Activation of proto-oncogenes by disruption of chromosome neighborhoods

Mango: a bias-correcting ChIA-PET analysis pipeline

(2015) Douglas H. Phanstiel et al.   BIOINFORMATICS

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

(2015) Fabian Grubert et al.   CELL

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

(2015) Zhonghui Tang et al.   CELL

Convergence of Developmental and Oncogenic Signaling Pathways at Transcriptional Super-Enhancers

(2015) Denes Hnisz et al.   MOLECULAR CELL

Whole–genome characterization of chemoresistant ovarian cancer

(2015) Ann-Marie Patch et al.   NATURE

Chemically modified guide RNAs enhance CRISPR-Cas genome editing in human primary cells

(2015) Ayal Hendel et al.   NATURE BIOTECHNOLOGY

CTCF/cohesin-binding sites are frequently mutated in cancer

(2015) Riku Katainen et al.   NATURE GENETICS

Whole-genome sequencing provides new insights into the clonal architecture of Barrett's esophagus and esophageal adenocarcinoma

(2015) Caryn S Ross-Innes et al.   NATURE GENETICS

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

(2014) Suhas S.P. Rao et al.   CELL

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

(2014) Jill M. Dowen et al.   CELL

Genome-wide map of regulatory interactions in the human genome

(2014) Nastaran Heidari et al.   GENOME RESEARCH

RAG-mediated recombination is the predominant driver of oncogenic rearrangement in ETV6-RUNX1 acute lymphoblastic leukemia

(2014) Elli Papaemmanuil et al.   NATURE GENETICS

CTCF: an architectural protein bridging genome topology and function

(2014) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions

(2014) Jonas Paulsen et al.   NUCLEIC ACIDS RESEARCH

Downregulation of microRNA-214 and overexpression of FGFR-1 contribute to hepatocellular carcinoma metastasis

(2013) Jian Wang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Chromatin looping defines expression of TAL1, its flanking genes, and regulation in T-ALL

(2013) Y. Zhou et al.   BLOOD

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

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

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

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Lessons from the Cancer Genome

(2013) Levi A. Garraway et al.   CELL

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

(2013) Jennifer E. Phillips-Cremins et al.   CELL

Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments

(2013) V. C. Seitan et al.   GENOME RESEARCH

The Hierarchy of the 3D Genome

(2013) Johan H. Gibcus et al.   MOLECULAR CELL

The genomic landscape of hypodiploid acute lymphoblastic leukemia

(2013) Linda Holmfeldt et al.   NATURE GENETICS

Exploring long-range genome interactions using the WashU Epigenome Browser

(2013) Xin Zhou et al.   NATURE METHODS

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Actionable Gene Expression-Based Patient Stratification for Molecular Targeted Therapy in Hepatocellular Carcinoma

(2013) Jung-Hee Kwon et al.   PLoS One

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

Revisiting Global Gene Expression Analysis

(2012) Jakob Lovén et al.   CELL

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

(2012) Guoliang Li et al.   CELL

The molecular basis of T cell acute lymphoblastic leukemia

(2012) Pieter Van Vlierberghe et al.   JOURNAL OF CLINICAL INVESTIGATION

From cells to chromatin: Capturing snapshots of genome organization with 5C technology

(2012) Maria A. Ferraiuolo et al.   METHODS

Analysis of long-range chromatin interactions using Chromosome Conformation Capture

(2012) Natalia Naumova et al.   METHODS

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

The genetic basis of early T-cell precursor acute lymphoblastic leukaemia

(2012) Jinghui Zhang et al.   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

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

(2012) Maxim Imakaev et al.   NATURE METHODS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

An NK and T Cell Enhancer Lies 280 Kilobase Pairs 3' to the Gata3 Structural Gene

(2011) S. Hosoya-Ohmura et al.   MOLECULAR AND CELLULAR BIOLOGY

CTCF-mediated functional chromatin interactome in pluripotent cells

(2011) Lusy Handoko et al.   NATURE GENETICS

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

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

(2010) Guoliang Li et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

My5C: web tools for chromosome conformation capture studies

(2009) Bryan R Lajoie et al.   NATURE METHODS

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

Cohesins Functionally Associate with CTCF on Mammalian Chromosome Arms

(2008) Vania Parelho et al.   CELL

Cohesin mediates transcriptional insulation by CCCTC-binding factor

(2008) Kerstin S. Wendt et al.   NATURE

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Oncogenes and Cancer

(2008) Carlo M. Croce   NEW ENGLAND JOURNAL OF MEDICINE

CTCF physically links cohesin to chromatin

(2008) E. D. Rubio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY