DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation

Century-scale Methylome Stability in a Recently Diverged Arabidopsis thaliana Lineage

(2015) Jörg Hagmann et al.   PLoS Genetics

Keeping It Local: Evidence for Positive Selection in Swedish Arabidopsis thaliana

(2014) Christian D. Huber et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic Distribution of H3K9me2 and DNA Methylation in a Maize Genome

(2014) Patrick T. West et al.   PLoS One

How a Retrotransposon Exploits the Plant's Heat Stress Response for Its Activation

(2014) Vladimir V. Cavrak et al.   PLoS Genetics

Evolution of DNA Methylation Patterns in the Brassicaceae is Driven by Differences in Genome Organization

(2014) Danelle K. Seymour et al.   PLoS Genetics

Natural CMT2 Variation Is Associated With Genome-Wide Methylation Changes and Temperature Seasonality

(2014) Xia Shen et al.   PLoS Genetics

Estimating heritability of complex traits from genome-wide association studies using IBS-based Haseman–Elston regression

(2014) Guo-Bo Chen   Frontiers in Genetics

NextGenMap: fast and accurate read mapping in highly polymorphic genomes

(2013) Fritz J. Sedlazeck et al.   BIOINFORMATICS

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

Inheritance Patterns and Stability of DNA Methylation Variation in Maize Near-Isogenic Lines

(2013) Q. Li et al.   GENETICS

Estimating and interpreting FST: The impact of rare variants

(2013) G. Bhatia et al.   GENOME RESEARCH

Patterns of population epigenomic diversity

(2013) Robert J. Schmitz et al.   NATURE

Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden

(2013) Quan Long et al.   NATURE GENETICS

QST–FST comparisons: evolutionary and ecological insights from genomic heterogeneity

(2013) Tuomas Leinonen et al.   NATURE REVIEWS GENETICS

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis

(2013) Hume Stroud et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Epigenetic and Genetic Influences on DNA Methylation Variation in Maize Populations

(2013) S. R. Eichten et al.   PLANT CELL

RNA Silencing Is Resistant to Low-Temperature in Grapevine

(2013) Marjorie Romon et al.   PLoS One

Passive and active DNA methylation and the interplay with genetic variation in gene regulation

(2013) Maria Gutierrez-Arcelus et al.   eLife

An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations

(2012) Vincent Segura et al.   NATURE GENETICS

DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons

(2012) Xuehua Zhong et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Advanced Methylome Analysis after Bisulfite Deep Sequencing: An Example in Arabidopsis

(2012) Huy Q. Dinh et al.   PLoS One

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions

(2012) Kasper D Hansen et al.   GENOME BIOLOGY

Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data

(2012) Yaping Liu et al.   GENOME BIOLOGY

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

Body-Methylated Genes in Arabidopsis thaliana Are Functionally Important and Evolve Slowly

(2011) S. Takuno et al.   MOLECULAR BIOLOGY AND EVOLUTION

An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress

(2011) Hidetaka Ito et al.   NATURE

Adaptation to Climate Across the Arabidopsis thaliana Genome

(2011) A. M. Hancock et al.   SCIENCE

Repitools: an R package for the analysis of enrichment-based epigenomic data

(2010) A. L. Statham et al.   BIOINFORMATICS

R/qtl: high-throughput multiple QTL mapping: Fig. 1.

(2010) Danny Arends et al.   BIOINFORMATICS

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

(2010) Lihua J Zhu et al.   BMC BIOINFORMATICS

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

(2010) Susanna Atwell et al.   NATURE

Variance component model to account for sample structure in genome-wide association studies

(2010) Hyun Min Kang et al.   NATURE GENETICS

Epigenetic Regulation of Repetitive Elements Is Attenuated by Prolonged Heat Stress inArabidopsis

(2010) Ales Pecinka et al.   PLANT CELL

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

BSMAP: whole genome bisulfite sequence MAPping program

(2009) Yuanxin Xi et al.   BMC BIOINFORMATICS

H2A.Z-Containing Nucleosomes Mediate the Thermosensory Response in Arabidopsis

(2009) S. Vinod Kumar et al.   CELL

A stepwise pathway for biogenesis of 24-nt secondary siRNAs and spreading of DNA methylation

(2008) Lucia Daxinger et al.   EMBO JOURNAL