Integrative analysis of reference epigenomes in 20 rice varieties

Autophagy contributes to sulfonylurea herbicide tolerance via GCN2-independent regulation of amino acid homeostasis

(2018) Lun Zhao et al.   Autophagy

Rice Information GateWay: A Comprehensive Bioinformatics Platform for Indica Rice Genomes

(2018) Jia-Ming Song et al.   Molecular Plant

PCSD: a plant chromatin state database

(2017) Yue Liu et al.   NUCLEIC ACIDS RESEARCH

Suppressor of rid1 (SID1) shares common targets with RID1 on florigen genes to initiate floral transition in rice

(2017) Li Deng et al.   PLoS Genetics

Tug of war: adding and removing histone lysine methylation in Arabidopsis

(2016) Jun Xiao et al.   CURRENT OPINION IN PLANT BIOLOGY

RPAN: rice pan-genome browser for ∼3000 rice genomes

(2016) Chen Sun et al.   NUCLEIC ACIDS RESEARCH

Epigenetic regulation and epigenomic landscape in rice

(2016) Xian Deng et al.   National Science Review

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

Crop Epigenomics: Identifying, Unlocking, and Harnessing Cryptic Variation in Crop Genomes

(2015) Lexiang Ji et al.   Molecular Plant

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Genome-Wide Prediction and Validation of Intergenic Enhancers in Arabidopsis Using Open Chromatin Signatures

(2015) Bo Zhu et al.   PLANT CELL

Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection

(2015) Weibo Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq

(2015) Laurent Vanhille et al.   Nature Communications

pENCODE: A Plant Encyclopedia of DNA Elements

(2014) Amanda K. Lane et al.   Annual Review of Genetics

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

The Functional Topography of the Arabidopsis Genome Is Organized in a Reduced Number of Linear Motifs of Chromatin States

(2014) J. Sequeira-Mendes et al.   PLANT CELL

Rice epigenomics and epigenetics: challenges and opportunities

(2013) Xiangsong Chen et al.   CURRENT OPINION IN PLANT BIOLOGY

A step-by-step protocol for formaldehyde-assisted isolation of regulatory elements fromArabidopsis thaliana

(2013) Mohammad Amin Omidbakhshfard et al.   Journal of Integrative Plant Biology

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

(2013) Zhou Du et al.   Molecular Plant

Genome-Wide Binding Analysis of the Transcription Activator IDEAL PLANT ARCHITECTURE1 Reveals a Complex Network Regulating Rice Plant Architecture

(2013) Z. Lu et al.   PLANT CELL

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

ChIA-PET analysis of transcriptional chromatin interactions

(2012) Jingyao Zhang et al.   METHODS

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA

(2012) Jeremy M Simon et al.   Nature Protocols

Integrative epigenomic mapping defines four main chromatin states in Arabidopsis

(2011) François Roudier et al.   EMBO JOURNAL

Histone Methylation in Higher Plants

(2010) Chunyan Liu et al.   Annual Review of Plant Biology

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP)

(2010) Kerstin Kaufmann et al.   Nature Protocols

Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids

(2010) G. He et al.   PLANT CELL

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein 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