Integrated analysis and transcript abundance modelling of H3K4me3 and H3K27me3 in developing secondary xylem

The Eucalyptus linker histone variant EgH1.3 cooperates with the transcription factor EgMYB1 to control lignin biosynthesis during wood formation

(2016) Marçal Soler et al.   NEW PHYTOLOGIST

Transcriptional Regulation of Arabidopsis Polycomb Repressive Complex 2 Coordinates Cell-Type Proliferation and Differentiation

(2016) Miguel de Lucas et al.   PLANT CELL

CURLY LEAFRegulates Gene Sets Coordinating Seed Size and Lipid Biosynthesis

(2016) Jun Liu et al.   PLANT PHYSIOLOGY

Genome-wide mapping of histone H3 lysine 4 trimethylation in Eucalyptus grandis developing xylem

(2015) Steven G Hussey et al.   BMC PLANT BIOLOGY

Genome-wide analysis of the lignin toolbox ofEucalyptus grandis

(2015) Victor Carocha et al.   NEW PHYTOLOGIST

Co-ordination of Flower Development Through Epigenetic Regulation in Two Model Species: Rice and Arabidopsis

(2015) S. Guo et al.   PLANT AND CELL PHYSIOLOGY

Chromatin and Epigenetics

(2015) Anna Amtmann et al.   PLANT PHYSIOLOGY

A Genome-Wide Chronological Study of Gene Expression and Two Histone Modifications, H3K4me3 and H3K9ac, during Developmental Leaf Senescence

(2015) Judy A. Brusslan et al.   PLANT PHYSIOLOGY

Flowering Locus C’s Lessons: Conserved Chromatin Switches Underpinning Developmental Timing and Adaptation

(2015) Jo Hepworth et al.   PLANT PHYSIOLOGY

Integrative analysis of histone ChIP-seq and transcription data using Bayesian mixture models

(2014) Hans-Ulrich Klein et al.   BIOINFORMATICS

Predictive modelling of gene expression from transcriptional regulatory elements

(2014) David M. Budden et al.   BRIEFINGS IN BIOINFORMATICS

H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency

(2014) Bérénice A. Benayoun et al.   CELL

Antagonistic Roles for H3K36me3 and H3K27me3 in the Cold-Induced Epigenetic Switch at Arabidopsis FLC

(2014) Hongchun Yang et al.   CURRENT BIOLOGY

Comparative analysis of the transcriptome across distant species

(2014) Mark B. Gerstein et al.   NATURE

A robust chromatin immunoprecipitation protocol for studying transcription factor–DNA interactions and histone modifications in wood-forming tissue

(2014) Wei Li et al.   Nature Protocols

The floral transcriptome ofEucalyptus grandis

(2014) Kelly J. Vining et al.   NEW PHYTOLOGIST

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

Predicting expression: the complementary power of histone modification and transcription factor binding data

(2014) David M Budden et al.   Epigenetics & Chromatin

Arabidopsis AL PHD-PRC1 Complexes Promote Seed Germination through H3K4me3-to-H3K27me3 Chromatin State Switch in Repression of Seed Developmental Genes

(2014) Anne Marie Molitor et al.   PLoS Genetics

Arabidopsis Polycomb Repressive Complex 2 binding sites contain putative GAGA factor binding motifs within coding regions of genes

(2013) Weiwei Deng et al.   BMC GENOMICS

Root responses to flooding

(2013) Margret Sauter   CURRENT OPINION IN PLANT BIOLOGY

Genomic Distribution of Maize Facultative Heterochromatin Marked by Trimethylation of H3K27

(2013) I. Makarevitch et al.   PLANT CELL

Profiling spatial enrichment of chromatin marks suggests an additional epigenomic dimension in gene regulation

(2013) Claudia Chica et al.   Frontiers in Life Science

Genome-wide in silico prediction of gene expression

(2012) Robert C. McLeay et al.   BIOINFORMATICS

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

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

Xylem cell death: emerging understanding of regulation and function

(2012) B. Bollhoner et al.   JOURNAL OF EXPERIMENTAL BOTANY

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for natural antisense transcript production

(2012) Chongyuan Luo et al.   PLANT JOURNAL

Reprogramming of H3K27me3 Is Critical for Acquisition of Pluripotency from Cultured Arabidopsis Tissues

(2012) Chongsheng He et al.   PLoS Genetics

Natural variation of H3K27me3 distribution between two Arabidopsis accessions and its association with flanking transposable elements

(2012) Xue Dong et al.   GENOME BIOLOGY

Modeling gene expression using chromatin features in various cellular contexts

(2012) Xianjun Dong et al.   GENOME BIOLOGY

Histone modifications in transcriptional activation during plant development

(2011) Alexandre Berr et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Epigenetic control of gene regulation in plants

(2011) Massimiliano Lauria et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Integrative epigenomic mapping defines four main chromatin states in Arabidopsis

(2011) François Roudier et al.   EMBO JOURNAL

Arabidopsis REF6 is a histone H3 lysine 27 demethylase

(2011) Falong Lu et al.   NATURE GENETICS

Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq

(2011) Mazhar Adli et al.   Nature Protocols

Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells

(2011) Chao Cheng et al.   NUCLEIC ACIDS RESEARCH

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

Tissue-Specific Expression ofFLOWERING LOCUS TinArabidopsisIs Maintained Independently of Polycomb Group Protein Repression

(2011) Sara Farrona et al.   PLANT CELL

Histone modification: cause or cog?

(2011) Steven Henikoff et al.   TRENDS IN GENETICS

Dynamic Regulation of H3K27 Trimethylation during Arabidopsis Differentiation

(2011) Marcel Lafos et al.   PLoS Genetics

Polycomb Repressive Complex 2 Controls the Embryo-to-Seedling Phase Transition

(2011) Daniel Bouyer et al.   PLoS Genetics

A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets

(2011) Chao Cheng et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Wood formation in Angiosperms

(2010) Annabelle Déjardin et al.   COMPTES RENDUS BIOLOGIES

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Histone modification levels are predictive for gene expression

(2010) R. Karlic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

H3K27me3 Profiling of the Endosperm Implies Exclusion of Polycomb Group Protein Targeting by DNA Methylation

(2010) Isabelle Weinhofer et al.   PLoS Genetics

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Recruitment of Polycomb group complexes and their role in the dynamic regulation of cell fate choice

(2009) B. Schuettengruber et al.   DEVELOPMENT

Unlocking the secrets of the genome

(2009) Susan E. Celniker et al.   NATURE

Dynamic Landscapes of Four Histone Modifications during Deetiolation in Arabidopsis

(2009) J.-B. F. Charron et al.   PLANT CELL

Molecular implementation and physiological roles for histone H3 lysine 4 (H3K4) methylation

(2008) Ali Shilatifard   CURRENT OPINION IN CELL BIOLOGY

Genic and Global Functions for Paf1C in Chromatin Modification and Gene Expression in Arabidopsis

(2008) Sookyung Oh et al.   PLoS Genetics

Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains

(2008) Manching Ku et al.   PLoS Genetics

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY