Random sampling causes the low reproducibility of rare eukaryotic OTUs in Illumina COI metabarcoding

A framework for inferring biological communities from environmental DNA

(2016) Andrew Olaf Shelton et al.   ECOLOGICAL APPLICATIONS

Censusing marine eukaryotic diversity in the twenty-first century

(2016) Matthieu Leray et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Indexed PCR Primers Induce Template-Specific Bias in Large-Scale DNA Sequencing Studies

(2016) James L. O’Donnell et al.   PLoS One

Estimating beta diversity for under-sampled communities using the variably weighted Odum dissimilarity index and OTUshuff

(2015) Daniel K. Manter et al.   BIOINFORMATICS

BFC: correcting Illumina sequencing errors

(2015) Heng Li   BIOINFORMATICS

Error filtering, pair assembly and error correction for next-generation sequencing reads

(2015) Robert C. Edgar et al.   BIOINFORMATICS

Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA

(2015) Kristy Deiner et al.   BIOLOGICAL CONSERVATION

Modeling false positive detections in species occurrence data under different study designs

(2015) Thierry Chambert et al.   ECOLOGY

Effects of plankton net characteristics on metagenetic community analysis of metazoan zooplankton in a coastal marine ecosystem

(2015) Junya Hirai et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

Meiofaunal community analysis by high-throughput sequencing: Comparison of extraction, quality filtering, and clustering methods

(2015) Pamela M. Brannock et al.   Marine Genomics

Metabarcoding approach for the ballast water surveillance – An advantageous solution or an awkward challenge?

(2015) Anastasija Zaiko et al.   MARINE POLLUTION BULLETIN

Not all are free-living: high-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoa

(2015) S. Geisen et al.   MOLECULAR ECOLOGY

Statistical approaches to account for false-positive errors in environmental DNA samples

(2015) José J. Lahoz-Monfort et al.   Molecular Ecology Resources

Tag jumps illuminated - reducing sequence-to-sample misidentifications in metabarcoding studies

(2015) Ida Baerholm Schnell et al.   Molecular Ecology Resources

DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity

(2015) Matthieu Leray et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

Performance of species occurrence estimators when basic assumptions are not met: a test using field data where true occupancy status is known

(2015) David A. W. Miller et al.   Methods in Ecology and Evolution

High-throughput monitoring of wild bee diversity and abundance via mitogenomics

(2015) Min Tang et al.   Methods in Ecology and Evolution

Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities?

(2015) Emily A. Brown et al.   Ecology and Evolution

Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods

(2015) Jullien M. Flynn et al.   Ecology and Evolution

Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist diet

(2015) Matthieu Leray et al.   PeerJ

Environmental DNA (eDNA) Sampling Improves Occurrence and Detection Estimates of Invasive Burmese Pythons

(2015) Margaret E. Hunter et al.   PLoS One

Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol

(2015) Vasco Elbrecht et al.   PLoS One

High-throughput sequencing and morphology perform equally well for benthic monitoring of marine ecosystems

(2015) Franck Lejzerowicz et al.   Scientific Reports

Rare biosphere exploration using high-throughput sequencing: research progress and perspectives

(2014) Aibin Zhan et al.   CONSERVATION GENETICS

Universal and blocking primer mismatches limit the use of high-throughput DNA sequencing for the quantitative metabarcoding of arthropods

(2014) J. Piñol et al.   Molecular Ecology Resources

Using Environmental DNA to Census Marine Fishes in a Large Mesocosm

(2014) Ryan P. Kelly et al.   PLoS One

Current noise-removal methods can create false signals in ecogenomic data

(2014) A. G. Rossberg et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Gateway for Phylogenetic Analysis Powered by Grid Computing Featuring GARLI 2.0

(2014) Adam L. Bazinet et al.   SYSTEMATIC BIOLOGY

Reproducibility of pyrosequencing data for biodiversity assessment in complex communities

(2014) Aibin Zhan et al.   Methods in Ecology and Evolution

Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding

(2013) Yinqiu Ji et al.   ECOLOGY LETTERS

A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents

(2013) Matthieu Leray et al.   Frontiers in Zoology

Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count?

(2013) Bruce E. Deagle et al.   Molecular Ecology Resources

Undersampling and the measurement of beta diversity

(2013) Jan Beck et al.   Methods in Ecology and Evolution

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

(2012) Laure Guillou et al.   NUCLEIC ACIDS RESEARCH

PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets

(2012) Ameet J. Pinto et al.   PLoS One

Sequencing our way towards understanding global eukaryotic biodiversity

(2012) Holly M. Bik et al.   TRENDS IN ECOLOGY & EVOLUTION

Barcoded Primers Used in Multiplex Amplicon Pyrosequencing Bias Amplification

(2011) David Berry et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering

(2011) Xiaolin Hao et al.   BIOINFORMATICS

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

RNA-seq: technical variability and sampling

(2011) Lauren M McIntyre et al.   BMC GENOMICS

Reproducibility and quantitation of amplicon sequencing-based detection

(2011) Jizhong Zhou et al.   ISME Journal

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

(2011) Vincent Ranwez et al.   PLoS One

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

(2011) Patrick D. Schloss et al.   PLoS One

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Tissue-specific differences in mitochondrial activity and biogenesis

(2010) Erika Fernández-Vizarra et al.   MITOCHONDRION

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Zooplankton diversity analysis through single-gene sequencing of a community sample

(2009) Ryuji J Machida et al.   BMC GENOMICS

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified

(2008) H. Song et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA