The unique epigenetic features of Pack-MULEs and their impact on chromosomal base composition and expression spectrum

Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice

(2017) Marta Brozynska et al.   PLANT BIOTECHNOLOGY JOURNAL

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

Sequencing and de novo assembly of a near complete indica rice genome

(2017) Huilong Du et al.   Nature Communications

What makes up plant genomes: The vanishing line between transposable elements and genes

(2016) Dongyan Zhao et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

The First Rule of Plant Transposable Element Silencing: Location, Location, Location

(2016) Meredith J. Sigman et al.   PLANT CELL

Extensive sequence divergence between the reference genomes of two eliteindicarice varieties Zhenshan 97 and Minghui 63

(2016) Jianwei Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis of Ribosome-Associated mRNAs in Rice Reveals the Importance of Transcript Size and GC Content in Translation

(2016) Dongyan Zhao et al.   G3-Genes Genomes Genetics

Quantification of GC-biased gene conversion in the human genome

(2015) Sylvain Glémin et al.   GENOME RESEARCH

RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome

(2015) Qing Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TAL effectors and activation of predicted host targets distinguish Asian from African strains of the rice pathogen Xanthomonas oryzae pv. oryzicola while strict conservation suggests universal importance of five TAL effectors

(2015) Katherine E. Wilkins et al.   Frontiers in Plant Science

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The Bimodal Distribution of Genic GC Content Is Ancestral to Monocot Species

(2014) Yves Clément et al.   Genome Biology and Evolution

Comparative analyses of C4 and C3 photosynthesis in developing leaves of maize and rice

(2014) Lin Wang et al.   NATURE BIOTECHNOLOGY

Nested Insertions and Accumulation of Indels Are Negatively Correlated with Abundance of Mutator-Like Transposable Elements in Maize and Rice

(2014) Dongyan Zhao et al.   PLoS One

Genomic Distribution of H3K9me2 and DNA Methylation in a Maize Genome

(2014) Patrick T. West et al.   PLoS One

Genome-Wide Nucleosome Positioning Is Orchestrated by Genomic Regions Associated with DNase I Hypersensitivity in Rice

(2014) Yufeng Wu et al.   PLoS Genetics

RNA-sequencing reveals previously unannotated protein- and microRNA-coding genes expressed in aleurone cells of rice seeds

(2013) Kenneth A. Watanabe et al.   GENOMICS

Genome-Wide Analysis of Histone Modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica

(2013) Zhou Du et al.   Molecular Plant

Transcriptomes of isolatedOryza sativagametes characterized by deep sequencing: evidence for distinct sex-dependent chromatin and epigenetic states before fertilization

(2013) Sarah N. Anderson et al.   PLANT JOURNAL

Selective Acquisition and Retention of Genomic Sequences by Pack-Mutator-Like Elements Based on Guanine-Cytosine Content and the Breadth of Expression

(2013) A. A. Ferguson et al.   PLANT PHYSIOLOGY

Developmental relaxation of transposable element silencing in plants: functional or byproduct?

(2012) Germán Martínez et al.   CURRENT OPINION IN PLANT BIOLOGY

Evidence for Widespread GC-biased Gene Conversion in Eukaryotes

(2012) Eugénie Pessia et al.   Genome Biology and Evolution

CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize

(2012) J. I. Gent et al.   GENOME RESEARCH

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Spreading of Heterochromatin Is Limited to Specific Families of Maize Retrotransposons

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

The Rice Proteogenomics Database OryzaPG-DB: Development, Expansion, and New Features

(2012) Mohamed Helmy et al.   Frontiers in Plant Science

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

(2011) Felix Krueger et al.   BIOINFORMATICS

Epigenetic modifications in plants: an evolutionary perspective

(2011) Suhua Feng et al.   CURRENT OPINION IN PLANT BIOLOGY

Gene Capture by Helitron Transposons Reshuffles the Transcriptome of Maize

(2011) A. M. Barbaglia et al.   GENETICS

Retrogenes in Rice (Oryza sativa L. ssp. japonica) Exhibit Correlated Expression with Their Source Genes

(2011) Hiroaki Sakai et al.   Genome Biology and Evolution

High-resolution mapping of open chromatin in the rice genome

(2011) W. Zhang et al.   GENOME RESEARCH

Euchromatic Subdomains in Rice Centromeres Are Associated with Genes and Transcription

(2011) Yufeng Wu et al.   PLANT CELL

Pack-Mutator-like transposable elements (Pack-MULEs) induce directional modification of genes through biased insertion and DNA acquisition

(2011) N. Jiang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Origins, evolution, and phenotypic impact of new genes

(2010) H. Kaessmann   GENOME RESEARCH

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

The MuDR transposon terminal inverted repeat contains a complex plant promoter directing distinct somatic and germinal programs

(2010) Manish N. Raizada et al.   PLANT JOURNAL

Histone modification patterns and epigenetic codes

(2009) Andreas Lennartsson et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

(2009) Chongzhi Zang et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?

(2009) Z. Tian et al.   GENOME RESEARCH

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

The Contribution of Transposable Elements to Expressed Coding Sequence in Arabidopsis thaliana

(2009) Steven Lockton et al.   JOURNAL OF MOLECULAR EVOLUTION

The Functional Role of Pack-MULEs in Rice Inferred from Purifying Selection and Expression Profile

(2009) K. Hanada et al.   PLANT CELL

Distribution, diversity, evolution, and survival of Helitrons in the maize genome

(2009) L. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mu Transposon Insertion Sites and Meiotic Recombination Events Co-Localize with Epigenetic Marks for Open Chromatin across the Maize Genome

(2009) Sanzhen Liu et al.   PLoS Genetics

Removal of high-abundance proteins for nuclear subproteome studies in rice (Oryza sativa) endosperm

(2008) Guosheng Li et al.   ELECTROPHORESIS

Dynamic Evolution of Oryza Genomes Is Revealed by Comparative Genomic Analysis of a Genus-Wide Vertical Data Set

(2008) J. S.S. Ammiraju et al.   PLANT CELL

The Epigenetic Landscape of Plants

(2008) X. Zhang   SCIENCE