Use of prior knowledge for the analysis of high-throughput transcriptomics and metabolomics data

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

(2012) Christine Staiger et al.   PLoS One

Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development

(2011) Philip J. Stephens et al.   CELL

Graph Constrained Discriminant Analysis: A New Method for the Integration of a Graph into a Classification Process

(2011) Vincent Guillemot et al.   PLoS One

Protein Networks as Logic Functions in Development and Cancer

(2011) Janusz Dutkowski et al.   PLoS Computational Biology

Over-optimism in bioinformatics: an illustration

(2010) M. Jelizarow et al.   BIOINFORMATICS

Trimming of mammalian transcriptional networks using network component analysis

(2010) Linh M Tran et al.   BMC BIOINFORMATICS

MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data

(2010) J. Xia et al.   NUCLEIC ACIDS RESEARCH

Metabolomics data exploration guided by prior knowledge

(2009) Robert A. van den Berg et al.   ANALYTICA CHIMICA ACTA

A general modular framework for gene set enrichment analysis

(2009) Marit Ackermann et al.   BMC BIOINFORMATICS

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

(2008) C. Li et al.   BIOINFORMATICS

The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation

(2008) E. Wingender   BRIEFINGS IN BIOINFORMATICS