The Compact Macronuclear Genome of the Ciliate Halteria grandinella: A Transcriptome-Like Genome with 23,000 Nanochromosomes

Single-Cell Transcriptomics Reveal a Correlation between Genome Architecture and Gene Family Evolution in Ciliates

(2020) Ying Yan et al.   mBio

ADFinder: accurate detection of programmed DNA elimination using NGS high-throughput sequencing data

(2020) Weibo Zheng et al.   BIOINFORMATICS

The completed macronuclear genome of a model ciliate Tetrahymena thermophila and its application in genome scrambling and copy number analyses

(2020) Yalan Sheng et al.   Science China-Life Sciences

Cyclin Cyc2p is required for micronuclear bouquet formation in Tetrahymena thermophila

(2019) Jing Xu et al.   Science China-Life Sciences

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

(2019) Yurui Wang et al.   Science China-Life Sciences

Identification of a DNA N6-Adenine Methyltransferase Complex and Its Impact on Chromatin Organization

(2019) Leslie Y. Beh et al.   CELL

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

Environmentally induced plasticity of programmed DNA elimination boosts somatic variability in Paramecium tetraurelia

(2019) Valerio Vitali et al.   GENOME RESEARCH

rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data

(2019) Elena Bushmanova et al.   GigaScience

A distinct class of eukaryotic MT-A70 methyltransferases maintain symmetric DNA N6-adenine methylation at the ApT dinucleotides as an epigenetic mark associated with transcription

(2019) Yuanyuan Wang et al.   NUCLEIC ACIDS RESEARCH

EOGD: the Euplotes octocarinatus genome database

(2018) Ruan-lin Wang et al.   BMC GENOMICS

Insights into an Extensively Fragmented Eukaryotic Genome: De Novo Genome Sequencing of the Multinuclear Ciliate Uroleptopsis citrina

(2018) Weibo Zheng et al.   Genome Biology and Evolution

“Twisted Tales: Insights into Genome Diversity of Ciliates Using Single-Cell ‘omics”

(2018) Xyrus X Maurer-Alcalá et al.   Genome Biology and Evolution

Small RNA-mediated regulation of DNA dosage in the ciliate Oxytricha

(2017) Jaspreet S. Khurana et al.   RNA

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

(2016) Estienne Carl Swart et al.   CELL

High frequency of +1 programmed ribosomal frameshifting in Euplotes octocarinatus

(2016) Ruanlin Wang et al.   Scientific Reports

Combinatorial DNA rearrangement facilitates the origin of new genes in ciliates

(2015) Xiao Chen et al.   Genome Biology and Evolution

: a database of ciliate genome rearrangements

(2015) Jonathan Burns et al.   NUCLEIC ACIDS RESEARCH

Analyses of Alternatively Processed Genes in Ciliates Provide Insights into the Origins of Scrambled Genomes and May Provide a Mechanism for Speciation

(2015) Feng Gao et al.   mBio

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Genome-Wide Linkage-Disequilibrium Profiles from Single Individuals

(2014) Michael Lynch et al.   GENETICS

The Draft Assembly of the Radically Organized Stylonychia lemnae Macronuclear Genome

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

Population-Genetic Inference from Pooled-Sequencing Data

(2014) Michael Lynch et al.   Genome Biology and Evolution

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Spliced DNA Sequences in the Paramecium Germline: Their Properties and Evolutionary Potential

(2013) Francesco Catania et al.   Genome Biology and Evolution

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

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

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

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

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control

(2011) Robert S Coyne et al.   GENOME BIOLOGY

Alternative processing of scrambled genes generates protein diversity in the ciliate Chilodonella uncinata

(2010) Laura A. Katz et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

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

(2008) Guénola Ricard et al.   BMC GENOMICS

Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure

(2008) Robert S Coyne et al.   BMC GENOMICS

Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: A somatic view of the germline

(2008) L. Duret et al.   GENOME RESEARCH

Translational control of intron splicing in eukaryotes

(2008) Olivier Jaillon et al.   NATURE

NCBI BLAST: a better web interface

(2008) M. Johnson et al.   NUCLEIC ACIDS RESEARCH