COMPADRE: an R and web resource for pathway activity analysis by component decompositions

Pathway Analysis of Expression Data: Deciphering Functional Building Blocks of Complex Diseases

(2011) Frank Emmert-Streib et al.   PLoS Computational Biology

Circadian signatures in rat liver: from gene expression to pathways

(2010) Meric A Ovacik et al.   BMC BIOINFORMATICS

Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling

(2010) Ignacio Medina et al.   NUCLEIC ACIDS RESEARCH

Mapping Drug Physico-Chemical Features to Pathway Activity Reveals Molecular Networks Linked to Toxicity Outcome

(2010) Philipp Antczak et al.   PLoS One

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

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

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

(2009) Junjie Su et al.   PLoS One

Knowledge-based gene expression classification via matrix factorization

(2008) R. Schachtner et al.   BIOINFORMATICS