Enhancer–promoter interactions are encoded by complex genomic signatures on looping chromatin

Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin

(2015) Elizabeth Ing-Simmons et al.   GENOME RESEARCH

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements

(2015) Stefan Schoenfelder et al.   GENOME RESEARCH

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

A method for calculating probabilities of fitness consequences for point mutations across the human genome

(2015) Brad Gulko et al.   NATURE GENETICS

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

(2015) Borbala Mifsud et al.   NATURE GENETICS

Nanoscale spatial organization of theHoxDgene cluster in distinct transcriptional states

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

Integrative modeling reveals the principles of multi-scale chromatin boundary formation in human nuclear organization

(2015) Benjamin L Moore et al.   GENOME BIOLOGY

ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters

(2015) Swneke D. Bailey et al.   Nature Communications

Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases

(2014) Alexander Gusev et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Epigenetic control of hematopoiesis: the PU.1 chromatin connection

(2014) Boet van Riel et al.   BIOLOGICAL CHEMISTRY

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Checks and Balances between Cohesin and Polycomb in Gene Silencing and Transcription

(2014) Dale Dorsett et al.   CURRENT BIOLOGY

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

Transcription factor binding predicts histone modifications in human cell lines

(2014) Dan Benveniste et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Antagonistic actions of Rcor proteins regulate LSD1 activity and cellular differentiation

(2014) G. Upadhyay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enhancer variants: evaluating functions in common disease

(2014) Olivia Corradin et al.   Genome Medicine

Candidate genes and functional noncoding variants identified in a canine model of obsessive-compulsive disorder

(2014) Ruqi Tang et al.   GENOME BIOLOGY

HCFC1 is a common component of active human CpG-island promoters and coincides with ZNF143, THAP11, YY1, and GABP transcription factor occupancy

(2013) J. Michaud et al.   GENOME RESEARCH

Chromatin connectivity maps reveal dynamic promoter–enhancer long-range associations

(2013) Yubo Zhang et al.   NATURE

DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes

(2013) Dvir Aran et al.   GENOME BIOLOGY

A decade of 3C technologies: insights into nuclear organization

(2012) E. de Wit et al.   GENES & DEVELOPMENT

Linking disease associations with regulatory information in the human genome

(2012) M. A. Schaub et al.   GENOME RESEARCH

Annotation of functional variation in personal genomes using RegulomeDB

(2012) A. P. Boyle et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

(2012) Michael M Hoffman et al.   NATURE METHODS

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

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

Transcription factor and chromatin features predict genes associated with eQTLs

(2012) Dennis Wang et al.   NUCLEIC ACIDS RESEARCH

Predicting Spatial and Temporal Gene Expression Using an Integrative Model of Transcription Factor Occupancy and Chromatin State

(2012) Bartek Wilczynski et al.   PLoS Computational Biology

Genomic Variation and Its Impact on Gene Expression in Drosophila melanogaster

(2012) Andreas Massouras et al.   PLoS Genetics

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

(2012) Kevin Y Yip et al.   GENOME BIOLOGY

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

Control of Embryonic Stem Cell Lineage Commitment by Core Promoter Factor, TAF3

(2011) Zhe Liu et al.   CELL

Selective targeting of histone methylation

(2011) Abul BMMK Islam et al.   CELL CYCLE

Polycomb eviction as a new distant enhancer function

(2011) D. Vernimmen et al.   GENES & DEVELOPMENT

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

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

(2011) Jason Ernst et al.   NATURE

The Polycomb complex PRC2 and its mark in life

(2011) Raphaël Margueron et al.   NATURE

HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants

(2011) L. D. Ward et al.   NUCLEIC ACIDS RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Sp1 Regulates Chromatin Looping between an Intronic Enhancer and Distal Promoter of the Human Heme Oxygenase-1 Gene in Renal Cells

(2010) Jessy Deshane et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Integrative analysis of genomic, functional and protein interaction data predicts long-range enhancer-target gene interactions

(2010) Christian Rödelsperger et al.   NUCLEIC ACIDS RESEARCH

Human genetic variation recognizes functional elements in noncoding sequence

(2009) D. Lomelin et al.   GENOME RESEARCH

Unlocking the secrets of the genome

(2009) Susan E. Celniker et al.   NATURE

A histone H3 lysine 36 trimethyltransferase links Nkx2-5 to Wolf–Hirschhorn syndrome

(2009) Keisuke Nimura et al.   NATURE

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Human genetic variation and its contribution to complex traits

(2009) Kelly A. Frazer et al.   NATURE REVIEWS GENETICS

Transcription factors mediate long-range enhancer-promoter interactions

(2009) I. K. Nolis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

(2009) Daniel Ramsköld et al.   PLoS Computational Biology

A HapMap harvest of insights into the genetics of common disease

(2008) Teri A. Manolio et al.   JOURNAL OF CLINICAL INVESTIGATION

The CTCF Insulator Protein Is Posttranslationally Modified by SUMO

(2008) M. J. MacPherson et al.   MOLECULAR AND CELLULAR BIOLOGY

What are decision trees?

(2008) Carl Kingsford et al.   NATURE BIOTECHNOLOGY

Whole-genome sequencing and variant discovery in C. elegans

(2008) LaDeana W Hillier et al.   NATURE METHODS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY