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

Dicer-like Enzymes with Sequence Cleavage Preferences

(2018) Cristina Hoehener et al.   CELL

Discovery of the First Germline-Restricted Gene by Subtractive Transcriptomic Analysis in the Zebra Finch, Taeniopygia guttata

(2018) Michelle K. Biederman et al.   CURRENT BIOLOGY

Small RNA-Mediated trans -Nuclear and trans -Element Communications in Tetrahymena DNA Elimination

(2018) Tomoko Noto et al.   CURRENT BIOLOGY

Plasticity of Meiotic Recombination Rates in Response to Temperature inArabidopsis

(2018) Andrew Lloyd et al.   GENETICS

The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution

(2018) Jeramiah J. Smith et al.   NATURE GENETICS

Plasticity of Meiotic Recombination Rates in Response to Temperature inArabidopsis

(2018) Andrew Lloyd et al.   GENETICS

Six domesticated PiggyBac transposases together carry out programmed DNA elimination in Paramecium

(2018) Julien Bischerour et al.   eLife

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

(2018) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Necessity Is the Mother of Invention: Ciliates, Transposons, and Transgenerational Inheritance

(2017) Sarah E. Allen et al.   TRENDS IN GENETICS

Whats, hows and whys of programmed DNA elimination in Tetrahymena

(2017) Tomoko Noto et al.   Open Biology

Atropos: specific, sensitive, and speedy trimming of sequencing reads

(2017) John P. Didion et al.   PeerJ

BBMerge – Accurate paired shotgun read merging via overlap

(2017) Brian Bushnell et al.   PLoS One

ParTIES: a toolbox forParameciuminterspersed DNA elimination studies

(2015) Cyril Denby Wilkes et al.   BIOINFORMATICS

Cis-acting signals modulate the efficiency of programmed DNA elimination inParamecium tetraurelia

(2015) Diana Ferro et al.   NUCLEIC ACIDS RESEARCH

TFIIS-Dependent Non-coding Transcription Regulates Developmental Genome Rearrangements

(2015) Kamila Maliszewska-Olejniczak et al.   PLoS Genetics

On the path to genetic novelties: insights from programmed DNA elimination and RNA splicing

(2015) Francesco Catania et al.   Wiley Interdisciplinary Reviews-RNA

Programmed DNA elimination in multicellular organisms

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

Functional Diversification of Dicer-like Proteins and Small RNAs Required for Genome Sculpting

(2014) Pamela Y. Sandoval et al.   DEVELOPMENTAL CELL

Genome-defence small RNAs exapted for epigenetic mating-type inheritance

(2014) Deepankar Pratap Singh et al.   NATURE

Local Effect of Enhancer of Zeste-Like Reveals Cooperation of Epigenetic and cis-Acting Determinants for Zygotic Genome Rearrangements

(2014) Maoussi Lhuillier-Akakpo et al.   PLoS Genetics

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

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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

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

Coping with Temperature at the Warm Edge – Patterns of Thermal Adaptation in the Microbial Eukaryote Paramecium caudatum

(2012) Sascha Krenek 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

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Thermal performance curves of Paramecium caudatum: A model selection approach

(2011) Sascha Krenek et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Versatile TPR domains accommodate different modes of target protein recognition and function

(2010) Rudi Kenneth Allan et al.   CELL STRESS & CHAPERONES

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 Relationship among Gene Expression, the Evolution of Gene Dosage, and the Rate of Protein Evolution

(2010) Jean-François Gout et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

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

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Maternal noncoding transcripts antagonize the targeting of DNA elimination by scanRNAs in Paramecium tetraurelia

(2008) G. Lepere et al.   GENES & DEVELOPMENT

Study of an RNA helicase implicates small RNA-noncoding RNA interactions in programmed DNA elimination in Tetrahymena

(2008) L. Aronica et al.   GENES & DEVELOPMENT

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

(2008) L. Duret et al.   GENOME RESEARCH

Silencing-associated and meiosis-specific small RNA pathways in Paramecium tetraurelia

(2008) Gersende Lepère et al.   NUCLEIC ACIDS RESEARCH