ArticlePloS one2016
Design Principles of Biological Oscillators through Optimization: Forward and Reverse Analysis.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- A model-based design strategy to engineer miRNA-regulated detection systems.Frontiers in systems biology · 2025Article
- Automated Design of Synthetic Gene Circuits in the Presence of Molecular Noise.ACS synthetic biology · 2023Article
- Robotic automation and unsupervised cluster assisted modeling for solving the forward and reverse design problem of paper airplanes.Scientific reports · 2023Article
- A microfluidic optimal experimental design platform for forward design of cell-free genetic networks.Nature communications · 2022Article
- Discovering design principles for biological functionalities:Perspectives from systems biology.Journal of biosciences · 2022Review
- Discovering adaptation-capable biological network structures using control-theoretic approaches.PLoS computational biology · 2022Article
- Basal leakage in oscillation: Coupled transcriptional and translational control using feed-forward loops.PLoS computational biology · 2020Article
- Asymmetry between Activators and Deactivators in Functional Protein Networks.Scientific reports · 2020Article
- Parameter estimation in models of biological oscillators: an automated regularised estimation approach.BMC bioinformatics · 2019Article
- Combining a Toggle Switch and a Repressilator within the AC-DC Circuit Generates Distinct Dynamical Behaviors.Cell systems · 2018Article
- Computing with biological switches and clocks.Natural computing · 2018Article
- A novel interaction perturbation analysis reveals a comprehensive regulatory principle underlying various biochemical oscillators.BMC systems biology · 2017Article
- A parallel metaheuristic for large mixed-integer dynamic optimization problems, with applications in computational biology.PloS one · 2017Article
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2 authors.
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Abstract
From cyanobacteria to human, sustained oscillations coordinate important biological functions. Although much has been learned concerning the sophisticated molecular mechanisms underlying biological oscillators, design principles linking structure and functional behavior are not yet fully understood. Here we explore design principles of biological oscillators from a multiobjective optimization perspective, taking into account the trade-offs between conflicting performance goals or demands. We develop a comprehensive tool for automated design of oscillators, based on multicriteria global optimization that allows two modes: (i) the automatic design (forward problem) and (ii) the inference of design principles (reverse analysis problem). From the perspective of synthetic biology, the forward mode allows the solution of design problems that mimic some of the desirable properties appearing in natural oscillators. The reverse analysis mode facilitates a systematic exploration of the design space based on Pareto optimality concepts. The method is illustrated with two case studies: the automatic design of synthetic oscillators from a library of biological parts, and the exploration of design principles in 3-gene oscillatory systems.
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