Computational approaches for the identification of cancer genes and pathways

TiMEx: a waiting time model for mutually exclusive cancer alterations

(2015) Simona Constantinescu et al.   BIOINFORMATICS

MEMCover: integrated analysis of mutual exclusivity and functional network reveals dysregulated pathways across multiple cancer types

(2015) Yoo-Ah Kim et al.   BIOINFORMATICS

Inferring synthetic lethal interactions from mutual exclusivity of genetic events in cancer

(2015) Sriganesh Srihari et al.   Biology Direct

Kinome-wide Decoding of Network-Attacking Mutations Rewiring Cancer Signaling

(2015) Pau Creixell et al.   CELL

Understanding multicellular function and disease with human tissue-specific networks

(2015) Casey S Greene et al.   NATURE GENETICS

A copy number variation map of the human genome

(2015) Mehdi Zarrei et al.   NATURE REVIEWS GENETICS

Patient-specific driver gene prediction and risk assessment through integrated network analysis of cancer omics profiles

(2015) Denis Bertrand et al.   NUCLEIC ACIDS RESEARCH

NCG 5.0: updates of a manually curated repository of cancer genes and associated properties from cancer mutational screenings

(2015) Omer An et al.   NUCLEIC ACIDS RESEARCH

Identification of Constrained Cancer Driver Genes Based on Mutation Timing

(2015) Thomas Sakoparnig et al.   PLoS Computational Biology

Distinctive Behaviors of Druggable Proteins in Cellular Networks

(2015) Costas Mitsopoulos et al.   PLoS Computational Biology

Network-Based Integration of Disparate Omic Data To Identify "Silent Players" in Cancer

(2015) Matthew Ruffalo et al.   PLoS Computational Biology

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

(2015) Özgün Babur et al.   GENOME BIOLOGY

Quantitative network mapping of the human kinome interactome reveals new clues for rational kinase inhibitor discovery and individualized cancer therapy

(2015) Feixiong Cheng et al.   Oncotarget

DrugComboRanker: drug combination discovery based on target network analysis

(2014) L. Huang et al.   BIOINFORMATICS

Discovery of co-occurring driver pathways in cancer

(2014) Junhua Zhang et al.   BMC BIOINFORMATICS

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

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

Cancer3D: understanding cancer mutations through protein structures

(2014) Eduard Porta-Pardo et al.   NUCLEIC ACIDS RESEARCH

Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine

(2014) Benjamin J Raphael et al.   Genome Medicine

Modeling Mutual Exclusivity of Cancer Mutations

(2014) Ewa Szczurek et al.   PLoS Computational Biology

Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE)

(2013) Evan O. Paull et al.   BIOINFORMATICS

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

(2013) Sepideh Babaei et al.   BMC BIOINFORMATICS

A survey of tools for variant analysis of next-generation genome sequencing data

(2013) S. Pabinger et al.   BRIEFINGS IN BIOINFORMATICS

Lessons from the Cancer Genome

(2013) Levi A. Garraway et al.   CELL

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas

(2013) Larsson Omberg et al.   NATURE GENETICS

Emerging landscape of oncogenic signatures across human cancers

(2013) Giovanni Ciriello et al.   NATURE GENETICS

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

eXtasy: variant prioritization by genomic data fusion

(2013) Alejandro Sifrim et al.   NATURE METHODS

Network-based stratification of tumor mutations

(2013) Matan Hofree et al.   NATURE METHODS

IntOGen-mutations identifies cancer drivers across tumor types

(2013) Abel Gonzalez-Perez et al.   NATURE METHODS

TCPA: a resource for cancer functional proteomics data

(2013) Jun Li et al.   NATURE METHODS

DGIdb: mining the druggable genome

(2013) Malachi Griffith et al.   NATURE METHODS

Analysis of microRNA-target interactions across diverse cancer types

(2013) Anders Jacobsen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Crizotinib versus Chemotherapy in Advanced ALK-Positive Lung Cancer

(2013) Alice T. Shaw et al.   NEW ENGLAND JOURNAL OF MEDICINE

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Exploring TCGA Pan-Cancer Data at the UCSC Cancer Genomics Browser

(2013) Melissa S. Cline et al.   Scientific Reports

The mutational landscape of phosphorylation signaling in cancer

(2013) Jüri Reimand et al.   Scientific Reports

Simultaneous Identification of Multiple Driver Pathways in Cancer

(2013) Mark D. M. Leiserson et al.   PLoS Computational Biology

DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer

(2013) Ali Bashashati et al.   GENOME BIOLOGY

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

nFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing

(2012) A. McPherson et al.   GENOME RESEARCH

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

Chromoanagenesis and cancer: mechanisms and consequences of localized, complex chromosomal rearrangements

(2012) Andrew J Holland et al.   NATURE MEDICINE

Detecting overlapping protein complexes in protein-protein interaction networks

(2012) Tamás Nepusz et al.   NATURE METHODS

The RCSB Protein Data Bank: new resources for research and education

(2012) Peter W. Rose et al.   NUCLEIC ACIDS RESEARCH

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

Inter-tumor heterogeneity

(2012) Mike Cusnir et al.   Human Vaccines & Immunotherapeutics

A Mathematical Methodology for Determining the Temporal Order of Pathway Alterations Arising during Gliomagenesis

(2012) Yu-Kang Cheng et al.   PLoS Computational Biology

PathScan: a tool for discerning mutational significance in groups of putative cancer genes

(2011) Michael C. Wendl et al.   BIOINFORMATICS

Discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors

(2011) Christopher A Miller et al.   BMC Medical Genomics

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

(2011) Philip J. Stephens et al.   CELL

Interactome Networks and Human Disease

(2011) Marc Vidal et al.   CELL

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

Protein-network modeling of prostate cancer gene signatures reveals essential pathways in disease recurrence

(2011) James L Chen et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

The genomic complexity of primary human prostate cancer

(2011) Michael F. Berger et al.   NATURE

The Temporal Order of Genetic and Pathway Alterations in Tumorigenesis

(2011) Moritz Gerstung et al.   PLoS One

A Genome-Wide RNAi Screen Identifies Core Components of the G2-M DNA Damage Checkpoint

(2011) S. Kondo et al.   Science Signaling

The NCGC Pharmaceutical Collection: A Comprehensive Resource of Clinically Approved Drugs Enabling Repurposing and Chemical Genomics

(2011) R. Huang et al.   Science Translational Medicine

iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence

(2011) B. Turner et al.   Database-The Journal of Biological Databases and Curation

Patient-oriented gene set analysis for cancer mutation data

(2011) Simina M Boca et al.   GENOME BIOLOGY

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM

(2010) Charles J. Vaske et al.   BIOINFORMATICS

Candidate gene prioritization by network analysis of differential expression using machine learning approaches

(2010) Daniela Nitsch et al.   BMC BIOINFORMATICS

Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1

(2010) Roel G.W. Verhaak et al.   CANCER CELL

An Integrated Approach to Uncover Drivers of Cancer

(2010) Uri David Akavia et al.   CELL

International network of cancer genome projects

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

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

Automated Network Analysis Identifies Core Pathways in Glioblastoma

(2010) Ethan Cerami et al.   PLoS One

A human functional protein interaction network and its application to cancer data analysis

(2010) Guanming Wu et al.   GENOME BIOLOGY

Identification of rare cancer driver mutations by network reconstruction

(2009) A. Torkamani et al.   GENOME RESEARCH

A Network Model of a Cooperative Genetic Landscape in Brain Tumors

(2009) Markus Bredel et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

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

COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer

(2009) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Sorafenib in Unresectable Hepatocellular Carcinoma from Mild to Advanced Stage Liver Cirrhosis

(2009) M. Pinter et al.   ONCOLOGIST

Multiple testing on the directed acyclic graph of gene ontology

(2008) Jelle J. Goeman et al.   BIOINFORMATICS

Combinatorial patterns of somatic gene mutations in cancer

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

Variations in DNA elucidate molecular networks that cause disease

(2008) Yanqing Chen et al.   NATURE

Cost-effective strategies for completing the interactome

(2008) Ariel S Schwartz et al.   NATURE METHODS

An empirical framework for binary interactome mapping

(2008) Kavitha Venkatesan et al.   NATURE METHODS

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH

Reactome knowledgebase of human biological pathways and processes

(2008) L. Matthews et al.   NUCLEIC ACIDS RESEARCH