Rewiring of 3D Chromatin Topology Orchestrates Transcriptional Reprogramming and the Development of Human Dilated Cardiomyopathy

Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression

(2021) Anthony M. Gacita et al.   CIRCULATION

Mitochondrial Function and Dysfunction in Dilated Cardiomyopathy

(2021) Daniela Ramaccini et al.   Frontiers in Cell and Developmental Biology

Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization

(2020) Joachim Wolff et al.   NUCLEIC ACIDS RESEARCH

Epigenomes of Human Hearts Reveal New Genetic Variants Relevant for Cardiac Disease and Phenotype

(2020) Wilson Lek Wen Tan et al.   CIRCULATION RESEARCH

Phosphorylation of cardiac myosin–binding protein-C contributes to calcium homeostasis

(2020) Mohit Kumar et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

An Overview of the Cytoskeleton-Associated Role of PDLIM5

(2020) Xiaolan Huang et al.   Frontiers in Physiology

The Self-Organizing Genome: Principles of Genome Architecture and Function

(2020) Tom Misteli   CELL

Altered Enhancer and Promoter Usage Leads to Differential Gene Expression in the Normal and Failed Human Heart

(2020) Anthony M. Gacita et al.   Circulation-Heart Failure

The Gridlock transcriptional repressor impedes vertebrate heart regeneration by restricting expression of lysine methyltransferase

(2020) Peilu She et al.   DEVELOPMENT

Promoter-interacting expression quantitative trait loci are enriched for functional genetic variants

(2020) Vivek Chandra et al.   NATURE GENETICS

Chromatin accessibility and the regulatory epigenome

(2019) Sandy L. Klemm et al.   NATURE REVIEWS GENETICS

Mapping the Global Chromatin Connectivity Network for Sox2 Function in Neural Stem Cell Maintenance

(2019) Jessica A. Bertolini et al.   Cell Stem Cell

Epigenetics in dilated cardiomyopathy

(2019) Junyi Yu et al.   CURRENT OPINION IN CARDIOLOGY

Long-range enhancer–promoter contacts in gene expression control

(2019) Stefan Schoenfelder et al.   NATURE REVIEWS GENETICS

Cooler: scalable storage for Hi-C data and other genomically labeled arrays

(2019) Nezar Abdennur et al.   BIOINFORMATICS

The role of 3D genome organization in development and cell differentiation

(2019) Hui Zheng et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Histone methyltransferase SMYD2: ubiquitous regulator of disease

(2019) Xin Yi et al.   Clinical Epigenetics

Chromatin Interaction Analysis with Updated ChIA-PET Tool (V3)

(2019) Li et al.   Genes

Novel polymorphisms in PDLIM3 and PDLIM5 gene encoding Z ‐line proteins increase risk of idiopathic dilated cardiomyopathy

(2019) Dongfei Wang et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs

(2019) William A. Flavahan et al.   NATURE

Circular ecDNA promotes accessible chromatin and high oncogene expression

(2019) Sihan Wu et al.   NATURE

Genetics of dilated cardiomyopathy: practical implications for heart failure management

(2019) Andrew N. Rosenbaum et al.   Nature Reviews Cardiology

Integrated Multiomics Approach to Identify Genetic Underpinnings of Heart Failure and Its Echocardiographic Precursors

(2019) Charlotte Andersson et al.   Circulation-Genomic and Precision Medicine

Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element

(2018) Seung Woo Cho et al.   CELL

AIF1L regulates actomyosin contractility and filopodial extensions in human podocytes

(2018) Mako Yasuda-Yamahara et al.   PLoS One

Stratification of TAD boundaries reveals preferential insulation of super-enhancers by strong boundaries

(2018) Yixiao Gong et al.   Nature Communications

Loss of microRNA-128 promotes cardiomyocyte proliferation and heart regeneration

(2018) Wei Huang et al.   Nature Communications

Progesterone Protects Against Bisphenol A–Induced Arrhythmias in Female Rat Cardiac Myocytes via Rapid Signaling

(2017) Jianyong Ma et al.   ENDOCRINOLOGY

Evolving concepts in dilated cardiomyopathy

(2017) Marco Merlo et al.   EUROPEAN JOURNAL OF HEART FAILURE

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

(2017) Tao Yang et al.   GENOME RESEARCH

Genome-wide characterization of mammalian promoters with distal enhancer functions

(2017) Lan T M Dao et al.   NATURE GENETICS

Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements

(2017) Maxwell R Mumbach et al.   NATURE GENETICS

A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells

(2017) Yarui Diao et al.   NATURE METHODS

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq

(2016) Rongxin Fang et al.   CELL RESEARCH

HAND1 loss-of-function mutation associated with familial dilated cardiomyopathy

(2016) Yi-Meng Zhou et al.   CLINICAL CHEMISTRY AND LABORATORY MEDICINE

Chromatin Domains: The Unit of Chromosome Organization

(2016) Jesse R. Dixon et al.   MOLECULAR CELL

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

(2016) Maxwell R Mumbach et al.   NATURE METHODS

Epidemiology and aetiology of heart failure

(2016) Boback Ziaeian et al.   Nature Reviews Cardiology

PDE1C deficiency antagonizes pathological cardiac remodeling and dysfunction

(2016) Walter E. Knight et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Mango: a bias-correcting ChIA-PET analysis pipeline

(2015) Douglas H. Phanstiel et al.   BIOINFORMATICS

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

Condensin-driven remodelling of X chromosome topology during dosage compensation

(2015) Emily Crane et al.   NATURE

A mouse model for adult cardiac-specific gene deletion with CRISPR/Cas9

(2015) Kelli J. Carroll et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Progressive decay of Ca2+ homeostasis in the development of diabetic cardiomyopathy

(2014) Shu-Mei Zhao et al.   Cardiovascular Diabetology

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Regulation of fetal gene expression in heart failure

(2013) Ellen Dirkx et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

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

(2012) Guoliang Li et al.   CELL

Analysis of long-range chromatin interactions using Chromosome Conformation Capture

(2012) Natalia Naumova et al.   METHODS

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

Ablation of the Cardiac-Specific Gene Leucine-Rich Repeat Containing 10 (Lrrc10) Results in Dilated Cardiomyopathy

(2012) Matthew J. Brody et al.   PLoS One

Patient-Specific Induced Pluripotent Stem Cells as a Model for Familial Dilated Cardiomyopathy

(2012) N. Sun et al.   Science Translational Medicine

Large-Scale Functional Organization of Long-Range Chromatin Interaction Networks

(2012) Kuljeet Singh Sandhu et al.   Cell Reports

A novel Fbxo25 acts as an E3 ligase for destructing cardiac specific transcription factors

(2011) Jae-Woo Jang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Reduced Collagen Deposition in Infarcted Myocardium Facilitates Induced Pluripotent Stem Cell Engraftment and Angiomyogenesis for Improvement of Left Ventricular Function

(2011) Bo Dai et al.   JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY

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

(2011) Jason Ernst et al.   NATURE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Slowing of cardiomyocyte Ca2+ release and contraction during heart failure progression in postinfarction mice

(2009) Halvor K. Mørk et al.   AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY

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

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

(2009) J. Chen et al.   NUCLEIC ACIDS RESEARCH

Regulation of Estrogen Receptor-mediated Long Range Transcription via Evolutionarily Conserved Distal Response Elements

(2008) You Fu Pan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The MEF2D transcription factor mediates stress-dependent cardiac remodeling in mice

(2008) Yuri Kim et al.   JOURNAL OF CLINICAL INVESTIGATION