Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks

APOBEC signature mutation generates an oncogenic enhancer that drives LMO1 expression in T-ALL

(2017) Z Li et al.   LEUKEMIA

Parkinson-associated risk variant in distal enhancer of α-synuclein modulates target gene expression

(2016) Frank Soldner et al.   NATURE

Landscape of somatic mutations in 560 breast cancer whole-genome sequences

(2016) Serena Nik-Zainal et al.   NATURE

Role of non-coding sequence variants in cancer

(2016) Ekta Khurana et al.   NATURE REVIEWS GENETICS

GeneAnalytics: An Integrative Gene Set Analysis Tool for Next Generation Sequencing, RNAseq and Microarray Data

(2016) Shani Ben-Ari Fuchs et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome

(2016) Anthony D. Schmitt et al.   Cell Reports

COP1, the negative regulator of ETV1, influences prognosis in triple-negative breast cancer

(2015) Mao Ouyang et al.   BMC CANCER

In Silico Prescription of Anticancer Drugs to Cohorts of 28 Tumor Types Reveals Targeting Opportunities

(2015) Carlota Rubio-Perez et al.   CANCER CELL

Genomic Classification of Cutaneous Melanoma

(2015) Rehan Akbani et al.   CELL

A method to predict the impact of regulatory variants from DNA sequence

(2015) Dongwon Lee et al.   NATURE GENETICS

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

FTO Obesity Variant Circuitry and Adipocyte Browning in Humans

(2015) Melina Claussnitzer et al.   NEW ENGLAND JOURNAL OF MEDICINE

i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly

(2015) Hana Imrichová et al.   NUCLEIC ACIDS RESEARCH

Identification of altered cis-regulatory elements in human disease

(2015) Anthony Mathelier et al.   TRENDS IN GENETICS

Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state

(2015) Annelien Verfaillie et al.   Nature Communications

Identification of High-Impact cis-Regulatory Mutations Using Transcription Factor Specific Random Forest Models

(2015) Dmitry Svetlichnyy et al.   PLoS Computational Biology

Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas

(2015) Anthony Mathelier et al.   GENOME BIOLOGY

Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells

(2014) Suhn Rhie et al.   BMC GENOMICS

Phosphorylation of ETS1 by Src Family Kinases Prevents Its Recognition by the COP1 Tumor Suppressor

(2014) Gang Lu et al.   CANCER CELL

Cross-Species Regulatory Network Analysis Identifies a Synergistic Interaction between FOXM1 and CENPF that Drives Prostate Cancer Malignancy

(2014) Alvaro Aytes et al.   CANCER CELL

Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer

(2014) Phillippa C. Taberlay et al.   GENOME RESEARCH

Genome-wide analysis of noncoding regulatory mutations in cancer

(2014) Nils Weinhold et al.   NATURE GENETICS

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

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

(2014) M. R. Mansour et al.   SCIENCE

Effect of Down-Regulated Transcriptional Repressor ZEB1 on the Epithelial-Mesenchymal Transition of Ovarian Cancer Cells

(2013) Dengyu Chen et al.   INTERNATIONAL JOURNAL OF GYNECOLOGICAL CANCER

Mutations close in on gene regulation

(2013) Stein Aerts et al.   NATURE

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

Emerging landscape of oncogenic signatures across human cancers

(2013) Giovanni Ciriello et al.   NATURE GENETICS

Elevated levels of FOXA1 facilitate androgen receptor chromatin binding resulting in a CRPC-like phenotype

(2013) J L L Robinson et al.   ONCOGENE

TERT Promoter Mutations in Familial and Sporadic Melanoma

(2013) S. Horn et al.   SCIENCE

Highly Recurrent TERT Promoter Mutations in Human Melanoma

(2013) F. W. Huang et al.   SCIENCE

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Comprehensive identification of mutational cancer driver genes across 12 tumor types

(2013) David Tamborero et al.   Scientific Reports

Annotation of functional variation in personal genomes using RegulomeDB

(2012) A. P. Boyle et al.   GENOME RESEARCH

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Reverse engineering of TLX oncogenic transcriptional networks identifies RUNX1 as tumor suppressor in T-ALL

(2012) Giusy Della Gatta et al.   NATURE MEDICINE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Nrf2 Enhances Cell Proliferation and Resistance to Anticancer Drugs in Human Lung Cancer

(2009) S. Homma et al.   CLINICAL CANCER RESEARCH

Reversibility of Epithelial-Mesenchymal Transition (EMT) Induced in Breast Cancer Cells by Activation of Urokinase Receptor-dependent Cell Signaling

(2009) Minji Jo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The transcriptional network for mesenchymal transformation of brain tumours

(2009) Maria Stella Carro et al.   NATURE

Cancer attractors: A systems view of tumors from a gene network dynamics and developmental perspective

(2009) Sui Huang et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY

Krüppel-Like Factor 5 Mediates Cellular Transformation During Oncogenic KRAS-Induced Intestinal Tumorigenesis

(2007) Mandayam O. Nandan et al.   GASTROENTEROLOGY