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Cited by 31Gene Regulatory Network AnalysisBacterial Genetics and BiotechnologyMicrobial Metabolic Engineering and Bioproduction

The DOI matches its Crossref record; 59 of the 59 references it cites were found in a registry or an index.

Incorporating genome-wide DNA sequence information into a dynamic whole-cell model of Escherichia coli : application to DNA replication

Atlas, J.C., Nikolaev, E.V., Browning, S.T., Shuler, M.L.·2008·IET Systems Biology
DOI 10.1049/iet-syb:20070079
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Abstract

The advent of thousands of annotated genomes, detailed metabolic reconstructions and databases within the flourishing field of systems biology necessitates the development of functionally complete computer models of whole cells and cellular systems. Such models would realistically describe fundamental properties of living systems such as growth, division and chromosome replication. This will inevitably bridge bioinformatic technologies with ongoing mathematical modelling efforts and would allow for in silico prediction of important dynamic physiological events. To demonstrate a potential for the anticipated merger of bioinformatic genome-wide data with a whole-cell computer model, the authors present here an updated version of a dynamic model of Escherichia coli, including a module that correctly describes the initiation and control of DNA replication by nucleoprotein DnaA-ATP molecules. Specifically, a rigorous mathematical approach used to explicitly include the genome-wide distribution of DnaA-binding sites on the replicating chromosome into a computer model of a bacterial cell is discussed. A new simple deterministic approximation of the complex stochastic process of DNA replication initiation is also provided. It is shown for the first time that reasonable assumptions about the mechanism of DNA replication initiation can be implemented in a deterministic whole-cell model to make predictions about the timing of chromosome replication. Furthermore, it is proposed that a la…

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59 of 59 references verified0 citation errors · 0 not checkable

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  • Early ODE-based models of cellular physiology were limited by difficulty in obtaining required parameters.

    “The first approaches to modeling cellular physiology, based on ordinary differential equations (ODEs) (Atlas et al., 2008; Browning et al., 2004; Castellanos et al., 2004; Castellanos et al., 2007; Domach et al., 1984; Tomita et al., 1999), were limited by the difficulty in obtaining the necessary model parameters.”

    From A Whole-Cell Computational Model Predicts Phenotype from Genotype (2012) · cites this paper as Atlas et al., 2008

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Research works printed but not linked: 53

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Metadata

Authors
Atlas, J. C., Nikolaev, E. V., Browning, S. T., & Shuler, M. L.
Affiliations
Cornell University (US)
ORCID
Venue
IET Systems Biology
Publisher
Institution of Engineering and Technology (IET)
Published
2008-09-15
Volume
2
Issue
5
Pages
369-382
ISSN
  • 1751-8849 (ISSN-L)
  • 1751-8857
DOI
10.1049/iet-syb:20070079
OpenAlex
W1976043669
Cited by
31
References
59
Citations by year
2023: 1 · 2021: 1 · 2020: 4 · 2019: 3 · 2018: 1 · 2017: 2 · 2016: 1 · 2015: 3 · 2014: 1 · 2013: 4 · 2012: 4
FWCI
0.82
Type
journal article
Language
en
Open access
closed
Locations
  • IET Systems Biology (publishedVersion)
  • PubMed (publishedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
Keywords
whole-cell model, Escherichia coli, DNA replication initiation, DNA replication timing, bacterial growth rate, genome-scale metabolic reconstruction
MeSH terms
Base Sequence, Chromosome Mapping, Computer Simulation, DNA Replication, DNA, Bacterial, Escherichia coli, Models, Genetic, Molecular Sequence Data, Genome, Bacterial, Sequence Analysis, DNA, Escherichia coli Proteins

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