Computer model for glucose‐limited growth of a single cell of <i>Escherichia coli</i> B/r‐A

Domach, Michael M.; Leung, S. K.; Cahn, R. E.; Cocks, George G.; Shuler, Michael L.

doi:10.1002/bit.260260925

Cited by 52 publications

(21 citation statements)

References 36 publications

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“…An event is a discrete change in cell state. The initial model formulation 6,16 was expanded to include a much larger array of components including plasmids encoding synthesis of recombinant proteins 1,10 and interaction of plasmid encoded functions and cellular metabolism. 11 The E. coli model has always had the capability of linking genomic structure with cellular response.…”

Section: Model Of a Minimal Bacterial Cellmentioning

confidence: 99%

Modeling Life

Shuler

2012

Ann Biomed Eng

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Abstract-We seek to construct physical and mathematical models of life. Such models allow us to test our understanding of how living systems function and how they respond to human imposed stimuli. One system is a genomically and chemically complete model of a minimal cell. This cell is a hypothetical bacterium with the fewest number of genes possible. Such a minimal cell provides a platform to ask about the essential features of a living cell and forms a platform to investigate ''synthetic biology.'' A second system is ''Body-on-a-Chip'' which is a microfabricated microfluidic system with cells or tissue constructs representing various organs in the body. It can be constructed from human or animal cells and used in drug discovery development. That model is a physical representation of a physiologically based pharmacokinetic model. Both the computer and the physical models provide insight into the underlying biology and provide new tools to make use of that understanding to provide benefits to society.

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Section: Model Of a Minimal Bacterial Cellmentioning

confidence: 99%

Modeling Life

Shuler

2012

Ann Biomed Eng

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“…In the absence of experimental data, the motivation to write very detailed models is indeed limited. The model of Domach and Shuler (Domach et al, 1984) is a rare example of a model with a large amount of detail long before the omic measurement revolution. However, recent advances in analytical technologies has enabled genome wide measurements of gene, protein expression as well as metabolite profiling (Ferea and Brown, 1999;Fiehn et al, 2000;Pandey and Mann, 2000), which again has led to the development of more sophisticated models that can describe a number of physiological descriptors.…”

Section: Role Of Models In Systems Biology: Can Mathematics Be a Goodmentioning

confidence: 99%

“…Many purely descriptive models are of the bottom-up type (such as the e-cell, virtual cell modelling framework developed by Tomita et al (1999), Takahashi et al (2003), and Loew et al (2001)). One of the earliest examples of a bottom-up descriptive model was that of Domach-Shuler (Domach et al, 1984). More recently, Castellanos et al (2004) have been working on making these detailed descriptions more modular.…”

Section: Mathematical Model Complexity Versus Degree Of Biological Dementioning

confidence: 99%

Systems Biology: The synergistic interplay between biology and mathematics

Dhurjati

Mahadevan

2008

Can J Chem Eng

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Systems Biology is a nascent field that arose from the technology driven omics measurement revolution. It goes beyond mere data analysis and focuses on the biological behaviour emerging from the dynamic interactions between system components that are organized in a hierarchical and highly connected manner. Mathematical models have been used as a conceptual framework to study such systems and their impact is maximal when there is a synergistic interplay of the models with experimental data and biological domain knowledge. The review provides an introduction to the modelling process and selectively highlights manuscripts that have strong biological impact.La biologie des systèmes est un domaine qui est apparu récemment avec la révolution dans les mesures omiques dues aux progrès technologiques. Ce domaine va au-delà de la simple analyse et s'intéresse au comportement biologique venant des interactions dynamiques entre les composantes de systèmes qui sont organisées de façon hiérarchique et hautement interreliées. Des modèles mathématiques ontété utilisés comme cadre conceptuel afin d'étudier ces systèmes, et leur impact est maximal lorsqu'il y a une interrelation synergétique entre d'une part, les modèles, et d'autre part, les données expérimentales et les connaissances dans le domaine biologique. Cette revue de la littérature fournit une introduction aux articles mettant en lumière les procédés de modélisation et la sélectivité et qui ont un fort impact biologique.

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“…In response to these limitations and challenges, a number of research groups have undertaken the development of plausible large-scale kinetic models. Prominent modeling projects include large-scale kinetic models of Saccharomyces cerevisiae (Hynne et al 2001;Rizzi et al 1997) and Escherichia coli (Chassagnole et al 2002;Visser et al 2004), the kinetic model of central metabolism coupled with tryptophan gene expression in E.coli , and computer models of single cells capturing dynamic effects of chromosome replication and changes in the cell geometry (Atlas et al, 2008;Castellanos et al 2007;Domach et al 1984;Nikolaev et al 2006). The discussed models are highly nonlinear, stiff and include many kinetic parameters which are hard to identify from the measurements.…”

Section: Introductionmentioning

confidence: 99%

The elucidation of metabolic pathways and their improvements using stable optimization of large-scale kinetic models of cellular systems

Nikolaev

2010

Metabolic Engineering

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Computer model for glucose‐limited growth of a single cell of Escherichia coli B/r‐A

Cited by 52 publications

References 36 publications

Modeling Life

Modeling Life

Systems Biology: The synergistic interplay between biology and mathematics

The elucidation of metabolic pathways and their improvements using stable optimization of large-scale kinetic models of cellular systems

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