Modeling Hybridoma Cell Metabolism Using a Generic Genome‐Scale Metabolic Model of Mus musculus

@article{Sheikh2005ModelingHC,
  title={Modeling Hybridoma Cell Metabolism Using a Generic Genome‐Scale Metabolic Model of Mus musculus},
  author={Kashif M. Sheikh and Jochen F{\"o}rster and Lars Keld Nielsen},
  journal={Biotechnology Progress},
  year={2005},
  volume={21}
}
The reconstructed cellular metabolic network of Mus musculus, based on annotated genomic data, pathway databases, and currently available biochemical and physiological information, is presented. Although incomplete, it represents the first attempt to collect and characterize the metabolic network of a mammalian cell on the basis of genomic data. The reaction network is generic in nature and attempts to capture the carbon, energy, and nitrogen metabolism of the cell. The metabolic reactions were… Expand
On the reconstruction of the Mus musculus genome-scale metabolic network model.
  • L. Quek, L. Nielsen
  • Biology, Medicine
  • Genome informatics. International Conference on Genome Informatics
  • 2008
TLDR
Effectively, this work can focus its curation efforts into establishing better model annotations and gene-protein-reaction associations within the core metabolism, while relying on genome and proteome databases to build new annotations for peripheral pathways, which may bear less relevance to the modeling interest. Expand
Genome-scale modeling and in silico analysis of mouse cell metabolic network.
TLDR
Overall mouse metabolic network is topologically dominated by highly connected and bridging metabolites, and functionally by lipid metabolism that most of essential genes and metabolites are from, revealing that the current in silico mouse model can be exploited for understanding and characterizing the cellular physiology. Expand
Metabolic flux balance analysis of an industrially useful microorganism Corynebacerium glutamicum by a genome-scale reconstructed model
TLDR
The newly reconstructed genome-scale metabolic model of an industrially useful microorganism, Corynebacterium glutamicum, is reconstructed based on genome sequence annotation and physiological data to provide a better understanding for evaluating metabolic capabilities and predicting metabolic characteristics of C. glutamum. Expand
Development and experimental verification of a genome-scale metabolic model for Corynebacterium glutamicum
TLDR
This study reconstructed a genome-scale metabolic model of Corynebacterium glutamicum on the basis of genome sequence annotation and physiological data and simulated the changes in the metabolic flux profiles that occur on changing the oxygen uptake rate to help identify several genes whose deletion resulted in an improvement in organic acid production. Expand
Genome-Scale In Silico Models
TLDR
This chapter discusses how to reconstruct a metabolic network starting from a genome annotation, and introduces the philosophy of constraint-based modeling, which can be used to investigate network properties and metabolic capabilities of the reconstructed system. Expand
Bringing Genomes to Life: The Use of Genome-Scale In Silico Models
TLDR
This chapter discusses how to reconstruct a metabolic network starting from a genome annotation, and introduces the philosophy of constraint-based modeling, which can be used to investigate network properties and metabolic capabilities of the reconstructed system. Expand
Reconstruction of a generic genome-scale metabolic network for chicken: investigating network connectivity and finding potential biomarkers
TLDR
The results indicated robustness to genetic manipulation for iES1300 similar to the results for human, and it was found that the normal model has notable metabolic flexibility in the utilization of various metabolic pathways, especially in metabolic pathways of the carbohydrate metabolism, compared to the others. Expand
Global reconstruction of the human metabolic network based on genomic and bibliomic data
TLDR
The reconstruction process is described and it is demonstrated how the resulting genome-scale (or global) network can be used for the discovery of missing information, for the formulation of an in silico model, and as a structured context for analyzing high-throughput biological data sets. Expand
Reconstruction of metabolic pathways for the cattle genome
TLDR
The aims of this study were to reconstruct conserved metabolic pathways in the cattle genome and to identify metabolic pathways with missing genes and proteins and to provide a framework for the metabolic reconstruction of other newly sequenced mammalian genomes. Expand
A genome-scale, constraint-based approach to systems biology of human metabolism.
TLDR
Homo sapiens Recon 1 is described, a functionally tested, genome-scale reconstruction of human cellular metabolism, and its capabilities for facilitating the understanding of physiological and disease metabolic states. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 40 REFERENCES
Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network.
TLDR
The reconstructed metabolic network in the yeast Saccharomyces cerevisiae was reconstructed using currently available genomic, biochemical, and physiological information and may be used as the basis for in silico analysis of phenotypic functions. Expand
Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model.
TLDR
This study systematically identified inconsistencies in knowledge of yeast metabolism that require specific further experimental investigation and identified false predictions caused by iND750's limited inclusion of cellular processes outside of metabolism. Expand
Metabolic modeling of microbial strains in silico.
TLDR
The use of quantitative analysis methods to generate testable hypotheses and drive experimentation at a whole-genome level signals the advent of a systemic modeling approach to cellular and molecular biology. Expand
Integration of gene expression data into genome-scale metabolic models.
A framework for integration of transcriptome data into stoichiometric metabolic models to obtain improved flux predictions is presented. The key idea is to exploit the regulatory information in theExpand
The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities.
  • J. Edwards, B. Palsson
  • Biology, Medicine
  • Proceedings of the National Academy of Sciences of the United States of America
  • 2000
TLDR
It was shown that based on stoichiometric and capacity constraints the in silico analysis was able to qualitatively predict the growth potential of mutant strains in 86% of the cases examined. Expand
Metabolic Pathway Analysis: Basic Concepts and Scientific Applications in the Post‐genomic Era
TLDR
A better understanding of the architecture of cellular metabolism and the enormous amount of genomic data available today, biochemists and biotechnologists will be able to draw the entire metabolic map of a cell and redesign it by rational and directed metabolic engineering. Expand
Genome-scale microbial in silico models: the constraints-based approach.
TLDR
This work has shown that genome sequencing and annotation has enabled the reconstruction of genome-scale metabolic networks, including substrate preference, consequences of gene deletions, optimal growth patterns, outcomes of adaptive evolution and shifts in expression profiles, are useful as a basis for iterative model building and for several practical applications. Expand
Systems Properties of the Haemophilus influenzaeRd Metabolic Genotype*
TLDR
It is shown that the synthesis ofin silico metabolic genotypes from annotated genome sequences is possible and that systems analysis methods are available that can be used to analyze and interpret phenotypic behavior of such genotypes. Expand
Examination of primary metabolic pathways in a murine hybridoma with carbon‐13 nuclear magnetic resonance spectroscopy
TLDR
Primary metabolism of a murine hybridoma was probed with 13C nuclear magnetic resonance (NMR) spectroscopy to determine the intracellular concentration of several metabolic intermediates and to determine fluxes for primary metabolic pathways. Expand
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
TLDR
iJR904 will help to outline the genotype-phenotype relationship for E. coli K-12, as it can account for genomic, transcriptomic, proteomic and fluxomic data simultaneously, and has improved capabilities over iJE660a. Expand
...
1
2
3
4
...