Bioinformatic challenges for DNA metabarcoding of plants and animals

Tracking earthworm communities from soil DNA

(2012) FRIEDERIKE BIENERT et al.   MOLECULAR ECOLOGY

New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems

(2012) LAURA S. EPP et al.   MOLECULAR ECOLOGY

Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

Prey Preference of Snow Leopard (Panthera uncia) in South Gobi, Mongolia

(2012) Wasim Shehzad et al.   PLoS One

Hydrocarbon-Degrading Bacteria and the Bacterial Community Response in Gulf of Mexico Beach Sands Impacted by the Deepwater Horizon Oil Spill

(2011) Joel E. Kostka et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

Potential efficacy of mitochondrial genes for animal DNA barcoding: a case study using eutherian mammals

(2011) Arong Luo et al.   BMC GENOMICS

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

Meta-barcoding of ‘dirt’ DNA from soil reflects vertebrate biodiversity

(2011) KENNETH ANDERSEN et al.   MOLECULAR ECOLOGY

A fuzzy-set-theory-based approach to analyse species membership in DNA barcoding

(2011) A.-B. ZHANG et al.   MOLECULAR ECOLOGY

Who is eating what: diet assessment using next generation sequencing

(2011) FRANCOIS POMPANON et al.   MOLECULAR ECOLOGY

Two decades of describing the unseen majority of aquatic microbial diversity

(2011) LUCIE ZINGER et al.   MOLECULAR ECOLOGY

ABGD, Automatic Barcode Gap Discovery for primary species delimitation

(2011) N. PUILLANDRE et al.   MOLECULAR ECOLOGY

Use of the Genealogical Sorting Index (GSI) to delineate species boundaries in the Neofusicoccum parvum–Neofusicoccum ribis species complex

(2011) Monique L. Sakalidis et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis

(2011) Tiayyba Riaz et al.   NUCLEIC ACIDS RESEARCH

jMOTU and Taxonerator: Turning DNA Barcode Sequences into Annotated Operational Taxonomic Units

(2011) Martin Jones et al.   PLoS One

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

(2011) Mehrdad Hajibabaei et al.   PLoS One

DNA Barcode Sequence Identification Incorporating Taxonomic Hierarchy and within Taxon Variability

(2011) Damon P. Little   PLoS One

Microbial Biogeography of Public Restroom Surfaces

(2011) Gilberto E. Flores et al.   PLoS One

DNA-Based Faecal Dietary Analysis: A Comparison of qPCR and High Throughput Sequencing Approaches

(2011) Dáithí C. Murray et al.   PLoS One

Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood

(2011) Simon A. Berger et al.   SYSTEMATIC BIOLOGY

Caspase deficiency alters the murine gut microbiome

(2011) B M Brinkman et al.   Cell Death & Disease

An evaluation of candidate plant DNA barcodes and assignment methods in diagnosing 29 species in the genus Agalinis (Orobanchaceae)

(2010) James B. Pettengill et al.   AMERICAN JOURNAL OF BOTANY

Spatial patterns of bacterial richness and evenness in the NW Mediterranean Sea explored by pyrosequencing of the 16S rRNA

(2010) T Pommier et al.   AQUATIC MICROBIAL ECOLOGY

Integrating DNA barcode data and taxonomic practice: Determination, discovery, and description

(2010) Paul Z. Goldstein et al.   BIOESSAYS

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

An In silico approach for the evaluation of DNA barcodes

(2010) Gentile Ficetola et al.   BMC GENOMICS

ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases

(2010) Eva Bellemain et al.   BMC MICROBIOLOGY

Performance of distance-based DNA barcoding in the molecular identification of Primates

(2010) Vincent Nijman et al.   COMPTES RENDUS BIOLOGIES

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

(2010) Susan M. Huse et al.   ENVIRONMENTAL MICROBIOLOGY

The integrative future of taxonomy

(2010) Jose M. Padial et al.   Frontiers in Zoology

Water mass-specificity of bacterial communities in the North Atlantic revealed by massively parallel sequencing

(2010) HÉLÈNE AGOGUÉ et al.   MOLECULAR ECOLOGY

Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water

(2010) THORSTEN STOECK et al.   MOLECULAR ECOLOGY

Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate

(2010) J. H. SØNSTEBØ et al.   Molecular Ecology Resources

SpedeSTEM: a rapid and accurate method for species delimitation

(2010) DANIEL D. ENCE et al.   Molecular Ecology Resources

Assigning sequences to species in the absence of large interspecific differences

(2010) Melanie Lou et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

The UNITE database for molecular identification of fungi - recent updates and future perspectives

(2010) Kessy Abarenkov et al.   NEW PHYTOLOGIST

Structural Analysis of Biodiversity

(2010) Lawrence Sirovich et al.   PLoS One

Using Population Genetic Theory and DNA Sequences for Species Detection and Identification in Asexual Organisms

(2010) C. William Birky et al.   PLoS One

Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus)

(2010) A. D. Leache et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Species Delimitation Using Dominant and Codominant Multilocus Markers

(2010) Bernhard Hausdorf et al.   SYSTEMATIC BIOLOGY

Species Delimitation Using a Combined Coalescent and Information-Theoretic Approach: An Example from North American Myotis Bats

(2010) Bryan C. Carstens et al.   SYSTEMATIC BIOLOGY

Integrative taxonomy, or iterative taxonomy?

(2010) DAVID K. YEATES et al.   SYSTEMATIC ENTOMOLOGY

Assessment of Microbial Communities by Graph Partitioning in a Study of Soil Fungi in Two Alpine Meadows

(2009) L. Zinger et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

STEM: species tree estimation using maximum likelihood for gene trees under coalescence

(2009) Laura S. Kubatko et al.   BIOINFORMATICS

Googling DNA sequences on the World Wide Web

(2009) Mehrdad Hajibabaei et al.   BMC BIOINFORMATICS

Rapid DNA barcoding analysis of large datasets using the composition vector method

(2009) Ka Chu et al.   BMC BIOINFORMATICS

DNA barcode analysis: a comparison of phylogenetic and statistical classification methods

(2009) Frederic Austerlitz et al.   BMC BIOINFORMATICS

Efficient alignment-free DNA barcode analytics

(2009) Pavel Kuksa et al.   BMC BIOINFORMATICS

Learning to classify species with barcodes

(2009) Paola Bertolazzi et al.   BMC BIOINFORMATICS

BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing

(2009) Daniel N Frank   BMC BIOINFORMATICS

The seasonal structure of microbial communities in the Western English Channel

(2009) Jack A. Gilbert et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures

(2009) Eeva M Soininen et al.   Frontiers in Zoology

Universal DNA-Based Methods for Assessing the Diet of Grazing Livestock and Wildlife from Feces

(2009) Anthony Pegard et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: thetrnL approach

(2009) ALICE VALENTINI et al.   Molecular Ecology Resources

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

PrimerHunter: a primer design tool for PCR-based virus subtype identification

(2009) Jorge Duitama et al.   NUCLEIC ACIDS RESEARCH

A Scalable Method for Analysis and Display of DNA Sequences

(2009) Lawrence Sirovich et al.   PLoS One

A DNA barcode for land plants

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

Species Delimitation: A Case Study in a Problematic Ant Taxon

(2009) Kenneth G. Ross et al.   SYSTEMATIC BIOLOGY

Accelerated Species Inventory on Madagascar Using Coalescent-Based Models of Species Delineation

(2009) Michael T. Monaghan et al.   SYSTEMATIC BIOLOGY

Estimating Species Trees: Methods of Phylogenetic Analysis When There Is Incongruence across Genes

(2009) L. Lacey Knowles   SYSTEMATIC BIOLOGY

New Heuristic Methods for Joint Species Delimitation and Species Tree Inference

(2009) Brian C. O'Meara   SYSTEMATIC BIOLOGY

A universal DNA mini-barcode for biodiversity analysis

(2008) Isabelle Meusnier et al.   BMC GENOMICS

Four years of DNA barcoding: Current advances and prospects

(2008) Lise Frézal et al.   INFECTION GENETICS AND EVOLUTION

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex

(2008) Micah Hamady et al.   NATURE METHODS

UniPrime: a workflow-based platform for improved universal primer design

(2008) Michaël Bekaert et al.   NUCLEIC ACIDS RESEARCH

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH

DNA barcoding the floras of biodiversity hotspots

(2008) R. Lahaye et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Testing the Reliability of Genetic Methods of Species Identification via Simulation

(2008) Howard A. Ross et al.   SYSTEMATIC BIOLOGY

Inferring Species Membership Using DNA Sequences with Back-Propagation Neural Networks

(2008) A. B. Zhang et al.   SYSTEMATIC BIOLOGY

Statistical Assignment of DNA Sequences Using Bayesian Phylogenetics

(2008) Kasper Munch et al.   SYSTEMATIC BIOLOGY

DNA barcoding for ecologists

(2008) Alice Valentini et al.   TRENDS IN ECOLOGY & EVOLUTION

Character-based DNA barcoding allows discrimination of genera, species and populations in Odonata

(2007) J Rach et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES