14 Result(s)
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Article
Open AccessUsing optimal control to understand complex metabolic pathways
Optimality principles have been used to explain the structure and behavior of living matter at different levels of organization, from basic phenomena at the molecular level, up to complex dynamics in whole pop...
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Article
Open AccessParameter estimation in models of biological oscillators: an automated regularised estimation approach
Dynamic modelling is a core element in the systems biology approach to understanding complex biosystems. Here, we consider the problem of parameter estimation in models of biological oscillators described by d...
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Article
Open AccessParameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy
The development of large-scale kinetic models is one of the current key issues in computational systems biology and bioinformatics. Here we consider the problem of parameter estimation in nonlinear dynamic mod...
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Chapter and Conference Paper
PREMER: Parallel Reverse Engineering of Biological Networks with Information Theory
A common approach for reverse engineering biological networks from data is to deduce the existence of interactions among nodes from information theoretic measures. Estimating these quantities in a multidimensi...
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Article
Open AccessEnabling network inference methods to handle missing data and outliers
The inference of complex networks from data is a challenging problem in biological sciences, as well as in a wide range of disciplines such as chemistry, technology, economics, or sociology. The quantity and q...
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Article
Open AccessOptimal programs of pathway control: dissecting the influence of pathway topology and feedback inhibition on pathway regulation
Adjusting the capacity of metabolic pathways in response to rapidly changing environmental conditions is an important component of microbial adaptation strategies to stochastic environments. In this work, we u...
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Article
Open AccessMEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics
Optimization is the key to solving many problems in computational biology. Global optimization methods, which provide a robust methodology, and metaheuristics in particular have proven to be the most efficient...
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Chapter and Conference Paper
Optimization Based Design of Synthetic Oscillators from Standard Biological Parts
We consider the problem of optimal design of synthetic biological oscillators. Our aim is, given a set of standard biological parts and some pre-specified performance requirements, to automatically find the ci...
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Chapter and Conference Paper
Improved Parameter Estimation in Kinetic Models: Selection and Tuning of Regularization Methods
Kinetic models are being increasingly used as a systematic framework to understand function in biological systems. Calibration of these nonlinear dynamic models remains challenging due to the nonconvexity and ...
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Reference Work Entry In depth
Optimal Dynamic Experiments
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Chapter and Conference Paper
On the Verification and Correction of Large-Scale Kinetic Models in Systems Biology
In this paper we consider the problem of verification of large dynamic models of biological systems. We present syntactical criteria based on biochemical kinetics to ensure the plausibility of a model and the ...
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Chapter
Computational Procedures for Model Identification
Mathematical models provide abstract representations of the information gained from experimental observations on the structure and function of a particular biological system. Conferring a predictive character ...
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Article
Open AccessDOTcvpSB, a software toolbox for dynamic optimization in systems biology
Mathematical optimization aims to make a system or design as effective or functional as possible, computing the quality of the different alternatives using a mathematical model. Most models in systems biology ...
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Article
Open AccessNovel metaheuristic for parameter estimation in nonlinear dynamic biological systems
We consider the problem of parameter estimation (model calibration) in nonlinear dynamic models of biological systems. Due to the frequent ill-conditioning and multi-modality of many of these problems, traditi...
