Species-wide patterns of DNA methylation variation inQuercus lobataand their association with climate gradients

Landscape genomic analysis of candidate genes for climate adaptation in a California endemic oak, Quercus lobata

(2016) V. L. Sork et al.   AMERICAN JOURNAL OF BOTANY

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

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

Natural epigenetic variation contributes to heritable flowering divergence in a widespread asexual dandelion lineage

(2016) Rutger A. Wilschut et al.   MOLECULAR ECOLOGY

The multivariate association between genomewide DNA methylation and climate across the range ofArabidopsis thaliana

(2016) Thomas E. Keller et al.   MOLECULAR ECOLOGY

Association of transcriptome-wide sequence variation with climate gradients in valley oak (Quercus lobata)

(2016) Paul F. Gugger et al.   Tree Genetics & Genomes

Evolutionary insights from de novo transcriptome assembly and SNP discovery in California white oaks

(2015) Shawn J. Cokus et al.   BMC GENOMICS

Epigenome-Wide Association of Liver Methylation Patterns and Complex Metabolic Traits in Mice

(2015) Luz D. Orozco et al.   Cell Metabolism

Genome-wide signature of local adaptation linked to variable CpG methylation in oak populations

(2015) Alexander Platt et al.   MOLECULAR ECOLOGY

Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies

(2015) Christophe Plomion et al.   Molecular Ecology Resources

CG gene body DNA methylation changes and evolution of duplicated genes in cassava

(2015) Haifeng Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rate, spectrum, and evolutionary dynamics of spontaneous epimutations

(2015) Adriaan van der Graaf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptive plasticity and epigenetic variation in response to warming in an Alpine plant

(2015) Adrienne B. Nicotra et al.   Ecology and Evolution

Century-scale Methylome Stability in a Recently Diverged Arabidopsis thaliana Lineage

(2015) Jörg Hagmann et al.   PLoS Genetics

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

(2015) Manu J Dubin et al.   eLife

Genomic Signature of Adaptation to Climate inMedicago truncatula

(2014) Jeremy B. Yoder et al.   GENETICS

Epigenetics, plasticity, and evolution: How do we link epigenetic change to phenotype?

(2014) Elizabeth J. Duncan et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

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

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

Epigenetics: Beyond Chromatin Modifications and Complex Genetic Regulation

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

Efecto de la reproducción clonal en la estructura genética de Pentaclethra macroloba (Fabaceae: Mimosoideae)

(2014) Keith D. Gaddis et al.   REVISTA DE BIOLOGIA TROPICAL

The Secret Garden--Epigenetic Alleles Underlie Complex Traits

(2014) R. J. Schmitz   SCIENCE

Mapping the Epigenetic Basis of Complex Traits

(2014) S. Cortijo et al.   SCIENCE

Temperature-dependent differential transcriptomes during formation of an epigenetic memory in Norway spruce embryogenesis

(2014) Igor A. Yakovlev et al.   Tree Genetics & Genomes

Natural CMT2 Variation Is Associated With Genome-Wide Methylation Changes and Temperature Seasonality

(2014) Xia Shen et al.   PLoS Genetics

How epigenetic mutations can affect genetic evolution: Model and mechanism

(2013) Filippos D. Klironomos et al.   BIOESSAYS

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

(2013) Weilong Guo et al.   BMC GENOMICS

Epigenetic differences between shoots and roots inArabidopsisreveals tissue-specific regulation

(2013) Nicolas Widman et al.   Epigenetics

Influence of late Quaternary climate change on present patterns of genetic variation in valley oak,Quercus lobataNée

(2013) Paul F. Gugger et al.   MOLECULAR ECOLOGY

Patterns of population epigenomic diversity

(2013) Robert J. Schmitz et al.   NATURE

Mixed models can correct for population structure for genomic regions under selection

(2013) Jae Hoon Sul et al.   NATURE REVIEWS GENETICS

Transgenerational epigenetic inheritance: how important is it?

(2013) Ueli Grossniklaus et al.   NATURE REVIEWS GENETICS

Changes in DNA methylation fingerprint ofQuercus ilextrees in response to experimental field drought simulating projected climate change

(2013) L. Rico et al.   PLANT BIOLOGY

Characterising a Eucalyptus cladocalyx breeding population using SNP markers

(2013) David Bush et al.   Tree Genetics & Genomes

The impact of climate change on plant epigenomes

(2013) Qiong A. Liu   TRENDS IN GENETICS

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

(2013) Katharina Bräutigam et al.   Ecology and Evolution

Genetics of Climate Change Adaptation

(2012) Steven J. Franks et al.   Annual Review of Genetics

Epigenetic correlates of plant phenotypic plasticity: DNA methylation differs between prickly and nonprickly leaves in heterophyllousIlex aquifolium(Aquifoliaceae) trees

(2012) Carlos M. Herrera et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Epigenetic variation: origin and transgenerational inheritance

(2012) Claude Becker et al.   CURRENT OPINION IN PLANT BIOLOGY

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Characterizing genomic variation ofArabidopsis thaliana: the roles of geography and climate

(2012) JESSE R. LASKY et al.   MOLECULAR ECOLOGY

Epigenetic variation creates potential for evolution of plant phenotypic plasticity

(2012) Yuan-Ye Zhang et al.   NEW PHYTOLOGIST

Transgenerational Effects of Stress Exposure on Offspring Phenotypes in Apomictic Dandelion

(2012) Koen J.F. Verhoeven et al.   PLoS One

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

An adaptive epigenetic memory in conifers with important implications for seed production

(2012) Igor Yakovlev et al.   SEED SCIENCE RESEARCH

Transgenerational defense induction and epigenetic inheritance in plants

(2012) Liza M. Holeski et al.   TRENDS IN ECOLOGY & EVOLUTION

Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data

(2012) Yaping Liu et al.   GENOME BIOLOGY

Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing

(2011) Brian Walenz et al.   BIOINFORMATICS

Predicting species responses to climate change: demography and climate microrefugia in California valley oak (Quercus lobata)

(2011) BLAIR C. Mclaughlin et al.   GLOBAL CHANGE BIOLOGY

Molecular and genetic characterization of the gene family encoding the voltage-dependent anion channel in Arabidopsis

(2011) Chika Tateda et al.   JOURNAL OF EXPERIMENTAL BOTANY

Body-Methylated Genes in Arabidopsis thaliana Are Functionally Important and Evolve Slowly

(2011) S. Takuno et al.   MOLECULAR BIOLOGY AND EVOLUTION

Untangling individual variation in natural populations: ecological, genetic and epigenetic correlates of long-term inequality in herbivory

(2011) C. M. HERRERA et al.   MOLECULAR ECOLOGY

Divergent DNA Methylation Patterns Associated with Abiotic Stress in Hevea brasiliensis

(2011) Thomas K. Uthup et al.   Molecular Plant

Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

(2011) Claude Becker et al.   NATURE

Transgenerational Epigenetic Instability Is a Source of Novel Methylation Variants

(2011) R. J. Schmitz et al.   SCIENCE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Gene movement and genetic association with regional climate gradients in California valley oak (Quercus lobata Née) in the face of climate change

(2010) VICTORIA L. SORK et al.   MOLECULAR ECOLOGY

Variance component model to account for sample structure in genome-wide association studies

(2010) Hyun Min Kang et al.   NATURE GENETICS

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

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

Epigenetic differentiation and relationship to adaptive genetic divergence in discrete populations of the violet Viola cazorlensis

(2010) Carlos M. Herrera et al.   NEW PHYTOLOGIST

Differential gene expression related to an epigenetic memory affecting climatic adaptation in Norway spruce

(2010) Igor A. Yakovlev et al.   PLANT SCIENCE

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

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

Transgenerational Epigenetic Inheritance: Prevalence, Mechanisms, and Implications for the Study of Heredity and Evolution

(2009) Eva Jablonka et al.   QUARTERLY REVIEW OF BIOLOGY

Efficient Control of Population Structure in Model Organism Association Mapping

(2008) H. M. Kang et al.   GENETICS

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE