Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening

The tomato genome sequence provides insights into fleshy fruit evolution

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The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters

(2012) Yun-Ru Chen et al.   Plant Methods

Genetics and Control of Tomato Fruit Ripening and Quality Attributes

(2011) Harry J. Klee et al.   Annual Review of Genetics

Identification of potential target genes for the tomato fruit-ripening regulator RIN by chromatin immunoprecipitation

(2011) Masaki Fujisawa et al.   BMC PLANT BIOLOGY

Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

(2011) Claude Becker et al.   NATURE

The Tomato MADS-Box Transcription Factor RIPENING INHIBITOR Interacts with Promoters Involved in Numerous Ripening Processes in a COLORLESS NONRIPENING-Dependent Manner

(2011) C. Martel et al.   PLANT PHYSIOLOGY

Transgenerational Epigenetic Instability Is a Source of Novel Methylation Variants

(2011) R. J. Schmitz et al.   SCIENCE

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

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

Protocol: fine-tuning of a Chromatin Immunoprecipitation (ChIP) protocol in tomato

(2010) Martiniano M Ricardi et al.   Plant Methods

Local DNA hypomethylation activates genes in rice endosperm

(2010) A. Zemach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epigenetic Reprogramming in Plant and Animal Development

(2010) Suhua Feng et al.   SCIENCE

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

(2009) Likun Wang et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Regulatory Features Underlying Pollination-Dependent and -Independent Tomato Fruit Set Revealed by Transcript and Primary Metabolite Profiling

(2009) H. Wang et al.   PLANT CELL

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

DNA-binding specificity, transcriptional activation potential, and therinmutation effect for the tomato fruit-ripening regulator RIN

(2008) Yasuhiro Ito et al.   PLANT JOURNAL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY

Genetics and epigenetics of fruit development and ripening

(2007) Graham Seymour et al.   CURRENT OPINION IN PLANT BIOLOGY