Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions

3D Chromosome Regulatory Landscape of Human Pluripotent Cells

(2016) Xiong Ji et al.   Cell Stem Cell

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

(2015) Zhonghui Tang et al.   CELL

Integrative analysis of haplotype-resolved epigenomes across human tissues

(2015) Danny Leung et al.   NATURE

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

(2014) Suhas S.P. Rao et al.   CELL

Genome-wide map of regulatory interactions in the human genome

(2014) Nastaran Heidari et al.   GENOME RESEARCH

The Spatial Organization of the Human Genome

(2013) Wendy A. Bickmore   Annual Review of Genomics and Human Genetics

Interactome Maps of Mouse Gene Regulatory Domains Reveal Basic Principles of Transcriptional Regulation

(2013) Kyong-Rim Kieffer-Kwon et al.   CELL

The genomic landscape of cohesin-associated chromatin interactions

(2013) L. E. DeMare et al.   GENOME RESEARCH

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

(2013) Yubo Zhang et al.   NATURE

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

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

(2012) Guoliang Li et al.   CELL

Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization

(2012) Iouri Chepelev et al.   CELL RESEARCH

ChIA-PET analysis of transcriptional chromatin interactions

(2012) Jingyao Zhang et al.   METHODS

CTCF-mediated functional chromatin interactome in pluripotent cells

(2011) Lusy Handoko et al.   NATURE GENETICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans

(2010) R. McDaniell et al.   SCIENCE

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing

(2010) Guoliang Li et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

ChIP-based methods for the identification of long-range chromatin interactions

(2009) Melissa J. Fullwood et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

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

(2009) E. Lieberman-Aiden et al.   SCIENCE

Mass spectrometric identification of formaldehyde-induced peptide modifications under in vivo protein cross-linking conditions

(2008) Judy Toews et al.   ANALYTICA CHIMICA ACTA