(Q38205653)

31 August 2017

title

Kinetic models in industrial biotechnology - Improving cell factory performance (English)

1 reference

31 August 2017

0 references

4

1 reference

31 August 2017

Vassily Hatzimanikatis

object named as

Vassily Hatzimanikatis

3

0 references

Mats Jirstrand

object named as

Mats Jirstrand

5

0 references

author name string

Joachim Almquist

1

1 reference

31 August 2017

Marija Cvijovic

2

1 reference

31 August 2017

publication date

16 April 2014

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31 August 2017

published in

Metabolic Engineering

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31 August 2017

volume

24

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31 August 2017

page(s)

38-60

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Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks

31 August 2017

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Genome-scale metabolic reconstruction and in silico analysis of methylotrophic yeast Pichia pastoris for strain improvement

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Quantitative analysis of the fermentative metabolism of glycerol in Escherichia coli.

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Ensemble modeling for strain development of L-lysine-producing Escherichia coli

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Kinetics of L-lysine fermentation: a continuous culture model incorporating oxygen uptake rate

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Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification

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Systems analysis of cellular networks under uncertainty

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Genome-based metabolic engineering of Mannheimia succiniciproducens for succinic acid production

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Model-based optimization of viral capsid protein production in fed-batch culture of recombinant Escherichia coli

7 January 2021

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An improved kinetic model for the acetone-butanol-ethanol pathway of Clostridium acetobutylicum and model-based perturbation analysis

7 January 2021

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The role of physiological heterogeneity in microbial population behavior.

7 January 2021

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Biochemical network models simplified by balanced truncation.

7 January 2021

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7 January 2021

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

7 January 2021

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

7 January 2021

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

7 January 2021

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Modeling of Xanthophyllomyces dendrorhous growth on glucose and overflow metabolism in batch and fed-batch cultures for astaxanthin production.

7 January 2021

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On global identifiability for arbitrary model parametrizations

7 January 2021

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The identification of enzyme targets for the optimization of a valine producing Corynebacterium glutamicum strain using a kinetic model

7 January 2021

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Dynamic flux balance analysis of diauxic growth in Escherichia coli

7 January 2021

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Dynamical modeling and multi-experiment fitting with PottersWheel

7 January 2021

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Differential algebra methods for the study of the structural identifiability of rational function state-space models in the biosciences.

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Optimization of tryptophan production in bacteria. Design of a strategy for genetic manipulation of the tryptophan operon for tryptophan flux maximization

7 January 2021

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An Algorithm for Least-Squares Estimation of Nonlinear Parameters

7 January 2021

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Versatile modeling and optimization of fed batch processes for the production of secreted heterologous proteins with Pichia pastoris

7 January 2021

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An empirical modeling platform to evaluate the relative control discrete CHO cell synthetic processes exert over recombinant monoclonal antibody production process titer.

7 January 2021

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Computational modeling of biochemical networks using COPASI

7 January 2021

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

7 January 2021

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Mathematical modelling of industrial pilot-plant penicillin-G fed-batch fermentations.

7 January 2021

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Finding identifiable parameter combinations in nonlinear ODE models and the rational reparameterization of their input-output equations.

7 January 2021

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The frequency dependence of osmo-adaptation in Saccharomyces cerevisiae

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

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How can biochemical reactions within cells differ from those in test tubes?

7 January 2021

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Production of biofuels and biochemicals: in need of an ORACLE.

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Modeling of uncertainties in biochemical reactions.

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Continuous modeling of metabolic networks with gene regulation in yeast and in vivo determination of rate parameters.

7 January 2021

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7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

A Simplex Method for Function Minimization

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Optimization of erythropoietin production with controlled glycosylation-PEGylated erythropoietin produced in glycoengineered Pichia pastoris

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Mixed glucose and lactate uptake by Corynebacterium glutamicum through metabolic engineering

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Metabolic engineering: techniques for analysis of targets for genetic manipulations

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

A method for estimation of elasticities in metabolic networks using steady state and dynamic metabolomics data and linlog kinetics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Model reduction and a priori kinetic parameter identifiability analysis using metabolome time series for metabolic reaction networks with linlog kinetics.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Visualizing regulatory interactions in metabolic networks

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Dynamic model of CHO cell metabolism.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Dynamic model for CHO cell engineering

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Fifteen years of large scale metabolic modeling of yeast: developments and impacts

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

A dynamic, genome-scale flux model of Lactococcus lactis to increase specific recombinant protein expression

