Network perturbation by recurrent regulatory variants in cancer

Harmful somatic amino acid substitutions affect key pathways in cancers

(2015) Abhishek Niroula et al.   BMC Medical Genomics

Global transcription network incorporating distal regulator binding reveals selective cooperation of cancer drivers and risk genes

(2015) Kwoneel Kim et al.   NUCLEIC ACIDS RESEARCH

Uncovering disease-disease relationships through the incomplete interactome

(2015) J. Menche et al.   SCIENCE

Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations

(2015) Özgün Babur et al.   GENOME BIOLOGY

Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis

(2014) Simon Merid et al.   BMC BIOINFORMATICS

A Proteome-Scale Map of the Human Interactome Network

(2014) Thomas Rolland et al.   CELL

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Obesity-associated variants within FTO form long-range functional connections with IRX3

(2014) Scott Smemo et al.   NATURE

Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes

(2014) Mark D M Leiserson et al.   NATURE GENETICS

Genome-wide analysis of noncoding regulatory mutations in cancer

(2014) Nils Weinhold et al.   NATURE GENETICS

Global view of enhancer-promoter interactome in human cells

(2014) B. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detecting recurrent gene mutation in interaction network context using multi-scale graph diffusion

(2013) Sepideh Babaei et al.   BMC BIOINFORMATICS

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair

(2013) Paz Polak et al.   NATURE BIOTECHNOLOGY

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

Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics

(2013) Ekta Khurana et al.   SCIENCE

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

HINT: High-quality protein interactomes and their applications in understanding human disease

(2012) Jishnu Das et al.   BMC Systems Biology

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Sleeping Beauty mutagenesis reveals cooperating mutations and pathways in pancreatic adenocarcinoma

(2012) K. M. Mann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Prioritizing candidate disease genes by network-based boosting of genome-wide association data

(2011) I. Lee et al.   GENOME RESEARCH

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

(2011) Jason Ernst et al.   NATURE

Insertional mutagenesis identifies multiple networks of cooperating genes driving intestinal tumorigenesis

(2011) H Nikki March et al.   NATURE GENETICS

Next-generation sequencing to generate interactome datasets

(2011) Haiyuan Yu et al.   NATURE METHODS