Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing technology and application

Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes

(2014) Jill M. Dowen et al.   CELL

Functional gene groups are concentrated within chromosomes, among chromosomes and in the nuclear space of the human genome

(2014) Annelyse Thévenin et al.   NUCLEIC ACIDS RESEARCH

Nucleosome eviction and multiple co-factor binding predict estrogen-receptor-alpha-associated long-range interactions

(2014) C. He et al.   NUCLEIC ACIDS RESEARCH

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

3D Chromosome Modeling with Semi-Definite Programming and Hi-C Data

(2013) ZhiZhuo Zhang et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

(2013) Yubo Zhang et al.   NATURE

Dissecting the chromatin interactome of microRNA genes

(2013) D. Chen et al.   NUCLEIC ACIDS RESEARCH

The sequencing bias relaxed characteristics of Hi-C derived data and implications for chromatin 3D modeling

(2013) Cheng Peng et al.   NUCLEIC ACIDS RESEARCH

Quantitative analysis of genomic element interactions by molecular colony technique

(2013) Alexey A. Gavrilov et al.   NUCLEIC ACIDS RESEARCH

Bayesian Inference of Spatial Organizations of Chromosomes

(2013) Ming Hu et al.   PLoS Computational Biology

BatMis: a fast algorithm for k-mismatch mapping

(2012) Chandana Tennakoon et al.   BIOINFORMATICS

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

TNFα signals through specialized factories where responsive coding and miRNA genes are transcribed

(2012) Argyris Papantonis et al.   EMBO JOURNAL

A decade of 3C technologies: insights into nuclear organization

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

ChIA-PET analysis of transcriptional chromatin interactions

(2012) Jingyao Zhang et al.   METHODS

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

(2012) Kuljeet Singh Sandhu et al.   Cell Reports

Chromatin interaction networks and higher order architectures of eukaryotic genomes

(2011) Kuljeet Singh Sandhu et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

CTCF-mediated functional chromatin interactome in pluripotent cells

(2011) Lusy Handoko et al.   NATURE GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY