Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation

ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream from transcription start sites at the majority of CpG island promoters

(2018) Suhn Kyong Rhie et al.   GENOME RESEARCH

Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk

(2018) Prashanth Rajarajan et al.   SCIENCE

Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes

(2017) Yinxiu Zhan et al.   GENOME RESEARCH

Genome-wide association analysis identifies 30 new susceptibility loci for schizophrenia

(2017) Zhiqiang Li et al.   NATURE GENETICS

Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control

(2016) Denes Hnisz et al.   CELL

3D Chromosome Regulatory Landscape of Human Pluripotent Cells

(2016) Xiong Ji et al.   Cell Stem Cell

Chromosome conformation elucidates regulatory relationships in developing human brain

(2016) Hyejung Won et al.   NATURE

Activation of proto-oncogenes by disruption of chromosome neighborhoods

(2016) D. Hnisz et al.   SCIENCE

motifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites: Fig. 1.

(2015) Simon G. Coetzee et al.   BIOINFORMATICS

The role of DNA methylation in directing the functional organization of the cancer epigenome

(2015) Fides D. Lay et al.   GENOME RESEARCH

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

TopDom: an efficient and deterministic method for identifying topological domains in genomes

(2015) Hanjun Shin et al.   NUCLEIC ACIDS RESEARCH

Correspondence of DNA Methylation Between Blood and Brain Tissue and Its Application to Schizophrenia Research

(2015) Esther Walton et al.   SCHIZOPHRENIA BULLETIN

Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome

(2015) Yu Gyoung Tak et al.   Epigenetics & Chromatin

The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation

(2015) Fan Yang et al.   GENOME BIOLOGY

Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells

(2014) Suhn Rhie et al.   BMC GENOMICS

H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency

(2014) Bérénice A. Benayoun et al.   CELL

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

(2014) Suhas S.P. Rao et al.   CELL

Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts

(2014) F. Ay et al.   GENOME RESEARCH

Biological insights from 108 schizophrenia-associated genetic loci

(2014)   NATURE

B-myb is an essential regulator of hematopoietic stem cell and myeloid progenitor cell development

(2014) S. J. Baker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional annotation of colon cancer risk SNPs

(2014) Lijing Yao et al.   Nature Communications

Comprehensive Functional Annotation of 77 Prostate Cancer Risk Loci

(2014) Dennis J. Hazelett et al.   PLoS Genetics

Functional implications of genome topology

(2013) Giacomo Cavalli et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments

(2013) P. Kheradpour et al.   NUCLEIC ACIDS RESEARCH

Comprehensive Functional Annotation of Seventy-One Breast Cancer Risk Loci

(2013) Suhn Kyong Rhie et al.   PLoS One

HiTC: exploration of high-throughput ‘C’ experiments

(2012) Nicolas Servant et al.   BIOINFORMATICS

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

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

Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules

(2012) T. K. Kelly et al.   GENOME RESEARCH

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

(2012) Caryn S. Ross-Innes et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

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

(2012) Elphège P. Nora et al.   NATURE

HOCOMOCO: a comprehensive collection of human transcription factor binding sites models

(2012) Ivan V. Kulakovskiy et al.   NUCLEIC ACIDS RESEARCH

FunciSNP: an R/bioconductor tool integrating functional non-coding data sets with genetic association studies to identify candidate regulatory SNPs

(2012) Simon G. Coetzee et al.   NUCLEIC ACIDS RESEARCH

Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium

(2012) J. Wang et al.   NUCLEIC ACIDS RESEARCH

Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data

(2012) Yaping Liu et al.   GENOME BIOLOGY

H3K4 tri-methylation provides an epigenetic signature of active enhancers

(2011) Aleksandra Pekowska et al.   EMBO JOURNAL

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

Myb Controls Intestinal Stem Cell Genes and Self-Renewal

(2011) Dane Cheasley et al.   STEM CELLS

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

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY