Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes

Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2

(2020) Arya Kaul et al.   Nature Protocols

13q12.2 deletions in acute lymphoblastic leukemia lead to upregulation of FLT3 through enhancer hijacking

(2020) Minjun Yang et al.   BLOOD

A supervised learning framework for chromatin loop detection in genome-wide contact maps

(2020) Tarik J. Salameh et al.   Nature Communications

Diverse noncoding mutations contribute to deregulation of cis-regulatory landscape in pediatric cancers

(2020) Bing He et al.   Science Advances

Enhancer hijacking activates oncogenic transcription factor NR4A3 in acinic cell carcinomas of the salivary glands

(2019) Florian Haller et al.   Nature Communications

Distinct structural classes of activating FOXA1 alterations in advanced prostate cancer

(2019) Abhijit Parolia et al.   NATURE

Functional dissection of the Sox9–Kcnj2 locus identifies nonessential and instructive roles of TAD architecture

(2019) Alexandra Despang et al.   NATURE GENETICS

PVT1 Signaling Is a Mediator of Cancer Progression

(2019) Camille Derderian et al.   Frontiers in Oncology

Integrated paired-end enhancer profiling and whole-genome sequencing reveals recurrent CCNE1 and IGF2 enhancer hijacking in primary gastric adenocarcinoma

(2019) Wen Fong Ooi et al.   GUT

Therapeutic Targeting of CDK12/CDK13 in Triple-Negative Breast Cancer

(2019) Victor Quereda et al.   CANCER CELL

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

(2018) Jianfang Liu et al.   CELL

Structural variation in the 3D genome

(2018) Malte Spielmann et al.   NATURE REVIEWS GENETICS

OneD: increasing reproducibility of Hi-C samples with abnormal karyotypes

(2018) Enrique Vidal et al.   NUCLEIC ACIDS RESEARCH

Effective normalization for copy number variation in Hi-C data

(2018) Nicolas Servant et al.   BMC BIOINFORMATICS

Integrative detection and analysis of structural variation in cancer genomes

(2018) Jesse R. Dixon et al.   NATURE GENETICS

Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis

(2018) Bjørt K. Kragesteen et al.   NATURE GENETICS

CCND2 and CCND3 hijack immunoglobulin light chain enhancers in cyclin D1-negative mantle cell lymphoma

(2018) David Martín-Garcia et al.   BLOOD

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

(2017) Tao Yang et al.   GENOME RESEARCH

The whole-genome landscape of medulloblastoma subtypes

(2017) Paul A. Northcott et al.   NATURE

HiTAD: detecting the structural and functional hierarchies of topologically associating domains from chromatin interactions

(2017) Xiao-Tao Wang et al.   NUCLEIC ACIDS RESEARCH

MYC Drives a Subset of High-Risk Pediatric Neuroblastomas and Is Activated through Mechanisms Including Enhancer Hijacking and Focal Enhancer Amplification

(2017) Mark W. Zimmerman et al.   Cancer Discovery

A computational strategy to adjust for copy number in tumor Hi-C data

(2016) Hua-Jun Wu et al.   BIOINFORMATICS

Formation of new chromatin domains determines pathogenicity of genomic duplications

(2016) Martin Franke et al.   NATURE

Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking

(2016) Joachim Weischenfeldt et al.   NATURE GENETICS

An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma

(2016) Yotam Drier et al.   NATURE GENETICS

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

PI3K/AKT Signaling Regulates H3K4 Methylation in Breast Cancer

(2016) Jennifer M. Spangle et al.   Cell Reports

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Condensin-driven remodelling of X chromosome topology during dosage compensation

(2015) Emily Crane et al.   NATURE

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

(2015) Adrian L. Sanborn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection of Enhancer-Associated Rearrangements Reveals Mechanisms of Oncogene Dysregulation in B-cell Lymphoma

(2015) R. J. H. Ryan et al.   Cancer Discovery

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

(2014) Suhas S.P. Rao et al.   CELL

A Single Oncogenic Enhancer Rearrangement Causes Concomitant EVI1 and GATA2 Deregulation in Leukemia

(2014) Stefan Gröschel et al.   CELL

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

(2014) F. Ay et al.   GENOME RESEARCH

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

(2014) Paul A. Northcott et al.   NATURE

ETV1 directs androgen metabolism and confers aggressive prostate cancer in targeted mice and patients

(2013) E. Baena et al.   GENES & DEVELOPMENT

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

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

(2012) Maxim Imakaev et al.   NATURE METHODS

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data

(2011) Valentina Boeva et al.   BIOINFORMATICS

Overexpression of Full-Length ETV1 Transcripts in Clinical Prostate Cancer Due to Gene Translocation

(2011) Delila Gasi et al.   PLoS One

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

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

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