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

Comparative Meta-analysis of Prognostic Gene Signatures for Late-Stage Ovarian Cancer

(2014) Levi Waldron et al.   JNCI-Journal of the National Cancer Institute

An Integrated mRNA and microRNA Expression Signature for Glioblastoma Multiforme Prognosis

(2014) Jie Xiong et al.   PLoS One

OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes

(2013) David Tamborero et al.   BIOINFORMATICS

BRAF Fusions Define a Distinct Molecular Subset of Melanomas with Potential Sensitivity to MEK Inhibition

(2013) K. E. Hutchinson et al.   CLINICAL CANCER RESEARCH

Epigenome-wide DNA methylation landscape of melanoma progression to brain metastasis reveals aberrations on homeobox D cluster associated with prognosis

(2013) Diego M. Marzese et al.   HUMAN MOLECULAR GENETICS

Over-expression of BCAT1, a c-Myc target gene, induces cell proliferation, migration and invasion in nasopharyngeal carcinoma

(2013) Wen Zhou et al.   Molecular Cancer

Integrated genomic characterization of endometrial carcinoma

(2013) Gad Getz et al.   NATURE

Network-based stratification of tumor mutations

(2013) Matan Hofree et al.   NATURE METHODS

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

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

(2013) Ali Bashashati et al.   GENOME BIOLOGY

PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis

(2012) Sam Ng et al.   BIOINFORMATICS

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

(2012) Jordi Barretina et al.   NATURE

Functional impact bias reveals cancer drivers

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

Whole-Genome Sequencing: The New Standard of Care?

(2012) L. R. Brunham et al.   SCIENCE

Correlation of Somatic Mutation and Expression Identifies Genes Important in Human Glioblastoma Progression and Survival

(2011) D. L. Masica et al.   CANCER RESEARCH

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

Algorithms for Detecting Significantly Mutated Pathways in Cancer

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

Gene expression profiling in breast cancer: classification, prognostication, and prediction

(2011) Jorge S Reis-Filho et al.   LANCET

Practical limits for reverse engineering of dynamical systems: a statistical analysis of sensitivity and parameter inferability in systems biology models

(2011) Kamil Erguler et al.   Molecular BioSystems

Initial genome sequencing and analysis of multiple myeloma

(2011) Michael A. Chapman et al.   NATURE

Integrated genomic analyses of ovarian carcinoma

(2011) D. Bell et al.   NATURE

Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia

(2011) Xose S. Puente et al.   NATURE

Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder

(2011) Yaoting Gui et al.   NATURE GENETICS

Exome sequencing identifies GRIN2A as frequently mutated in melanoma

(2011) Xiaomu Wei et al.   NATURE GENETICS

Exome sequencing identifies frequent mutation of ARID1A in molecular subtypes of gastric cancer

(2011) Kai Wang et al.   NATURE GENETICS

Cancer genomics: from discovery science to personalized medicine

(2011) Lynda Chin et al.   NATURE MEDICINE

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

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

Exome sequencing identifies a spectrum of mutation frequencies in advanced and lethal prostate cancers

(2011) A. Kumar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer

(2011) H. W. Cheung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identifying Causal Genes and Dysregulated Pathways in Complex Diseases

(2011) Yoo-Ah Kim et al.   PLoS Computational Biology

Identifying cancer driver genes in tumor genome sequencing studies

(2010) Ahrim Youn et al.   BIOINFORMATICS

A flexible R package for nonnegative matrix factorization

(2010) Renaud Gaujoux et al.   BMC BIOINFORMATICS

Integrative Genomic Profiling of Human Prostate Cancer

(2010) Barry S. Taylor et al.   CANCER CELL

An Integrated Approach to Uncover Drivers of Cancer

(2010) Uri David Akavia et al.   CELL

How accurate are cancer cell lines?

(2010) Brendan Borrell   NATURE

International network of cancer genome projects

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

Personalized medicine in oncology: the future is now

(2010) Richard L. Schilsky   NATURE REVIEWS DRUG DISCOVERY

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

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

American Society of Clinical Oncology Provisional Clinical Opinion: Testing forKRASGene Mutations in Patients With Metastatic Colorectal Carcinoma to Predict Response to Anti–Epidermal Growth Factor Receptor Monoclonal Antibody Therapy

(2009) Carmen J. Allegra et al.   JOURNAL OF CLINICAL ONCOLOGY

The cancer genome

(2009) Michael R. Stratton et al.   NATURE

Trim24 targets endogenous p53 for degradation

(2009) Kendra Allton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein networks in disease

(2008) T. Ideker et al.   GENOME RESEARCH

Enabling personalized cancer medicine through analysis of gene-expression patterns

(2008) Laura J. van 't Veer et al.   NATURE

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