title: Computational approaches for analyzing information flow in biological          networks.
abstract: The advancements in "omics" (proteomics, genomics, lipidomics, and                    metabolomics) technologies have yielded large inventories of genes, transcripts,                    proteins, and metabolites. The challenge is to find out how these entities work                    together to regulate the processes by which cells respond to external and                    internal signals. Mathematical and computational modeling of signaling networks                    has a key role in this task, and network analysis provides insights into                    biological systems and has applications for medicine. Here, we review                    experimental and theoretical progress and future challenges toward this goal. We                    focus on how networks are reconstructed from data, how these networks are                    structured to control the flow of biological information, and how the design                    features of the networks specify biological decisions.
authors.affiliation: Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland.
authors.forename: Boris
authors.initials: B
authors.lastname: Kholodenko
authors.forename: Michael B
authors.initials: MB
authors.lastname: Yaffe
authors.forename: Walter
authors.initials: W
authors.lastname: Kolch
mesh_terms: D019295:Computational Biology; D003198:Computer Simulation; D040901:Proteomics / Q000379:methods; D015398:Signal Transduction; D049490:Systems Biology / Q000379:methods*