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

Canonical Notch signalling is inactive in urothelial carcinoma

(2014) Annemarie Greife et al.   BMC CANCER

Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin

(2014) Katherine A. Hoadley et al.   CELL

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

Utilizing protein structure to identify non-random somatic mutations

(2013) Gregory A Ryslik et al.   BMC BIOINFORMATICS

Lessons from the Cancer Genome

(2013) Levi A. Garraway et al.   CELL

Integrated genomic characterization of endometrial carcinoma

(2013) Gad Getz et al.   NATURE

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms

(2013) Ayana Kon et al.   NATURE GENETICS

Frequent truncating mutations of STAG2 in bladder cancer

(2013) David A Solomon 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

Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancy

(2013) Cigall Kadoch et al.   NATURE GENETICS

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Network-based stratification of tumor mutations

(2013) Matan Hofree et al.   NATURE METHODS

Integrative approaches for finding modular structure in biological networks

(2013) Koyel Mitra et al.   NATURE REVIEWS GENETICS

Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

(2013)   NEW ENGLAND JOURNAL OF MEDICINE

Oncodrive-CIS: A Method to Reveal Likely Driver Genes Based on the Impact of Their Copy Number Changes on Expression

(2013) David Tamborero et al.   PLoS One

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Interpretation of Genomic Variants Using a Unified Biological Network Approach

(2013) Ekta Khurana et al.   PLoS Computational Biology

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

(2012) Jishnu Das et al.   BMC Systems Biology

Condensins: universal organizers of chromosomes with diverse functions

(2012) T. Hirano   GENES & DEVELOPMENT

MuSiC: Identifying mutational significance in cancer genomes

(2012) N. D. Dees et al.   GENOME RESEARCH

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Comprehensive genomic characterization of squamous cell lung cancers

(2012)   NATURE

The mutational landscape of lethal castration-resistant prostate cancer

(2012) Catherine S. Grasso et al.   NATURE

BAP1 loss defines a new class of renal cell carcinoma

(2012) Samuel Peña-Llopis et al.   NATURE GENETICS

Integrated genomic analyses identify ARID1A and ARID1B alterations in the childhood cancer neuroblastoma

(2012) Mark Sausen et al.   NATURE GENETICS

Mutations affecting components of the SWI/SNF complex cause Coffin-Siris syndrome

(2012) Yoshinori Tsurusaki et al.   NATURE GENETICS

Functional impact bias reveals cancer drivers

(2012) Abel Gonzalez-Perez et al.   NUCLEIC ACIDS RESEARCH

Molecular mechanisms for the regulation of Nrf2-mediated cell proliferation in non-small-cell lung cancers

(2012) T Yamadori et al.   ONCOGENE

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

De novo discovery of mutated driver pathways in cancer

(2011) F. Vandin et al.   GENOME RESEARCH

Mutual exclusivity analysis identifies oncogenic network modules

(2011) G. Ciriello et al.   GENOME RESEARCH

Algorithms for Detecting Significantly Mutated Pathways in Cancer

(2011) Fabio Vandin et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma

(2011) Ignacio Varela et al.   NATURE

Integrated genomic analyses of ovarian carcinoma

(2011) D. Bell et al.   NATURE

Next-generation sequencing to generate interactome datasets

(2011) Haiyuan Yu et al.   NATURE METHODS

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

(2011) Craig H Mermel et al.   GENOME BIOLOGY

Statistical method on nonrandom clustering with application to somatic mutations in cancer

(2010) Jingjing Ye et al.   BMC BIOINFORMATICS

Nrf2 and Keap1 Abnormalities in Non-Small Cell Lung Carcinoma and Association with Clinicopathologic Features

(2010) L. M. Solis et al.   CLINICAL CANCER RESEARCH

A CTCF-independent role for cohesin in tissue-specific transcription

(2010) D. Schmidt et al.   GENOME RESEARCH

Human LSD2/KDM1b/AOF1 Regulates Gene Transcription by Modulating Intragenic H3K4me2 Methylation

(2010) Rui Fang et al.   MOLECULAR CELL

Condensin and cohesin complexity: the expanding repertoire of functions

(2010) Andrew J. Wood et al.   NATURE REVIEWS GENETICS

hCAP-D3 Expression Marks a Prostate Cancer Subtype With Favorable Clinical Behavior and Androgen Signaling Signature

(2009) Jacques Lapointe et al.   AMERICAN JOURNAL OF SURGICAL PATHOLOGY

The cancer genome

(2009) Michael R. Stratton et al.   NATURE

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

iRefIndex: A consolidated protein interaction database with provenance

(2008) Sabry Razick et al.   BMC BIOINFORMATICS

Combinatorial patterns of somatic gene mutations in cancer

(2008) Chen-Hsiang Yeang et al.   FASEB JOURNAL

CHD8 Is an ATP-Dependent Chromatin Remodeling Factor That Regulates  -Catenin Target Genes

(2008) B. A. Thompson et al.   MOLECULAR AND CELLULAR BIOLOGY

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

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