From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems

PathWave: discovering patterns of differentially regulated enzymes in metabolic pathways

(2010) Gunnar Schramm et al.   BIOINFORMATICS

Heading Down the Wrong Pathway: on the Influence of Correlation within Gene Sets

(2010) Daniel M Gatti et al.   BMC GENOMICS

Petri Nets with Fuzzy Logic (PNFL): Reverse Engineering and Parametrization

(2010) Robert Küffner et al.   PLoS One

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis

(2009) Andreas Keller et al.   BIOINFORMATICS

Gene-set analysis and reduction

(2008) I. Dinu et al.   BRIEFINGS IN BIOINFORMATICS