Beyond the visual: using metabarcoding to characterize the hidden reef cryptobiome

MIDORI server: a webserver for taxonomic assignment of unknown metazoan mitochondrial-encoded sequences using a curated database

(2018) Matthieu Leray et al.   BIOINFORMATICS

The hidden half: ecology and evolution of cryptobenthic fishes on coral reefs

(2018) Simon J. Brandl et al.   BIOLOGICAL REVIEWS

Automated high throughput animal CO1 metabarcode classification

(2018) Teresita M. Porter et al.   Scientific Reports

Cross-shelf investigation of coral reef cryptic benthic organisms reveals diversity patterns of the hidden majority

(2018) J. K. Pearman et al.   Scientific Reports

Adapting metabarcoding-based benthic biomonitoring into routine marine ecological status assessment networks

(2018) Eva Aylagas et al.   ECOLOGICAL INDICATORS

Over 2.5 million COI sequences in GenBank and growing

(2018) Teresita M. Porter et al.   PLoS One

A comparative analysis of metabarcoding and morphology-based identification of benthic communities across different regional seas

(2018) Abigail E. Cahill et al.   Ecology and Evolution

Metapopulation theory identifies biogeographical patterns among core and satellite marine bacteria scaling from tens to thousands of kilometers

(2017) Markus V. Lindh et al.   ENVIRONMENTAL MICROBIOLOGY

Where less may be more: how the rare biosphere pulls ecosystems strings

(2017) Alexandre Jousset et al.   ISME Journal

Microbial planktonic communities in the Red Sea: high levels of spatial and temporal variability shaped by nutrient availability and turbulence

(2017) John K. Pearman et al.   Scientific Reports

Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment

(2017) Michael Stat et al.   Scientific Reports

Sorting things out: Assessing effects of unequal specimen biomass on DNA metabarcoding

(2017) Vasco Elbrecht et al.   Ecology and Evolution

Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies

(2017) Laurence J. Clarke et al.   Ecology and Evolution

Abundance and local-scale processes contribute to multi-phyla gradients in global marine diversity

(2017) Graham J. Edgar et al.   Science Advances

dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering

(2015) Tal Galili   BIOINFORMATICS

A review of contemporary patterns of endemism for shallow water reef fauna in the Red Sea

(2015) Joseph D. DiBattista et al.   JOURNAL OF BIOGEOGRAPHY

Metagenetic tools for the census of marine meiofaunal biodiversity: An overview

(2015) Laura Carugati et al.   Marine Genomics

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

(2015) Eddy J. Dowle et al.   Molecular Ecology Resources

Ecology and exploration of the rare biosphere

(2015) Michael D. J. Lynch et al.   NATURE REVIEWS MICROBIOLOGY

DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity

(2015) Matthieu Leray et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Temporal patterns of rarity provide a more complete view of microbial diversity

(2015) Ashley Shade et al.   TRENDS IN MICROBIOLOGY

Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods

(2015) Jullien M. Flynn et al.   Ecology and Evolution

Microbial Ecology: Finding Structure in the Rare Biosphere

(2014) Charles Bachy et al.   CURRENT BIOLOGY

Patterns of Rare and Abundant Marine Microbial Eukaryotes

(2014) Ramiro Logares et al.   CURRENT BIOLOGY

Invertebrate biodiversity associated with algal turfs on a coral-dominated reef

(2014) Rebecca Milne et al.   Marine Biodiversity

Beta diversity as the variance of community data: dissimilarity coefficients and partitioning

(2013) Pierre Legendre 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

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Rare Species Support Vulnerable Functions in High-Diversity Ecosystems

(2013) David Mouillot et al.   PLOS BIOLOGY

Species richness of motile cryptofauna across a gradient of reef framework erosion

(2012) I. C. Enochs et al.   CORAL REEFS

The importance of structural complexity in coral reef ecosystems

(2012) N. A. J. Graham et al.   CORAL REEFS

The Magnitude of Global Marine Species Diversity

(2012) Ward Appeltans et al.   CURRENT BIOLOGY

Motile cryptofauna associated with live and dead coral substrates: implications for coral mortality and framework erosion

(2011) Ian C. Enochs   MARINE BIOLOGY

Cnidarians as a Source of New Marine Bioactive Compounds—An Overview of the Last Decade and Future Steps for Bioprospecting

(2011) Joana Rocha et al.   Marine Drugs

Environmental determinants of motile cryptofauna on an eastern Pacific coral reef

(2011) IC Enochs et al.   MARINE ECOLOGY PROGRESS SERIES

Contrasting changes in taxonomic vs. functional diversity of tropical fish communities after habitat degradation

(2010) Sébastien Villéger et al.   ECOLOGICAL APPLICATIONS

Predicting the number of known and unknown species in European seas using rates of description

(2010) Mark J. Costello et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Linking Social and Ecological Systems to Sustain Coral Reef Fisheries

(2009) Joshua E. Cinner et al.   CURRENT BIOLOGY

Estimating and controlling for spatial structure in the study of ecological communities

(2009) Pedro R. Peres-Neto et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Climate change and coral reef bleaching: An ecological assessment of long-term impacts, recovery trends and future outlook

(2008) Andrew C. Baker et al.   ESTUARINE COASTAL AND SHELF SCIENCE

Poorly cemented coral reefs of the eastern tropical Pacific: Possible insights into reef development in a high-CO2 world

(2008) D. P. Manzello et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA