Assessment of littoral algal diversity from the northern Gulf of Mexico using environmental DNA metabarcoding

Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing

(2020) Andrei Prodan et al.   PLoS One

Minimizing polymerase biases in metabarcoding

(2018) Ruth V. Nichols et al.   Molecular Ecology Resources

Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences

(2018) Robert C. Edgar   PeerJ

Toward an ecoregion scale evaluation of eDNA metabarcoding primers: A case study for the freshwater fish biodiversity of the Murray-Darling Basin (Australia)

(2018) Jonas Bylemans et al.   Ecology and Evolution

IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences

(2018) Adithya Murali et al.   Microbiome

Environmental DNA (eDNA) metabarcoding reveals strong discrimination among diverse marine habitats connected by water movement

(2018) Gert-Jan Jeunen et al.   Molecular Ecology Resources

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

A metabarcoding comparison of windward and leeward airborne algal diversity across the Ko‘olau mountain range on the island of O'ahu, Hawai‘i1

(2017) Alison R. Sherwood et al.   JOURNAL OF PHYCOLOGY

DNA metabarcoding for high-throughput monitoring of estuarine macrobenthic communities

(2017) Jorge Lobo et al.   Scientific Reports

Non-native molluscan colonizers on deliberately placed shipwrecks in the Florida Keys, with description of a new species of potentially invasive worm-snail (Gastropoda: Vermetidae)

(2017) Rüdiger Bieler et al.   PeerJ

From reads to operational taxonomic units: an ensemble processing pipeline for MiSeq amplicon sequencing data

(2017) Mohamed Mysara et al.   GigaScience

The best of both worlds: A combined approach for analyzing microalgal diversity via metabarcoding and morphology-based methods

(2017) Sophie Groendahl et al.   PLoS One

Wanted dead or alive? Using metabarcoding of environmental DNA and RNA to distinguish living assemblages for biosecurity applications

(2017) Xavier Pochon et al.   PLoS One

An adaptive decorrelation method removes Illumina DNA base-calling errors caused by crosstalk between adjacent clusters

(2017) Bo Wang et al.   Scientific Reports

Quality filtering of Illumina index reads mitigates sample cross-talk

(2016) Erik Scott Wright et al.   BMC GENOMICS

How DNA barcoding can be more effective in microalgae identification: a case of cryptic diversity revelation in Scenedesmus (Chlorophyceae)

(2016) Shanmei Zou et al.   Scientific Reports

Multi-marker metabarcoding of coral skeletons reveals a rich microbiome and diverse evolutionary origins of endolithic algae

(2016) Vanessa Rossetto Marcelino et al.   Scientific Reports

A metabarcoding framework for facilitated survey of endolithic phototrophs with tufA

(2016) Thomas Sauvage et al.   BMC ECOLOGY

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Error filtering, pair assembly and error correction for next-generation sequencing reads

(2015) Robert C. Edgar et al.   BIOINFORMATICS

Estimating Oceanic Primary Production Using Vertical Irradiance and Chlorophyll Profiles from Ocean Gliders in the North Atlantic

(2015) Victoria S. Hemsley et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

Swarm v2: highly-scalable and high-resolution amplicon clustering

(2015) Frédéric Mahé et al.   PeerJ

Metabarcoding Is Powerful yet Still Blind: A Comparative Analysis of Morphological and Molecular Surveys of Seagrass Communities

(2015) Dominique A. Cowart et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Vertical zonation is the main distribution pattern of littoral assemblages on rocky shores at a regional scale

(2014) Eglantine Chappuis et al.   ESTUARINE COASTAL AND SHELF SCIENCE

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

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

From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity

(2014) Melania E. Cristescu   TRENDS IN ECOLOGY & EVOLUTION

Environmental DNA for wildlife biology and biodiversity monitoring

(2014) Kristine Bohmann et al.   TRENDS IN ECOLOGY & EVOLUTION

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing

(2014) Patrick J. Keeling et al.   PLOS BIOLOGY

Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding

(2013) Yinqiu Ji et al.   ECOLOGY LETTERS

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Has the Earth’s sixth mass extinction already arrived?

(2011) Anthony D. Barnosky et al.   NATURE

Eukaryotic Richness in the Abyss: Insights from Pyrotag Sequencing

(2011) Jan Pawlowski et al.   PLoS One

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

The role of constructed reefs in non-indigenous species introductions and range expansions

(2009) Daniel J. Sheehy et al.   ECOLOGICAL ENGINEERING