Constructing kinetic models of metabolism at genome-scales: A review (Q38579075)

4 September 2017

Constructing kinetic models of metabolism at genome-scales: A review (English)

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4 September 2017

Shyam Srinivasan

1

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PubMed ID

26332243

4 September 2017

William R Cluett

series ordinal

2

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PubMed ID

26332243

4 September 2017

Radhakrishnan Mahadevan

series ordinal

3

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4 September 2017

1 September 2015

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4 September 2017

Biotechnology Journal

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4 September 2017

10

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4 September 2017

9

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4 September 2017

1345-1359

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Modeling formalisms in Systems Biology

4 September 2017

1 reference

https://api.crossref.org/works/10.1002%2FBIOT.201400522

Metabolic shifts: a fitness perspective for microbial cell factories

21 January 2018

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Cancer systems biology: a network modeling perspective

21 January 2018

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Modelling reveals novel roles of two parallel signalling pathways and homeostatic feedbacks in yeast

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201400522

Constraint-based models predict metabolic and associated cellular functions.

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201400522

A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information

21 January 2018

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Towards genome-scale signalling network reconstructions

21 January 2018

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A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201400522

Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism.

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201400522

High-throughput generation, optimization and analysis of genome-scale metabolic models

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIOT.201400522

Optimizing genome-scale network reconstructions

21 January 2018

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Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201400522

What is flux balance analysis?

21 January 2018

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Something from nothing: bridging the gap between constraint-based and kinetic modelling.

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201400522

Ensemble modeling of metabolic networks

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201400522

Thermodynamically feasible kinetic models of reaction networks

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201400522

Exploring the gap between dynamic and constraint-based models of metabolism.

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201400522

k-OptForce: integrating kinetics with flux balance analysis for strain design

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201400522

Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation

21 January 2018

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Network motifs: theory and experimental approaches

21 January 2018

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When ubiquitination meets phosphorylation: a systems biology perspective of EGFR/MAPK signalling

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201400522

Phenotypic bistability in Escherichia coli's central carbon metabolism

21 January 2018

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Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201400522

Structural kinetic modeling of metabolic networks

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201400522

Sustained glycolytic oscillations in individual isolated yeast cells.

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201400522

Towards a theory of biological robustness

21 January 2018

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Robustness of cellular functions

21 January 2018

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Multidimensional optimality of microbial metabolism

21 January 2018

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Evolutionary tradeoffs between economy and effectiveness in biological homeostasis systems

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201400522

Bacterial adaptation through distributed sensing of metabolic fluxes

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201400522

Thermodynamics-based metabolic flux analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIOT.201400522

Kinetic models in industrial biotechnology - Improving cell factory performance

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIOT.201400522

Advancing metabolic models with kinetic information.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIOT.201400522

A computational procedure for optimal engineering interventions using kinetic models of metabolism.

21 January 2018

1 reference

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Systems and synthetic metabolic engineering for amino acid production - the heartbeat of industrial strain development

21 January 2018

1 reference

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Metabolic flux responses to genetic modification for shikimic acid production by Bacillus subtilis strains

21 January 2018

1 reference

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Microbial engineering for the production of advanced biofuels

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIOT.201400522

Advances in metabolic pathway and strain engineering paving the way for sustainable production of chemical building blocks

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIOT.201400522

Systems biology of yeast: enabling technology for development of cell factories for production of advanced biofuels

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIOT.201400522

New types of experimental data shape the use of enzyme kinetics for dynamic network modeling

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201400522

Metabolic dynamics in the human red cell. Part I--A comprehensive kinetic model.

21 January 2018

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https://api.crossref.org/works/10.1002%2FBIOT.201400522

Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIOT.201400522

Tendency modeling: a new approach to obtain simplified kinetic models of metabolism applied to Saccharomyces cerevisiae.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIOT.201400522

Dynamic modeling of the central carbon metabolism of Escherichia coli.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIOT.201400522

Kinetic modelling of central carbon metabolism in Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIOT.201400522

Metabolic control analysis under uncertainty: framework development and case studies

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIOT.201400522

Approximative kinetic formats used in metabolic network modeling

21 January 2018

1 reference

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Towards a genome-scale kinetic model of cellular metabolism

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIOT.201400522

Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis-Menten and approximate kinetic equations.

21 January 2018

1 reference

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Biochemical systems analysis. I. Some mathematical properties of the rate law for the component enzymatic reactions.

21 January 2018

1 reference

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Metabolic control analysis: a survey of its theoretical and experimental development

21 January 2018

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Systematic construction of kinetic models from genome-scale metabolic networks

21 January 2018

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Bringing metabolic networks to life: convenience rate law and thermodynamic constraints

21 January 2018

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Likelihood based observability analysis and confidence intervals for predictions of dynamic models

21 January 2018

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Metabolic flux analysis of Escherichia coli knockouts: lessons from the Keio collection and future outlook

21 January 2018

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Contribution of network connectivity in determining the relationship between gene expression and metabolite concentration changes

21 January 2018

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Recent advances in reconstruction and applications of genome-scale metabolic models

21 January 2018

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Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism

21 January 2018

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Modeling of uncertainties in biochemical reactions.

21 January 2018

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Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints.

21 January 2018

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Reducing the allowable kinetic space by constructing ensemble of dynamic models with the same steady-state flux.

21 January 2018

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Optimization-driven identification of genetic perturbations accelerates the convergence of model parameters in ensemble modeling of metabolic networks

21 January 2018

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Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models

21 January 2018

1 reference

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Top-down analysis of temporal hierarchy in biochemical reaction networks

21 January 2018

1 reference

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Random sampling of elementary flux modes in large-scale metabolic networks

21 January 2018

1 reference

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A probabilistic approach to identify putative drug targets in biochemical networks

21 January 2018

1 reference

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Computational approaches to the topology, stability and dynamics of metabolic networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIOT.201400522

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIOT.201400522

Coordination of microbial metabolism

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIOT.201400522

Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models.

21 January 2018

1 reference

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Large-scale metabolome analysis and quantitative integration with genomics and proteomics data in Mycoplasma pneumoniae.

21 January 2018

1 reference

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A whole-cell computational model predicts phenotype from genotype

21 January 2018

1 reference

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Prediction of microbial growth rate versus biomass yield by a metabolic network with kinetic parameters

21 January 2018

1 reference

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Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood

21 January 2018

1 reference

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The stability and robustness of metabolic states: identifying stabilizing sites in metabolic networks

21 January 2018

1 reference

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Systems analysis of cellular networks under uncertainty

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FBIOT.201400522

21 January 2018

Identifiers

DOI

10.1002/BIOT.201400522

1 reference

4 September 2017

1 reference

PubMed ID

26332243