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Dynamic modeling of lactic acid fermentation metabolism with Lactococcus lactis.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Simplification of Mathematical Models of Chemical Reaction Systems.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Kinetic modeling and sensitivity analysis of xylose metabolism in Lactococcus lactis IO-1.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Industrial systems biology

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Kinetic modelling reveals current limitations in the production of ethanol from xylose by recombinant Saccharomyces cerevisiae.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Fed-batch culture of Escherichia coli for L-valine production based on in silico flux response analysis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Use of genome-scale microbial models for metabolic engineering

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Summing up the noise in gene networks

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Modeling and measuring intracellular fluxes of secreted recombinant protein in Pichia pastoris with a novel 34S labeling procedure

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Diverse metabolic model parameters generate similar methionine cycle dynamics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Yield optimization of regulated metabolic systems using deterministic branch-and-reduce methods

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Steady-state global optimization of metabolic non-linear dynamic models through recasting into power-law canonical models

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Metabolic control analysis of xylose catabolism in Aspergillus

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Schemes of flux control in a model of Saccharomyces cerevisiae glycolysis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Metabolic design of macroscopic bioreaction models: application to Chinese hamster ovary cells

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Modelling hybridoma cell growth and metabolism--a comparison of selected models and data

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Identifiability and observability analysis for experimental design in nonlinear dynamical models

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Addressing parameter identifiability by model-based experimentation.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

A hybrid approach for efficient and robust parameter estimation in biochemical pathways.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Cellular signaling identifiability analysis: a case study

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Examples of testing global identifiability of biological and biomedical models with the DAISY software.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Model-based inference of biochemical parameters and dynamic properties of microbial signal transduction networks

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Nested uncertainties in biochemical models

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

BRENDA, the enzyme information system in 2011

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Metabolic design based on a coupled gene expression-metabolic network model of tryptophan production in Escherichia coli

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

SBaddon: high performance simulation for the Systems Biology Toolbox for MATLAB.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Complexity reduction of biochemical rate expressions

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Estimating the Dimension of a Model

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

The ABC of reverse engineering biological signalling systems.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Kinetic modeling and sensitivity analysis of acetone-butanol-ethanol production

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Towards a genome-scale kinetic model of cellular metabolism

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Towards building the silicon cell: a modular approach

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

From network models to network responses: integration of thermodynamic and kinetic properties of yeast genome-scale metabolic networks

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Genome-scale metabolic model of methylotrophic yeast Pichia pastoris and its use for in silico analysis of heterologous protein production.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Parameter identifiability of power-law biochemical system models

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Zooming of states and parameters using a lumping approach including back-translation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

A method for zooming of nonlinear models of biochemical systems.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Experimental design for the identification of macrokinetic models and model discrimination.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Industrial biotechnology: tools and applications

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Hybrid elementary flux analysis/nonparametric modeling: application for bioprocess control

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Metabolic control analysis of the penicillin biosynthetic pathway: the influence of the LLD-ACV:bisACV ratio on the flux control

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Why are nonlinear fits to data so challenging?

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Rationalizing translation attenuation in the network architecture of the unfolded protein response.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

The unfolded protein response and translation attenuation: a modelling approach

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Toward design-based engineering of industrial microbes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Stochastic approaches in systems biology

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

A mathematical model of N-linked glycoform biosynthesis.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Dynamic modeling of Escherichia coli metabolic and regulatory systems for amino-acid production.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

The mathematics of metabolic control analysis revisited

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Dynamic simulation and metabolic re-design of a branched pathway using linlog kinetics.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Optimal re-design of primary metabolism in Escherichia coli using linlog kinetics.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Metabolic control analysis under uncertainty: framework development and case studies

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Metabolic engineering under uncertainty--II: analysis of yeast metabolism.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Metabolic engineering under uncertainty. I: framework development.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Bistability, stochasticity, and oscillations in the mitogen-activated protein kinase cascade

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Mechanistic pathway modeling for industrial biotechnology: challenging but worthwhile

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

An Adaptable Standard for Protein Export from the Endoplasmic Reticulum

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Optimization of a glycoengineered Pichia pastoris cultivation process for commercial antibody production

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

On-line evolutionary optimization of an industrial fed-batch yeast fermentation process.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

Dynamic metabolic models of CHO cell cultures through minimal sets of elementary flux modes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

A quantitative study of the Hog1 MAPK response to fluctuating osmotic stress in Saccharomyces cerevisiae

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMBEN.2014.03.007

10.1016/J.YMBEN.2014.03.007

7 January 2021

Identifiers

DOI

1 reference

31 August 2017

1 reference