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

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iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types

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The 3D Genome as Moderator of Chromosomal Communication

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Chromatin Domains: The Unit of Chromosome Organization

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Chromosome conformation elucidates regulatory relationships in developing human brain

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Formation of new chromatin domains determines pathogenicity of genomic duplications

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Erratum: Organization and function of the 3D genome

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

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Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions

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CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

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

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The Role of Chromosome Domains in Shaping the Functional Genome

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Integrative analysis of 111 reference human epigenomes

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Insulator dysfunction and oncogene activation in IDH mutant gliomas

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WASP: allele-specific software for robust molecular quantitative trait locus discovery

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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

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Enhancer loops appear stable during development and are associated with paused polymerase

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3D genome reconstruction from chromosomal contacts

(2014) Annick Lesne et al.   NATURE METHODS

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

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Genome Architecture: Domain Organization of Interphase Chromosomes

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A high-resolution map of the three-dimensional chromatin interactome in human cells

(2013) Fulai Jin et al.   NATURE

Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing

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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

Higher-order chromatin domains link eQTLs with the expression of far-away genes

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Divergence of Mammalian Higher Order Chromatin Structure Is Associated with Developmental Loci

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Distinct Metabolic Flow Enables Large-Scale Purification of Mouse and Human Pluripotent Stem Cell-Derived Cardiomyocytes

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Directed cardiomyocyte differentiation from human pluripotent stem cells by modulating Wnt/β-catenin signaling under fully defined conditions

(2012) Xiaojun Lian et al.   Nature Protocols

Gene Loops Enhance Transcriptional Directionality

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Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

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RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

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Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture

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Efficient generation of transgene-free human induced pluripotent stem cells (iPSCs) by temperature-sensitive Sendai virus vectors

(2011) H. Ban et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

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Chromatin loops in gene regulation

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