Similarity between soybean andArabidopsisseed methylomes and loss of non-CG methylation does not affect seed development

Endosperm and Imprinting, Inextricably Linked

(2016) Mary Gehring et al.   PLANT PHYSIOLOGY

Seed maturation: Simplification of control networks in plants

(2016) Martine Devic et al.   PLANT SCIENCE

DNA demethylation is initiated in the central cells ofArabidopsisand rice

(2016) Kyunghyuk Park et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA methylation pathways and their crosstalk with histone methylation

(2015) Jiamu Du et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Down-Regulating the Expression of 53 Soybean Transcription Factor Genes Uncovers a Role for SPEECHLESS in Initiating Stomatal Cell Lineages during Embryo Development

(2015) John Danzer et al.   PLANT PHYSIOLOGY

A Comparative Epigenomic Analysis of Polyploidy-Derived Genes in Soybean and Common Bean

(2015) Kyung Do Kim et al.   PLANT PHYSIOLOGY

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

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

Epigenetic reprogramming in plant sexual reproduction

(2014) Tomokazu Kawashima et al.   NATURE REVIEWS GENETICS

DNA methylation as a system of plant genomic immunity

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

Genomic dissection of the seed

(2014) Michael G. Becker et al.   Frontiers in Plant Science

Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

(2013) Wei Xie et al.   CELL

Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population

(2013) R. J. Schmitz et al.   GENOME RESEARCH

Genome-Wide Analysis of DNA Methylation in Soybean

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

Reconstructing de novo silencing of an active plant retrotransposon

(2013) Arturo Marí-Ordóñez et al.   NATURE GENETICS

Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis

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

Genomic Imprinting in the Arabidopsis Embryo Is Partly Regulated by PRC2

(2013) Michael T. Raissig et al.   PLoS Genetics

Dual Binding of Chromomethylase Domains to H3K9me2-Containing Nucleosomes Directs DNA Methylation in Plants

(2012) Jiamu Du et al.   CELL

RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats

(2012) Tzuu-fen Lee et al.   Epigenetics

Maternal and paternal genomes contribute equally to the transcriptome of early plant embryos

(2012) Michael D. Nodine et al.   NATURE

MORC Family ATPases Required for Heterochromatin Condensation and Gene Silencing

(2012) G. Moissiard et al.   SCIENCE

Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes

(2012) C. A. Ibarra et al.   SCIENCE

Evolution of Gene Regulatory Networks Controlling Body Plan Development

(2011) Isabelle S. Peter et al.   CELL

Genome demethylation and imprinting in the endosperm

(2011) Matthew J Bauer et al.   CURRENT OPINION IN PLANT BIOLOGY

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

(2011) Xiangchao Gan et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Seed maturation in Arabidopsis thaliana is characterized by nuclear size reduction and increased chromatin condensation

(2011) M. van Zanten et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

BS Seeker: precise mapping for bisulfite sequencing

(2010) Pao-Yang Chen et al.   BMC BIOINFORMATICS

SoyTEdb: a comprehensive database of transposable elements in the soybean genome

(2010) Jianchang Du et al.   BMC GENOMICS

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors

(2010) B. H. Le et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Sensitive and accurate detection of copy number variants using read depth of coverage

(2009) S. Yoon et al.   GENOME RESEARCH

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

VirtualPlant: A Software Platform to Support Systems Biology Research

(2009) M. S. Katari et al.   PLANT PHYSIOLOGY

Genome-Wide Demethylation of Arabidopsis Endosperm

(2009) T.-F. Hsieh et al.   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME 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

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Germination, Genetics, and Growth of an Ancient Date Seed

(2008) S. Sallon et al.   SCIENCE