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

Molecular and Genetic Properties of Tumors Associated with Local Immune Cytolytic Activity

(2015) Michael S. Rooney et al.   CELL

Widespread Macromolecular Interaction Perturbations in Human Genetic Disorders

(2015) Nidhi Sahni et al.   CELL

Inconsistency and features of single nucleotide variants detected in whole exome sequencing versus transcriptome sequencing: A case study in lung cancer

(2015) Timothy D. O’Brien et al.   METHODS

Systematic Prioritization of Druggable Mutations in ∼5000 Genomes Across 16 Cancer Types Using a Structural Genomics-based Approach

(2015) Junfei Zhao et al.   MOLECULAR & CELLULAR PROTEOMICS

End of cancer-genome project prompts rethink

(2015) Heidi Ledford   NATURE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

(2015) Silvana Konermann et al.   NATURE

Startups use short-read data to expand long-read sequencing market

(2015) Michael Eisenstein   NATURE BIOTECHNOLOGY

Stromal gene expression defines poor-prognosis subtypes in colorectal cancer

(2015) Alexandre Calon et al.   NATURE GENETICS

Stromal contribution to the colorectal cancer transcriptome

(2015) Claudio Isella et al.   NATURE GENETICS

Large-scale whole-genome sequencing of the Icelandic population

(2015) Daniel F Gudbjartsson et al.   NATURE GENETICS

Toward understanding and exploiting tumor heterogeneity

(2015) Ash A Alizadeh et al.   NATURE MEDICINE

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection

(2015) Adam D Ewing et al.   NATURE METHODS

dSysMap: exploring the edgetic role of disease mutations

(2015) Roberto Mosca et al.   NATURE METHODS

A New Initiative on Precision Medicine

(2015) Francis S. Collins et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

(2015) Denis Bertrand et al.   NUCLEIC ACIDS RESEARCH

Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants

(2015) Aziz Belkadi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Uncovering disease-disease relationships through the incomplete interactome

(2015) J. Menche et al.   SCIENCE

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer

(2015) N. A. Rizvi et al.   SCIENCE

Personalized genomic analyses for cancer mutation discovery and interpretation

(2015) Siân Jones et al.   Science Translational Medicine

Reconfiguring phosphorylation signaling by genetic polymorphisms affects cancer susceptibility

(2015) Yongbo Wang et al.   Journal of Molecular Cell Biology

Protein Domain-Level Landscape of Cancer-Type-Specific Somatic Mutations

(2015) Fan Yang et al.   PLoS Computational 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

e-Driver: a novel method to identify protein regions driving cancer

(2014) Eduard Porta-Pardo et al.   BIOINFORMATICS

ContrastRank: a new method for ranking putative cancer driver genes and classification of tumor samples

(2014) Rui Tian et al.   BIOINFORMATICS

OncodriveROLE classifies cancer driver genes in loss of function and activating mode of action

(2014) Michael P. Schroeder et al.   BIOINFORMATICS

An assessment of computational methods for estimating purity and clonality using genomic data derived from heterogeneous tumor tissue samples

(2014) V. K. Yadav et al.   BRIEFINGS IN BIOINFORMATICS

Comparative analysis of methods for identifying somatic copy number alterations from deep sequencing data

(2014) A. Alkodsi et al.   BRIEFINGS IN BIOINFORMATICS

A Proteome-Scale Map of the Human Interactome Network

(2014) Thomas Rolland et al.   CELL

Integration of Genomic Data Enables Selective Discovery of Breast Cancer Drivers

(2014) Félix Sanchez-Garcia et al.   CELL

Synonymous Mutations Frequently Act as Driver Mutations in Human Cancers

(2014) Fran Supek et al.   CELL

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

(2014) Katherine A. Hoadley et al.   CELL

Application of oncoproteomics to aberrant signalling networks in changing the treatment paradigm in acute lymphoblastic leukaemia

(2014) Elena López Villar et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

Studying Tumorigenesis through Network Evolution and Somatic Mutational Perturbations in the Cancer Interactome

(2014) Feixiong Cheng et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Meta-analysis of Somatic Mutations from Next Generation Sequencing of 241 Melanomas: A Road Map for the Study of Genes with Potential Clinical Relevance

