Topologically inferring pathway activity for precise survival outcome prediction: breast cancer as a case

Personalized characterization of diseases using sample-specific networks

(2016) Xiaoping Liu et al.   NUCLEIC ACIDS RESEARCH

Investigating the utility of clinical outcome-guided mutual information network in network-based Cox regression

(2015) Hyun-hwan Jeong et al.   BMC Systems Biology

Integration of pathway structure information into a reweighted partial Cox regression approach for survival analysis on high-dimensional gene expression data

(2015) Wei Liu et al.   Molecular BioSystems

Topologically inferring pathway activity toward precise cancer classification via integrating genomic and metabolomic data: prostate cancer as a case

(2015) Wei Liu et al.   Scientific Reports

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

Systematic Pathway Enrichment Analysis of a Genome-Wide Association Study on Breast Cancer Survival Reveals an Influence of Genes Involved in Cell Adhesion and Calcium Signaling on the Patients’ Clinical Outcome

(2014) Andrea Woltmann et al.   PLoS One

A Novel Model to Combine Clinical and Pathway-Based Transcriptomic Information for the Prognosis Prediction of Breast Cancer

(2014) Sijia Huang et al.   PLoS Computational Biology

Design, Synthesis, and Mechanistic Investigations of Bile Acid–Tamoxifen Conjugates for Breast Cancer Therapy

(2013) Vedagopuram Sreekanth et al.   BIOCONJUGATE CHEMISTRY

Topologically inferring risk-active pathways toward precise cancer classification by directed random walk

(2013) Wei Liu et al.   BIOINFORMATICS

Calcium influx pathways in breast cancer: opportunities for pharmacological intervention

(2013) I Azimi et al.   BRITISH JOURNAL OF PHARMACOLOGY

Network and Data Integration for Biomarker Signature Discovery via Network Smoothed T-Statistics

(2013) Yupeng Cun et al.   PLoS One

APG: an Active Protein-Gene Network Model to Quantify Regulatory Signals in Complex Biological Systems

(2013) Jiguang Wang et al.   Scientific Reports

Network-based Survival Analysis Reveals Subnetwork Signatures for Predicting Outcomes of Ovarian Cancer Treatment

(2013) Wei Zhang et al.   PLoS Computational Biology

Interactions between immunity, proliferation and molecular subtype in breast cancer prognosis

(2013) Srikanth Nagalla et al.   GENOME BIOLOGY

The Gut-To-Breast Connection - Interdependence of Sterols and Sphingolipids in Multidrug Resistance and Breast Cancer Therapy

(2012) Stefka Spassieva et al.   Anti-Cancer Agents in Medicinal Chemistry

SurvNet: a web server for identifying network-based biomarkers that most correlate with patient survival data

(2012) J. Li et al.   NUCLEIC ACIDS RESEARCH

Detecting early-warning signals for sudden deterioration of complex diseases by dynamical network biomarkers

(2012) Luonan Chen et al.   Scientific Reports

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

(2012) Christof Winter et al.   PLoS Computational Biology

pathClass: an R-package for integration of pathway knowledge into support vector machines for biomarker discovery

(2011) M. Johannes 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

Pathway-based analysis for genome-wide association studies using supervised principal components

(2010) Xi Chen et al.   GENETIC EPIDEMIOLOGY

An integrative pathway-based clinical–genomic model for cancer survival prediction

(2010) Xi Chen et al.   STATISTICS & PROBABILITY LETTERS

Incorporating pathway information into boosting estimation of high-dimensional risk prediction models

(2009) Harald Binder et al.   BMC BIOINFORMATICS

Integrating Biological Knowledge with Gene Expression Profiles for Survival Prediction of Cancer

(2009) Xi Chen et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

SubpathwayMiner: a software package for flexible identification of pathways

(2009) C. Li et al.   NUCLEIC ACIDS RESEARCH

Accurate and Reliable Cancer Classification Based on Probabilistic Inference of Pathway Activity

(2009) Junjie Su et al.   PLoS One

Random survival forests

(2008) Hemant Ishwaran et al.   Annals of Applied Statistics

Sparse kernel methods for high-dimensional survival data

(2008) L. Evers et al.   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH

Inferring Pathway Activity toward Precise Disease Classification

(2008) Eunjung Lee et al.   PLoS Computational Biology