Pathway and network analysis of cancer genomes

HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery

(2014) Alvin Leung et al.   BIOINFORMATICS

Cross-Species Regulatory Network Analysis Identifies a Synergistic Interaction between FOXM1 and CENPF that Drives Prostate Cancer Malignancy

(2014) Alvaro Aytes et al.   CANCER CELL

The Transcriptional Regulatory Network of Proneural Glioma Determines the Genetic Alterations Selected during Tumor Progression

(2014) A. M. Sonabend et al.   CANCER RESEARCH

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

(2014) Katherine A. Hoadley et al.   CELL

Epigenomic alterations define lethal CIMP-positive ependymomas of infancy

(2014) S. C. Mack et al.   NATURE

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

Delivery of a Clinical Genomics Service

(2014) William Newman et al.   Genes

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

(2013) Evan O. Paull et al.   BIOINFORMATICS

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Direct Reversal of Glucocorticoid Resistance by AKT Inhibition in Acute Lymphoblastic Leukemia

(2013) Erich Piovan et al.   CANCER CELL

RHPN2 Drives Mesenchymal Transformation in Malignant Glioma by Triggering RhoA Activation

(2013) C. Danussi et al.   CANCER RESEARCH

Lessons from the Cancer Genome

(2013) Levi A. Garraway et al.   CELL

ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing

(2013) Robert C. Green et al.   GENETICS IN MEDICINE

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

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

Pan-cancer patterns of somatic copy number alteration

(2013) Travis I Zack et al.   NATURE GENETICS

Accelerated discovery via a whole-cell model

(2013) Jayodita C Sanghvi et al.   NATURE METHODS

Computational approaches to identify functional genetic variants in cancer genomes

(2013)   NATURE METHODS

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Pathway-based personalized analysis of cancer

(2013) Y. Drier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Power calculation for overall hypothesis testing with high-dimensional commensurate outcomes

(2013) Yueh-Yun Chi et al.   STATISTICS IN MEDICINE

Simultaneous Identification of Multiple Driver Pathways in Cancer

(2013) Mark D. M. Leiserson et al.   PLoS Computational Biology

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

(2012) Sam Ng et al.   BIOINFORMATICS

Bayesian Inference of Signaling Network Topology in a Cancer Cell Line

(2012) Steven M. Hill et al.   BIOINFORMATICS

EnrichNet: network-based gene set enrichment analysis

(2012) Enrico Glaab et al.   BIOINFORMATICS

Mapping the Hallmarks of Lung Adenocarcinoma with Massively Parallel Sequencing

(2012) Marcin Imielinski et al.   CELL

Sequential Application of Anticancer Drugs Enhances Cell Death by Rewiring Apoptotic Signaling Networks

(2012) Michael J. Lee et al.   CELL

Sequence analysis of mutations and translocations across breast cancer subtypes

(2012) Shantanu Banerji et al.   NATURE

Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes

(2012) Andrew V. Biankin et al.   NATURE

Leveraging models of cell regulation and GWAS data in integrative network-based association studies

(2012) Andrea Califano et al.   NATURE GENETICS

Oncogenic NRAS signaling differentially regulates survival and proliferation in melanoma

(2012) Lawrence N Kwong et al.   NATURE MEDICINE

Camera: a competitive gene set test accounting for inter-gene correlation

(2012) Di Wu 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

Sample-level enrichment analysis unravels shared stress phenotypes among multiple cancer types

(2012) Gunes Gundem et al.   Genome Medicine

A network module-based method for identifying cancer prognostic signatures

(2012) Guanming Wu et al.   GENOME BIOLOGY

The PathOlogist: an automated tool for pathway-centric analysis

(2011) Sharon I Greenblum et al.   BMC BIOINFORMATICS

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text

(2011) Martin Krallinger et al.   BMC BIOINFORMATICS

Principles and Strategies for Developing Network Models in Cancer

(2011) Dana Pe'er et al.   CELL

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

Integrated genomic analyses of ovarian carcinoma

(2011) D. Bell et al.   NATURE

ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data

(2011) A. Lan et al.   NUCLEIC ACIDS RESEARCH

The IntAct molecular interaction database in 2012

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

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

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

Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli

(2011) Melody K. Morris et al.   PLoS Computational Biology

Logic-Based Models for the Analysis of Cell Signaling Networks

(2010) Melody K. Morris et al.   BIOCHEMISTRY

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

Adaptive Clinical Trials: The Promise and the Caution

(2010) Donald A. Berry   JOURNAL OF CLINICAL ONCOLOGY

Interaction between Ras V12 and scribbled clones induces tumour growth and invasion

(2010) Ming Wu et al.   NATURE

International network of cancer genome projects

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

A human MAP kinase interactome

(2010) Sourav Bandyopadhyay et al.   NATURE METHODS

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

(2010) David Warde-Farley et al.   NUCLEIC ACIDS RESEARCH

Reactome: a database of reactions, pathways and biological processes

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

Automated Network Analysis Identifies Core Pathways in Glioblastoma

(2010) Ethan Cerami et al.   PLoS One

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

(2010) Daniele Merico et al.   PLoS One

The transcriptional network for mesenchymal transformation of brain tumours

(2009) Maria Stella Carro et al.   NATURE

The Gene Ontology in 2010: extensions and refinements

(2009)   NUCLEIC ACIDS RESEARCH

Identifying functional modules in protein-protein interaction networks: an integrated exact approach

(2008) M. T. Dittrich et al.   BIOINFORMATICS

Flexible informatics for linking experimental data to mathematical models via DataRail

(2008) Julio Saez-Rodriguez et al.   BIOINFORMATICS

A novel signaling pathway impact analysis

(2008) Adi Laurentiu Tarca et al.   BIOINFORMATICS

iRefIndex: A consolidated protein interaction database with provenance

(2008) Sabry Razick et al.   BMC BIOINFORMATICS

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE