Chromatin state analysis of the barley epigenome reveals a higher-order structure defined by H3K27me1 and H3K27me3 abundance

Antagonistic Roles for H3K36me3 and H3K27me3 in the Cold-Induced Epigenetic Switch at Arabidopsis FLC

(2014) Hongchun Yang et al.   CURRENT BIOLOGY

The chromatin landscape of Drosophila: comparisons between species, sexes, and chromosomes

(2014) E. J. Brown et al.   GENOME RESEARCH

The Functional Topography of the Arabidopsis Genome Is Organized in a Reduced Number of Linear Motifs of Chromatin States

(2014) J. Sequeira-Mendes et al.   PLANT CELL

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

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

The low-recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression

(2014) Katie Baker et al.   PLANT JOURNAL

Genomic Distribution of H3K9me2 and DNA Methylation in a Maize Genome

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

Exploitation of interspecific diversity for monocot crop improvement

(2013) J King et al.   HEREDITY

Genomic Distribution of Maize Facultative Heterochromatin Marked by Trimethylation of H3K27

(2013) I. Makarevitch et al.   PLANT CELL

Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)

(2013) Martin Mascher et al.   PLANT JOURNAL

Regional control of histone H3 lysine 27 methylation in Neurospora

(2013) K. Jamieson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Heterochromatin and gene positioning: inside, outside, any side?

(2012) K. Laurence Jost et al.   CHROMOSOMA

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Spatiotemporal Asymmetry of the Meiotic Program Underlies the Predominantly Distal Distribution of Meiotic Crossovers in Barley

(2012) James D. Higgins et al.   PLANT CELL

GenomicTools: a computational platform for developing high-throughput analytics in genomics

(2011) Aristotelis Tsirigos et al.   BIOINFORMATICS

Association of tissue lineage and gene expression: conservatively and differentially expressed genes define common and special functions of tissues

(2011) Yao Yu et al.   BMC BIOINFORMATICS

Integrative epigenomic mapping defines four main chromatin states in Arabidopsis

(2011) François Roudier et al.   EMBO JOURNAL

Nucleosomes in the neighborhood

(2011) Elizabeth Suzanne Dorn et al.   Epigenetics

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

Euchromatic Subdomains in Rice Centromeres Are Associated with Genes and Transcription

(2011) Yufeng Wu et al.   PLANT CELL

Polycomb Group Complexes Mediate Developmental Transitions in Plants

(2011) S. Holec et al.   PLANT PHYSIOLOGY

Dynamic Regulation of H3K27 Trimethylation during Arabidopsis Differentiation

(2011) Marcel Lafos et al.   PLoS Genetics

A signal–noise model for significance analysis of ChIP-seq with negative control

(2010) Han Xu et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

(2010) Guillaume J. Filion et al.   CELL

Rice SUVH Histone Methyltransferase Genes Display Specific Functions in Chromatin Modification and Retrotransposon Repression

(2010) Fu-Jun Qin et al.   Molecular Plant

Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases

(2010) Yannick Jacob et al.   NATURE

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids

(2010) G. He et al.   PLANT CELL

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

JBrowse: A next-generation genome browser

(2009) M. E. Skinner et al.   GENOME RESEARCH

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

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

FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology

(2008) A. P. Fejes et al.   BIOINFORMATICS

Histone modifications associated with both A and B chromosomes of maize

(2008) Weiwei Jin et al.   CHROMOSOME RESEARCH

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data

(2008) R. Jothi et al.   NUCLEIC ACIDS RESEARCH

High-Resolution Mapping of Epigenetic Modifications of the Rice Genome Uncovers Interplay between DNA Methylation, Histone Methylation, and Gene Expression

(2008) X. Li et al.   PLANT CELL