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

Robust estimation of microbial diversity in theory and in practice

(2013) Bart Haegeman et al.   ISME Journal

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

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

Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay

(2012) Lucie Bittner et al.   MOLECULAR ECOLOGY

Fast, accurate error-correction of amplicon pyrosequences using Acacia

(2012) Lauren Bragg et al.   NATURE METHODS

PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets

(2012) Ameet J. Pinto et al.   PLoS One

Molecular Phylogeny of Tintinnid Ciliates (Tintinnida, Ciliophora)

(2012) Charles Bachy et al.   PROTIST

CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms

(2012) Jan Pawlowski et al.   PLOS BIOLOGY

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

(2012) Sophie Charvet et al.   Frontiers in Microbiology

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

Morphological and molecular phylogeny of dileptid and tracheliid ciliates: Resolution at the base of the class Litostomatea (Ciliophora, Rhynchostomatia)

(2011) Peter Vďačný et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

Microbial eukaryote life in the new hypersaline deep-sea basin Thetis

(2011) Alexandra Stock et al.   EXTREMOPHILES

Class Cariacotrichea, a novel ciliate taxon from the anoxic Cariaco Basin, Venezuela

(2011) W. Orsi et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Accessing marine protists from the anoxic Cariaco Basin

(2011) V Edgcomb et al.   ISME Journal

Reproducibility and quantitation of amplicon sequencing-based detection

(2011) Jizhong Zhou et al.   ISME Journal

Protist diversity in a permanently ice-covered Antarctic Lake during the polar night transition

(2011) Scott Bielewicz et al.   ISME Journal

Spatiotemporal distribution and activity patterns of bacteria from three phylogenetic groups in an oligomesotrophic lake

(2011) Michaela M. Salcher et al.   LIMNOLOGY AND OCEANOGRAPHY

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

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

Identification of Paramecium bursaria Syngens through Molecular Markers – Comparative Analysis of Three Loci in the Nuclear and Mitochondrial DNA

(2011) Magdalena Greczek-Stachura et al.   PROTIST

JAGUC — A SOFTWARE PACKAGE FOR ENVIRONMENTAL DIVERSITY ANALYSES

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

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Some considerations for analyzing biodiversity using integrative metagenomics and gene networks

(2010) Lucie Bittner et al.   Biology Direct

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

Spatio-temporal variations in protistan communities along an O2/H2S gradient in the anoxic Framvaren Fjord (Norway)

(2010) Anke Behnke et al.   FEMS MICROBIOLOGY 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

Quantifying microbial communities with 454 pyrosequencing: does read abundance count?

(2010) ANTHONY S. AMEND et al.   MOLECULAR ECOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

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

(2010) Markus Nebel et al.   Environmental Microbiology Reports

High-Level Genetic Diversity but No Population Structure Inferred from Nuclear and Mitochondrial Markers of the Peritrichous Ciliate Carchesium polypinum in the Grand River Basin (North America)

(2009) E. Gentekaki et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences

(2009) Yijun Sun et al.   NUCLEIC ACIDS RESEARCH

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

High mitochondrial haplotype diversity of Coleps sp. (Ciliophora: Prostomatida)

(2008) Dana Barth et al.   ENVIRONMENTAL MICROBIOLOGY

Spatio-temporal niche separation of planktonicBetaproteobacteriain an oligo-mesotrophic lake

(2008) Michaela M. Salcher et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial eukaryotes in the hypersaline anoxic L'Atalante deep-sea basin

(2008) Eva Alexander et al.   ENVIRONMENTAL MICROBIOLOGY

Protistan community patterns within the brine and halocline of deep hypersaline anoxic basins in the eastern Mediterranean Sea

(2008) Virginia Edgcomb et al.   EXTREMOPHILES

Multigene phylogenies of clonal Spumella-like strains, a cryptic heterotrophic nanoflagellate, isolated from different geographical regions

(2008) T. Stoeck et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY