RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome

Post-conversion targeted capture of modified cytosines in mammalian and plant genomes

(2015) Qing Li et al.   NUCLEIC ACIDS RESEARCH

Examining the Causes and Consequences of Context-Specific Differential DNA Methylation in Maize

(2015) Qing Li et al.   PLANT PHYSIOLOGY

Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements

(2015) David Secco et al.   eLife

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Diverse Gene-Silencing Mechanisms with Distinct Requirements for RNA Polymerase Subunits in Zea mays

(2014) A. E. Sloan et al.   GENETICS

Detection of Pol IV/RDR2-dependent transcripts at the genomic scale inArabidopsisreveals features and regulation of siRNA biogenesis

(2014) Shaofang Li et al.   GENOME RESEARCH

SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation

(2014) Lianna M. Johnson et al.   NATURE

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity

(2014) Marjori A. Matzke et al.   NATURE REVIEWS GENETICS

Accessible DNA and Relative Depletion of H3K9me2 at Maize Loci Undergoing RNA-Directed DNA Methylation

(2014) Jonathan I. Gent et al.   PLANT CELL

Genetic Perturbation of the Maize Methylome

(2014) Qing Li et al.   PLANT CELL

Maize Gene Atlas Developed by RNA Sequencing and Comparative Evaluation of Transcriptomes Based on RNA Sequencing and Microarrays

(2014) Rajandeep S. Sekhon et al.   PLoS One

Genomic Distribution of H3K9me2 and DNA Methylation in a Maize Genome

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

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

(2013) Assaf Zemach et al.   CELL

The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA

(2013) M. Regulski et al.   GENOME RESEARCH

Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1

(2013) Julie A. Law et al.   NATURE

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

Automated conserved non-coding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses

(2013) Gina Turco et al.   Frontiers in Plant Science

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize

(2012) J. I. Gent et al.   GENOME RESEARCH

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

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

RNA polymerase V targets transcriptional silencing components to promoters of protein-coding genes

(2012) Qi Zheng et al.   PLANT JOURNAL

‘Leveling’ the playing field for analyses of single-base resolution DNA methylomes

(2012) Matthew D. Schultz et al.   TRENDS IN GENETICS

Spreading of Heterochromatin Is Limited to Specific Families of Maize Retrotransposons

(2012) Steven R. Eichten et al.   PLoS Genetics

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

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

Conservation and divergence of methylation patterning in plants and animals

(2010) S. Feng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BSMAP: whole genome bisulfite sequence MAPping program

(2009) Yuanxin Xi et al.   BMC BIOINFORMATICS

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

A Dominant Mutation in mediator of paramutation2, One of Three Second-Largest Subunits of a Plant-Specific RNA Polymerase, Disrupts Multiple siRNA Silencing Processes

(2009) Lyudmila Sidorenko et al.   PLoS Genetics

Loss of RNA–Dependent RNA Polymerase 2 (RDR2) Function Causes Widespread and Unexpected Changes in the Expression of Transposons, Genes, and 24-nt Small RNAs

(2009) Yi Jia et al.   PLoS Genetics