Published in Ecol Evol on May 13, 2015
Deep-Sea, Deep-Sequencing: Metabarcoding Extracellular DNA from Sediments of Marine Canyons. PLoS One (2015) 1.45
Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities? Ecol Evol (2015) 0.86
Censusing marine eukaryotic diversity in the twenty-first century. Philos Trans R Soc Lond B Biol Sci (2016) 0.81
Pipeline for amplifying and analyzing amplicons of the V1-V3 region of the 16S rRNA gene. BMC Res Notes (2016) 0.79
The best of both worlds: A combined approach for analyzing microalgal diversity via metabarcoding and morphology-based methods. PLoS One (2017) 0.75
The establishment of species-specific primers for the molecular identification of ten stored-product psocids based on ITS2 rDNA. Sci Rep (2016) 0.75
Critical Issues in Mycobiota Analysis. Front Microbiol (2017) 0.75
Comparison of three clustering approaches for detecting novel environmental microbial diversity. PeerJ (2016) 0.75
Population attenuation in zooplankton communities during transoceanic transfer in ballast water. Ecol Evol (2016) 0.75
ESPRIT-Forest: Parallel clustering of massive amplicon sequence data in subquadratic time. PLoS Comput Biol (2017) 0.75
Random sampling causes the low reproducibility of rare eukaryotic OTUs in Illumina COI metabarcoding. PeerJ (2017) 0.75
DAMe: a toolkit for the initial processing of datasets with PCR replicates of double-tagged amplicons for DNA metabarcoding analyses. BMC Res Notes (2016) 0.75
Bacterial Diversity in the Soda Saline Crater Lake from Isabel Island, Mexico. Microb Ecol (2015) 0.75
DNA metabarcoding of orchid-derived products reveals widespread illegal orchid trade. Proc Biol Sci (2017) 0.75
Basic local alignment search tool. J Mol Biol (1990) 659.07
QIIME allows analysis of high-throughput community sequencing data. Nat Methods (2010) 85.34
Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol (2009) 77.55
Biological identifications through DNA barcodes. Proc Biol Sci (2003) 54.14
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res (2008) 52.43
Search and clustering orders of magnitude faster than BLAST. Bioinformatics (2010) 51.97
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics (2006) 43.68
MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol (2013) 34.34
UCHIME improves sensitivity and speed of chimera detection. Bioinformatics (2011) 29.22
Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol (2007) 23.64
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res (2012) 19.48
Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods (2009) 15.25
Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol (2009) 14.17
Removing noise from pyrosequenced amplicons. BMC Bioinformatics (2011) 13.45
Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol (2010) 13.19
UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods (2013) 12.05
ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences. Nucleic Acids Res (2009) 4.93
Who is eating what: diet assessment using next generation sequencing. Mol Ecol (2011) 3.53
The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol (2010) 3.26
Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nat Commun (2010) 2.77
Sequencing our way towards understanding global eukaryotic biodiversity. Trends Ecol Evol (2012) 2.70
Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA. Nucleic Acids Res (2000) 2.56
454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases. New Phytol (2010) 2.49
SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read. BMC Bioinformatics (2010) 2.43
CANGS: a user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies. BMC Res Notes (2010) 2.16
Next-generation gap. Nat Methods (2009) 2.01
A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis. Brief Bioinform (2011) 1.87
Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions. Environ Microbiol (2010) 1.84
Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering. Bioinformatics (2011) 1.82
ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time. Nucleic Acids Res (2011) 1.76
DNACLUST: accurate and efficient clustering of phylogenetic marker genes. BMC Bioinformatics (2011) 1.66
Swarm: robust and fast clustering method for amplicon-based studies. PeerJ (2014) 1.55
Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing. Genome Res (2009) 1.28
A comparison of methods for clustering 16S rRNA sequences into OTUs. PLoS One (2013) 1.15
Two-stage clustering (TSC): a pipeline for selecting operational taxonomic units for the high-throughput sequencing of PCR amplicons. PLoS One (2012) 1.15
Evolution of Hypervariable Regions, V4 and V7, of Insect 18S rRNA and Their Phylogenetic Implications. Zoolog Sci (2000) 1.13
A Clustering Optimization Strategy for Molecular Taxonomy Applied to Planktonic Foraminifera SSU rDNA. Evol Bioinform Online (2010) 1.12
Assessment of replicate bias in 454 pyrosequencing and a multi-purpose read-filtering tool. BMC Res Notes (2011) 1.12
Comparing clustering and pre-processing in taxonomy analysis. Bioinformatics (2012) 1.06
454 pyrosequencing to describe microbial eukaryotic community composition, diversity and relative abundance: a test for marine haptophytes. PLoS One (2013) 1.05
Estimation of bacterial diversity using next generation sequencing of 16S rDNA: a comparison of different workflows. BMC Bioinformatics (2011) 1.02
A grammar-based distance metric enables fast and accurate clustering of large sets of 16S sequences. BMC Bioinformatics (2010) 0.99
Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations. Bioinformatics (2014) 0.97
The origin and evolution of variable-region helices in V4 and V7 of the small-subunit ribosomal RNA of branchiopod crustaceans. Mol Biol Evol (1998) 0.94
Analysis of the primary sequence and secondary structure of the unusually long SSU rRNA of the soil bug, Armadillidium vulgare. J Mol Evol (1999) 0.93
Selection on the structural stability of a ribosomal RNA expansion segment in Daphnia obtusa. Mol Biol Evol (2005) 0.91
Environmental monitoring through protist next-generation sequencing metabarcoding: assessing the impact of fish farming on benthic foraminifera communities. Mol Ecol Resour (2014) 0.91
The contribution of DNA slippage to eukaryotic nuclear 18S rRNA evolution. J Mol Evol (1995) 0.88
M-pick, a modularity-based method for OTU picking of 16S rRNA sequences. BMC Bioinformatics (2013) 0.84
Testing three pipelines for 18S rDNA-based metabarcoding of soil faunal diversity. Sci China Life Sci (2012) 0.83
MSClust: A Multi-Seeds based Clustering algorithm for microbiome profiling using 16S rRNA sequence. J Microbiol Methods (2013) 0.80
A molecular-based approach for examining responses of eukaryotes in microcosms to contaminant-spiked estuarine sediments. Environ Toxicol Chem (2014) 0.79