994 | 3,892 |
| 9 | Emerging threats and persistent conservation challenges for freshwater biodiversity Andrea J. Reid, Andrew K. Carlson, Irena F. Creed et al. · Biological reviews/Biological reviews of the Cambridge Philosophical Society | 22 Nov 2018 | 3,663 |
| 10 | The biodiversity of species and their rates of extinction, distribution, and protection Stuart L. Pimm, Clinton N. Jenkins, Robin Abell et al. · Science | 29 May 2014 | 3,588 |
| 11 | Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons Brian J. Haas, Dirk Gevers, Ashlee M. Earl et al. · Genome Research | 6 Jan 2011 | 3,584 |
| 12 | Genome Fingerprinting by Simple Sequence Repeat (SSR)-Anchored Polymerase Chain Reaction Amplification Ewa Ziętkiewicz, Antoni J. Rafalski, Damian Labuda · Genomics | Mar 1994 | 3,415 |
| 13 | Impacts of biological invasions: what's what and the way forward Daniel Simberloff, Jean‐Louis Martin, Piero Genovesi et al. · Trends in Ecology & Evolution | 10 Aug 2012 | 3,381 |
| 14 | A general species delimitation method with applications to phylogenetic placements Jiajie Zhang, Paschalia Kapli, Pavlos Pavlidis et al. · Bioinformatics | 29 Aug 2013 | 3,139 |
| 15 | TimeTree: A Resource for Timelines, Timetrees, and Divergence Times Sudhir Kumar, Glen Stecher, Michael Suleski et al. · Molecular Biology and Evolution | 25 Mar 2017 | 3,027 |
| 16 | Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea Daniel P. R. Herlemann, Matthias Labrenz, Klaus Jürgens et al. · The ISME Journal | 7 Apr 2011 | 3,025 |
| 17 | Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton Amy M. Apprill, Sean P. McNally, Rachel J. Parsons et al. · Aquatic Microbial Ecology | 17 Apr 2015 | 2,990 |
| 18 | DNA recovery from soils of diverse composition Jizhong Z. Zhou, Mary Ann Bruns, Jim M. Tiedje · Applied and Environmental Microbiology | Feb 1996 | 2,934 |
| 19 | Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences Pablo Yarza, Pelin Yilmaz, Elmar Pruesse et al. · Nature Reviews Microbiology | 14 Aug 2014 | 2,706 |
| 20 | SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information Gaurav Vaidya, David J. Lohman, Rudolf Meier · Cladistics | 7 Jul 2010 | 2,692 |
| 21 | Structure and function of the global topsoil microbiome Mohammad Bahram et al. · Nature | 31 Jul 2018 | 2,659 |
| 22 | The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy Laure Guillou et al. · Nucleic Acids Research | 26 Nov 2012 | 2,499 |
| 23 | Illumina Sequencing Library Preparation for Highly Multiplexed Target Capture and Sequencing Matthias Meyer, Martin Kircher · Cold Spring Harbor Protocols | Jun 2010 | 2,393 |
| 24 | Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys William Anton Walters, Embriette R. Hyde, Donna Berg-Lyons et al. · mSystems | 18 Dec 2015 | 2,329 |
| 25 | Virioplankton: Viruses in Aquatic Ecosystems K. Eric Wommack, Rita R. Colwell · Microbiology and Molecular Biology Reviews | Mar 2000 | 2,198 |
| 26 | Eukaryotic plankton diversity in the sunlit ocean Colomban de Vargas et al. · Science | 22 May 2015 | 2,162 |
| 27 | Environmental DNA – An emerging tool in conservation for monitoring past and present biodiversity Philip Francis Thomsen, Eske Willerslev · Biological Conservation | 19 Dec 2014 | 2,154 |
| 28 | Environmental DNA metabarcoding: Transforming how we survey animal and plant communities Kristy Deiner, Holly M. Bik, Elvira Mächler et al. · Molecular Ecology | 18 Sep 2017 | 2,065 |
| 29 | Antibiotics and antibiotic resistance in water environments Fernando Baquero, José Luis Martínez, Rafael Cantón · Current Opinion in Biotechnology | Jun 2008 | 2,064 |
| 30 | eBird: A citizen-based bird observation network in the biological sciences Brian L. Sullivan, Christopher Wood, Marshall J. Iliff et al. · Biological Conservation | 29 May 2009 | 2,063 |
| 31 | Microsatellite analysis of population structure in Canadian polar bears David Paetkau, Wendy A. Calvert, I Stirling et al. · Molecular Ecology | Jun 1995 | 2,061 |
| 32 | Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis Friedrich von Wintzingerode, Ulf Berthold Göbel, Erko Stackebrandt · FEMS Microbiology Reviews | Nov 1997 | 2,060 |
| 33 | MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics Rémi Allio, Alex Schomaker-Bastos, Jonathan Romiguier et al. · Molecular Ecology Resources | 3 Apr 2020 | 2,042 |
| 34 | Towards next‐generation biodiversity assessment using DNA metabarcoding Pierre Taberlet, Éric Coissac, François Pompanon et al. · Molecular Ecology | Apr 2012 | 2,025 |
| 35 | DNA Barcoding: Error Rates Based on Comprehensive Sampling Chris Meyer, Gustav Paulay · PLoS Biology | 18 Nov 2005 | 1,997 |
| 36 | Antibiotic Resistance Genes as Emerging Contaminants: Studies in Northern Colorado Amy J. Pruden, Ruoting Pei, Heather N. Storteboom et al. · Environmental Science & Technology | 15 Aug 2006 | 1,963 |
| 37 | The Genome Sequence Archive Family: Toward Explosive Data Growth and Diverse Data Types Tingting Chen et al. · Genomics Proteomics & Bioinformatics | Aug 2021 | 1,943 |
| 38 | UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing R. C. Edgar · bioRxiv (Cold Spring Harbor Laboratory) | 15 Oct 2016 | 1,940 |
| 39 | Environmental pollution by antibiotics and by antibiotic resistance determinants José Luis Martínez · Environmental Pollution | 28 Jun 2009 | 1,939 |
| 40 | Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR Marcelino T. Suzuki, Stephen J. Giovannoni · Applied and Environmental Microbiology | Feb 1996 | 1,913 |
| 41 | Review and re-analysis of domain-specific 16S primers Gillian C. Baker, Jacques J. Smith, Don Arthur Cowan · Journal of Microbiological Methods | 6 Nov 2003 | 1,883 |
| 42 | Pyrosequencing enumerates and contrasts soil microbial diversity Luiz Fernando Würdig Roesch, Roberta R. Fulthorpe, Alberto Riva et al. · The ISME Journal | 5 Jul 2007 | 1,878 |
| 43 | The Sequence Manipulation Suite: JavaScript Programs for Analyzing and Formatting Protein and DNA Sequences Paul Stothard · BioTechniques | Jun 2000 | 1,868 |
| 44 | Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water Thorsten Stoeck, David Bass, Markus E. Nebel et al. · Molecular Ecology | 10 Feb 2010 | 1,865 |
| 45 | Global Dispersal of Free-Living Microbial Eukaryote Species Bland J. Finlay · Science | 10 May 2002 | 1,852 |
| 46 | Identifying the Dominant Soil Bacterial Taxa in Libraries of 16S rRNA and 16S rRNA Genes Peter H. Janssen · Applied and Environmental Microbiology | Mar 2006 | 1,845 |
| 47 | mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters Hákon Jónsson, Aurélien Ginolhac, Mikkel Schubert et al. · Bioinformatics | 23 Apr 2013 | 1,831 |
| 48 | Species detection using environmental DNA from water samples Gentile Francesco Ficetola, Claude Miaud, François Pompanon et al. · Biology Letters | 9 Apr 2008 | 1,785 |
| 49 | Rapid Method for Coextraction of DNA and RNA from Natural Environments for Analysis of Ribosomal DNA- and rRNA-Based Microbial Community Composition Robert Iwan Griffiths, Andrew Steven Whiteley, Anthony G. O’Donnell et al. · Applied and Environmental Microbiology | Dec 2000 | 1,743 |
| 50 | BBMerge – Accurate paired shotgun read merging via overlap Brian Bushnell, Jonathan Rood, Esther Singer · PLoS ONE | 26 Oct 2017 | 1,741 |
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.