Investigating Microbial Eukaryotic Diversity from a Global Census: Insights from a Comparison of Pyrotag and Full-Length Sequences of 18S rRNA Genes

Pyrosequencing for assessing diversity of eukaryotic microbes: analysis of data on marine planktonic ciliates and comparison with traditional methods

(2014) Luciana F. Santoferrara et al.   ENVIRONMENTAL MICROBIOLOGY

Regional variability in eukaryotic protist communities in the Amundsen Sea

(2013) Christian Wolf et al.   ANTARCTIC SCIENCE

Robust estimation of microbial diversity in theory and in practice

(2013) Bart Haegeman et al.   ISME Journal

Towards a Molecular Taxonomy for Protists: Benefits, Risks, and Applications in Plankton Ecology

(2013) David A. Caron   JOURNAL OF EUKARYOTIC MICROBIOLOGY

454 Pyrosequencing to Describe Microbial Eukaryotic Community Composition, Diversity and Relative Abundance: A Test for Marine Haptophytes

(2013) Elianne Egge et al.   PLoS One

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

Comparing the Hyper-Variable V4 and V9 Regions of the Small Subunit rDNA for Assessment of Ciliate Environmental Diversity

(2012) Micah Dunthorn et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

(2012) Laure Guillou et al.   NUCLEIC ACIDS RESEARCH

Microplanktonic Community Structure in a Coastal System Relative to a Phaeocystis Bloom Inferred from Morphological and Tag Pyrosequencing Methods

(2012) Sébastien Monchy et al.   PLoS One

Sequencing our way towards understanding global eukaryotic biodiversity

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

Marine Protistan Diversity

(2011) David A. Caron et al.   Annual Review of Marine Science

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Protistan microbial observatory in the Cariaco Basin, Caribbean. I. Pyrosequencing vs Sanger insights into species richness

(2011) Virginia Edgcomb et al.   ISME Journal

Two decades of describing the unseen majority of aquatic microbial diversity

(2011) LUCIE ZINGER et al.   MOLECULAR ECOLOGY

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

(2011) Patrick D. Schloss et al.   PLoS One

JAGUC — A SOFTWARE PACKAGE FOR ENVIRONMENTAL DIVERSITY ANALYSES

(2011) MARKUS E. NEBEL et al.   Journal of Bioinformatics and Computational Biology

Microbial Metagenomics: Beyond the Genome

(2010) Jack A. Gilbert et al.   Annual Review of Marine Science

Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions

(2010) Anke Behnke et al.   ENVIRONMENTAL MICROBIOLOGY

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

(2010) Susan M. Huse et al.   ENVIRONMENTAL MICROBIOLOGY

Composition and genetic diversity of picoeukaryotes in subtropical coastal waters as revealed by 454 pyrosequencing

(2010) Man Kit Cheung et al.   ISME Journal

Seasonal analysis of protistan community structure and diversity at the USC Microbial Observatory (San Pedro Channel, North Pacific Ocean)

(2010) Peter D. Countway et al.   LIMNOLOGY AND OCEANOGRAPHY

Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity

(2010) VIOLA NOLTE et al.   MOLECULAR ECOLOGY

Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water

(2010) THORSTEN STOECK et al.   MOLECULAR ECOLOGY

Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms

(2010) RALPH MEDINGER et al.   MOLECULAR ECOLOGY

Insidious effects of sequencing errors on perceived diversity in molecular surveys

(2010) Ian A. Dickie   NEW PHYTOLOGIST

Delimiting operational taxonomic units for assessing ciliate environmental diversity using small-subunit rRNA gene sequences

(2010) Markus Nebel et al.   Environmental Microbiology Reports

Comparison of Species Richness Estimates Obtained Using Nearly Complete Fragments and Simulated Pyrosequencing-Generated Fragments in 16S rRNA Gene-Based Environmental Surveys

(2009) N. Youssef et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Defining DNA-Based Operational Taxonomic Units for Microbial-Eukaryote Ecology

(2009) D. A. Caron et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure

(2009) Julie A. Huber et al.   ENVIRONMENTAL MICROBIOLOGY

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit Ribosomal RNA Genes

(2009) Linda A. Amaral-Zettler et al.   PLoS One

Extreme diversity in noncalcifying haptophytes explains a major pigment paradox in open oceans

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

Widespread occurrence and genetic diversity of marine parasitoids belonging toSyndiniales(Alveolata)

(2008) L. Guillou et al.   ENVIRONMENTAL MICROBIOLOGY

Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing

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