The Draft Assembly of the Radically Organized Stylonychia lemnae Macronuclear Genome

Differential expression of histone H3 genes and selective association of the variant H3.7 with a specific sequence class in Stylonychia macronuclear development

(2014) Sakeh Forcob et al.   Epigenetics & Chromatin

Space-efficient and exact de Bruijn graph representation based on a Bloom filter

(2013) Rayan Chikhi et al.   Algorithms for Molecular Biology

GAGE-B: an evaluation of genome assemblers for bacterial organisms

(2013) Tanja Magoc et al.   BIOINFORMATICS

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

BayesHammer: Bayesian clustering for error correction in single-cell sequencing

(2013) Sergey I Nikolenko et al.   BMC GENOMICS

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

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

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

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

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

A permissive chromatin structure is adopted prior to site-specific DNA demethylation of developmentally expressed genes involved in macronuclear differentiation

(2013) Aneta Bulic et al.   Epigenetics & Chromatin

RNA-dependent genome processing during nuclear differentiation: the model systems of stichotrichous ciliates

(2013) Gloria Fuhrmann et al.   Epigenomics

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

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

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

(2013) Alexander Vogt et al.   PLoS Genetics

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Parameters for accurate genome alignment

(2012) Martin C Frith et al.   BMC BIOINFORMATICS

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

(2012) Ke Xu et al.   GENE

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

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

Draft macronucleus genome of Euplotes crassus ciliate

(2012) D. V. Vinogradov et al.   MOLECULAR BIOLOGY

Rfam 11.0: 10 years of RNA families

(2012) Sarah W. Burge et al.   NUCLEIC ACIDS RESEARCH

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

(2012) Toshiaki Namiki et al.   NUCLEIC ACIDS RESEARCH

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

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

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

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

The Pfam protein families database

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

Transgenerational Epigenetic Instability Is a Source of Novel Methylation Variants

(2011) R. J. Schmitz et al.   SCIENCE

The evolutionary history of histone H3 suggests a deep eukaryotic root of chromatin modifying mechanisms

(2010) Jan Postberg et al.   BMC EVOLUTIONARY BIOLOGY

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

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

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li 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

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Transgenerational Epigenetic Inheritance: Prevalence, Mechanisms, and Implications for the Study of Heredity and Evolution

(2009) Eva Jablonka et al.   QUARTERLY REVIEW OF BIOLOGY

A Functional Role for Transposases in a Large Eukaryotic Genome

(2009) M. Nowacki et al.   SCIENCE

G-quadruplex structures: in vivo evidence and function

(2009) Hans J. Lipps et al.   TRENDS IN CELL BIOLOGY

SHRiMP: Accurate Mapping of Short Color-space Reads

(2009) Stephen M. Rumble et al.   PLoS Computational Biology

Quickly evolving histones, nucleosome stability and chromatin folding: All about histone H2A.Bbd

(2008) Rodrigo González-Romero et al.   GENE

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH

Spatial and temporal plasticity of chromatin during programmed DNA-reorganization in Stylonychia macronuclear development

(2008) Jan Postberg et al.   Epigenetics & Chromatin