Driver gene classification reveals a substantial overrepresentation of tumor suppressors among very large chromatin-regulating proteins

MOZ (MYST3, KAT6A) inhibits senescence via the INK4A-ARF pathway

(2015) B N Sheikh et al.   ONCOGENE

High nuclear/cytoplasmic ratio of Cdk1 expression predicts poor prognosis in colorectal cancer patients

(2015) Wen-Wei Sung et al.   BMC CANCER

Building Predictive Models inRUsing thecaretPackage

(2015) Max Kuhn   Journal of Statistical Software

Snail regulates Nanog status during the epithelial–mesenchymal transition via the Smad1/Akt/GSK3β signaling pathway in non-small-cell lung cancer

(2015) Chen-Wei Liu et al.   Oncotarget

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

(2014) Michael P. Schroeder et al.   BIOINFORMATICS

Targeting cyclin-dependent kinase 1 (CDK1) but not CDK4/6 or CDK2 is selectively lethal to MYC-dependent human breast cancer cells

(2014) Jian Kang et al.   BMC CANCER

Identification of synthetic lethality of PRKDC in MYC-dependent human cancers by pooled shRNA screening

(2014) Zongxiang Zhou et al.   BMC CANCER

Integration of Genomic Data Enables Selective Discovery of Breast Cancer Drivers

(2014) Félix Sanchez-Garcia et al.   CELL

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

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

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

Expanding the computational toolbox for mining cancer genomes

(2014) Li Ding et al.   NATURE REVIEWS GENETICS

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

SUPT6H controls estrogen receptor activity and cellular differentiation by multiple epigenomic mechanisms

(2014) U Bedi et al.   ONCOGENE

A Functional Cancer Genomics Screen Identifies a Druggable Synthetic Lethal Interaction between MSH3 and PRKDC

(2014) F. Dietlein et al.   Cancer Discovery

KAT6A, a Chromatin Modifier from the 8p11-p12 Amplicon is a Candidate Oncogene in Luminal Breast Cancer

(2014) Brittany Turner-Ivey et al.   NEOPLASIA

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

(2013) David Tamborero et al.   BIOINFORMATICS

Cumulative Haploinsufficiency and Triplosensitivity Drive Aneuploidy Patterns and Shape the Cancer Genome

(2013) Teresa Davoli et al.   CELL

Lessons from the Cancer Genome

(2013) Levi A. Garraway et al.   CELL

Analysis of 41 cancer cell lines reveals excessive allelic loss and novel mutations in theSIRT1gene

(2013) Jeehae Han et al.   CELL CYCLE

dbNSFP v2.0: A Database of Human Non-synonymous SNVs and Their Functional Predictions and Annotations

(2013) Xiaoming Liu et al.   HUMAN MUTATION

Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics

(2013) Linn Fagerberg et al.   MOLECULAR & CELLULAR PROTEOMICS

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

Pan-cancer patterns of somatic copy number alteration

(2013) Travis I Zack et al.   NATURE GENETICS

Computational approaches to identify functional genetic variants in cancer genomes

(2013)   NATURE METHODS

Systematic identification of transcriptional regulatory modules from protein–protein interaction networks

(2013) Diego Diez et al.   NUCLEIC ACIDS RESEARCH

A bagging SVM to learn from positive and unlabeled examples

(2013) F. Mordelet et al.   PATTERN RECOGNITION LETTERS

The Spectrum of SWI/SNF Mutations, Ubiquitous in Human Cancers

(2013) A. Hunter Shain et al.   PLoS One

Prediction and Validation of Gene-Disease Associations Using Methods Inspired by Social Network Analyses

(2013) U. Martin Singh-Blom et al.   PLoS One

DNA-PKcs Inhibition Sensitizes Cancer Cells to Carbon-Ion Irradiation via Telomere Capping Disruption

(2013) Xin Zhou et al.   PLoS One

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Genome-wide survey of interindividual differences of RNA stability in human lymphoblastoid cell lines

(2013) Jubao Duan et al.   Scientific Reports

Identifying potential cancer driver genes by genomic data integration

(2013) Yong Chen et al.   Scientific Reports

From Mouse to Human: Evolutionary Genomics Analysis of Human Orthologs of Essential Genes

(2013) Benjamin Georgi et al.   PLoS Genetics

In silico identification of oncogenic potential of fyn-related kinase in hepatocellular carcinoma

(2012) Jia-Shing Chen et al.   BIOINFORMATICS

Positive-unlabeled learning for disease gene identification

(2012) Peng Yang et al.   BIOINFORMATICS

Cancer Genetics and Epigenetics: Two Sides of the Same Coin?

(2012) Jueng Soo You et al.   CANCER CELL

Cancer Epigenetics: From Mechanism to Therapy

(2012) Mark A. Dawson et al.   CELL

Mapping the Hallmarks of Lung Adenocarcinoma with Massively Parallel Sequencing

(2012) Marcin Imielinski et al.   CELL

Global analysis reveals multiple pathways for unique regulation of mRNA decay in induced pluripotent stem cells

(2012) A. T. Neff et al.   GENOME RESEARCH

MuSiC: Identifying mutational significance in cancer genomes

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

Systematic identification of genomic markers of drug sensitivity in cancer cells

(2012) Mathew J. Garnett et al.   NATURE

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

(2012) Jordi Barretina et al.   NATURE

TSGene: a web resource for tumor suppressor genes

(2012) Min Zhao et al.   NUCLEIC ACIDS RESEARCH

Functional impact bias reveals cancer drivers

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

Association between TGFBR1 Polymorphisms and Cancer Risk: A Meta-Analysis of 35 Case-Control Studies

(2012) Yong-qiang Wang et al.   PLoS One

The Duplicated Genes Database: Identification and Functional Annotation of Co-Localised Duplicated Genes across Genomes

(2012) Marion Ouedraogo et al.   PLoS One

ProDiGe: Prioritization Of Disease Genes with multitask machine learning from positive and unlabeled examples

(2011) Fantine Mordelet et al.   BMC BIOINFORMATICS

Specific activity of cyclin-dependent kinase I is a new potential predictor of tumour recurrence in stage II colon cancer

(2011) E C M Zeestraten et al.   BRITISH JOURNAL OF CANCER

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

dbNSFP: A lightweight database of human nonsynonymous SNPs and their functional predictions

(2011) Xiaoming Liu et al.   HUMAN MUTATION

A Quantitative Spatial Proteomics Analysis of Proteome Turnover in Human Cells

(2011) François-Michel Boisvert et al.   MOLECULAR & CELLULAR PROTEOMICS

Compromised CDK1 activity sensitizes BRCA-proficient cancers to PARP inhibition

(2011) Neil Johnson et al.   NATURE MEDICINE

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

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

(2011) Craig H Mermel et al.   GENOME BIOLOGY

The landscape of somatic copy-number alteration across human cancers

(2010) Rameen Beroukhim et al.   NATURE

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Characterising and Predicting Haploinsufficiency in the Human Genome

(2010) Ni Huang et al.   PLoS Genetics

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

(2009) J. Chen et al.   NUCLEIC ACIDS RESEARCH

Monocytic Leukemia Zinc Finger (MOZ) Interacts with p53 to Induce p21 Expression and Cell-cycle Arrest

(2008) Susumu Rokudai et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Identification of candidate disease genes by integrating Gene Ontologies and protein-interaction networks: case study of primary immunodeficiencies

(2008) Csaba Ortutay et al.   NUCLEIC ACIDS RESEARCH

Bone morphogenetic protein signaling enhances invasion and bone metastasis of breast cancer cells through Smad pathway

(2008) Y Katsuno et al.   ONCOGENE

Global Protein Stability Profiling in Mammalian Cells

(2008) H.-C. S. Yen et al.   SCIENCE