Whole-genome DNA methylation patterns and complex associations with gene structure and expression during flower development in Arabidopsis

High-throughput sequencing of methylated cytosine enriched by modification-dependent restriction endonuclease MspJI

(2013) Xiaojun Huang et al.   BMC GENETICS

Patterns of population epigenomic diversity

(2013) Robert J. Schmitz et al.   NATURE

Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening

(2013) Silin Zhong et al.   NATURE BIOTECHNOLOGY

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis

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

Sexual dimorphic floral development in dioecious plants revealed by transcriptome, phytohormone, and DNA methylation analysis in Populus tomentosa

(2013) Yuepeng Song et al.   PLANT MOLECULAR BIOLOGY

A Potential Role for CHH DNA Methylation in Cotton Fiber Growth Patterns

(2013) Xiang Jin et al.   PLoS One

GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data

(2012) Jianxing Feng et al.   BIOINFORMATICS

DNA Methylation Dynamics during Sexual Reproduction in Arabidopsis thaliana

(2012) Pauline E. Jullien et al.   CURRENT BIOLOGY

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

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

Structure and cleavage activity of the tetrameric MspJI DNA modification-dependent restriction endonuclease

(2012) John R. Horton et al.   NUCLEIC ACIDS RESEARCH

Molecular basis for the specification of floral organs by APETALA3 and PISTILLATA

(2012) S. E. Wuest et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Position-dependent correlations between DNA methylation and the evolutionary rates of mammalian coding exons

(2012) T.-J. Chuang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

First Exon Length Controls Active Chromatin Signatures and Transcription

(2012) Nicole I. Bieberstein et al.   Cell Reports

Regulation and function of DNA methylation in plants and animals

(2011) Xin-Jian He et al.   CELL RESEARCH

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

(2011) Ikhlak Ahmed et al.   NUCLEIC ACIDS RESEARCH

DNA Methylation of the First Exon Is Tightly Linked to Transcriptional Silencing

(2011) Fabienne Brenet et al.   PLoS One

The MspJI family of modification-dependent restriction endonucleases for epigenetic studies

(2011) D. Cohen-Karni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Merged consensus clustering to assess and improve class discovery with microarray data

(2010) T Ian Simpson et al.   BMC BIOINFORMATICS

Signaling and Transcriptional Control of Reproductive Development in Arabidopsis

(2010) Xiaochun Ge et al.   CURRENT BIOLOGY

Molecular control of microsporogenesis in Arabidopsis

(2010) Fang Chang et al.   CURRENT OPINION IN PLANT BIOLOGY

Relationship between nucleosome positioning and DNA methylation

(2010) Ramakrishna K. Chodavarapu et al.   NATURE

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

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

A unique family of Mrr-like modification-dependent restriction endonucleases

(2010) Yu Zheng et al.   NUCLEIC ACIDS RESEARCH

The transcriptome landscape of Arabidopsis male meiocytes from high-throughput sequencing: the complexity and evolution of the meiotic process

(2010) Hongxing Yang et al.   PLANT JOURNAL

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

Orchestration of Floral Initiation by APETALA1

(2010) K. Kaufmann et al.   SCIENCE

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

DNA methylation reprogramming during plant sexual reproduction?

(2010) Pauline E. Jullien et al.   TRENDS IN GENETICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen

(2009) R. Keith Slotkin et al.   CELL

Floral stem cell termination involves the direct regulation of AGAMOUS by PERIANTHIA

(2009) P. Das et al.   DEVELOPMENT

Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells

(2009) Madeleine P Ball et al.   NATURE BIOTECHNOLOGY

Extensive Demethylation of Repetitive Elements During Seed Development Underlies Gene Imprinting

(2009) M. Gehring et al.   SCIENCE

Genome-Wide Demethylation of Arabidopsis Endosperm

(2009) T.-F. Hsieh et al.   SCIENCE

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

(2008) Ryan Lister et al.   CELL

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

DNA methylation landscapes: provocative insights from epigenomics

(2008) Miho M. Suzuki et al.   NATURE REVIEWS GENETICS

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

Longer First Introns Are a General Property of Eukaryotic Gene Structure

(2008) Keith R. Bradnam et al.   PLoS One

Three SRA-Domain Methylcytosine-Binding Proteins Cooperate to Maintain Global CpG Methylation and Epigenetic Silencing in Arabidopsis

(2008) Hye Ryun Woo et al.   PLoS Genetics