Application of dual reading domains as novel reagents in chromatin biology reveals a new H3K9me3 and H3K36me2/3 bivalent chromatin state

ATRX binds to atypical chromatin domains at the 3′ exons of zinc finger genes to preserve H3K9me3 enrichment

(2016) David Valle-García et al.   Epigenetics

Structural basis for recognition of histone H3K36me3 nucleosome by human de novo DNA methyltransferases 3A and 3B

(2016) Grégoire Rondelet et al.   JOURNAL OF STRUCTURAL BIOLOGY

Co-ChIP enables genome-wide mapping of histone mark co-occurrence at single-molecule resolution

(2016) Assaf Weiner et al.   NATURE BIOTECHNOLOGY

Single-molecule decoding of combinatorially modified nucleosomes

(2016) E. Shema et al.   SCIENCE

H3K9me3-Dependent Heterochromatin: Barrier to Cell Fate Changes

(2016) Justin S. Becker et al.   TRENDS IN GENETICS

Application of recombinant TAF3 PHD domain instead of anti-H3K4me3 antibody

(2016) Goran Kungulovski et al.   Epigenetics & Chromatin

Analysis of Combinatorial Epigenomic States

(2015) Paul D. Soloway   ACS Chemical Biology

Reading the Combinatorial Histone Language

(2015) Zhangli Su et al.   ACS Chemical Biology

Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation

(2015) Tuncay Baubec et al.   NATURE

Sound of silence: the properties and functions of repressive Lys methyltransferases

(2015) Chiara Mozzetta et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Combinatorial epigenetic patterns as quantitative predictors of chromatin biology

(2014) Marcin Cieślik et al.   BMC GENOMICS

Application of histone modification-specific interaction domains as an alternative to antibodies

(2014) Goran Kungulovski et al.   GENOME RESEARCH

Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape

(2014) Aurélien Griffon et al.   NUCLEIC ACIDS RESEARCH

ChIP-Enrich: gene set enrichment testing for ChIP-seq data

(2014) Ryan P. Welch et al.   NUCLEIC ACIDS RESEARCH

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Readout of Epigenetic Modifications

(2013) Dinshaw J. Patel et al.   Annual Review of Biochemistry

A double take on bivalent promoters

(2013) P. Voigt et al.   GENES & DEVELOPMENT

High-resolution mapping of transcription factor binding sites on native chromatin

(2013) Sivakanthan Kasinathan et al.   NATURE METHODS

Epigenetic Reprogramming in Cancer

(2013) M. L. Suva et al.   SCIENCE

Bivalent histone modifications in early embryogenesis

(2012) Nadine L Vastenhouw et al.   CURRENT OPINION IN CELL BIOLOGY

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Understanding the language of Lys36 methylation at histone H3

(2012) Eric J. Wagner et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange

(2012) Michaela Smolle et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Perceiving the epigenetic landscape through histone readers

(2012) Catherine A Musselman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

EpiExplorer: live exploration and global analysis of large epigenomic datasets

(2012) Konstantin Halachev et al.   GENOME BIOLOGY

Signals and Combinatorial Functions of Histone Modifications

(2011) Tamaki Suganuma et al.   Annual Review of Biochemistry

Application of Celluspots peptide arrays for the analysis of the binding specificity of epigenetic reading domains to modified histone tails

(2011) Ina Bock et al.   BMC BIOCHEMISTRY

Chipster: user-friendly analysis software for microarray and other high-throughput data

(2011) M Aleksi Kallio et al.   BMC GENOMICS

Recognition of a Mononucleosomal Histone Modification Pattern by BPTF via Multivalent Interactions

(2011) Alexander J. Ruthenburg et al.   CELL

Identification of 67 Histone Marks and Histone Lysine Crotonylation as a New Type of Histone Modification

(2011) Minjia Tan et al.   CELL

Regulation of chromatin by histone modifications

(2011) Andrew J Bannister et al.   CELL RESEARCH

Structure and Function of Histone H3 Lysine 9 Methyltransferases and Demethylases

(2011) Swathi Krishnan  et al.   CHEMBIOCHEM

Detailed specificity analysis of antibodies binding to modified histone tails with peptide arrays

(2011) Ina Bock et al.   Epigenetics

Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions

(2011) Gabriel E. Zentner et al.   GENOME RESEARCH

Structural Insights for MPP8 Chromodomain Interaction with Histone H3 Lysine 9: Potential Effect of Phosphorylation on Methyl-Lysine Binding

(2011) Yanqi Chang et al.   JOURNAL OF MOLECULAR BIOLOGY

CelluSpots Arrays as an Alternative to Peptide Arrays on Membrane Supports

(2011) Daniel Maisch et al.   MINI-REVIEWS IN ORGANIC CHEMISTRY

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons

(2011) Violaine Saint-André et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Characterization of the Contradictory Chromatin Signatures at the 3′ Exons of Zinc Finger Genes

(2011) Kimberly R. Blahnik et al.   PLoS One

Identification of a second DNA binding site in human DNA methyltransferase 3A by substrate inhibition and domain deletion

(2010) Matthew M. Purdy et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Nucleosome-Interacting Proteins Regulated by DNA and Histone Methylation

(2010) Till Bartke et al.   CELL

The significance, development and progress of high-throughput combinatorial histone code analysis

(2010) Nicolas L. Young et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

The Dnmt3a PWWP Domain Reads Histone 3 Lysine 36 Trimethylation and Guides DNA Methylation

(2010) Arunkumar Dhayalan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Epigenetic modifications and human disease

(2010) Anna Portela et al.   NATURE BIOTECHNOLOGY

seqMINER: an integrated ChIP-seq data interpretation platform

(2010) Tao Ye et al.   NUCLEIC ACIDS RESEARCH

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

High Throughput Characterization of Combinatorial Histone Codes

(2009) Nicolas L. Young et al.   MOLECULAR & CELLULAR PROTEOMICS

Differential chromatin marking of introns and expressed exons by H3K36me3

(2009) Paulina Kolasinska-Zwierz et al.   NATURE GENETICS

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Cell cycle control of centromeric repeat transcription and heterochromatin assembly

(2008) Ee Sin Chen et al.   NATURE

Protein lysine methyltransferase G9a acts on non-histone targets

(2008) Philipp Rathert et al.   Nature Chemical Biology

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY