Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivo

Improved regulatory element prediction based on tissue-specific local epigenomic signatures

(2017) Yupeng He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA methylation signatures follow preformed chromatin compartments in cardiac myocytes

(2017) Stephan Nothjunge et al.   Nature Communications

Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells

(2017) Sebastian Pott   eLife

Epigenetic response to environmental stress: Assembly of BRG1–G9a/GLP–DNMT3 repressive chromatin complex on Myh6 promoter in pathologically stressed hearts

(2016) Pei Han et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis

(2016) Luis Luna-Zurita et al.   CELL

The H3K9 dimethyltransferases EHMT1/2 protect against pathological cardiac hypertrophy

(2016) Bernard Thienpont et al.   JOURNAL OF CLINICAL INVESTIGATION

Phospholamban is concentrated in the nuclear envelope of cardiomyocytes and involved in perinuclear/nuclear calcium handling

(2016) Adonis Z. Wu et al.   JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

Ablation of biglycan attenuates cardiac hypertrophy and fibrosis after left ventricular pressure overload

(2016) Nadine Beetz et al.   JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

Active DNA demethylation at enhancers during the vertebrate phylotypic period

(2016) Ozren Bogdanović et al.   NATURE GENETICS

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

DNA hydroxymethylation controls cardiomyocyte gene expression in development and hypertrophy

(2016) Carolina M. Greco et al.   Nature Communications

Genome-wide compendium and functional assessment of in vivo heart enhancers

(2016) Diane E. Dickel et al.   Nature Communications

Discovery and validation of sub-threshold genome-wide association study loci using epigenomic signatures

(2016) Xinchen Wang et al.   eLife

Mapping Human Pluripotent-to-Cardiomyocyte Differentiation: Methylomes, Transcriptomes, and Exon DNA Methylation “Memories”

(2016) Joshua D. Tompkins et al.   EBioMedicine

Genetic and Epigenetic Regulation of Human Cardiac Reprogramming and Differentiation in Regenerative Medicine

(2015) Paul W. Burridge et al.   Annual Review of Genetics

Dynamics of Cell Generation and Turnover in the Human Heart

(2015) Olaf Bergmann et al.   CELL

Deciphering the Epigenetic Code of Cardiac Myocyte TranscriptionNovelty and Significance

(2015) Sebastian Preissl et al.   CIRCULATION RESEARCH

metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data

(2015) Frank Jühling et al.   GENOME RESEARCH

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Human body epigenome maps reveal noncanonical DNA methylation variation

(2015) Matthew D. Schultz et al.   NATURE

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing

(2014) Volker Hovestadt et al.   NATURE

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease

(2014) Ralf Gilsbach et al.   Nature Communications

DNA Sequence Explains Seemingly Disordered Methylation Levels in Partially Methylated Domains of Mammalian Genomes

(2014) Dimos Gaidatzis et al.   PLoS Genetics

Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

(2013) Wei Xie et al.   CELL

BET Bromodomains Mediate Transcriptional Pause Release in Heart Failure

(2013) Priti Anand et al.   CELL

Alterations in cardiac DNA methylation in human dilated cardiomyopathy

(2013) Jan Haas et al.   EMBO Molecular Medicine

BET acetyl-lysine binding proteins control pathological cardiac hypertrophy

(2013) Jessica I. Spiltoir et al.   JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

Charting a dynamic DNA methylation landscape of the human genome

(2013) Michael J. Ziller et al.   NATURE

Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues

(2013) Gary C Hon et al.   NATURE GENETICS

Recommendations for the design and analysis of epigenome-wide association studies

(2013) Karin B Michels et al.   NATURE METHODS

Tagmentation-based whole-genome bisulfite sequencing

(2013) Qi Wang et al.   Nature Protocols

TETonic shift: biological roles of TET proteins in DNA demethylation and transcription

(2013) William A. Pastor et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Identification of active regulatory regions from DNA methylation data

(2013) Lukas Burger et al.   NUCLEIC ACIDS RESEARCH

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: 2014 update

(2013) Donna Karolchik et al.   NUCLEIC ACIDS RESEARCH

Genome-wide analysis of histone marks identifying an epigenetic signature of promoters and enhancers underlying cardiac hypertrophy

(2013) R. Papait et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global Epigenomic Reconfiguration During Mammalian Brain Development

(2013) R. Lister et al.   SCIENCE

Transcription Factor Occupancy Can Mediate Active Turnover of DNA Methylation at Regulatory Regions

(2013) Angelika Feldmann et al.   PLoS Genetics

A Temporal Chromatin Signature in Human Embryonic Stem Cells Identifies Regulators of Cardiac Development

(2012) Sharon L. Paige et al.   CELL

Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage

(2012) Joseph A. Wamstad et al.   CELL

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Cole Trapnell et al.   Nature Protocols

Nuclear RNA Sequencing of the Mouse Erythroid Cell Transcriptome

(2012) Jennifer A. Mitchell et al.   PLoS One

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

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

(2011) Felix Krueger et al.   BIOINFORMATICS

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

(2011) Ryan Lister et al.   NATURE

SIRPA is a specific cell-surface marker for isolating cardiomyocytes derived from human pluripotent stem cells

(2011) Nicole C Dubois et al.   NATURE BIOTECHNOLOGY

Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart

(2011) A. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide DNA methylation in human heart failure

(2011) Mehregan Movassagh et al.   Epigenomics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Redefining CpG islands using hidden Markov models

(2010) H. Wu et al.   BIOSTATISTICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

(2009) Gabriela Bindea et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genomic views of distant-acting enhancers

(2009) Axel Visel et al.   NATURE

Evidence for Cardiomyocyte Renewal in Humans

(2009) Olaf Bergmann et al.   SCIENCE

SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap

(2008) A. D. Johnson et al.   BIOINFORMATICS