Two New Computational Methods for Universal DNA Barcoding: A Benchmark Using Barcode Sequences of Bacteria, Archaea, Animals, Fungi, and Land Plants

Community composition of root-associated fungi in aQuercus-dominated temperate forest: “codominance” of mycorrhizal and root-endophytic fungi

(2013) Hirokazu Toju et al.   Ecology and Evolution

Accuracy of protist diversity assessments: morphology compared with cloning and direct pyrosequencing of 18S rRNA genes and ITS regions using the conspicuous tintinnid ciliates as a case study

(2012) Charles Bachy et al.   ISME Journal

Bioinformatic challenges for DNA metabarcoding of plants and animals

(2012) ERIC COISSAC et al.   MOLECULAR ECOLOGY

Biodiversity loss and its impact on humanity

(2012) Bradley J. Cardinale et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Estimation of Fish Biomass Using Environmental DNA

(2012) Teruhiko Takahara et al.   PLoS One

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

(2012) C. L. Schoch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Surveillance of fish species composition using environmental DNA

(2011) Toshifumi Minamoto et al.   LIMNOLOGY

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

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

Taxonomic metagenome sequence assignment with structured output models

(2011) Kaustubh R Patil et al.   NATURE METHODS

PhymmBL expanded: confidence scores, custom databases, parallelization and more

(2011) Arthur Brady et al.   NATURE METHODS

Taxonomic classification of metagenomic shotgun sequences with CARMA3

(2011) Wolfgang Gerlach et al.   NUCLEIC ACIDS RESEARCH

DNA Barcode Sequence Identification Incorporating Taxonomic Hierarchy and within Taxon Variability

(2011) Damon P. Little   PLoS One

Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences

(2011) David S. Hibbett et al.   Fungal Biology Reviews

Comparative performances of DNA barcoding across insect orders

(2010) Massimiliano Virgilio et al.   BMC BIOINFORMATICS

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

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies

(2010) Manuel Stark et al.   BMC GENOMICS

SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences

(2009) M. Monzoorul Haque et al.   BIOINFORMATICS

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

(2009) Frederic Austerlitz et al.   BMC BIOINFORMATICS

TACOA – Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach

(2009) Naryttza N Diaz et al.   BMC BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Progress towards DNA barcoding of fungi

(2009) KEITH A. SEIFERT   Molecular Ecology Resources

Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama

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

A DNA barcode for land plants

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

A universal DNA mini-barcode for biodiversity analysis

(2008) Isabelle Meusnier et al.   BMC GENOMICS

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

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

Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing

(2008) Susan M. Huse et al.   PLoS Genetics