25 Result(s)
within
Julio R Banga
Bioinformatics
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Protocol
Synthetic Gene Circuit Analysis and Optimization
Synthetic biology aims at engineering synthetic circuits with pre-defined target functions. From a systems (model-based) perspective, the following problems are of central importance: (1) given the model of a ...
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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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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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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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Reference Work Entry In depth
Optimal Dynamic Experiments
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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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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 ...