(2014) J. Xia et al.   MOLECULAR CANCER THERAPEUTICS

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens

(2014) Matthew M. Gubin et al.   NATURE

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer

(2014) Jens G Lohr et al.   NATURE BIOTECHNOLOGY

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

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

Genome-wide analysis of noncoding regulatory mutations in cancer

(2014) Nils Weinhold et al.   NATURE GENETICS

Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types

(2014) Nils J Fredriksson et al.   NATURE GENETICS

Rationale for co-targeting IGF-1R and ALK in ALK fusion–positive lung cancer

(2014) Christine M Lovly et al.   NATURE MEDICINE

An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage

(2014) Aaron M Newman et al.   NATURE MEDICINE

Expanding the computational toolbox for mining cancer genomes

(2014) Li Ding et al.   NATURE REVIEWS GENETICS

Genetic Basis for Clinical Response to CTLA-4 Blockade in Melanoma

(2014) Alexandra Snyder et al.   NEW ENGLAND JOURNAL OF MEDICINE

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins

(2014) Pablo Minguez et al.   NUCLEIC ACIDS RESEARCH

Cancer3D: understanding cancer mutations through protein structures

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

Only three driver gene mutations are required for the development of lung and colorectal cancers

(2014) Cristian Tomasetti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direct in Vivo RNAi Screen Unveils Myosin IIa as a Tumor Suppressor of Squamous Cell Carcinomas

(2014) D. Schramek et al.   SCIENCE

Functional consequences of somatic mutations in cancer using protein pocket-based prioritization approach

(2014) Huy Vuong et al.   Genome Medicine

DawnRank: discovering personalized driver genes in cancer

(2014) Jack P Hou et al.   Genome Medicine

DOTS-Finder: a comprehensive tool for assessing driver genes in cancer genomes

(2014) Giorgio EM Melloni 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

Predicting the functional consequences of cancer-associated amino acid substitutions

(2013) Hashem A. Shihab et al.   BIOINFORMATICS

CRAVAT: cancer-related analysis of variants toolkit

(2013) Christopher Douville et al.   BIOINFORMATICS

INstruct: a database of high-quality 3D structurally resolved protein interactome networks

(2013) Michael J. Meyer et al.   BIOINFORMATICS

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

(2013) David Tamborero et al.   BIOINFORMATICS

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

(2013) Evan O. Paull et al.   BIOINFORMATICS

Utilizing protein structure to identify non-random somatic mutations

(2013) Gregory A Ryslik et al.   BMC BIOINFORMATICS

Comparing somatic mutation-callers: beyond Venn diagrams

(2013) Su Kim et al.   BMC BIOINFORMATICS

Next-generation sequencing of paired tyrosine kinase inhibitor-sensitive and -resistant EGFR mutant lung cancer cell lines identifies spectrum of DNA changes associated with drug resistance

(2013) P. Jia et al.   GENOME RESEARCH

Network-assisted analysis to prioritize GWAS results: principles, methods and perspectives

(2013) Peilin Jia et al.   HUMAN GENETICS

Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers

(2013) J. Reimand et al.   Molecular Systems Biology

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

(2013) Michael S. Lawrence et al.   NATURE

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Computational approaches to identify functional genetic variants in cancer genomes

(2013)   NATURE METHODS

Network-based stratification of tumor mutations

(2013) Matan Hofree et al.   NATURE METHODS

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

Analysis of Circulating Tumor DNA to Monitor Metastatic Breast Cancer

(2013) Sarah-Jane Dawson et al.   NEW ENGLAND JOURNAL OF MEDICINE

Interaction-based discovery of functionally important genes in cancers

(2013) Dario Ghersi et al.   NUCLEIC ACIDS RESEARCH

3did: a catalog of domain-based interactions of known three-dimensional structure

(2013) Roberto Mosca et al.   NUCLEIC ACIDS RESEARCH

The Reactome pathway knowledgebase

(2013) David Croft et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

CanDrA: Cancer-Specific Driver Missense Mutation Annotation with Optimized Features

(2013) Yong Mao et al.   PLoS One

Functional Roles of Pulsing in Genetic Circuits

(2013) J. H. Levine et al.   SCIENCE

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

Inferring tumour purity and stromal and immune cell admixture from expression data

(2013) Kosuke Yoshihara et al.   Nature Communications

Connecting Genomic Alterations to Cancer Biology with Proteomics: The NCI Clinical Proteomic Tumor Analysis Consortium

(2013) M. J. Ellis et al.   Cancer Discovery

Identifying potential cancer driver genes by genomic data integration

(2013) Yong Chen et al.   Scientific Reports

Comprehensive identification of mutational cancer driver genes across 12 tumor types

(2013) David Tamborero et al.   Scientific Reports

The mutational landscape of phosphorylation signaling in cancer

(2013) Jüri Reimand et al.   Scientific Reports

Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers

(2013) Qingguo Wang et al.   Genome Medicine

Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing

(2013) Jason O'Rawe et al.   Genome Medicine

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

Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives

(2012) Q. Wang et al.   BRIEFINGS IN BIOINFORMATICS

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Mapping the Hallmarks of Lung Adenocarcinoma with Massively Parallel Sequencing

(2012) Marcin Imielinski et al.   CELL

The cancer antigenome

(2012) Bianca Heemskerk et al.   EMBO JOURNAL

MuSiC: Identifying mutational significance in cancer genomes

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

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Interactome3D: adding structural details to protein networks

(2012) Roberto Mosca et al.   NATURE METHODS

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

(2012) Marco Gerlinger et al.   NEW ENGLAND JOURNAL OF MEDICINE

Functional impact bias reveals cancer drivers

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

SIFT web server: predicting effects of amino acid substitutions on proteins

(2012) Ngak-Leng Sim 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

The BioGRID interaction database: 2013 update

(2012) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

Personalized Pathway Enrichment Map of Putative Cancer Genes from Next Generation Sequencing Data

(2012) Peilin Jia et al.   PLoS One

Predicting the Functional Effect of Amino Acid Substitutions and Indels

(2012) Yongwook Choi et al.   PLoS One

BRAF L597 Mutations in Melanoma Are Associated with Sensitivity to MEK Inhibitors

(2012) Kimberly Brown Dahlman et al.   Cancer Discovery

Improving the Assessment of the Outcome of Nonsynonymous SNVs with a Consensus Deleteriousness Score, Condel

(2011) Abel González-Pérez et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Unraveling the Genetics of Cancer: Genome Sequencing and Beyond

(2011) Kit Man Wong et al.   Annual Review of Genomics and Human Genetics

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer

(2011) Wing Chung Wong et al.   BIOINFORMATICS

Principles and Strategies for Developing Network Models in Cancer

(2011) Dana Pe'er et al.   CELL

Algorithms for Detecting Significantly Mutated Pathways in Cancer

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

Structural and Functional Impact of Cancer-Related Missense Somatic Mutations

(2011) Zhen Shi et al.   JOURNAL OF MOLECULAR BIOLOGY

The structural impact of cancer-associated missense mutations in oncogenes and tumor suppressors

(2011) Henning Stehr et al.   Molecular Cancer

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

Cancer genomics: from discovery science to personalized medicine

(2011) Lynda Chin et al.   NATURE MEDICINE

PINA v2.0: mining interactome modules

(2011) Mark J. Cowley et al.   NUCLEIC ACIDS RESEARCH

MINT, the molecular interaction database: 2012 update

(2011) Luana Licata et al.   NUCLEIC ACIDS RESEARCH

The IntAct molecular interaction database in 2012

(2011) S. Kerrien et al.   NUCLEIC ACIDS RESEARCH

WikiPathways: building research communities on biological pathways

(2011) T. Kelder et al.   NUCLEIC ACIDS RESEARCH

PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse

(2011) P. V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

CAERUS: Predicting CAncER oUtcomeS Using Relationship between Protein Structural Information, Protein Networks, Gene Expression Data, and Mutation Data

(2011) Kelvin Xi Zhang et al.   PLoS Computational Biology

Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly

(2011) Kim Wong et al.   GENOME BIOLOGY

Structural Variation in the Human Genome and its Role in Disease

(2010) Paweł Stankiewicz et al.   Annual Review of Medicine

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

(2010) Charles J. Vaske et al.   BIOINFORMATICS

An Integrated Approach to Uncover Drivers of Cancer

(2010) Uri David Akavia et al.   CELL

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

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

MutationTaster evaluates disease-causing potential of sequence alterations

(2010) Jana Marie Schwarz et al.   NATURE METHODS

Advances in understanding cancer genomes through second-generation sequencing

(2010) Matthew Meyerson et al.   NATURE REVIEWS GENETICS

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami et al.   NUCLEIC ACIDS RESEARCH

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

(2009) H. Carter et al.   CANCER RESEARCH

Edgetic perturbation models of human inherited disorders

(2009) Quan Zhong et al.   Molecular Systems Biology

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols

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

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

(2008) Timothy J. Ley et al.   NATURE

PID: the Pathway Interaction Database

(2008) Carl F. Schaefer et al.   NUCLEIC ACIDS RESEARCH

Human Protein Reference Database--2009 update

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

Estimating the size of the human interactome

(2008) M. P. H. Stumpf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA