This article is addressing a recurrent problem in biology: mining newly built large scale networks. Our approach consists in comparing these new networks to well known ones. The v...
Phylogenetic trees are built by examining differences in the biological traits of a set of species. An example of such a trait is a biological network such as a metabolic pathway,...
Background: This paper considers the problem of identifying pathways through metabolic networks that relate to a specific biological response. Our proposed model, HME3M, first ide...
PathwayTools is a production-quality software environment for creating a type of model-organism database called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc integrates ...
Peter D. Karp, Suzanne M. Paley, Markus Krummenack...
Systemic pathways-oriented approaches to analysis of metabolic networks are effective for small networks but are computationally infeasible for genome scale networks. Current comp...
Nagiza F. Samatova, Al Geist, George Ostrouchov, A...