ArticleChaos (Woodbury, N.Y.)2013
Phenotypic deconstruction of gene circuitry.
Article in Chaos (Woodbury, N.Y.), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
11 citing papers in PubMed.
- Topological Environment in Genetic and Metabolic Networks.bioRxiv : the preprint server for biology · 2026Article
- Using Monoids for the Integration of Genomic and Metabolic Parameters in the Prediction of Phenotypes in Regulatory Cascades.bioRxiv : the preprint server for biology · 2025Article
- Phenotype Design Space Provides a Mechanistic Framework Relating Molecular Parameters to Phenotype Diversity Available for Selection.Journal of molecular evolution · 2023Article
- Predictive nonlinear modeling of malignant myelopoiesis and tyrosine kinase inhibitor therapy.eLife · 2023Article
- Cyclin/Forkhead-mediated coordination of cyclin waves: an autonomous oscillator rationalizing the quantitative model of Cdk control for budding yeast.NPJ systems biology and applications · 2021Review
- Clb3-centered regulations are recurrent across distinct parameter regions in minimal autonomous cell cycle oscillator designs.NPJ systems biology and applications · 2020Article
- 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
- Nonlinear Dynamics in Gene Regulation Promote Robustness and Evolvability of Gene Expression Levels.PloS one · 2016Article
- Strategy revealing phenotypic differences among synthetic oscillator designs.ACS synthetic biology · 2014Article
- Elucidating the genotype-phenotype map by automatic enumeration and analysis of the phenotypic repertoire.NPJ systems biology and applicationsArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
It remains a challenge to obtain a global perspective on the behavioral repertoire of complex nonlinear gene circuits. In this paper, we describe a method for deconstructing complex systems into nonlinear sub-systems, based on mathematically defined phenotypes, which are then represented within a system design space that allows the repertoire of qualitatively distinct phenotypes of the complex system to be identified, enumerated, and analyzed. This method efficiently characterizes large regions of system design space and quickly generates alternative hypotheses for experimental testing. We describe the motivation and strategy in general terms, illustrate its use with a detailed example involving a two-gene circuit with a rich repertoire of dynamic behavior, and discuss experimental means of navigating the system design space.
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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.