De novo pathway-based biomarker identification

FERAL: network-based classifier with application to breast cancer outcome prediction

(2015) Amin Allahyar et al.   BIOINFORMATICS

Comparing the performance of biomedical clustering methods

(2015) Christian Wiwie et al.   NATURE METHODS

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Reactome pathway Knowledgebase

(2015) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

Oncotype DX® colon cancer assay for prediction of recurrence risk in patients with stage II and III colon cancer: A review of the evidence

(2015) Y. Nancy You et al.   SURGICAL ONCOLOGY-OXFORD

Robustness of Random Forest-based gene selection methods

(2014) Miron Bartosz Kursa   BMC BIOINFORMATICS

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

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Analytical validation of the Oncotype DX prostate cancer assay – a clinical RT-PCR assay optimized for prostate needle biopsies

(2013) Dejan Knezevic et al.   BMC GENOMICS

A T cell gene expression panel for the diagnosis and monitoring of disease activity in patients with systemic lupus erythematosus

(2013) Alexandros P. Grammatikos et al.   CLINICAL IMMUNOLOGY

Validation of a Genomic Classifier that Predicts Metastasis Following Radical Prostatectomy in an At Risk Patient Population

(2013) R. Jeffrey Karnes et al.   JOURNAL OF UROLOGY

Characterizing Genes with Distinct Methylation Patterns in the Context of Protein-Protein Interaction Network: Application to Human Brain Tissues

(2013) Yongsheng Li et al.   PLoS One

Robustness and accuracy of functional modules in integrated network analysis

(2012) Daniela Beisser et al.   BIOINFORMATICS

Pathway-based classification of cancer subtypes

(2012) Shinuk Kim et al.   Biology Direct

Prognostic gene signatures for patient stratification in breast cancer - accuracy, stability and interpretability of gene selection approaches using prior knowledge on protein-protein interactions

(2012) Yupeng Cun et al.   BMC BIOINFORMATICS

HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions

(2012) Luiz A Bovolenta et al.   BMC GENOMICS

PAM50 assay and the three-gene model for identifying the major and clinically relevant molecular subtypes of breast cancer

(2012) A. Prat et al.   BREAST CANCER RESEARCH AND TREATMENT

Efficient key pathway mining: combining networks and OMICS data

(2012) Nicolas Alcaraz et al.   Integrative Biology

A molecular signature in blood identifies early Parkinson’s disease

(2012) Leonid Molochnikov et al.   Molecular Neurodegeneration

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

The ConsensusPathDB interaction database: 2013 update

(2012) Atanas Kamburov et al.   NUCLEIC ACIDS RESEARCH

A Critical Evaluation of Network and Pathway-Based Classifiers for Outcome Prediction in Breast Cancer

(2012) Christine Staiger et al.   PLoS One

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

Classification with correlated features: unreliability of feature ranking and solutions

(2011) Laura Toloşi et al.   BIOINFORMATICS

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Prioritizing candidate disease genes by network-based boosting of genome-wide association data

(2011) I. Lee et al.   GENOME RESEARCH

BioNet: an R-Package for the functional analysis of biological networks

(2010) D. Beisser et al.   BIOINFORMATICS

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

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

Predictive value of epithelial gene expression profiles for response to infliximab in Crohnʼs disease‡

(2010) Ingrid Arijs et al.   INFLAMMATORY BOWEL DISEASES

Partitioning biological data with transitivity clustering

(2010) Tobias Wittkop et al.   NATURE METHODS

Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes

(2009) Joel S. Parker et al.   JOURNAL OF CLINICAL ONCOLOGY

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

(2009) David A. Barbie et al.   NATURE

Dynamic modularity in protein interaction networks predicts breast cancer outcome

(2009) Ian W Taylor et al.   NATURE BIOTECHNOLOGY

A comprehensive comparison of random forests and support vector machines for microarray-based cancer classification

(2008) Alexander Statnikov et al.   BMC BIOINFORMATICS

Pooling breast cancer datasets has a synergetic effect on classification performance and improves signature stability

(2008) Martin H van Vliet et al.   BMC GENOMICS

Human Protein Reference Database--2009 update

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

A general framework for multiple testing dependence

(2008) J. T. Leek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inferring Pathway Activity toward Precise Disease Classification

(2008) Eunjung Lee et al.   PLoS Computational Biology