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

Distribution and diversity of oligotrich and choreotrich ciliates assessed by morphology and DGGE in temperate coastal waters

(2013) JD Grattepanche et al.   AQUATIC MICROBIAL ECOLOGY

A morphogenetic survey on ciliate plankton from a mountain lake pinpoints the necessity of lineage-specific barcode markers in microbial ecology

(2013) Thorsten Stoeck et al.   ENVIRONMENTAL MICROBIOLOGY

Multigene-Based Analyses of the Phylogenetic Evolution of Oligotrich Ciliates, with Consideration of the Internal Transcribed Spacer 2 Secondary Structure of Three Systematically Ambiguous Genera

(2013) Jiamei Li et al.   EUKARYOTIC CELL

Extremely High Copy Numbers and Polymorphisms of the rDNA Operon Estimated from Single Cell Analysis of Oligotrich and Peritrich Ciliates

(2013) Jun Gong et al.   PROTIST

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

Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing

(2012) Ramiro Logares et al.   ISME Journal

Phylogeny of the Order Tintinnida (Ciliophora, Spirotrichea) Inferred from Small- and Large-Subunit rRNA Genes

(2012) Luciana F. Santoferrara et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Reconciling Cladistic and Genetic Analyses in Choreotrichid Ciliates (Ciliophora, Spirotricha, Oligotrichea)

(2012) Sabine Agatha et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Abundance and diversity of tintinnids (planktonic ciliates) under contrasting levels of productivity in the Argentine Shelf and Drake Passage

(2012) Luciana F. Santoferrara et al.   JOURNAL OF SEA RESEARCH

Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay

(2012) Lucie Bittner et al.   MOLECULAR ECOLOGY

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

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

Utility of Genetic Markers and Morphology for Species Discrimination within the Order Tintinnida (Ciliophora, Spirotrichea)

(2012) Luciana F. Santoferrara et al.   PROTIST

Sequencing our way towards understanding global eukaryotic biodiversity

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

Phylogeny of three choreotrich genera (Protozoa, Ciliophora, Spirotrichea), with morphological, morphogenetic and molecular investigations on three strobilidiid species

(2012) Weiwei Liu et al.   ZOOLOGICA SCRIPTA

Pyrosequencing analysis of the protist communities in a High Arctic meromictic lake: DNA preservation and change

(2012) Sophie Charvet et al.   Frontiers in Microbiology

Distribution and diversity of oligotrich and choreotrich ciliates across an environmental gradient in a large temperate estuary

(2011) M Tamura et al.   AQUATIC MICROBIAL ECOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

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

(2011) Virginia Edgcomb et al.   ISME Journal

Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments

(2011) HOLLY M. BIK et al.   MOLECULAR ECOLOGY

Two decades of describing the unseen majority of aquatic microbial diversity

(2011) LUCIE ZINGER et al.   MOLECULAR ECOLOGY

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Are similarity- or phylogeny-based methods more appropriate for classifying internal transcribed spacer (ITS) metagenomic amplicons?

(2011) Teresita M. Porter et al.   NEW PHYTOLOGIST

Diversity and Vertical Distribution of Microbial Eukaryotes in the Snow, Sea Ice and Seawater Near the North Pole at the End of the Polar Night

(2011) Charles Bachy et al.   Frontiers in Microbiology

Diversity of Oligotrichia and Choreotrichia Ciliates in Coastal Marine Sediments and in Overlying Plankton

(2010) M. Doherty et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Ciliate diversity and distribution across an environmental and depth gradient in Long Island Sound, USA

(2010) Mary Doherty et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

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

Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions

(2010) Jens Reeder et al.   NATURE METHODS

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

Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities

(2009) Thorsten Stoeck et al.   BMC BIOLOGY

Eukaryotic diversity and phylogeny using small- and large-subunit ribosomal RNA genes from environmental samples

(2009) William Marande 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

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS