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Systems Biology: necessary developments and trends
At the end of this definition of Systems Biology through exampling, we discuss ambitions, goals, and challenges relating to this new discipline. We...
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From Genetic Variation to Probabilistic Modeling
Genetic algorithms ⦓GAs) [53, 83] are stochastic optimization methods inspired by natural evolution and genetics. Over the last few decades, GAs have...
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Hierarchical Bayesian Optimization Algorithm
The previous chapter has discussed how hierarchy can be used to reduce problem complexity in black-box optimization. Additionally, the chapter has...
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Scientific and technical challenges for systems biology
Systems biology is an emergent discipline, yet can be rooted back almost a century when pioneering thoughts on system-oriented views were discussed....
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From isolation to integration, a systems biology approach for building the Silicon Cell
In the last decade, the field now commonly referred to as systems biology has developed rapidly. With the sequencing of whole genomes and the...
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Systems biology of apoptosis
New approaches are required for the mathematical modelling and system identification of complex signal transduction networks, which are characterized...
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Modelling signalling pathways – a yeast approach
MAP kinase pathways are conserved signalling systems in eukaryotes that control stress responses, cell growth, and proliferation, as well as...
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Metabolic flux analysis: A key methodology for systems biology of metabolism
Genome-wide analyses of mRNA, protein, or metabolite complements of biological systems produce unprecedented data sets. In contrast to such cellular...
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Mechanistic and modular approaches to modeling and inference of cellular regulatory networks
In this chapter we wish to present a vision of systems biology as a discipline that generates new insight and knowledge with quantitative and...
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Mathematical modelling of the Wnt-pathway
A kinetic model of the Wnt-signal transduction pathway is presented which includes the main molecular components of this system. It is based on a set...
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Systems Biology: Did we know it all along?
It is often suggested that Systems Biology is nothing new, or that it is irrelevant. Its central paradigm, i.e. that much of biological function...
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Systems biology of the yeast cell cycle engine
One goal of systems biology is to obtain an integrated understanding of the physiological properties of cells from the detailed molecular machinery...
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A modular systems biology analysis of cell cycle entrance into S-phase
A modular systems biology approach to the study of the cell cycle of the budding yeast Saccharomyces cerevisiae is presented. Literature on the...
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What is systems biology? From genes to function and back
The essence of the grand contributions of physiology and molecular biology to biology is discussed in relation to what may be needed to understand...
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Modeling the E. coli cell: The need for computing, cooperation, and consortia
Escherichia coli K-12 is an ideal test bed for pushing forward the limits of our ability to understand cellular systems through computational...
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The Challenge of Hierarchical Difficulty
Thus far, we have examined the Bayesian optimization algorithm (BOA), empirical results of its application to several problems of bounded difficulty,...
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Mesoscopic kinetics and its applications in protein synthesis
Molecular biology emerged through unification of genetics and nucleic acid chemistry that took place with the discovery of the double helix (Watson...
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Kinetic modelling of the E. coli metabolism
We describe a general strategy that enables us to develop kinetic models of large-scale metabolic systems by collecting and using available metabolic...
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Metabolic networks: biology meets engineering sciences
A hallmark of systems biology is the interdisciplinary approach to the complexity of biological systems, in which mathematical modeling constitutes...
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Hierarchical BOA in the Real World
The last chapter designed hBOA, which was shown to provide scalable solution for hierarchical traps. Since hierarchical traps were designed to test...