16 Result(s)
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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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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 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 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
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...
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Article
Open AccessInference of complex biological networks: distinguishability issues and optimization-based solutions
The inference of biological networks from high-throughput data has received huge attention during the last decade and can be considered an important problem class in systems biology. However, it has been recog...
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Article
Open AccessAn iterative identification procedure for dynamic modeling of biochemical networks
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 AccessOptimization in computational systems biology
Optimization aims to make a system or design as effective or functional as possible. Mathematical optimization methods are widely used in engineering, economics and science. This commentary is focused on appli...
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Article
Open AccessHybrid optimization method with general switching strategy for parameter estimation
Modeling and simulation of cellular signaling and metabolic pathways as networks of biochemical reactions yields sets of non-linear ordinary differential equations. These models usually depend on several param...
