Comparative analyses of the V4 and V9 regions of 18S rDNA for the extant eukaryotic community using the Illumina platform

Ecological and evolutionary patterns in the enigmatic protist genus Percolomonas (Heterolobosea; Discoba) from diverse habitats

(2019) Denis V. Tikhonenkov et al.   PLoS One

Temporal variation of eukaryotic community structures in UASB reactor treating domestic sewage as revealed by 18S rRNA gene sequencing

(2019) Yuga Hirakata et al.   Scientific Reports

Dactylomonas gen. nov., a Novel Lineage of Heterolobosean Flagellates with Unique Ultrastructure, Closely Related to the Amoeba Selenaion koniopes Park, De Jonckheere & Simpson, 2012

(2018) Pavla Hanousková et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Comparison of coastal phytoplankton composition estimated from the V4 and V9 regions of the 18S rRNA gene with a focus on photosynthetic groups and especially Chlorophyta

(2017) Margot Tragin et al.   ENVIRONMENTAL MICROBIOLOGY

A New Heterolobosean Amoeboflagellate, Tetramitus dokdoensis n. sp., Isolated from a Freshwater Pond on Dokdo Island in the East Sea, Korea

(2017) Jong Soo Park   JOURNAL OF EUKARYOTIC MICROBIOLOGY

An 18S rRNA Workflow for Characterizing Protists in Sewage, with a Focus on Zoonotic Trichomonads

(2017) Julia M. Maritz et al.   MICROBIAL ECOLOGY

Environmental Sequencing Provides Reasonable Estimates of the Relative Abundance of Specific Picoeukaryotes

(2016) Caterina R. Giner et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Design and Evaluation of Illumina MiSeq-Compatible, 18S rRNA Gene-Specific Primers for Improved Characterization of Mixed Phototrophic Communities

(2016) Ian M. Bradley et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Oligotrophic lagoons of the South Pacific Ocean are home to a surprising number of novel eukaryotic microorganisms

(2016) Eunsoo Kim et al.   ENVIRONMENTAL MICROBIOLOGY

Local diversity of heathland Cercozoa explored by in-depth sequencing

(2016) Christoffer Bugge Harder et al.   ISME Journal

Next-Generation Sequencing Assessment of Eukaryotic Diversity in Oil Sands Tailings Ponds Sediments and Surface Water

(2016) Maria Aguilar et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Phylogenetic diversity and biogeography of the Mamiellophyceae lineage of eukaryotic phytoplankton across the oceans

(2016) Adam Monier et al.   Environmental Microbiology Reports

Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing

(2015) Ramon Massana et al.   ENVIRONMENTAL MICROBIOLOGY

Estimating Protistan Diversity Using High-Throughput Sequencing

(2015) Sarah K. Hu et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Patterns of Rare and Abundant Marine Microbial Eukaryotes

(2014) Ramiro Logares et al.   CURRENT BIOLOGY

Placing Environmental Next-Generation Sequencing Amplicons from Microbial Eukaryotes into a Phylogenetic Context

(2014) Micah Dunthorn et al.   MOLECULAR BIOLOGY AND EVOLUTION

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Characterization of the 18S rRNA Gene for Designing Universal Eukaryote Specific Primers

(2014) Kenan Hadziavdic et al.   PLoS One

Intracellular Diversity of the V4 and V9 Regions of the 18S rRNA in Marine Protists (Radiolarians) Assessed by High-Throughput Sequencing

(2014) Johan Decelle et al.   PLoS One

Creneis carolina gen. et sp. nov. (Heterolobosea), a Novel Marine Anaerobic Protist with Strikingly Derived Morphology and Life Cycle

(2014) Tomáš Pánek et al.   PROTIST

The Phylogenetic Likelihood Library

(2014) T. Flouri et al.   SYSTEMATIC BIOLOGY

Ten years of next-generation sequencing technology

(2014) Erwin L. van Dijk et al.   TRENDS IN GENETICS

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

(2013) Ramiro Logares et al.   ENVIRONMENTAL MICROBIOLOGY

Choice of Pore Size Can Introduce Artefacts when Filtering Picoeukaryotes for Molecular Biodiversity Studies

(2013) Nikolaj Sørensen et al.   MICROBIAL ECOLOGY

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Phylogenetic Affiliation of SSU rRNA Genes Generated by Massively Parallel Sequencing: New Insights into the Freshwater Protist Diversity

(2013) Najwa Taib et al.   PLoS One

Ultrafast clustering algorithms for metagenomic sequence analysis

(2012) W. Li et al.   BRIEFINGS IN BIOINFORMATICS

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Characterization ofSelenaion koniopesn. gen., n. sp., an Amoeba that Represents a New Major Lineage within Heterolobosea, Isolated from the Wieliczka Salt Mine

(2012) Jong Soo Park et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

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 Revised Classification of Eukaryotes

(2012) Sina M. Adl et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on the Same Microbial Community DNA Sample

(2012) Chengwei Luo et al.   PLoS One

Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads

(2011) Andrea K. Bartram et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

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

(2011) T. Magoc et al.   BIOINFORMATICS

Illumina-based analysis of microbial community diversity

(2011) Patrick H Degnan et al.   ISME Journal

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

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

(2010) THORSTEN STOECK et al.   MOLECULAR ECOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Hypotheses on the role of the protistan rare biosphere in a changing world

(2009) DA Caron et al.   AQUATIC MICROBIAL ECOLOGY

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

Ultrastructure and Molecular Phylogeny of two Heterolobosean Amoebae, Euplaesiobystra hypersalinica gen. et sp. nov. and Tulamoeba peronaphora gen. et sp. nov., Isolated from an Extremely Hypersaline Habitat

(2009) Jong Soo Park et al.   PROTIST