Detecting invertebrate species in archived collections using next-generation sequencing

Delineating closely related species with DNA barcodes for routine biological monitoring

(2015) Melissa E. Carew et al.   FRESHWATER BIOLOGY

Large-Scale Biomonitoring of Remote and Threatened Ecosystems via High-Throughput Sequencing

(2015) Joel F. Gibson et al.   PLoS One

Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform

(2015) Shadi Shokralla et al.   Scientific Reports

Environmental metabarcodes for insects:in silicoPCR reveals potential for taxonomic bias

(2014) Laurence J. Clarke et al.   Molecular Ecology Resources

Environmental Status Assessment Using DNA Metabarcoding: Towards a Genetics Based Marine Biotic Index (gAMBI)

(2014) Eva Aylagas et al.   PLoS One

Taxonomic Reference Libraries for Environmental Barcoding: A Best Practice Example from Diatom Research

(2014) Jonas Zimmermann et al.   PLoS One

Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics

(2014) J. Gibson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A next-generation sequencing approach to river biomonitoring using benthic diatoms

(2014) Lenaïg Kermarrec et al.   Freshwater Science

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

Environmental monitoring using next generation sequencing: rapid identification of macroinvertebrate bioindicator species

(2013) Melissa E Carew et al.   Frontiers in Zoology

Ecological evidence links adverse biological effects to pesticide and metal contamination in an urban Australian watershed

(2013) Claudette R. Kellar et al.   JOURNAL OF APPLIED ECOLOGY

Evaluating Ethanol-based Sample Preservation to Facilitate Use of DNA Barcoding in Routine Freshwater Biomonitoring Programs Using Benthic Macroinvertebrates

(2013) Eric D. Stein et al.   PLoS One

Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification

(2013) Xin Zhou et al.   GigaScience

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing

(2012) DONALD J. BAIRD et al.   MOLECULAR ECOLOGY

Next-generation sequencing technologies for environmental DNA research

(2012) SHADI SHOKRALLA et al.   MOLECULAR ECOLOGY

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

(2012) Nicholas A Bokulich et al.   NATURE METHODS

Assessing biodiversity of a freshwater benthic macroinvertebrate community through non-destructive environmental barcoding of DNA from preservative ethanol

(2012) Mehrdad Hajibabaei et al.   BMC ECOLOGY

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

A combination of molecular and morphological approaches resolves species in the taxonomically difficult genus Procladius Skuse (Diptera: Chironomidae) despite high intra-specific morphological variation

(2011) M.E. Carew et al.   BULLETIN OF ENTOMOLOGICAL RESEARCH

Phylogenetic signals and ecotoxicological responses: potential implications for aquatic biomonitoring

(2011) Melissa E. Carew et al.   ECOTOXICOLOGY

Building freshwater macroinvertebrate DNA-barcode libraries from reference collection material: formalin preservation vs specimen age

(2011) Donald J. Baird et al.   JOURNAL OF THE NORTH AMERICAN BENTHOLOGICAL SOCIETY

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

(2011) Mehrdad Hajibabaei et al.   PLoS One

Direct PCR amplification and sequencing of specimens' DNA from preservative ethanol

(2010) Shadi Shokralla et al.   BIOTECHNIQUES

Taxon-specific PCR for DNA barcoding arthropod prey in bat faeces

(2010) MATT R. K. ZEALE et al.   Molecular Ecology Resources

454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases

(2010) Leho Tedersoo et al.   NEW PHYTOLOGIST

Barcode of Life

(2009) Mark Y. Stockle et al.   SCIENTIFIC AMERICAN

The effects of soil tillage on beneficial invertebrates within the vineyard

(2008) David J. Sharley et al.   AGRICULTURAL AND FOREST ENTOMOLOGY

DNA damage in preserved specimens and tissue samples: a molecular assessment

(2008) Juergen Zimmermann et al.   Frontiers in Zoology