Genetic and Methylome Variation in Turkish Brachypodium Distachyon Accessions Differentiate Two Geographically Distinct Subpopulations

Extending the Genotype in Brachypodium by Including DNA Methylation Reveals a Joint Contribution with Genetics on Adaptive Traits

(2020) Steven R. Eichten et al.   G3-Genes Genomes Genetics

Impact of transposable elements on methylation and gene expression across natural accessions of Brachypodium distachyon

(2020) Michele Wyler et al.   Genome Biology and Evolution

A Role for Epigenetic Regulation in the Adaptation and Stress Responses of Non-model Plants

(2019) Flávia Thiebaut et al.   Frontiers in Plant Science

Brachypodium: A monocot grass model system for plant biology

(2018) Karen-Beth G. Scholthof et al.   PLANT CELL

Comparison of the Relative Potential for Epigenetic and Genetic Variation To Contribute to Trait Stability

(2018) Emma S.T. Aller et al.   G3-Genes Genomes Genetics

The relationship between transgenerational acquired resistance and global DNA methylation in Arabidopsis

(2018) Joost H. M. Stassen et al.   Scientific Reports

Global Diversity of the Brachypodium Species Complex as a Resource for Genome-Wide Association Studies Demonstrated for Agronomic Traits in Response to Climate

(2018) Pip B. Wilson et al.   GENETICS

Contribution of epigenetic variation to adaptation in Arabidopsis

(2018) Marc W. Schmid et al.   Nature Communications

Recent Activity in Expanding Populations and Purifying Selection Have Shaped Transposable Element Landscapes across Natural Accessions of the Mediterranean Grass Brachypodium distachyon

(2017) Christoph Stritt et al.   Genome Biology and Evolution

WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas

(2017) Stephen E. Fick et al.   INTERNATIONAL JOURNAL OF CLIMATOLOGY

Establishment of a vernalization requirement inBrachypodium distachyonrequiresREPRESSOR OF VERNALIZATION1

(2017) Daniel P. Woods et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure

(2017) Sean P. Gordon et al.   Nature Communications

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

(2016) Taiji Kawakatsu et al.   CELL

DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity

(2016) Steven R. Eichten et al.   GENOME RESEARCH

Genetic and epigenetic differences associated with environmental gradients in replicate populations of two salt marsh perennials

(2016) C. M. Foust et al.   MOLECULAR ECOLOGY

Comparative spatial genetics and epigenetics of plant populations: heuristic value and a proof of concept

(2016) Carlos M. Herrera et al.   MOLECULAR ECOLOGY

Genetic and epigenetic divergence between disturbed and undisturbed subpopulations of a Mediterranean shrub: a 20-year field experiment

(2016) Carlos M. Herrera et al.   Ecology and Evolution

Linking Dynamic Phenotyping with Metabolite Analysis to Study Natural Variation in Drought Responses of Brachypodium distachyon

(2016) Lorraine H. C. Fisher et al.   Frontiers in Plant Science

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

(2016) Kyria Roessler et al.   PLoS One

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

Utilization of a high-throughput shoot imaging system to examine the dynamic phenotypic responses of a C4 cereal crop plant to nitrogen and water deficiency over time

(2015) E. H. Neilson et al.   JOURNAL OF EXPERIMENTAL BOTANY

TESS3: fast inference of spatial population structure and genome scans for selection

(2015) Kevin Caye et al.   Molecular Ecology Resources

Climate suitability for European ticks: assessing species distribution models against null models and projection under AR5 climate

(2015) Hefin Wyn Williams et al.   Parasites & Vectors

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

(2015) David Secco et al.   eLife

DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation

(2015) Manu J Dubin et al.   eLife

Targeting environmental adaptation in the monocot model Brachypodium distachyon: a multi-faceted approach

(2014) Matteo Dell’Acqua et al.   BMC GENOMICS

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

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

Analysis of Global Gene Expression in Brachypodium distachyon Reveals Extensive Network Plasticity in Response to Abiotic Stress

(2014) Henry D. Priest et al.   PLoS One

Epigenetic Regulation in Plant Responses to the Environment

(2014) D. C. Baulcombe et al.   Cold Spring Harbor Perspectives in Biology

A new statistical framework for the quantification of covariate associations with species distributions

(2014) Colin M. Beale et al.   Methods in Ecology and Evolution

The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin

(2013) Assaf Zemach et al.   CELL

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis

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

A high-performance computing toolset for relatedness and principal component analysis of SNP data

(2012) X. Zheng et al.   BIOINFORMATICS

Epigenetic and epigenomic variation in Arabidopsis thaliana

(2012) Robert J. Schmitz et al.   TRENDS IN PLANT SCIENCE

Cell wall composition throughout development for the model grass Brachypodium distachyon

(2012) David M. Rancour et al.   Frontiers in Plant Science

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

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

(2011) Felix Krueger et al.   BIOINFORMATICS

Exploiting the Brachypodium Tool Box in cereal and grass research

(2011) Luis A. J. Mur et al.   NEW PHYTOLOGIST

Transgenerational Epigenetic Instability Is a Source of Novel Methylation Variants

(2011) R. J. Schmitz et al.   SCIENCE

ENMTools: a toolbox for comparative studies of environmental niche models

(2010) Dan L. Warren et al.   ECOGRAPHY

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

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

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

Genome-wide DNA methylation alterations of Alternanthera philoxeroides in natural and manipulated habitats: implications for epigenetic regulation of rapid responses to environmental fluctuation and phenotypic variation

(2010) LEXUAN GAO et al.   PLANT CELL AND ENVIRONMENT

Epigenetic Variation in Mangrove Plants Occurring in Contrasting Natural Environment

(2010) Catarina Fonseca Lira-Medeiros et al.   PLoS One

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon

(2009) John P Vogel et al.   BMC PLANT BIOLOGY

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

Opening the climate envelope reveals no macroscale associations with climate in European birds

(2008) C. M. Beale et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA