Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome

Evolution of the RAG1-RAG2 locus: both proteins came from the same transposon

(2015) Vladimir V Kapitonov et al.   Biology Direct

Small-RNA-Mediated Genome-wide trans -Recognition Network in Tetrahymena DNA Elimination

(2015) Tomoko Noto et al.   MOLECULAR CELL

DNA deletion as a mechanism for developmentally programmed centromere loss

(2015) Maoussi Lhuillier-Akakpo et al.   NUCLEIC ACIDS RESEARCH

Centromeric Heterochromatin: The Primordial Segregation Machine

(2014) Kerry S. Bloom   Annual Review of Genetics

Billions of basepairs of recently expanded, repetitive sequences are eliminated from the somatic genome during copepod development

(2014) Cheng Sun et al.   BMC GENOMICS

The Architecture of a Scrambled Genome Reveals Massive Levels of Genomic Rearrangement during Development

(2014) Xiao Chen et al.   CELL

Centromere identity from the DNA point of view

(2014) Miroslav Plohl et al.   CHROMOSOMA

Programmed DNA elimination in multicellular organisms

(2014) Jianbin Wang et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Tetrahymena Pot2 Is a Developmentally Regulated Paralog of Pot1 That Localizes to Chromosome Breakage Sites but Not to Telomeres

(2014) Stacey Cranert et al.   EUKARYOTIC CELL

Msh4 and Msh5 Function in SC-Independent Chiasma Formation During the Streamlined Meiosis of Tetrahymena

(2014) A. Shodhan et al.   GENETICS

Methylation of histone H3K23 blocks DNA damage in pericentric heterochromatin during meiosis

(2014) Romeo Papazyan et al.   eLife

Loading and pre-loading processes generate a distinct siRNA population in Tetrahymena

(2013) Kazufumi Mochizuki et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Genomes on the Edge: Programmed Genome Instability in Ciliates

(2013) John R. Bracht et al.   CELL

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

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

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

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

Mus81 nuclease and Sgs1 helicase are essential for meiotic recombination in a protist lacking a synaptonemal complex

(2013) Agnieszka Lukaszewicz et al.   NUCLEIC ACIDS RESEARCH

A Model for the Evolution of Extremely Fragmented Macronuclei in Ciliates

(2013) David W. Morgens et al.   PLoS One

LIA5 Is Required for Nuclear Reorganization and Programmed DNA Rearrangements Occurring during Tetrahymena Macronuclear Differentiation

(2013) Annie Wan Yi Shieh et al.   PLoS One

Epigenetics of Ciliates

(2013) D. L. Chalker et al.   Cold Spring Harbor Perspectives in Biology

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

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

Transposon Domestication versus Mutualism in Ciliate Genome Rearrangements

(2013) Alexander Vogt et al.   PLoS Genetics

A Single Cohesin Complex Performs Mitotic and Meiotic Functions in the Protist Tetrahymena

(2013) Rachel A. Howard-Till et al.   PLoS Genetics

A Domesticated PiggyBac Transposase Interacts with Heterochromatin and Catalyzes Reproducible DNA Elimination in Tetrahymena

(2013) Alexander Vogt et al.   PLoS Genetics

Active Transposition in Genomes

(2012) Cheng Ran Lisa Huang et al.   Annual Review of Genetics

RNA-guided DNA rearrangements in ciliates: Is the best genome defence a good offence?

(2012) Robert S. Coyne et al.   BIOLOGY OF THE CELL

Composition and organization of active centromere sequences in complex genomes

(2012) Karen E Hayden et al.   BMC GENOMICS

Genetic Consequences of Programmed Genome Rearrangement

(2012) Jeramiah J. Smith et al.   CURRENT BIOLOGY

Biased transcription and selective degradation of small RNAs shape the pattern of DNA elimination in Tetrahymena

(2012) U. E. Schoeberl et al.   GENES & DEVELOPMENT

Transcriptome Analysis of the Model Protozoan, Tetrahymena thermophila, Using Deep RNA Sequencing

(2012) Jie Xiong et al.   PLoS One

The Paramecium Germline Genome Provides a Niche for Intragenic Parasitic DNA: Evolutionary Dynamics of Internal Eliminated Sequences

(2012) Olivier Arnaiz et al.   PLoS Genetics

Two large-scale analyses of Ty1 LTR-retrotransposon de novo insertion events indicate that Ty1 targets nucleosomal DNA near the H2A/H2B interface

(2012) Antoine Bridier-Nahmias et al.   Mobile DNA

DNA Elimination in Ciliates: Transposon Domestication and Genome Surveillance

(2011) Douglas L. Chalker et al.   Annual Review of Genetics

Keeping the Soma Free of Transposons: Programmed DNA Elimination in Ciliates

(2011) Ursula E. Schoeberl et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Absence of Positive Selection on Centromeric Histones in Tetrahymena Suggests Unsuppressed Centromere-Drive in Lineages Lacking Male Meiosis

(2011) Nels C. Elde et al.   JOURNAL OF MOLECULAR EVOLUTION

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Dynamic interactions between transposable elements and their hosts

(2011) Henry L. Levin et al.   NATURE REVIEWS GENETICS

Tetrahymena thermophila, a unicellular eukaryote with separate germline and somatic genomes

(2011) Eduardo Orias et al.   RESEARCH IN MICROBIOLOGY

Genome-Scale Analysis of Programmed DNA Elimination Sites in Tetrahymena thermophila

(2011) Joseph N. Fass et al.   G3-Genes Genomes Genetics

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

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries

(2011) Sheila Fisher et al.   GENOME BIOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Tetrahymena Argonaute-Binding Protein Giw1p Directs a Mature Argonaute-siRNA Complex to the Nucleus

(2010) Tomoko Noto et al.   CELL

Building centromeres: home sweet home or a nomadic existence?

(2010) Alessia Buscaino et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

A Domesticated piggyBac Transposase Plays Key Roles in Heterochromatin Dynamics and DNA Cleavage during Programmed DNA Deletion in Tetrahymena thermophila

(2010) Chao-Yin Cheng et al.   MOLECULAR BIOLOGY OF THE CELL

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

CDD: a Conserved Domain Database for the functional annotation of proteins

(2010) A. Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Major Evolutionary Transitions in Centromere Complexity

(2009) Harmit S. Malik et al.   CELL

Molecular domestication of transposable elements: From detrimental parasites to useful host genes

(2009) L. Sinzelle et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

 3, a transposable element that promotes host sexual reproduction

(2009) E. Barsoum et al.   GENES & DEVELOPMENT

PiggyMac, a domesticated piggyBac transposase involved in programmed genome rearrangements in the ciliate Paramecium tetraurelia

(2009) C. Baudry et al.   GENES & DEVELOPMENT

Exploring Repetitive DNA Landscapes Using REPCLASS, a Tool That Automates the Classification of Transposable Elements in Eukaryotic Genomes

(2009) Cédric Feschotte et al.   Genome Biology and Evolution

Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes

(2009) Iwanka Kozarewa et al.   NATURE METHODS

Microarray Analyses of Gene Expression during the Tetrahymena thermophila Life Cycle

(2009) Wei Miao et al.   PLoS One

A Functional Role for Transposases in a Large Eukaryotic Genome

(2009) M. Nowacki et al.   SCIENCE

The origins of the Rag genes—From transposition to V(D)J recombination

(2009) Sebastian D. Fugmann   SEMINARS IN IMMUNOLOGY

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

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY