ArticleBMC systems biology2014
Multicriteria global optimization for biocircuit design.
Article in BMC systems biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Optimal performance objectives in the highly conserved bone morphogenetic protein signaling pathway.NPJ systems biology and applications · 2024Article
- Automatic design of gene regulatory mechanisms for spatial pattern formation.NPJ systems biology and applications · 2024Article
- Topological descriptors of the parameter region of multistationarity: Deciding upon connectivity.PLoS computational biology · 2023Article
- Using optimal control to understand complex metabolic pathways.BMC bioinformatics · 2020Article
- Designing synthetic networks in silico: a generalised evolutionary algorithm approach.BMC systems biology · 2017Article
- Optimisation of an exemplar oculomotor model using multi-objective genetic algorithms executed on a GPU-CPU combination.BMC systems biology · 2017Article
- JuPOETs: a constrained multiobjective optimization approach to estimate biochemical model ensembles in the Julia programming language.BMC systems biology · 2017Article
- A parallel metaheuristic for large mixed-integer dynamic optimization problems, with applications in computational biology.PloS one · 2017Article
- A computational method for the investigation of multistable systems and its application to genetic switches.BMC systems biology · 2016Article
- Process-based design of dynamical biological systems.Scientific reports · 2016Article
- Multi-objective optimization framework to obtain model-based guidelines for tuning biological synthetic devices: an adaptive network case.BMC systems biology · 2016Article
- Design Principles of Biological Oscillators through Optimization: Forward and Reverse Analysis.PloS one · 2016Article
Corrections and comments
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Authors and funding
2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundOne of the challenges in Synthetic Biology is to design circuits with increasing levels of complexity. While circuits in Biology are complex and subject to natural tradeoffs, most synthetic circuits are simple in terms of the number of regulatory regions, and have been designed to meet a single design criterion.
resultsIn this contribution we introduce a multiobjective formulation for the design of biocircuits. We set up the basis for an advanced optimization tool for the modular and systematic design of biocircuits capable of handling high levels of complexity and multiple design criteria. Our methodology combines the efficiency of global Mixed Integer Nonlinear Programming solvers with multiobjective optimization techniques. Through a number of examples we show the capability of the method to generate non intuitive designs with a desired functionality setting up a priori the desired level of complexity.
conclusionsThe methodology presented here can be used for biocircuit design and also to explore and identify different design principles for synthetic gene circuits. The presence of more than one competing objective provides a realistic design setting where every solution represents an optimal trade-off between different criteria.
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