Genomic Distribution of H3K9me2 and DNA Methylation in a Maize Genome

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

Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea

(2014) Isobel AP Parkin et al.   GENOME BIOLOGY

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

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

(2013) M. Regulski et al.   GENOME RESEARCH

Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population

(2013) R. J. Schmitz et al.   GENOME RESEARCH

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

(2013) Julie A. Law et al.   NATURE

Epigenetic and Genetic Influences on DNA Methylation Variation in Maize Populations

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

Mechanism for full-length RNA processing of Arabidopsis genes containing intragenic heterochromatin

(2013) Hidetoshi Saze et al.   Nature Communications

Dual Binding of Chromomethylase Domains to H3K9me2-Containing Nucleosomes Directs DNA Methylation in Plants

(2012) Jiamu Du et al.   CELL

Genome-Wide Analysis of Syntenic Gene Deletion in the Grasses

(2012) James C. Schnable et al.   Genome Biology and Evolution

‘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

Strong epigenetic similarity between maize centromeric and pericentromeric regions at the level of small RNAs, DNA methylation and H3 chromatin modifications

(2011) Jonathan I. Gent et al.   NUCLEIC ACIDS RESEARCH

Transgenerational Epigenetic Instability Is a Source of Novel Methylation Variants

(2011) R. J. Schmitz et al.   SCIENCE

Heritable Epigenetic Variation among Maize Inbreds

(2011) Steve R. Eichten et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

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

Genome-wide profiling of histone H3 lysine 9 acetylation and dimethylation in Arabidopsis reveals correlation between multiple histone marks and gene expression

(2010) Junli Zhou et al.   PLANT MOLECULAR BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genome-Wide and Organ-Specific Landscapes of Epigenetic Modifications and Their Relationships to mRNA and Small RNA Transcriptomes in Maize

(2009) X. Wang et al.   PLANT CELL

The B73 Maize Genome: Complexity, Diversity, and Dynamics

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

Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome

(2009) Regina S. Baucom et al.   PLoS Genetics

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

(2008) Ryan Lister et al.   CELL

Histone modifications associated with both A and B chromosomes of maize

(2008) Weiwei Jin et al.   CHROMOSOME RESEARCH

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE