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

Activation of proto-oncogenes by disruption of chromosome neighborhoods

(2016) D. Hnisz et al.   SCIENCE

Fast and efficient QTL mapper for thousands of molecular phenotypes

(2015) Halit Ongen et al.   BIOINFORMATICS

FourCSeq: analysis of 4C sequencing data

(2015) Felix A. Klein et al.   BIOINFORMATICS

Population Variation and Genetic Control of Modular Chromatin Architecture in Humans

(2015) Sebastian M. Waszak et al.   CELL

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

(2015) Darío G. Lupiáñez et al.   CELL

IGF2 signaling and regulation in cancer

(2015) Jurriaan Brouwer-Visser et al.   CYTOKINE & GROWTH FACTOR REVIEWS

Structural and functional diversity of Topologically Associating Domains

(2015) Job Dekker et al.   FEBS LETTERS

Brg1 promotes both tumor-suppressive and oncogenic activities at distinct stages of pancreatic cancer formation

(2015) Nilotpal Roy et al.   GENES & DEVELOPMENT

A cell-based model system links chromothripsis with hyperploidy

(2015) B. R. Mardin et al.   Molecular Systems Biology

Telomerase activation by genomic rearrangements in high-risk neuroblastoma

(2015) Martin Peifer et al.   NATURE

Data analysis: Create a cloud commons

(2015) Lincoln D. Stein et al.   NATURE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Non-coding recurrent mutations in chronic lymphocytic leukaemia

(2015) Xose S. Puente et al.   NATURE

TERT rearrangements are frequent in neuroblastoma and identify aggressive tumors

(2015) Linda J Valentijn et al.   NATURE GENETICS

Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers

(2015) Xiaoyang Zhang et al.   NATURE GENETICS

Recurrent somatic mutations in regulatory regions of human cancer genomes

(2015) Collin Melton et al.   NATURE GENETICS

CTCF establishes discrete functional chromatin domains at theHoxclusters during differentiation

(2015) Varun Narendra et al.   SCIENCE

When Deletions Gain Functions: Commandeering Epigenetic Mechanisms

(2014) Justin Chen et al.   CANCER CELL

The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma

(2014) Caleb F. Davis et al.   CANCER CELL

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

Mapping the Shh long-range regulatory domain

(2014) E. Anderson et al.   DEVELOPMENT

Genomics of uterine leiomyomas: insights from high-throughput sequencing

(2014) Miika Mehine et al.   FERTILITY AND STERILITY

Functional and topological characteristics of mammalian regulatory domains

(2014) O. Symmons et al.   GENOME RESEARCH

Insulin Receptor Substrate-4 Binds to Slingshot-1 Phosphatase and Promotes Cofilin Dephosphorylation

(2014) Yuta Homma et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

(2014) Paul A. Northcott et al.   NATURE

Comprehensive molecular profiling of lung adenocarcinoma

(2014) Eric A. Collisson et al.   NATURE

Identification of genomic alterations in oesophageal squamous cell cancer

(2014) Yongmei Song et al.   NATURE

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

Genome-wide analysis of noncoding regulatory mutations in cancer

(2014) Nils Weinhold et al.   NATURE GENETICS

Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types

(2014) Nils J Fredriksson et al.   NATURE GENETICS

Oncogenic transformation of diverse gastrointestinal tissues in primary organoid culture

(2014) Xingnan Li et al.   NATURE MEDICINE

The landscape and therapeutic relevance of cancer-associated transcript fusions

(2014) K Yoshihara et al.   ONCOGENE

An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element

(2014) M. R. Mansour et al.   SCIENCE

Integrative Genomic Analyses Reveal an Androgen-Driven Somatic Alteration Landscape in Early-Onset Prostate Cancer

(2013) Joachim Weischenfeldt et al.   CANCER CELL

Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues

(2013) Jiang Zhu et al.   CELL

Punctuated Evolution of Prostate Cancer Genomes

(2013) Sylvan C. Baca et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Topology of mammalian developmental enhancers and their regulatory landscapes

(2013) Wouter de Laat et al.   NATURE

Maternal imprinting at the H19–Igf2 locus maintains adult haematopoietic stem cell quiescence

(2013) Aparna Venkatraman et al.   NATURE

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma

(2013) David T W Jones et al.   NATURE GENETICS

Pan-cancer patterns of somatic copy number alteration

(2013) Travis I Zack et al.   NATURE GENETICS

Emerging landscape of oncogenic signatures across human cancers

(2013) Giovanni Ciriello et al.   NATURE GENETICS

Effect of IRS4 Levels on PI 3-Kinase Signalling

(2013) Gerta Hoxhaj et al.   PLoS One

Mechanisms of FGFR-mediated carcinogenesis

(2012) Imran Ahmad et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

Genome Sequencing of Pediatric Medulloblastoma Links Catastrophic DNA Rearrangements with TP53 Mutations

(2012) Tobias Rausch et al.   CELL

Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: From fixation to computation

(2012) Erik Splinter et al.   METHODS

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

Dissecting the genomic complexity underlying medulloblastoma

(2012) David T. W. Jones et al.   NATURE

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

Comprehensive genomic characterization of squamous cell lung cancers

(2012)   NATURE

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

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development

(2011) Philip J. Stephens et al.   CELL

Distinct Types of Tumor-Initiating Cells Form Human Colon Cancer Tumors and Metastases

(2011) Sebastian M. Dieter et al.   Cell Stem Cell

Genomic inflation factors under polygenic inheritance

(2011) Jian Yang et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Transcriptional Enhancers in Animal Development and Evolution

(2010) Mike Levine   CURRENT BIOLOGY

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Signatures of mutation and selection in the cancer genome

(2010) Graham R. Bignell et al.   NATURE

The landscape of somatic copy-number alteration across human cancers

(2010) Rameen Beroukhim et al.   NATURE

Independent filtering increases detection power for high-throughput experiments

(2010) R. Bourgon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic copy number determination in cancer cells from single nucleotide polymorphism microarrays based on quantitative genotyping corrected for aneuploidy

(2009) E. F. Attiyeh et al.   GENOME RESEARCH

A comprehensive catalogue of somatic mutations from a human cancer genome

(2009) Erin D. Pleasance et al.   NATURE

Complex landscapes of somatic rearrangement in human breast cancer genomes

(2009) Philip J. Stephens et al.   NATURE

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

(2008) Timothy J. Ley et al.   NATURE

Adenovirus 5 E1A is responsible for increased expression of insulin receptor substrate 4 in established adenovirus 5-transformed cell lines and interacts with IRS components activating the PI3 kinase/Akt signalling pathway

(2008) N J Shimwell et al.   ONCOGENE