title: Design specifications for cellular regulation.
abstract: A critical feature of all cellular processes is the ability to control the rate of gene or protein expression and metabolic flux in changing environments through regulatory feedback. We review the many ways that regulation is represented through causal, logical, and dynamical components. Formalizing the nature of these components promotes effective comparison among distinct regulatory networks and provides a common framework for the potential design and control of regulatory systems in synthetic biology.
authors.affiliation: Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM, 87501, USA.
authors.forename: David C
authors.initials: DC
authors.lastname: Krakauer
authors.affiliation: Natural Language Processing Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University Leipzig, Härtelstrasse 16-18, 04107, Leipzig, Germany.
authors.forename: Lydia
authors.initials: L
authors.lastname: Müller
authors.affiliation: Computational EvoDevo Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University Leipzig, Härtelstrasse 16-18, 04107, Leipzig, Germany.
authors.forename: Sonja J
authors.initials: SJ
authors.lastname: Prohaska
authors.affiliation: Bioinformatics Group at the Department of Computer Science, Interdisciplinary Center for Bioinformatics, ScaDS, Competence Center for Scalable Data services and Solutions, and German Center for Integrative Biodiversity Research, University Leipzig, Härtelstrasse 16-18, 04107, Leipzig, Germany. studla@bioinf.uni-leipzig.de.|Max-Planck Institute for Mathematics in the Sciences, Inselstraße 22, 04103, Leipzig, Germany. studla@bioinf.uni-leipzig.de.|Fraunhofer Institut für Zelltherapie und Immunologie-IZI, Perlickstraße 1, 04103, Leipzig, Germany. studla@bioinf.uni-leipzig.de.|Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090, Wien, Austria. studla@bioinf.uni-leipzig.de.|Center for Non-Coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870, Frederiksberg C, Denmark. studla@bioinf.uni-leipzig.de.
authors.forename: Peter F
authors.identifier: http://orcid.org/0000-0002-5016-5191
authors.initials: PF
authors.lastname: Stadler
mesh_terms: D002453:Cell Cycle; D003198:Computer Simulation; D004926:Escherichia coli / Q000235:genetics; D005246:Feedback; D053263:Gene Regulatory Networks; D007763:Lac Operon / Q000235:genetics; D008957:Models, Genetic; D058615:Synthetic Biology / Q000379:methods*; D049490:Systems Biology / Q000379:methods*
keywords: Codes; Feedback; Memory; Typed I/O maps