Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring

Sequencing our way towards understanding global eukaryotic biodiversity

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

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

DNACLUST: accurate and efficient clustering of phylogenetic marker genes

(2011) Mohammadreza Ghodsi et al.   BMC BIOINFORMATICS

Phylogeny, phylogeography, phylobetadiversity and the molecular analysis of biological communities

(2011) B. C. Emerson et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Environmental Barcoding: A Next-Generation Sequencing Approach for Biomonitoring Applications Using River Benthos

(2011) Mehrdad Hajibabaei et al.   PLoS One

Molecular Detection of Vertebrates in Stream Water: A Demonstration Using Rocky Mountain Tailed Frogs and Idaho Giant Salamanders

(2011) Caren S. Goldberg et al.   PLoS One

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

(2011) Vincent Ranwez et al.   PLoS One

Implications of Goodhart's Law for monitoring global biodiversity loss

(2011) Adrian C. Newton   Conservation Letters

“Sight-unseen” detection of rare aquatic species using environmental DNA

(2011) Christopher L. Jerde et al.   Conservation Letters

PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data

(2011) Thomas J. Sharpton et al.   PLoS Computational Biology

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Arthropods as surrogates of diversity at different spatial scales

(2010) Clara Gaspar et al.   BIOLOGICAL CONSERVATION

The Effectiveness of Surrogate Taxa for the Representation of Biodiversity

(2010) ADAM S. LEWANDOWSKI et al.   CONSERVATION BIOLOGY

The potential of parasitoid Hymenoptera as bioindicators of arthropod diversity in agricultural grasslands

(2010) Annette Anderson et al.   JOURNAL OF APPLIED ECOLOGY

Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises

(2010) S. CREER et al.   MOLECULAR ECOLOGY

Ecometagenetics confirm high tropical rainforest nematode diversity

(2010) DOROTA L. PORAZINSKA et al.   MOLECULAR ECOLOGY

Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity

(2010) VIOLA NOLTE et al.   MOLECULAR ECOLOGY

Second-generation sequencing derived insights into the temporal biodiversity dynamics of freshwater protists

(2010) SIMON CREER   MOLECULAR ECOLOGY

Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms

(2010) RALPH MEDINGER et al.   MOLECULAR ECOLOGY

Quantifying microbial communities with 454 pyrosequencing: does read abundance count?

(2010) ANTHONY S. AMEND et al.   MOLECULAR ECOLOGY

Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions

(2010) Jens Reeder et al.   NATURE METHODS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Use of ITS2 Region as the Universal DNA Barcode for Plants and Animals

(2010) Hui Yao et al.   PLoS One

Second-generation environmental sequencing unmasks marine metazoan biodiversity

(2010) Vera G. Fonseca et al.   Nature Communications

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

Windshield splatter analysis with the Galaxy metagenomic pipeline

(2009) S. Kosakovsky Pond et al.   GENOME RESEARCH

Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data

(2009) Micah Hamady et al.   ISME Journal

Reproducibility of read numbers in high-throughput sequencing analysis of nematode community composition and structure

(2009) DOROTA L. PORAZINSKA et al.   Molecular Ecology Resources

Evaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversity

(2009) DOROTA L. PORAZINSKA et al.   Molecular Ecology Resources

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

iCODEHOP: a new interactive program for designing COnsensus-DEgenerate Hybrid Oligonucleotide Primers from multiply aligned protein sequences

(2009) R. Boyce et al.   NUCLEIC ACIDS RESEARCH

A DNA barcode for land plants

(2009) et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Species detection using environmental DNA from water samples

(2008) G. F. Ficetola et al.   Biology Letters

A universal DNA mini-barcode for biodiversity analysis

(2008) Isabelle Meusnier et al.   BMC GENOMICS

Simple approach to reduce PCR artefact formation leads to reliable genotyping of MHC and other highly polymorphic loci — Implications for evolutionary analysis

(2008) Tobias L. Lenz et al.   GENE

Statistical Assignment of DNA Sequences Using Bayesian Phylogenetics

(2008) Kasper Munch et al.   SYSTEMATIC BIOLOGY

DNA barcoding in surveys of small mammal communities: a field study in Suriname

(2007) ALEX V. BORISENKO et al.   Molecular Ecology Resources