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

Role of Collagen Matrix in Tumor Angiogenesis and Glioblastoma Multiforme Progression

(2013) Tadanori Mammoto et al.   AMERICAN JOURNAL OF PATHOLOGY

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

(2013) Sepideh Babaei et al.   BMC BIOINFORMATICS

MIMO: an efficient tool for molecular interaction maps overlap

(2013) Pietro Lena et al.   BMC BIOINFORMATICS

ATR Prohibits Replication Catastrophe by Preventing Global Exhaustion of RPA

(2013) Luis Ignacio Toledo et al.   CELL

Molecular Characteristics of Malignant Ovarian Germ Cell Tumors and Comparison With Testicular Counterparts: Implications for Pathogenesis

(2013) Sigrid Marie Kraggerud et al.   ENDOCRINE REVIEWS

What a difference a hydroxyl makes: mutant IDH, (R)-2-hydroxyglutarate, and cancer

(2013) J.-A. Losman et al.   GENES & DEVELOPMENT

Network analysis of genomic alteration profiles reveals co-altered functional modules and driver genes for glioblastoma

(2013) Yunyan Gu et al.   Molecular BioSystems

Emerging landscape of oncogenic signatures across human cancers

(2013) Giovanni Ciriello et al.   NATURE GENETICS

Statistical Assessment of Crosstalk Enrichment between Gene Groups in Biological Networks

(2013) Theodore McCormack et al.   PLoS One

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Network enrichment analysis: extension of gene-set enrichment analysis to gene networks

(2012) Andrey Alexeyenko et al.   BMC BIOINFORMATICS

Sequential Application of Anticancer Drugs Enhances Cell Death by Rewiring Apoptotic Signaling Networks

(2012) Michael J. Lee et al.   CELL

Exploiting Evolution To Treat Drug Resistance: Combination Therapy and the Double Bind

(2012) David Basanta et al.   MOLECULAR PHARMACEUTICS

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Mutual exclusivity analysis identifies oncogenic network modules

(2011) G. Ciriello et al.   GENOME RESEARCH

Integrated genomic analyses of ovarian carcinoma

(2011) D. Bell et al.   NATURE

Predicting the functional impact of protein mutations: application to cancer genomics

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

Novel EphB4 Monoclonal Antibodies Modulate Angiogenesis and Inhibit Tumor Growth

(2010) Valery Krasnoperov et al.   AMERICAN JOURNAL OF PATHOLOGY

The power of protein interaction networks for associating genes with diseases

(2010) Saket Navlakha et al.   BIOINFORMATICS

LYN Is a Mediator of Epithelial-Mesenchymal Transition and a Target of Dasatinib in Breast Cancer

(2010) Y.-L. Choi et al.   CANCER RESEARCH

An Integrated Approach to Uncover Drivers of Cancer

(2010) Uri David Akavia et al.   CELL

Genome-wide pathway analysis implicates intracellular transmembrane protein transport in Alzheimer disease

(2010) Mun-Gwan Hong et al.   JOURNAL OF HUMAN GENETICS

International network of cancer genome projects

(2010) Thomas J. Hudson (Chairperson) et al.   NATURE

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

CK1ε Is Required for Breast Cancers Dependent on β-Catenin Activity

(2010) So Young Kim et al.   PLoS One

Automated Network Analysis Identifies Core Pathways in Glioblastoma

(2010) Ethan Cerami et al.   PLoS One

Dynamic Zebrafish Interactome Reveals Transcriptional Mechanisms of Dioxin Toxicity

(2010) Andrey Alexeyenko et al.   PLoS One

Cancer-Specific High-Throughput Annotation of Somatic Mutations: Computational Prediction of Driver Missense Mutations

(2009) H. Carter et al.   CANCER RESEARCH

Identification of rare cancer driver mutations by network reconstruction

(2009) A. Torkamani et al.   GENOME RESEARCH

Global networks of functional coupling in eukaryotes from comprehensive data integration

(2009) A. Alexeyenko et al.   GENOME RESEARCH

Complex landscapes of somatic rearrangement in human breast cancer genomes

(2009) Philip J. Stephens 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

Prediction of Cancer Driver Mutations in Protein Kinases

(2008) A. Torkamani et al.   CANCER RESEARCH

Protein networks in disease

(2008) T. Ideker et al.   GENOME RESEARCH

Somatic mutations affect key pathways in lung adenocarcinoma

(2008) Li Ding et al.   NATURE

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE

Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers

(2008) R. J. Leary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses

(2008) S. Jones et al.   SCIENCE

An Integrated Genomic Analysis of Human Glioblastoma Multiforme

(2008) D. W. Parsons et al.   SCIENCE

Inhibition of casein kinase 1-epsilon induces cancer-cell-selective, PERIOD2-dependent growth arrest

(2008) Wan Seok Yang et al.   GENOME BIOLOGY