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

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

(2012) Ke Xu et al.   GENE

Characterization and Taxonomic Validity of the Ciliate Oxytricha trifallax (Class Spirotrichea) Based on Multiple Gene Sequences: Limitations in Identifying Genera Solely by Morphology

(2012) Stephen D. Zoller et al.   PROTIST

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

(2012) Olivier Arnaiz et al.   PLoS Genetics

SHRiMP2: Sensitive yet Practical Short Read Mapping

(2011) Matei David et al.   BIOINFORMATICS

The Oxytricha trifallax Mitochondrial Genome

(2011) Estienne C. Swart et al.   Genome Biology and Evolution

The Pot1a-associated proteins Tpt1 and Pat1 coordinate telomere protection and length regulation in Tetrahymena

(2011) Benjamin R. Linger et al.   MOLECULAR BIOLOGY OF THE CELL

Exploiting Oxytricha trifallax nanochromosomes to screen for non-coding RNA genes

(2011) S. Jung et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Targeted Assembly of Short Sequence Reads

(2011) René L. Warren et al.   PLoS One

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

(2011) Vincent Ranwez et al.   PLoS One

Estimating the timing of early eukaryotic diversification with multigene molecular clocks

(2011) L. W. Parfrey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

PE-Assembler: de novo assembler using short paired-end reads

(2010) Pramila Nuwantha Ariyaratne et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Assembly of large genomes using second-generation sequencing

(2010) M. C. Schatz et al.   GENOME RESEARCH

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

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

RNA-mediated epigenetic regulation of DNA copy number

(2010) M. Nowacki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-dependent control of gene amplification

(2010) G. Heyse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

(2009) Jacob F. Degner et al.   BIOINFORMATICS

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

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

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

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

POT1 proteins in green algae and land plants: DNA-binding properties and evidence of co-evolution with telomeric DNA

(2009) Eugene V. Shakirov et al.   NUCLEIC ACIDS RESEARCH

A Functional Role for Transposases in a Large Eukaryotic Genome

(2009) M. Nowacki et al.   SCIENCE

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

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

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

(2008) L. Duret et al.   GENOME RESEARCH

Analysis of the DDE Motif in the Mutator Superfamily

(2008) Aurélie Hua-Van et al.   JOURNAL OF MOLECULAR EVOLUTION

Genetic Diversity in the Paramecium aurelia Species Complex

(2008) F. Catania et al.   MOLECULAR BIOLOGY AND EVOLUTION

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH

tRNAdb 2009: compilation of tRNA sequences and tRNA genes

(2008) F. Juhling et al.   NUCLEIC ACIDS RESEARCH