ReviewJournal of biomedicine & biotechnology2010
Mathematical modeling: bridging the gap between concept and realization in synthetic biology.
Review in Journal of biomedicine & biotechnology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Applications of synthetic biology in biomedicine.Molecular biomedicine · 2026Review
- Detecting photoinduced symmetry-breaking charge separation with near-zero driving force in a perylene diimide cage.Physical chemistry chemical physics : PCCP · 2026Article
- Kinetic modeling of multiple-strain artificial consortium to improve fengycin production of Bacillus subtilis.Biotechnology for biofuels and bioproducts · 2026Article
- Mammalian synthetic gene circuits for biopharmaceutical development & manufacture.NPJ systems biology and applications · 2025Review
- Methods in quantitative biology-from analysis of single-cell microscopy images to inference of predictive models for stochastic gene expression.Physical biology · 2025Review
- Deconstructing synthetic biology across scales: a conceptual approach for training synthetic biologists.Nature communications · 2024Review
- Biomarkers or biotargets? Using competition to lure cancer cells into evolutionary traps.Evolution, medicine, and public health · 2023Article
- Lessons Learned from Two Decades of Modeling the Heat-Shock Response.Biomolecules · 2022Review
- A Brief Journey into the History of and Future Sources and Uses of Fatty Acids.Frontiers in nutrition · 2021Review
- A mechanistic model of the BLADE platform predicts performance characteristics of 256 different synthetic DNA recombination circuits.PLoS computational biology · 2020Article
- Mechanistic modelling of tyrosine recombination reveals key parameters determining the performance of a CAR T cell switching circuit.Engineering biology · 2020Article
- Optimization of Stimulation Parameters for Targeted Activation of Multiple Neurons Using Closed-Loop Search Methods.Processes (Basel, Switzerland) · 2017Article
- Artificially constructed quorum-sensing circuits are used for subtle control of bacterial population density.PloS one · 2014Article
- Synthetic approaches to study transcriptional networks and noise in mammalian systems.IET systems biology · 2013Article
- An evolutionary firefly algorithm for the estimation of nonlinear biological model parameters.PloS one · 2013Article
- Metabolic analyses elucidate non-trivial gene targets for amplifying dihydroartemisinic acid production in yeast.Frontiers in microbiology · 2013Article
- An improved swarm optimization for parameter estimation and biological model selection.PloS one · 2013Article
- Synthetic circuit of inositol phosphorylceramide synthase in Leishmania : a chemical biology approach.Journal of chemical biology · 2013Article
- A computational pipeline for identifying kinetic motifs to aid in the design and improvement of synthetic gene circuits.BMC bioinformatics · 2013Article
Corrections and comments
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Authors and funding
2 authors.
Funding
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Abstract
Mathematical modeling plays an important and often indispensable role in synthetic biology because it serves as a crucial link between the concept and realization of a biological circuit. We review mathematical modeling concepts and methodologies as relevant to synthetic biology, including assumptions that underlie a model, types of modeling frameworks (deterministic and stochastic), and the importance of parameter estimation and optimization in modeling. Additionally we expound mathematical techniques used to analyze a model such as sensitivity analysis and bifurcation analysis, which enable the identification of the conditions that cause a synthetic circuit to behave in a desired manner. We also discuss the role of modeling in phenotype analysis such as metabolic and transcription network analysis and point out some available modeling standards and software. Following this, we present three case studies-a metabolic oscillator, a synthetic counter, and a bottom--up gene regulatory network--which have incorporated mathematical modeling as a central component of synthetic circuit design.
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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.