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Design Specifications for Cellular Regulation

David C. Krakauer, Lydia Müller, Sonja J. Prohaska, Peter F. Stadler
doi: https://doi.org/10.1101/081729
David C. Krakauer
1Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA; E-mail: .
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  • For correspondence: krakauer@santafe.edu
Lydia Müller
2Natural Language Processing Group, Department of Computer Science,and Interdisciplinary Center for Bioinformatics, University Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany; E-mail: .
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  • For correspondence: lydia@bioinf.uni-leipzig.de
Sonja J. Prohaska
3Computational EvoDevo Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany; E-mail:
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  • For correspondence: sonja@bioinf.uni-leipzig.de
Peter F. Stadler
4Bioinformatics Group at the Department of Computer Science, Inter-disciplinary Center for Bioinformatics, ScaDS – Competence Center for Scalable Data services and Solutions, and German Center for Integrative Biodiversity Research, University Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany; Max-Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany; Fraunhofer Institut für Zelltherapie und Immunologie – IZI, Perlickstraße 1, D-04103 Leipzig, Germany; Department of Theoretical Chemistry University of Vienna, Währingerstraße 17, A-1090 Wien, Austria; Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark; Email:.
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  • For correspondence: studla@bioinf.uni-leipzig.de
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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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted October 18, 2016.
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Design Specifications for Cellular Regulation
David C. Krakauer, Lydia Müller, Sonja J. Prohaska, Peter F. Stadler
bioRxiv 081729; doi: https://doi.org/10.1101/081729
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Design Specifications for Cellular Regulation
David C. Krakauer, Lydia Müller, Sonja J. Prohaska, Peter F. Stadler
bioRxiv 081729; doi: https://doi.org/10.1101/081729

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