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

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

(2015) Itamar Sela et al.   NUCLEIC ACIDS RESEARCH

A case study to estimate the applicability of secondary structures of SSU-rRNA gene in taxonomy and phylogenetic analyses of ciliates

(2015) Pu Wang et al.   ZOOLOGICA SCRIPTA

Effect of the enzyme and PCR conditions on the quality of high-throughput DNA sequencing results

(2015) Claudia Brandariz-Fontes et al.   Scientific Reports

Genome of the facultative scuticociliatosis pathogen Pseudocohnilembus persalinus provides insight into its virulence through horizontal gene transfer

(2015) Jie Xiong et al.   Scientific Reports

The Draft Assembly of the Radically Organized Stylonychia lemnae Macronuclear Genome

(2014) Samuel H. Aeschlimann et al.   Genome Biology and Evolution

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

Taxonomy and molecular phylogeny of fourStrombidiumspecies, including description ofS. pseudostylifersp. nov. (Ciliophora, Oligotrichia)

(2014) Wen Song et al.   SYSTEMATICS AND BIODIVERSITY

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes

(2013) Estienne C. Swart et al.   PLOS BIOLOGY

Short-term dynamics of diversity patterns: evidence of continual reassembly within lacustrine small eukaryotes

(2012) Jean-François Mangot et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2012) Ke Xu et al.   GENE

Environmental microbiology through the lens of high-throughput DNA sequencing: Synopsis of current platforms and bioinformatics approaches

(2012) Ramiro Logares et al.   JOURNAL OF MICROBIOLOGICAL METHODS

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

Protist community composition during spring in an Arctic flaw lead polynya

(2011) Ramon Terrado et al.   POLAR BIOLOGY

Morphology and SSU rRNA gene-based phylogeny of two marine Euplotes species, E. orientalis spec. nov. and E. raikovi (Ciliophora, Euplotida)

(2010) Jiamei Jiang et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

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

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

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

(2009) P. Librado et al.   BIOINFORMATICS

Microarray and cDNA sequence analysis of transcription during nerve-dependent limb regeneration

(2009) James R Monaghan et al.   BMC BIOLOGY

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

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

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

The Dynamic Nature of Eukaryotic Genomes

(2008) L. W. Parfrey et al.   MOLECULAR BIOLOGY AND EVOLUTION

Intragenomic Variation of Fungal Ribosomal Genes Is Higher than Previously Thought

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

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY