Learning subgroup-specific regulatory interactions and regulator independence with PARADIGM

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

Regularization Paths for Cox's Proportional Hazards Model via Coordinate Descent

(2015) Noah Simon et al.   Journal of Statistical Software

Platinum compounds sensitize ovarian carcinoma cells to ABT-737 by modulation of the Mcl-1/Noxa axis

(2013) Karin Simonin et al.   APOPTOSIS

Causal reasoning on biological networks: interpreting transcriptional changes

(2012) Leonid Chindelevitch et al.   BIOINFORMATICS

Gene interaction enrichment and network analysis to identify dysregulated pathways and their interactions in complex diseases

(2012) Yu Liu et al.   BMC Systems Biology

Kidney Tumor Biomarkers Revealed by Simultaneous Multiple Matrix Metabolomics Analysis

(2012) S. Ganti et al.   CANCER RESEARCH

Fenofibrate triggers apoptosis of glioblastoma cells in vitro

(2012) Antonio Giordano et al.   CELL CYCLE

Proteomic Analyses Reveal High Expression of Decorin and Endoplasmin (HSP90B1) Are Associated with Breast Cancer Metastasis and Decreased Survival

(2012) Thomas R. Cawthorn et al.   PLoS One

Mutual exclusivity analysis identifies oncogenic network modules

(2011) G. Ciriello et al.   GENOME RESEARCH

The Integration of Biological Pathway Knowledge in Cancer Genomics: A review of existing computational approaches

(2011) Vinay Varadan et al.   IEEE SIGNAL PROCESSING MAGAZINE

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

(2010) Charles J. Vaske et al.   BIOINFORMATICS

Hypoxia inducible factor 1α gene (HIF-1α) splice variants: potential prognostic biomarkers in breast cancer

(2010) Jean-Philippe Dales et al.   BMC Medicine

An Integrated Approach to Uncover Drivers of Cancer

(2010) Uri David Akavia et al.   CELL

Automated Network Analysis Identifies Core Pathways in Glioblastoma

(2010) Ethan Cerami et al.   PLoS One

Analyses of Resected Human Brain Metastases of Breast Cancer Reveal the Association between Up-Regulation of Hexokinase 2 and Poor Prognosis

(2009) D. Palmieri et al.   MOLECULAR CANCER RESEARCH

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

A novel signaling pathway impact analysis

(2008) Adi Laurentiu Tarca et al.   BIOINFORMATICS

Unraveling the Biologic and Clinical Complexities of HER2

(2008) John W. Park et al.   Clinical Breast Cancer

Phase III Comparison of Vitespen, an Autologous Tumor-Derived Heat Shock Protein gp96 Peptide Complex Vaccine, With Physician's Choice of Treatment for Stage IV Melanoma: The C-100-21 Study Group

(2008) Alessandro Testori et al.   JOURNAL OF CLINICAL ONCOLOGY

K-rasMutations and Benefit from Cetuximab in Advanced Colorectal Cancer

(2008) Christos S. Karapetis et al.   NEW ENGLAND JOURNAL OF MEDICINE

PID: the Pathway Interaction Database

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

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Reactome knowledgebase of human biological pathways and processes

(2008) L. Matthews et al.   NUCLEIC ACIDS RESEARCH