title: Modular analysis of biological networks.
abstract: The analysis of complex biological networks has traditionally relied on decomposition into smaller, semi-autonomous units such as individual signaling pathways. With the increased scope of systems biology (models), rational approaches to modularization have become an important topic. With increasing acceptance of de facto modularity in biology, widely different definitions of what constitutes a module have sparked controversies. Here, we therefore review prominent classes of modular approaches based on formal network representations. Despite some promising research directions, several important theoretical challenges remain open on the way to formal, function-centered modular decompositions for dynamic biological networks.
authors.affiliation: Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland. hans-michael.kaltenbach
authors.forename: Hans-Michael
authors.initials: HM
authors.lastname: Kaltenbach
authors.forename: Jörg
authors.initials: J
authors.lastname: Stelling
mesh_terms: D000465:Algorithms; D000818:Animals; D053263:Gene Regulatory Networks; D006801:Humans; D053858:Metabolic Networks and Pathways / Q000235:genetics / Q000502:physiology*; D008954:Models, Biological; D011485:Protein Binding; D011506:Proteins / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction / Q000235:genetics / Q000502:physiology*; D049490:Systems Biology / Q000379:methods*
chemical_list: D011506:Proteins