Targeted gene enrichment and high-throughput sequencing for environmental biomonitoring: a case study using freshwater macroinvertebrates

Early detection of eukaryotic communities from marine biofilm using high-throughput sequencing: an assessment of different sampling devices

(2015) Xavier Pochon et al.   BIOFOULING

Environmental DNA – An emerging tool in conservation for monitoring past and present biodiversity

(2015) Philip Francis Thomsen et al.   BIOLOGICAL CONSERVATION

Environmental Monitoring: Inferring the Diatom Index from Next-Generation Sequencing Data

(2015) Joana Amorim Visco et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Accurate assessment of the impact of salmon farming on benthic sediment enrichment using foraminiferal metabarcoding

(2015) X. Pochon et al.   MARINE POLLUTION BULLETIN

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

(2015) Anastasija Zaiko et al.   MARINE POLLUTION BULLETIN

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

The Challenges of Resolving a Rapid, Recent Radiation: Empirical and Simulated Phylogenomics of Philippine Shrews

(2015) Thomas C. Giarla et al.   SYSTEMATIC BIOLOGY

Molecular Barcoding of Aquatic Oligochaetes: Implications for Biomonitoring

(2015) Régis Vivien 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

DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match

(2014) B. E. Deagle et al.   Biology Letters

Using metabarcoding to ask if easily collected soil and leaf-litter samples can be used as a general biodiversity indicator

(2014) Chenxue Yang et al.   ECOLOGICAL INDICATORS

Successional Change in Microbial Communities of Benthic Phormidium-Dominated Biofilms

(2014) Katie A. Brasell et al.   MICROBIAL ECOLOGY

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

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

Environmental monitoring through protist next-generation sequencing metabarcoding: assessing the impact of fish farming on benthic foraminifera communities

(2014) Jan Pawlowski et al.   Molecular Ecology Resources

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

Harnessing DNA to improve environmental management

(2014) R. P. Kelly et al.   SCIENCE

Does DNA barcoding improve performance of traditional stream bioassessment metrics?

(2014) Eric D. Stein et al.   Freshwater Science

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

(2014) Lenaïg Kermarrec et al.   Freshwater Science

Environmental bio-monitoring with high-throughput sequencing

(2013) J. Wang et al.   BRIEFINGS IN BIOINFORMATICS

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

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Redesign of PCR primers for mitochondrial cytochromecoxidase subunit I for marine invertebrates and application in all-taxa biotic surveys

(2013) J. Geller et al.   Molecular Ecology Resources

DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet

(2013) M. De Barba et al.   Molecular Ecology Resources

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

Molecular genetic tools for environmental monitoring of New Zealand's aquatic habitats, past, present and the future

(2013) SA Wood et al.   NEW ZEALAND JOURNAL OF MARINE AND FRESHWATER RESEARCH

A Phylogeny of Birds Based on Over 1,500 Loci Collected by Target Enrichment and High-Throughput Sequencing

(2013) John E. McCormack et al.   PLoS One

Evaluating Detection Limits of Next-Generation Sequencing for the Surveillance and Monitoring of International Marine Pests

(2013) Xavier Pochon et al.   PLoS One

Next Generation Sequencing Reveals the Hidden Diversity of Zooplankton Assemblages

(2013) Penelope K. Lindeque 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

Genetic diversity in widespread species is not congruent with species richness in alpine plant communities

(2012) Pierre Taberlet et al.   ECOLOGY LETTERS

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

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Sequencing our way towards understanding global eukaryotic biodiversity

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

CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms

(2012) Jan Pawlowski et al.   PLOS BIOLOGY

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

Targeted enrichment of genomic DNA regions for next-generation sequencing

(2011) F. Mertes et al.   Briefings in Functional Genomics

Can DNA barcodes of stream macroinvertebrates improve descriptions of community structure and water quality?

(2011) Bernard W. Sweeney et al.   JOURNAL OF THE NORTH AMERICAN BENTHOLOGICAL SOCIETY

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

(2011) KENNETH ANDERSEN et al.   MOLECULAR ECOLOGY

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

(2011) Mehrdad Hajibabaei et al.   PLoS One

Metagenomic Analyses: Past and Future Trends

(2010) Carola Simon et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

Ecological assessment of estuarine sediments by pyrosequencing eukaryotic ribosomal DNA

(2010) Anthony A Chariton et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises

(2010) S. CREER 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

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

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

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions

(2010) Marcus J. Claesson et al.   NUCLEIC ACIDS RESEARCH

Multiplexed DNA Sequence Capture of Mitochondrial Genomes Using PCR Products

(2010) Tomislav Maricic et al.   PLoS One

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

Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces

(2009) BRUCE E. DEAGLE et al.   MOLECULAR ECOLOGY

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

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

Genomics: catch me if you can

(2009) Nathan Blow   NATURE METHODS

A universal DNA mini-barcode for biodiversity analysis

(2008) Isabelle Meusnier et al.   BMC GENOMICS