New types of experimental data shape the use of enzyme kinetics for dynamic network modeling (Q26823013)

Timo Lubitz

series ordinal

2

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Max Schelker

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3

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language of work or name

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January 2014

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281

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issue

2

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page(s)

549-71

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In silico biology through "omics".

cites work

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Quantitative analysis of glycerol accumulation, glycolysis and growth under hyper osmotic stress

21 January 2018

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Dynamics and feedback loops in the transforming growth factor β signaling pathway

21 January 2018

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A Note on the Kinetics of Enzyme Action

21 January 2018

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Role of individual phosphorylation sites for the 14-3-3-protein-dependent activation of yeast neutral trehalase Nth1.

21 January 2018

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The addition compound theory of enzyme action

21 January 2018

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Studies on plant amylases: The effect of starch concentration upon the velocity of hydrolysis by the amylase of germinated barley

21 January 2018

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The direct linear plot. A new graphical procedure for estimating enzyme kinetic parameters

21 January 2018

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A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

The kinetics of enzyme-catalyzed reactions with two or more substrates or products

21 January 2018

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History of the enzyme nomenclature system

21 January 2018

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Allosteric proteins and cellular control systems

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL

21 January 2018

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Allostery and the Monod-Wyman-Changeux model after 50 years

21 January 2018

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Comparison of Experimental Binding Data and Theoretical Models in Proteins Containing Subunits*

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Glycolysis in bloodstream form Trypanosoma brucei can be understood in terms of the kinetics of the glycolytic enzymes.

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Information transfer in metabolic pathways. Effects of irreversible steps in computer models

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Approximative kinetic formats used in metabolic network modeling

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Use of implicit methods from general sensitivity theory to develop a systematic approach to metabolic control. II. Complex systems

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

The mathematics of metabolic control analysis revisited

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Effects of spatiotemporal variations on metabolic control: approximate analysis using (log)linear kinetic models

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

Responses of metabolic systems to large changes in enzyme activities and effectors. 2. The linear treatment of branched pathways and metabolite concentrations. Assessment of the general non-linear case.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

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

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

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

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Biochemical networks with uncertain parameters.

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA.

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

SABIO-RK--database for biochemical reaction kinetics

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

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

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism.

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Measuring enzyme activities under standardized in vivo-like conditions for systems biology

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Why in vivo may not equal in vitro - new effectors revealed by measurement of enzymatic activities under the same in vivo-like assay conditions.

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Macromolecular crowding: obvious but underappreciated

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Reaction kinetics in intracellular environments with macromolecular crowding: simulations and rate laws

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Implications of macromolecular crowding for signal transduction and metabolite channeling

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Channeling of substrates and intermediates in enzyme-catalyzed reactions

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

A systematic investigation of the rate laws valid in intracellular environments.

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Monte carlo simulations of enzyme reactions in two dimensions: fractal kinetics and spatial segregation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

The importance of uniformity in reporting protein-function data

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

21 January 2018

NMR-based metabolomics

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Comparing and combining NMR spectroscopy and mass spectrometry in metabolomics

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Metabolic networks in motion: 13C-based flux analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

21 January 2018

The PeptideAtlas project

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https://api.crossref.org/works/10.1111%2FFEBS.12525

High-throughput generation of selected reaction-monitoring assays for proteins and proteomes

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Absolute quantification of the glycolytic pathway in yeast: deployment of a complete QconCAT approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

RNA-Seq: a revolutionary tool for transcriptomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

Enzyme kinetic assays with surface plasmon resonance (BIAcore) based on competition between enzyme and creatinine antibody.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

KEGG: Kyoto Encyclopedia of Genes and Genomes

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Reorganizing the protein space at the Universal Protein Resource (UniProt)

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

Web-based kinetic modelling using JWS Online.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

An error model for protein quantification

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

Lessons learned from quantitative dynamical modeling in systems biology

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Parameter estimation in biochemical pathways: a comparison of global optimization methods

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Systems biology: parameter estimation for biochemical models

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

Sensitivity analysis approaches applied to systems biology models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

SBML-PET: a Systems Biology Markup Language-based parameter estimation tool.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

COPASI--a COmplex PAthway SImulator

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

Dynamical modeling and multi-experiment fitting with PottersWheel

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

Parameter balancing in kinetic models of cell metabolism

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

The pH dependence of the apparent equilibrium constant, K', of a biochemical reaction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

Calculation of standard transformed formation properties of biochemical reactants and standard apparent reduction potentials of half reactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

Annotation and merging of SBML models with semanticSBML

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Systematic assignment of thermodynamic constraints in metabolic network models

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

Thermodynamically feasible kinetic models of reaction networks

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Classic and contemporary approaches to modeling biochemical reactions

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

Joining forces of Bayesian and frequentist methodology: a study for inference in the presence of non-identifiability

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

Data-based identifiability analysis of non-linear dynamical models

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Profile likelihood in systems biology

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Exploiting the bootstrap method for quantifying parameter confidence intervals in dynamical systems.

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

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

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Sensitivity analysis of stoichiometric networks: an extension of metabolic control analysis to non-steady state trajectories.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

Therapeutically targeting ErbB3: a key node in ligand-induced activation of the ErbB receptor-PI3K axis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

Dynamic mathematical modeling of IL13-induced signaling in Hodgkin and primary mediastinal B-cell lymphoma allows prediction of therapeutic targets

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

A new strategy for assessing sensitivities in biochemical models

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Computational procedures for optimal experimental design in biological systems

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Optimal experimental design with the sigma point method.

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Addressing parameter identifiability by model-based experimentation.

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Identifiability and observability analysis for experimental design in nonlinear dynamical models

21 January 2018

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https://api.crossref.org/works/10.1111%2FFEBS.12525

Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

Systems biology: experimental design

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

Global analysis of protein expression in yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

Metabolomics: Current analytical platforms and methodologies

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

An Overview of Label-Free Quantitation Methods in Proteomics by Mass Spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

Enzyme flexibility and enzyme action

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

7 January 2021

Cross-platform comparison of methods for quantitative metabolomics of primary metabolism

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

7 January 2021

Mass spectrometry-based targeted proteomics

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https://api.crossref.org/works/10.1111%2FFEBS.12525

7 January 2021

Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

7 January 2021

The reversible Hill equation: how to incorporate cooperative enzymes into metabolic models.

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

7 January 2021

Effect of specific growth rate on fermentative capacity of baker's yeast

1 reference

https://api.crossref.org/works/10.1111%2FFEBS.12525

7 January 2021

release_fsr4dzhbw5cdxc6hdb46cc5yca

Identifiers

DOI

10.1111/FEBS.12525

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Fatcat ID

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PubMed publication ID

24034816

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