Massive Loss of DNA Methylation in Nitrogen-, but Not in Phosphorus-Deficient Zea mays Roots Is Poorly Correlated With Gene Expression Differences

Control of DEMETER DNA demethylase gene transcription in male and female gamete companion cells inArabidopsis thaliana

(2017) Jin-Sup Park et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Early nitrogen-deprivation responses in Arabidopsis roots reveal distinct differences on transcriptome and (phospho-) proteome levels between nitrate and ammonium nutrition

(2016) Jochen Menz et al.   PLANT JOURNAL

Control of eukaryotic phosphate homeostasis by inositol polyphosphate sensor domains

(2016) R. Wild et al.   SCIENCE

CG Methylation Covaries with Differential Gene Expression between Leaf and Floral Bud Tissues of Brachypodium distachyon

(2016) Kyria Roessler et al.   PLoS One

Transcriptome analysis of nitrogen-starvation-responsive genes in rice

(2015) Wenzhu Yang et al.   BMC PLANT BIOLOGY

Nitrogen deficiency in barley (Hordeum vulgare) seedlings induces molecular and metabolic adjustments that trigger aphid resistance

(2015) Gloria Comadira et al.   JOURNAL OF EXPERIMENTAL BOTANY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

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

(2015) Qing Li et al.   PLANT PHYSIOLOGY

Methylome analysis reveals an important role for epigenetic changes in the regulation of theArabidopsisresponse to phosphate starvation

(2015) Lenin Yong-Villalobos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2015) David Secco et al.   eLife

Transposable elements, a treasure trove to decipher epigenetic variation: insights from Arabidopsis and crop epigenomes

(2014) M. Mirouze et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

Epigenetics: Beyond Chromatin Modifications and Complex Genetic Regulation

(2014) S. R. Eichten et al.   PLANT PHYSIOLOGY

Comparative Proteomic Analyses Provide New Insights into Low Phosphorus Stress Responses in Maize Leaves

(2014) Kewei Zhang et al.   PLoS One

Epigenetic Regulation in Plants

(2014) C. S. Pikaard et al.   Cold Spring Harbor Perspectives in Biology

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

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

Detection of significantly differentially methylated regions in targeted bisulfite sequencing data

(2013) Katja Hebestreit et al.   BIOINFORMATICS

BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data

(2013) Weilong Guo et al.   BMC GENOMICS

Epigenetic and Genetic Influences on DNA Methylation Variation in Maize Populations

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

Spatio-Temporal Transcript Profiling of Rice Roots and Shoots in Response to Phosphate Starvation and Recovery

(2013) D. Secco et al.   PLANT CELL

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Maize Source Leaf Adaptation to Nitrogen Deficiency Affects Not Only Nitrogen and Carbon Metabolism But Also Control of Phosphate Homeostasis

(2012) U. Schluter et al.   PLANT PHYSIOLOGY

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

Spreading of Heterochromatin Is Limited to Specific Families of Maize Retrotransposons

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

Transposable element origins of epigenetic gene regulation

(2011) Damon Lisch et al.   CURRENT OPINION IN PLANT BIOLOGY

Genome Size and Transposable Element Content as Determined by High-Throughput Sequencing in Maize and Zea luxurians

(2011) Maud I. Tenaillon et al.   Genome Biology and Evolution

Heritable alteration in DNA methylation induced by nitrogen-deficiency stress accompanies enhanced tolerance by progenies to the stress in rice (Oryza sativa L.)

(2011) H.P. Kou et al.   JOURNAL OF PLANT PHYSIOLOGY

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

(2011) Ikhlak Ahmed et al.   NUCLEIC ACIDS RESEARCH

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

Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression

(2009) J. D. Hollister et al.   GENOME RESEARCH

High-throughput bisulfite sequencing in mammalian genomes

(2009) Zachary D. Smith et al.   METHODS

The B73 Maize Genome: Complexity, Diversity, and Dynamics

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

Effects of nitrogen deficiency on leaf photosynthesis, carbohydrate status and biomass production in two olive cultivars ‘Meski’ and ‘Koroneiki’

(2009) O. Boussadia et al.   SCIENTIA HORTICULTURAE

MaizeGDB becomes 'sequence-centric'

(2009) T. Z. Sen et al.   Database-The Journal of Biological Databases and Curation

Maize Centromere Structure and Evolution: Sequence Analysis of Centromeres 2 and 5 Reveals Dynamic Loci Shaped Primarily by Retrotransposons

(2009) Thomas K. Wolfgruber et al.   PLoS Genetics

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

(2008) Ryan Lister et al.   CELL

DNA methylation landscapes: provocative insights from epigenomics

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

Characterization of a sub-family of Arabidopsis genes with the SPX domain reveals their diverse functions in plant tolerance to phosphorus starvation

(2008) Ke Duan et al.   PLANT JOURNAL