ArticleBioinformatics (Oxford, England)2010
Automated construction and analysis of the design space for biochemical systems.
Article in Bioinformatics (Oxford, England), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Predictive nonlinear modeling of malignant myelopoiesis and tyrosine kinase inhibitor therapy.eLife · 2023Article
- Mechanistic Modeling of Biochemical Systems without A Priori Parameter Values Using the Design Space Toolbox v.3.0.iScience · 2020Article
- Clb3-centered regulations are recurrent across distinct parameter regions in minimal autonomous cell cycle oscillator designs.NPJ systems biology and applications · 2020Article
- The best models of metabolism.Wiley interdisciplinary reviews. Systems biology and medicine · 2017Review
- Rapid Discrimination Among Putative Mechanistic Models of Biochemical Systems.Scientific reports · 2016Article
- Design Space Toolbox V2: Automated Software Enabling a Novel Phenotype-Centric Modeling Strategy for Natural and Synthetic Biological Systems.Frontiers in genetics · 2016Article
- Unrelated toxin-antitoxin systems cooperate to induce persistence.Journal of the Royal Society, Interface · 2015Article
- Strategy revealing phenotypic differences among synthetic oscillator designs.ACS synthetic biology · 2014Article
- Molecular mechanisms of multiple toxin-antitoxin systems are coordinated to govern the persister phenotype.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- A bistable hysteretic switch in an activator-repressor regulated restriction-modification system.Nucleic acids research · 2013Article
- Phenotypic deconstruction of gene circuitry.Chaos (Woodbury, N.Y.) · 2013Article
- Article
- Design of the lac gene circuit revisited.Mathematical biosciences · 2011Review
- Biomedical engineering strategies in system design space.Annals of biomedical engineering · 2011Review
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Authors and funding
2 authors.
Funding
Abstract
motivationOur recent work introduced a generic method to construct the design space of biochemical systems: a representation of the relationships between system parameters, environmental variables and phenotypic behavior. In design space, the qualitatively distinct phenotypes of a biochemical system can be identified, counted, analyzed and compared. Boundaries in design space indicate a transition between phenotypic behaviors and can be used to measure a system's tolerance to large changes in parameters. Moreover, the relative size and arrangement of such phenotypic regions can suggest or confirm global properties of the system.
resultsOur work here demonstrates that the construction and analysis of design space can be automated. We present a formal description of design space and a detailed explanation of its construction. We also extend the notion to include variable kinetic orders. We describe algorithms that automate common steps of design space construction and analysis, introduce new analyses that are made possible by such automation and discuss challenges of implementation and scaling. In the end, we demonstrate the techniques using software we have created. AVAILABILITY: The Design Space Toolbox for MATLAB is freely available at http://www.bme.ucdavis.edu/savageaulab/ CONTACT: masavageau@ucdavis.edu
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.