Further analyses of variation of ribosome DNA copy number and polymorphism in ciliates provide insights relevant to studies of both molecular ecology and phylogeny

Species delimitation for the molecular taxonomy and ecology of the widely distributed microbial eukaryote genus Euplotes (Alveolata, Ciliophora)

(2018) Yan Zhao et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

N 6 -methyladenine DNA modification in the unicellular eukaryotic organism Tetrahymena thermophila

(2017) Yuanyuan Wang et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

Macronuclear Actin copy number variations in single cells of different Pseudokeronopsis (Alveolata, Ciliophora) populations

(2017) Lijuan Huang et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

Systematic studies on ciliates (Alveolata, Ciliophora) in China: Progress and achievements based on molecular information

(2017) Feng Gao et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

Unusual features of non-dividing somatic macronuclei in the ciliate class Karyorelictea

(2017) Ying Yan et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

A comparative study of genome organization and epigenetic mechanisms in model ciliates, with an emphasis on Tetrahymena , Paramecium and Oxytricha

(2017) Yurui Wang et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

Nuclear Features of the Heterotrich Ciliate Blepharisma americanum : Genomic Amplification, Life Cycle, and Nuclear Inclusion

(2017) Megan M. Wancura et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Single Cell Analysis Linking Ribosomal (r)DNA and rRNA Copy Numbers to Cell Size and Growth Rate Provides Insights into Molecular Protistan Ecology

(2017) Rao Fu et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Ecological Patterns Among Bacteria and Microbial Eukaryotes Derived from Network Analyses in a Low-Salinity Lake

(2017) Adriane Clark Jones et al.   MICROBIAL ECOLOGY

Further consideration on the phylogeny of the Ciliophora: Analyses using both mitochondrial and nuclear data with focus on the extremely confused class Phyllopharyngea

(2017) Pu Wang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

N6-adenine DNA methylation is associated with the linker DNA of H2A.Z-containing well-positioned nucleosomes in Pol II-transcribed genes in Tetrahymena

(2017) Yuanyuan Wang et al.   NUCLEIC ACIDS RESEARCH

Disentangling sources of variation in SSU rDNA sequences from single cell analyses of ciliates: impact of copy number variation and experimental error

(2017) Chundi Wang et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Distribution of Abundant and Active Planktonic Ciliates in Coastal and Slope Waters Off New England

(2017) Sarah J. Tucker et al.   Frontiers in Microbiology

Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests

(2017) Frédéric Mahé et al.   Nature Ecology & Evolution

Patterns and processes in microbial biogeography: do molecules and morphologies give the same answers?

(2016) Luciana F Santoferrara et al.   ISME Journal

Unexpected biodiversity of ciliates in marine samples from below the photic zone

(2016) Jean-David Grattepanche et al.   MOLECULAR ECOLOGY

Utility of combining morphological characters, nuclear and mitochondrial genes: An attempt to resolve the conflicts of species identification for ciliated protists

(2016) Yan Zhao et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Multigene-based phylogeny of the ciliate families Amphisiellidae and Trachelostylidae (Protozoa: Ciliophora: Hypotrichia)

(2016) Jie Huang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Histone methyltransferase TXR1 is required for both H3 and H3.3 lysine 27 methylation in the well-known ciliated protist Tetrahymena thermophila

(2016) Xiaolu Zhao et al.   Science China-Life Sciences

Enzymatic and chemical mapping of nucleosome distribution in purified micro- and macronuclei of the ciliated model organism, Tetrahymena thermophila

(2016) Xiao Chen et al.   Science China-Life Sciences

Patchiness of Ciliate Communities Sampled at Varying Spatial Scales along the New England Shelf

(2016) Jean-David Grattepanche et al.   PLoS One

The All-Data-Based Evolutionary Hypothesis of Ciliated Protists with a Revised Classification of the Phylum Ciliophora (Eukaryota, Alveolata)

(2016) Feng Gao et al.   Scientific Reports

GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters

(2015) Itamar Sela et al.   NUCLEIC ACIDS RESEARCH

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Do early colonization patterns of periphytic ciliate fauna reveal environmental quality status in coastal waters?

(2014) Henglong Xu et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

Nanochromosome Copy Number Does not Correlate with RNA Levels Though Patterns are Conserved between Strains of the Ciliate Morphospecies Chilodonella uncinata

(2014) Jie Huang et al.   PROTIST

Ribosomal DNA copy number is coupled with gene expression variation and mitochondrial abundance in humans

(2014) John G. Gibbons et al.   Nature Communications

Evidence for isolated evolution of deep-sea ciliate communities through geological separation and environmental selection

(2013) Alexandra Stock et al.   BMC MICROBIOLOGY

Impaired replication elongation in Tetrahymena mutants deficient in histone H3 Lys 27 monomethylation

(2013) S. Gao et al.   GENES & DEVELOPMENT

The D1-D2 region of the large subunit ribosomal DNA as barcode for ciliates

(2013) T. Stoeck et al.   Molecular Ecology Resources

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

Variability of Bacterial Community Composition on Leaves Between and Within Plant Species

(2012) Ido Izhaki et al.   CURRENT MICROBIOLOGY

Copy number variations of 11 macronuclear chromosomes and their gene expression in Oxytricha trifallax

(2012) Ke Xu et al.   GENE

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

Revealing the Diversity and Quantity of Peritrich Ciliates in Environmental Samples Using Specific Primer-based PCR and Quantitative PCR

(2012) Xihan Liu et al.   MICROBES AND ENVIRONMENTS

Intra-Genomic Ribosomal RNA Polymorphism and Morphological Variation in Elphidium macellum Suggests Inter-Specific Hybridization in Foraminifera

(2012) Loïc Pillet 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

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Molecular Diversity of the Syndinean Genus Euduboscquella Based on Single-Cell PCR Analysis

(2011) Tsvetan R. Bachvaroff et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Quantitative PCR assay for the detection of the parasitic ciliate Cryptocaryon irritans

(2011) Akito Taniguchi et al.   FISHERIES SCIENCE

Protist community composition during spring in an Arctic flaw lead polynya

(2011) Ramon Terrado et al.   POLAR BIOLOGY

Ribosomal DNA Deletions Modulate Genome-Wide Gene Expression: “rDNA–Sensitive” Genes and Natural Variation

(2011) Silvana Paredes et al.   PLoS Genetics

Redescription of Favella ehrenbergii (Claparède and Lachmann, 1858) Jörgensen, 1924 (Ciliophora: Choreotrichia), with Phylogenetic Analyses Based on Small Subunit rRNA Gene Sequences

(2010) SUN YOUNG KIM et al.   JOURNAL OF EUKARYOTIC 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

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

RNA-dependent control of gene amplification

(2010) G. Heyse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Evaluation of the Use of the LSU rRNA D1-D5 Domain for DNA-based Taxonomy of Eukaryotic Protists

(2010) Claudia Wylezich et al.   PROTIST

Abundance of Ribosomal RNA Gene Copies Maintains Genome Integrity

(2010) S. Ide et al.   SCIENCE

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

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

Effects of temperature increase on the grazing of planktonic bacteria by biofilm-dwelling consumers

(2009) M Kathol et al.   AQUATIC MICROBIAL ECOLOGY

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

(2009) P. Librado et al.   BIOINFORMATICS

Quantification of Diatom and Dinoflagellate Biomasses in Coastal Marine Seawater Samples by Real-Time PCR

(2008) A. Godhe et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Intragenomic Variation of Fungal Ribosomal Genes Is Higher than Previously Thought

(2008) U. K. Simon et al.   MOLECULAR BIOLOGY AND EVOLUTION