Discovering potential driver genes through an integrated model of somatic mutation profiles and gene functional information

Extracting Stage-Specific and Dynamic Modules Through Analyzing Multiple Networks Associated with Cancer Progression

(2018) Xiaoke Ma et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Comparison of algorithms for the detection of cancer drivers at subgene resolution

(2017) Eduard Porta-Pardo et al.   NATURE METHODS

Mutations in TSC1, TSC2, and MTOR Are Associated with Response to Rapalogs in Patients with Metastatic Renal Cell Carcinoma

(2016) D. J. Kwiatkowski et al.   CLINICAL CANCER RESEARCH

Discovering Recurrent Copy Number Aberrations in Complex Patterns via Non-Negative Sparse Singular Value Decomposition

(2016) Jianing Xi et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Detection of driver pathways using mutated gene network in cancer

(2016) Feng Li et al.   Molecular BioSystems

Discovering potential cancer driver genes by an integrated network-based approach

(2016) Kai Shi et al.   Molecular BioSystems

Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes

(2015) Feixiong Cheng et al.   BRIEFINGS IN BIOINFORMATICS

The Estrogen Receptor Cofactor SPEN Functions as a Tumor Suppressor and Candidate Biomarker of Drug Responsiveness in Hormone-Dependent Breast Cancers

(2015) S. Legare et al.   CANCER RESEARCH

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

(2015) Denis Bertrand et al.   NUCLEIC ACIDS RESEARCH

Comprehensive assessment of cancer missense mutation clustering in protein structures

(2015) Atanas Kamburov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Point mutations of the mTOR-RHEB pathway in renal cell carcinoma

(2015) Arindam P. Ghosh et al.   Oncotarget

Evaluation and integration of cancer gene classifiers: identification and ranking of plausible drivers

(2015) Yang Liu et al.   Scientific Reports

A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces

(2015) Eduard Porta-Pardo et al.   PLoS Computational Biology

Abstract 5324: Pan-cancer identification of mutated pathways and protein complexes

(2015) Mark D. Leiserson et al.   CANCER RESEARCH

Piecewise-constant and low-rank approximation for identification of recurrent copy number variations

(2014) X. Zhou et al.   BIOINFORMATICS

A graph theoretic approach to utilizing protein structure to identify non-random somatic mutations

(2014) Gregory A Ryslik et al.   BMC BIOINFORMATICS

A Diverse Array of Cancer-Associated MTOR Mutations Are Hyperactivating and Can Predict Rapamycin Sensitivity

(2014) B. C. Grabiner et al.   Cancer Discovery

NCG 4.0: the network of cancer genes in the era of massive mutational screenings of cancer genomes

(2014) Omer An et al.   Database-The Journal of Biological Databases and Curation

DawnRank: discovering personalized driver genes in cancer

(2014) Jack P Hou et al.   Genome Medicine

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

(2014) Benjamin J Raphael et al.   Genome Medicine

VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data

(2014) Peilin Jia et al.   PLoS Computational Biology

Utilizing protein structure to identify non-random somatic mutations

(2013) Gregory A Ryslik et al.   BMC BIOINFORMATICS

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

(2013) Sepideh Babaei et al.   BMC BIOINFORMATICS

Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives

(2013) Min Zhao et al.   BMC BIOINFORMATICS

Comprehensive molecular characterization of clear cell renal cell carcinoma

(2013)   NATURE

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

(2013) Michael S. Lawrence et al.   NATURE

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

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

(2013) J. Gao et al.   Science Signaling

Identification of ovarian cancer driver genes by using module network integration of multi-omics data

(2013) O. Gevaert et al.   Interface Focus

Interpretation of Genomic Variants Using a Unified Biological Network Approach

(2013) Ekta Khurana 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

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

(2012) Sam Ng et al.   BIOINFORMATICS

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

(2012) Jishnu Das et al.   BMC Systems Biology

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

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

(2012) Mark Sausen et al.   NATURE GENETICS

Robust biclustering by sparse singular value decomposition incorporating stability selection

(2011) Martin Sill et al.   BIOINFORMATICS

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

(2011) I. Lee et al.   GENOME RESEARCH

Next-Generation Sequencing

(2011) Momiao Xiong et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Algorithms for Detecting Significantly Mutated Pathways in Cancer

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

Identifying cancer driver genes in tumor genome sequencing studies

(2010) Ahrim Youn et al.   BIOINFORMATICS

Biclustering via Sparse Singular Value Decomposition

(2010) Mihee Lee et al.   BIOMETRICS

Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP

(2010) Troy Hawkins et al.   BMC BIOINFORMATICS

International network of cancer genome projects

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

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

GS2: an efficiently computable measure of GO-based similarity of gene sets

(2009) T. Ruths et al.   BIOINFORMATICS

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

Human Protein Reference Database--2009 update

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