Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana

The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin

(2013) Assaf Zemach et al.   CELL

Comprehensive Analysis of Silencing Mutants Reveals Complex Regulation of the Arabidopsis Methylome

(2013) Hume Stroud et al.   CELL

Genome-Wide Characterization of Endogenous Retroviruses in the Bat Myotis lucifugus Reveals Recent and Diverse Infections

(2013) X. Zhuo et al.   JOURNAL OF VIROLOGY

The impact of transposable elements in environmental adaptation

(2013) Elena Casacuberta et al.   MOLECULAR ECOLOGY

Reconstructing de novo silencing of an active plant retrotransposon

(2013) Arturo Marí-Ordóñez et al.   NATURE GENETICS

The Capsella rubella genome and the genomic consequences of rapid mating system evolution

(2013) Tanja Slotte et al.   NATURE GENETICS

Transposon Variants and Their Effects on Gene Expression in Arabidopsis

(2013) Xi Wang et al.   PLoS Genetics

Centromere-targeted de novo integrations of an LTR retrotransposon of Arabidopsis lyrata

(2012) S. Tsukahara et al.   GENES & DEVELOPMENT

NERD, a Plant-Specific GW Protein, Defines an Additional RNAi-Dependent Chromatin-Based Pathway in Arabidopsis

(2012) Dominique Pontier et al.   MOLECULAR CELL

Insights into salt tolerance from the genome ofThellungiella salsuginea

(2012) Hua-Jun Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transposable Elements, Epigenetics, and Genome Evolution

(2012) N. V. Fedoroff   SCIENCE

The genome of the mesopolyploid crop species Brassica rapa

(2011) Xiaowu Wang et al.   NATURE GENETICS

The genome of the extremophile crucifer Thellungiella parvula

(2011) Maheshi Dassanayake et al.   NATURE GENETICS

The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

(2011) Tina T Hu et al.   NATURE GENETICS

Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis

(2011) Ikhlak Ahmed et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

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

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

S-MART, A Software Toolbox to Aid RNA-seq Data Analysis

(2011) Matthias Zytnicki et al.   PLoS One

Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata

(2011) J. D. Hollister et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reference-guided assembly of four diverse Arabidopsis thaliana genomes

(2011) K. Schneeberger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

(2010) Julie A. Law et al.   NATURE REVIEWS GENETICS

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

(2010) S. Ossowski et al.   SCIENCE

Phylogeny of Methylomes

(2010) A. Jeltsch   SCIENCE

Cabbage family affairs: the evolutionary history of Brassicaceae

(2010) Andreas Franzke et al.   TRENDS IN PLANT SCIENCE

A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes

(2009) Stefan Kurtz et al.   BMC GENOMICS

Comparative analysis of Alu repeats in primate genomes

(2009) G. E. Liu et al.   GENOME RESEARCH

Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression

(2009) J. D. Hollister et al.   GENOME RESEARCH

Bursts of retrotransposition reproduced in Arabidopsis

(2009) Sayuri Tsukahara et al.   NATURE

Selective epigenetic control of retrotransposition in Arabidopsis

(2009) Marie Mirouze et al.   NATURE

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets

(2008) Nicolas Buisine et al.   GENOMICS

The Dynamic Ups and Downs of Genome Size Evolution in Brassicaceae

(2008) M. A. Lysak et al.   MOLECULAR BIOLOGY AND EVOLUTION

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

The shrunken genome of Arabidopsis thaliana

(2008) Ryan K. Oyama et al.   PLANT SYSTEMATICS AND EVOLUTION

A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation

(2008) Sean R. Eddy   PLoS Computational Biology

Evolution and Control of Imprinted FWA Genes in the Genus Arabidopsis

(2008) Ryo Fujimoto et al.   PLoS Genetics