28 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 identifiability analysis and visualization in large-scale kinetic models of biosystems
Kinetic models of biochemical systems usually consist of ordinary differential equations that have many unknown parameters. Some of these parameters are often practically unidentifiable, that is, their values ...
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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 AccessRobust and efficient parameter estimation in dynamic models of biological systems
Dynamic modelling provides a systematic framework to understand function in biological systems. Parameter estimation in nonlinear dynamic models remains a very challenging inverse problem due to its nonconvexi...
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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 AccessBioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology
Dynamic modelling is one of the cornerstones of systems biology. Many research efforts are currently being invested in the development and exploitation of large-scale kinetic models. The associated problems of...
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Article
Open AccessMulticriteria global optimization for biocircuit design
One 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...
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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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Article
Open AccessGlobal dynamic optimization approach to predict activation in metabolic pathways
During the last decade, a number of authors have shown that the genetic regulation of metabolic networks may follow optimality principles. Optimal control theory has been succesfully used to compute optimal en...
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Chapter and Conference Paper
A Parallel Differential Evolution Algorithm for Parameter Estimation in Dynamic Models of Biological Systems
Metaheuristics are gaining increased attention as efficient solvers for hard global optimization problems arising in bioinformatics and computational systems biology. Differential Evolution (DE) is one of the ...
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Chapter and Conference Paper
High-Confidence Predictions in Systems Biology Dynamic Models
Obtaining reliable predictions from large-scale dynamic models is a challenging task due to frequent lack of identifiability. This work presents a methodology for obtaining high confidence predictions in biote...
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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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Article
Open AccessSimultaneous model discrimination and parameter estimation in dynamic models of cellular systems
Model development is a key task in systems biology, which typically starts from an initial model candidate and, involving an iterative cycle of hypotheses-driven model modifications, leads to new experimentati...
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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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Article
Open AccessDynamic optimization of distributed biological systems using robust and efficient numerical techniques
Systems biology allows the analysis of biological systems behavior under different conditions through in silico experimentation. The possibility of perturbing biological systems in different manners calls for the...
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Article
Open AccessA cooperative strategy for parameter estimation in large scale systems biology models
Mathematical models play a key role in systems biology: they summarize the currently available knowledge in a way that allows to make experimentally verifiable predictions. Model calibration consists of findin...
