Pathway-Based Genomics Prediction using Generalized Elastic Net

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

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

(2014) Katherine A. Hoadley et al.   CELL

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

(2013) Evan O. Paull et al.   BIOINFORMATICS

Network-based stratification of tumor mutations

(2013) Matan Hofree et al.   NATURE METHODS

Pathways-Driven Sparse Regression Identifies Pathways and Genes Associated with High-Density Lipoprotein Cholesterol in Two Asian Cohorts

(2013) Matt Silver et al.   PLoS Genetics

Network-Induced Classification Kernels for Gene Expression Profile Analysis

(2012) Ofer Lavi et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Switching addictions between HER2 and FGFR2 in HER2-positive breast tumor cells: FGFR2 as a potential target for salvage after lapatinib failure

(2011) Koichi Azuma et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Optimally discriminative subnetwork markers predict response to chemotherapy

(2011) P. Dao et al.   BIOINFORMATICS

Algorithms for Detecting Significantly Mutated Pathways in Cancer

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

Penalized classification using Fisher's linear discriminant

(2011) Daniela M. Witten et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Subtype and pathway specific responses to anticancer compounds in breast cancer

(2011) L. M. Heiser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identifying differentially expressed genes in cancer patients using a non-parameter Ising model

(2011) Xumeng Li et al.   PROTEOMICS

Most Random Gene Expression Signatures Are Significantly Associated with Breast Cancer Outcome

(2011) David Venet et al.   PLoS Computational Biology

Protein Networks as Logic Functions in Development and Cancer

(2011) Janusz Dutkowski et al.   PLoS Computational Biology

Small-sample precision of ROC-related estimates

(2010) B. Hanczar et al.   BIOINFORMATICS

Integration of pathway knowledge into a reweighted recursive feature elimination approach for risk stratification of cancer patients

(2010) Marc Johannes et al.   BIOINFORMATICS

Detecting disease associated modules and prioritizing active genes based on high throughput data

(2010) Yu-Qing Qiu et al.   BMC BIOINFORMATICS

Increased entropy of signal transduction in the cancer metastasis phenotype

(2010) Andrew E Teschendorff et al.   BMC Systems Biology

Transcription factor KLF7 regulates differentiation of neuroectodermal and mesodermal cell lineages

(2010) Massimiliano Caiazzo et al.   EXPERIMENTAL CELL RESEARCH

Pathway Commons, a web resource for biological pathway data

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

Prognostic gene signatures for non-small-cell lung cancer

(2009) Paul C. Boutros et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Network-constrained regularization and variable selection for analysis of genomic data

(2008) C. Li et al.   BIOINFORMATICS

Direct functional assessment of the composite phenotype through multivariate projection strategies

(2008) Ana Conesa et al.   GENOMICS

Inferring Pathway Activity toward Precise Disease Classification

(2008) Eunjung Lee et al.   PLoS Computational Biology