Single-base methylome analysis reveals dynamic epigenomic differences associated with water deficit in apple

Epigenetic regulation of MdMYB1 is associated with paper bagging-induced red pigmentation of apples

(2016) Songling Bai et al.   PLANTA

Chilling-induced tomato flavor loss is associated with altered volatile synthesis and transient changes in DNA methylation

(2016) Bo Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA methylome of the 20-gigabase Norway spruce genome

(2016) Israel Ausin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Limited Contribution of DNA Methylation Variation to Expression Regulation in Arabidopsis thaliana

(2016) Dazhe Meng et al.   PLoS Genetics

Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm

(2015) Meilina Ong-Abdullah et al.   NATURE

Comparative epigenomics: a powerful tool to understand the evolution of DNA methylation

(2015) Xuehua Zhong   NEW PHYTOLOGIST

Global Analysis Reveals the Crucial Roles of DNA Methylation during Rice Seed Development

(2015) Mei-Qing Xing et al.   PLANT PHYSIOLOGY

Physiological and proteome analysis suggest critical roles for the photosynthetic system for high water-use efficiency under drought stress in Malus

(2015) Shasha Zhou et al.   PLANT SCIENCE

The R2R3-type MYB gene OsMYB91 has a function in coordinating plant growth and salt stress tolerance in rice

(2015) Ning Zhu et al.   PLANT SCIENCE

Autotetraploid rice methylome analysis reveals methylation variation of transposable elements and their effects on gene expression

(2015) Jie Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress

(2015) Irina Makarevitch et al.   PLoS Genetics

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

(2014) S. Anders et al.   BIOINFORMATICS

Single-base-resolution methylomes of populus trichocarpa reveal the association between DNA methylation and drought stress

(2014) Dan Liang et al.   BMC GENETICS

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

(2014) Sébastien A Smallwood et al.   NATURE METHODS

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

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

Genetic Perturbation of the Maize Methylome

(2014) Qing Li et al.   PLANT CELL

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

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

Genome-Wide Analysis of DNA Methylation in Soybean

(2013) Qing-Xin Song et al.   Molecular Plant

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

(2013) Silin Zhong et al.   NATURE BIOTECHNOLOGY

Epigenetic mechanisms of plant stress responses and adaptation

(2013) Pranav Pankaj Sahu et al.   PLANT CELL REPORTS

The Methylation of the PcMYB10 Promoter Is Associated with Green-Skinned Sport in Max Red Bartlett Pear

(2013) Z. Wang et al.   PLANT PHYSIOLOGY

Global Epigenomic Reconfiguration During Mammalian Brain Development

(2013) R. Lister et al.   SCIENCE

Epigenetic regulation of adaptive responses of forest tree species to the environment

(2013) Katharina Bräutigam et al.   Ecology and Evolution

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Programming of DNA Methylation Patterns

(2012) Howard Cedar et al.   Annual Review of Biochemistry

Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression

(2012) Xin Li et al.   BMC GENOMICS

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

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Widespread dynamic DNA methylation in response to biotic stress

(2012) R. H. Dowen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptome and methylome interactions in rice hybrids

(2012) Ramakrishna K. Chodavarapu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA methylation in higher plants: Past, present and future

(2011) Boris F. Vanyushin et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

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

(2011) Felix Krueger et al.   BIOINFORMATICS

Apple skin patterning is associated with differential expression of MYB10

(2011) Adriana Telias et al.   BMC PLANT BIOLOGY

Epigenetic contribution to stress adaptation in plants

(2011) Marie Mirouze et al.   CURRENT OPINION IN PLANT BIOLOGY

Drought-induced site-specific DNA methylation and its association with drought tolerance in rice (Oryza sativa L.)

(2010) Wen-Sheng Wang et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

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

Reactivation of a silenced minimal Mutator transposable element system following low-energy nitrogen ion implantation in maize

(2010) Yexiong Qian et al.   PLANT CELL REPORTS

Research on plant abiotic stress responses in the post-genome era: past, present and future

(2010) Takashi Hirayama et al.   PLANT JOURNAL

Dwarf apple MbDREB1 enhances plant tolerance to low temperature, drought, and salt stress via both ABA-dependent and ABA-independent pathways

(2010) Wei Yang et al.   PLANTA

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

Stress-induced DNA methylation changes and their heritability in asexual dandelions

(2009) Koen J. F. Verhoeven et al.   NEW PHYTOLOGIST

Drought tolerance in Arabidopsis is controlled by theOCP3disease resistance regulator

(2009) Vicente Ramírez et al.   PLANT JOURNAL

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