Single-Cell Genomic Sequencing of Three Peritrichs (Protista, Ciliophora) Reveals Less Biased Stop Codon Usage and More Prevalent Programmed Ribosomal Frameshifting Than in Other Ciliates

Morphology and molecular analyses of four epibiotic peritrichs on crustacean and polychaete hosts, including descriptions of two new species (Ciliophora, Peritrichia)

(2020) Borong Lu et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

Genome analyses of the new model protist Euplotes vannus focusing on genome rearrangement and resistance to environmental stressors

(2019) Xiao Chen et al.   Molecular Ecology Resources

Novel contributions to the peritrich family Vaginicolidae (Protista: Ciliophora), with morphological and phylogenetic analyses of poorly known species of Pyxicola, Cothurnia and Vaginicola

(2019) Borong Lu et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Comparative Genomics Analysis of Ciliates Provides Insights on the Evolutionary History Within “Nassophorea–Synhymenia–Phyllopharyngea” Assemblage

(2019) Bo Pan et al.   Frontiers in Microbiology

GPSit: An automated method for evolutionary analysis of nonculturable ciliated microeukaryotes

(2018) Xiao Chen et al.   Molecular Ecology Resources

Phylogeny of the families Zoothamniidae and Epistylididae (Protozoa: Ciliophora: Peritrichia) based on analyses of three rRNA-coding regions

(2018) Yuan Zhuang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Purifying and positive selection in the evolution of stop codons

(2018) Frida Belinky et al.   Scientific Reports

Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

(2018) Sina M. Adl et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Insights into the origin and evolution of Peritrichia (Oligohymenophorea, Ciliophora) based on analyses of morphology and phylogenomics

(2018) Chuan-Qi Jiang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenomics solves a long-standing evolutionary puzzle in the ciliate world: The subclass Peritrichia is monophyletic

(2017) Eleni Gentekaki et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genetic Codes with No Dedicated Stop Codon: Context-Dependent Translation Termination

(2016) Estienne Carl Swart et al.   CELL

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Position-dependent termination and widespread obligatory frameshifting in Euplotes translation

(2016) Alexei V Lobanov et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A new Peritrich Ciliate from a Hypersaline Habitat in Northern China

(2016) YUAN ZHUANG et al.   ZOOTAXA

Position-dependent termination and widespread obligatory frameshifting in Euplotes translation

(2016) Alexei V Lobanov et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

High frequency of +1 programmed ribosomal frameshifting in Euplotes octocarinatus

(2016) Ruanlin Wang et al.   Scientific Reports

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

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Comprehensive Analysis of Stop Codon Usage in Bacteria and Its Correlation with Release Factor Abundance

(2014) Gürkan Korkmaz et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Large-scale phylogenomic analysis reveals the phylogenetic position of the problematic taxon Protocruzia and unravels the deep phylogenetic affinities of the ciliate lineages

(2014) E. Gentekaki et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products

(2013) Sergey Nurk et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

An ITS-based phylogenetic framework for the genus Vorticella: finding the molecular and morphological gaps in a taxonomically difficult group

(2013) P. Sun et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell

(2012) C. Zong et al.   SCIENCE

Probing Meiotic Recombination and Aneuploidy of Single Sperm Cells by Whole-Genome Sequencing

(2012) S. Lu et al.   SCIENCE

OneZoom: A Fractal Explorer for the Tree of Life

(2012) J. Rosindell et al.   PLOS BIOLOGY

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Reconsideration of Phylogenetic Relationships of the Subclass Peritrichia (Ciliophora, Oligohymenophorea) Based on Small Subunit Ribosomal RNA Gene Sequences, with the Establishment of a New Subclass Mobilia Kahl, 1933

(2009) ZIFENG ZHAN et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Reconsideration of the Phylogenetic Positions of Five Peritrich Genera,Vorticella, Pseudovorticella, Zoothamnopsis, Zoothamnium, andEpicarchesium(Ciliophora, Peritrichia, Sessilida), Based on Small Subunit rRNA Gene Sequences

(2008) LIFANG LI et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY