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

Taxonomic studies on Aegyria apoliva sp. nov. and Trithigmostoma cucullulus (Müller, 1786) Jankowski, 1967 (Ciliophora, Cyrtophoria) with phylogenetic analyses

(2018) Xumiao Chen et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

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

(2018) Xiao Chen et al.   Molecular Ecology Resources

Phylogenomic Analysis of Nassula variabilis n. sp., Furgasonia blochmanni , and Pseudomicrothorax dubius Confirms a Nassophorean Clade

(2018) Denis H. Lynn et al.   PROTIST

Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

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

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

(2018) Alex L Mitchell et al.   NUCLEIC ACIDS RESEARCH

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

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

Morphology and Phylogeny of Two Novel Ciliates, Arcanisutura chongmingensis n. gen., n. sp. and Naxella paralucida n. sp. from Shanghai, China

(2017) Wanying Liao et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

A microtubule bestiary: structural diversity in tubulin polymers

(2017) Sami Chaaban et al.   MOLECULAR BIOLOGY OF THE CELL

Sensing Self and Foreign Circular RNAs by Intron Identity

(2017) Y. Grace Chen et al.   MOLECULAR CELL

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

Morphology of four cyrtophorian ciliates (Protozoa, Ciliophora) from Yangtze Delta, China, with notes on the phylogeny of the genus Phascolodon

(2016) Hongbo Pan et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

The small subunit rRNA gene sequence of the chonotrich Chilodochona carcini Jankowski, 1973 confirms chonotrichs as a dysteriid-derived clade (Phyllopharyngea, Ciliophora)

(2016) Denis H. Lynn   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Novel Ciliate Genetic Code Variants Including the Reassignment of All Three Stop Codons to Sense Codons inCondylostoma magnum

(2016) Stephen M. Heaphy et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

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

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

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

Identification of minimal eukaryotic introns through GeneBase, a user-friendly tool for parsing the NCBI Gene databank

(2015) Allison Piovesan et al.   DNA RESEARCH

The effects of modified atmosphere packaging on core browning and the expression patterns of PPO and PAL genes in ‘Yali’ pears during cold storage

(2015) Yudou Cheng et al.   LWT-FOOD SCIENCE AND TECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

New considerations on the phylogeny of cyrtophorian ciliates (Protozoa, Ciliophora): expanded sampling to understand their evolutionary relationships

(2015) Xiao Chen et al.   ZOOLOGICA SCRIPTA

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

GENOME STRUCTURE DRIVES PATTERNS OF GENE FAMILY EVOLUTION IN CILIATES, A CASE STUDY USINGCHILODONELLA UNCINATA(PROTISTA, CILIOPHORA, PHYLLOPHARYNGEA)

(2014) Feng Gao et al.   EVOLUTION

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

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

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

Further insights into the phylogeny of two ciliate classes Nassophorea and Prostomatea (Protista, Ciliophora)

(2013) Qianqian Zhang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

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

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

Molecular Phylogeny of the Cyrtophorid Ciliates (Protozoa, Ciliophora, Phyllopharyngea)

(2012) Shan Gao et al.   PLoS One

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

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

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

A novel hybrid gene prediction method employing protein multiple sequence alignments

(2011) Oliver Keller et al.   BIOINFORMATICS

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

(2011) Hanbo Chen et al.   BMC BIOINFORMATICS

Evidence of abundant stop codon readthrough in Drosophila and other metazoa

(2011) I. Jungreis et al.   GENOME RESEARCH

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

GUIDANCE: a web server for assessing alignment confidence scores

(2010) O. Penn et al.   NUCLEIC ACIDS RESEARCH

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

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

Phylogeny and Systematic Position ofZosterodasys(Ciliophora, Synhymeniida): A Combined Analysis of Ciliate Relationships Using Morphological and Molecular Data

(2009) K. LINDHOLM KIVIMAKI et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Small Subunit rRNA Phylogenies Show that the Class Nassophorea is Not Monophyletic (Phylum Ciliophora)

(2009) JUN GONG et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Macronuclear genome structure of the ciliate Nyctotherus ovalis: Single-gene chromosomes and tiny introns

(2008) Guénola Ricard et al.   BMC GENOMICS

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

The effect of intron length on exon creation ratios during the evolution of mammalian genomes

(2008) M. Roy et al.   RNA

A simple, fast, and accurate method of phylogenomic inference

(2008) Martin Wu et al.   GENOME BIOLOGY