Hidden variation in polyploid wheat drives local adaptation

A modified sequence capture approach allowing standard and methylation analyses of the same enriched genomic DNA sample

(2018) Lisa Olohan et al.   BMC GENOMICS

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations

(2017) Bernardo J. Clavijo et al.   GENOME RESEARCH

Exploiting induced and natural epigenetic variation for crop improvement

(2017) Nathan M. Springer et al.   NATURE REVIEWS GENETICS

A transposon-directed epigenetic change in ZmCCT underlies quantitative resistance to Gibberella stalk rot in maize

(2017) Chao Wang et al.   NEW PHYTOLOGIST

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

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Mapping-by-sequencing in complex polyploid genomes using genic sequence capture: a case study to map yellow rust resistance in hexaploid wheat

(2016) Laura-Jayne Gardiner et al.   PLANT JOURNAL

Epigenetic and developmental regulation in plant polyploids

(2015) Qingxin Song et al.   CURRENT OPINION IN PLANT BIOLOGY

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

(2015) Meilina Ong-Abdullah et al.   NATURE

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

(2015) Manu J Dubin et al.   eLife

A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

(2015) Jarrod A Chapman et al.   GENOME BIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Gene Body Methylation Can Alter Gene Expression and Is a Therapeutic Target in Cancer

(2014) Xiaojing Yang et al.   CANCER CELL

Functional DNA methylation in a transcript specific 3′UTR region of TrkB associates with suicide

(2014) Gilles Maussion et al.   Epigenetics

Ancient hybridizations among the ancestral genomes of bread wheat

(2014) T. Marcussen et al.   SCIENCE

Establishing the A. E. Watkins landrace cultivar collection as a resource for systematic gene discovery in bread wheat

(2014) Luzie U. Wingen et al.   THEORETICAL AND APPLIED GENETICS

DNA methylation as a system of plant genomic immunity

(2014) M. Yvonne Kim et al.   TRENDS IN PLANT SCIENCE

The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA

(2013) M. Regulski et al.   GENOME RESEARCH

Identification of QTLs associated with seedling root traits and their correlation with plant height in wheat

(2013) Caihong Bai et al.   JOURNAL OF EXPERIMENTAL BOTANY

Dirigent domain-containing protein is part of the machinery required for formation of the lignin-based Casparian strip in the root

(2013) P. S. Hosmani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Analysis of the bread wheat genome using whole-genome shotgun sequencing

(2012) Rachel Brenchley et al.   NATURE

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

Functional implication of the MYB transcription factor RVE8/LCL5 in the circadian control of histone acetylation

(2011) Benoit Farinas et al.   PLANT JOURNAL

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

(2011) Fabienne Brenet et al.   PLoS One

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

(2010) A. McKenna et al.   GENOME RESEARCH

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

(2010) S. Ossowski et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Assessing the Impact of Transgenerational Epigenetic Variation on Complex Traits

(2009) Frank Johannes et al.   PLoS Genetics

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

(2008) Ryan Lister et al.   CELL

Evaluation of metal-ion stress in sunflower (Helianthus annuus L.) leaves through proteomic changes

(2008) Jerusa Simone Garcia et al.   Metallomics