DawnRank: discovering personalized driver genes in cancer

A network-assisted co-clustering algorithm to discover cancer subtypes based on gene expression

(2014) Yiyi Liu et al.   BMC BIOINFORMATICS

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

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

(2014) Peilin Jia et al.   PLoS Computational Biology

CRAVAT: cancer-related analysis of variants toolkit

(2013) Christopher Douville 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

Amplification of FRS2 and Activation of FGFR/FRS2 Signaling Pathway in High-Grade Liposarcoma

(2013) K. Zhang et al.   CANCER RESEARCH

TRAF6 Upregulates Expression of HIF-1  and Promotes Tumor Angiogenesis

(2013) H. Sun et al.   CANCER RESEARCH

Journeys into the genome of cancer cells

(2013) Michael R. Stratton   EMBO Molecular Medicine

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

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

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

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Identification of a pharmacologically tractable Fra-1/ADORA2B axis promoting breast cancer metastasis

(2013) C. J. Desmet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics

(2013) Ekta Khurana et al.   SCIENCE

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

Lgr5-Expressing Cells Are Sufficient and Necessary for Postnatal Mammary Gland Organogenesis

(2013) Vicki Plaks et al.   Cell Reports

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

(2013) Ali Bashashati et al.   GENOME BIOLOGY

Integrated analysis of recurrent properties of cancer genes to identify novel drivers

(2013) Matteo D'Antonio et al.   GENOME BIOLOGY

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

(2012) Sam Ng et al.   BIOINFORMATICS

Molecular Pathways: Targeting the TGF-  Pathway for Cancer Therapy

(2012) A. L. Smith et al.   CLINICAL CANCER RESEARCH

Targeting the MAPK–RAS–RAF signaling pathway in cancer therapy

(2012) Libero Santarpia et al.   EXPERT OPINION ON THERAPEUTIC TARGETS

MuSiC: Identifying mutational significance in cancer genomes

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

Tumor-Associated Microglia/Macrophages Enhance the Invasion of Glioma Stem-like Cells via TGF- 1 Signaling Pathway

(2012) X.-z. Ye et al.   JOURNAL OF IMMUNOLOGY

WNT7A Regulates Tumor Growth and Progression in Ovarian Cancer through the WNT/ -Catenin Pathway

(2012) S. Yoshioka et al.   MOLECULAR CANCER RESEARCH

Sequence analysis of mutations and translocations across breast cancer subtypes

(2012) Shantanu Banerji et al.   NATURE

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

The translational landscape of mTOR signalling steers cancer initiation and metastasis

(2012) Andrew C. Hsieh et al.   NATURE

Functional impact bias reveals cancer drivers

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

Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes

(2012) Christof Winter et al.   PLoS Computational Biology

Principles and Strategies for Developing Network Models in Cancer

(2011) Dana Pe'er et al.   CELL

Targeting HIF1α Eliminates Cancer Stem Cells in Hematological Malignancies

(2011) Yin Wang et al.   Cell Stem 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

Therapeutic Potential of AZD1480 for the Treatment of Human Glioblastoma

(2011) B. C. McFarland et al.   MOLECULAR CANCER THERAPEUTICS

Charting a course for genomic medicine from base pairs to bedside

(2011) Eric D. Green et al.   NATURE

Integrated genomic analyses of ovarian carcinoma

(2011) D. Bell et al.   NATURE

Exome sequencing identifies GRIN2A as frequently mutated in melanoma

(2011) Xiaomu Wei et al.   NATURE GENETICS

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

PAK1 is a breast cancer oncogene that coordinately activates MAPK and MET signaling

(2011) Y Shrestha et al.   ONCOGENE

A refined molecular taxonomy of breast cancer

(2011) M Guedj et al.   ONCOGENE

Nuclear factor κB transcription factors are coexpressed and convey a poor outcome in ovarian cancer

(2010) Christina M. Annunziata et al.   CANCER

An Integrated Approach to Uncover Drivers of Cancer

(2010) Uri David Akavia et al.   CELL

Analysis of next-generation genomic data in cancer: accomplishments and challenges

(2010) L. Ding et al.   HUMAN MOLECULAR GENETICS

Proteoglycans in cancer biology, tumour microenvironment and angiogenesis

(2010) Renato V. Iozzo et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

Molecular Pharmacology and Antitumor Activity of PHT-427, a Novel Akt/Phosphatidylinositide-Dependent Protein Kinase 1 Pleckstrin Homology Domain Inhibitor

(2010) E. J. Meuillet et al.   MOLECULAR CANCER THERAPEUTICS

Reactome: a database of reactions, pathways and biological processes

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

Genetic inactivation of AKT1, AKT2, and PDPK1 in human colorectal cancer cells clarifies their roles in tumor growth regulation

(2010) K. Ericson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Guanming Wu et al.   GENOME BIOLOGY

Glioblastoma Proto-oncogene SEC61  Is Required for Tumor Cell Survival and Response to Endoplasmic Reticulum Stress

(2009) Z. Lu et al.   CANCER RESEARCH

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

(2009) H. Carter et al.   CANCER RESEARCH

Characterization of novel and complex genomic aberrations in glioblastoma using a 32K BAC array

(2009) Helena Nord et al.   NEURO-ONCOLOGY

A novel signaling pathway impact analysis

(2008) Adi Laurentiu Tarca et al.   BIOINFORMATICS

Lysosomotropic drugs inhibit maturation of transforming growth factor-β

(2008) Julie Basque et al.   CANADIAN JOURNAL OF PHYSIOLOGY AND PHARMACOLOGY

Centromere-Associated Protein E: A Motor That Puts the Brakes on the Mitotic Checkpoint

(2008) K. W. Wood et al.   CLINICAL CANCER RESEARCH

Basal-Like Breast Cancer Defined by Five Biomarkers Has Superior Prognostic Value than Triple-Negative Phenotype

(2008) M. C.U. Cheang et al.   CLINICAL CANCER RESEARCH

Finding common genes in multiple cancer types through meta–analysis of microarray experiments: A rank aggregation approach

(2008) V. Pihur et al.   GENOMICS

Somatic mutations affect key pathways in lung adenocarcinoma

(2008) Li Ding et al.   NATURE

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE

PID: the Pathway Interaction Database

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

Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses

(2008) S. Jones et al.   SCIENCE

JAB1 accelerates mitochondrial apoptosis by interaction with proapoptotic BclGs

(2007) Xiangjun Liu et al.   CELLULAR SIGNALLING