Building kinetic models for metabolic engineering

Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies

(2020) Milenko Tokic et al.   Biotechnology for Biofuels

K-FIT: An accelerated kinetic parameterization algorithm using steady-state fluxomic data

(2020) Saratram Gopalakrishnan et al.   METABOLIC ENGINEERING

An Enhanced Segment Particle Swarm Optimization Algorithm for Kinetic Parameters Estimation of the Main Metabolic Model of Escherichia Coli

(2020) Mohammed Adam Kunna et al.   Processes

Kinetic ensemble model of gas fermenting Clostridium autoethanogenum for improved ethanol production

(2019) Jennifer Greene et al.   BIOCHEMICAL ENGINEERING JOURNAL

A generalized computational framework to streamline thermodynamics and kinetics analysis of metabolic pathways

(2019) Chao Wu et al.   METABOLIC ENGINEERING

Metabolic flux responses to deletion of 20 core enzymes reveal flexibility and limits of E. coli metabolism

(2019) Christopher P. Long et al.   METABOLIC ENGINEERING

Synthetic N-terminal coding sequences for fine-tuning gene expression and metabolic engineering in Bacillus subtilis

(2019) Rongzhen Tian et al.   METABOLIC ENGINEERING

From Escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline

(2019) Charles J. Foster et al.   PLoS Computational Biology

Metabolic kinetic modeling provides insight into complex biological questions, but hurdles remain

(2019) Jonathan Strutz et al.   CURRENT OPINION IN BIOTECHNOLOGY

Bayesian inference of metabolic kinetics from genome-scale multiomics data

(2019) Peter C. St. John et al.   PLoS Computational Biology

Statistical inference in ensemble modeling of cellular metabolism

(2019) Tuure Hameri et al.   PLoS Computational Biology

Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures

(2018) Hiroyuki Kurata et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Dynamic modeling of subcellular phenylpropanoid metabolism in Arabidopsis lignifying cells

(2018) Longyun Guo et al.   METABOLIC ENGINEERING

Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology

(2018) J. Kyle Medley et al.   PLoS Computational Biology

Reserve Flux Capacity in the Pentose Phosphate Pathway Enables Escherichia coli 's Rapid Response to Oxidative Stress

(2018) Dimitris Christodoulou et al.   Cell Systems

Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations

(2018) Tuure Hameri et al.   METABOLIC ENGINEERING

COPASI and its applications in biotechnology

(2017) Frank T. Bergmann et al.   JOURNAL OF BIOTECHNOLOGY

Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints

(2017) Benjamín J Sánchez et al.   Molecular Systems Biology

Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks

(2017) Fabian Fröhlich et al.   PLoS Computational Biology

Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli

(2017) Pierre Millard et al.   PLoS Computational Biology

iSCHRUNK – I n S ilico Approach to Ch aracterization and R eduction of Un certainty in the K inetic Models of Genome-scale Metabolic Networks

(2016) Stefano Andreozzi et al.   METABOLIC ENGINEERING

A method for analysis and design of metabolism using metabolomics data and kinetic models: Application on lipidomics using a novel kinetic model of sphingolipid metabolism

(2016) Georgios Savoglidis et al.   METABOLIC ENGINEERING

Reaction kinetic analysis of the 3-hydroxypropionate/4-hydroxybutyrate CO 2 fixation cycle in extremely thermoacidophilic archaea

(2016) Andrew J. Loder et al.   METABOLIC ENGINEERING

Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli

(2016) Nusrat Jahan et al.   Microbial Cell Factories

BRENDA in 2017: new perspectives and new tools in BRENDA

(2016) Sandra Placzek et al.   NUCLEIC ACIDS RESEARCH

Enhanced limonene production in cyanobacteria reveals photosynthesis limitations

(2016) Xin Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitrokcatmeasurements

(2016) Dan Davidi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systems-level analysis of mechanisms regulating yeast metabolic flux

(2016) S. R. Hackett et al.   SCIENCE

A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains

(2016) Ali Khodayari et al.   Nature Communications

Construction of feasible and accurate kinetic models of metabolism: A Bayesian approach

(2016) Pedro A. Saa et al.   Scientific Reports

The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization

(2016) Elad Noor et al.   PLoS Computational Biology

The FAIR Guiding Principles for scientific data management and stewardship

(2016) Mark D. Wilkinson et al.   Scientific Data

Computational inference of the structure and regulation of the lignin pathway in Panicum virgatum

(2015) Mojdeh Faraji et al.   Biotechnology for Biofuels

Robust and efficient parameter estimation in dynamic models of biological systems

(2015) Attila Gábor et al.   BMC Systems Biology

Multiplicity of Steady States in Glycolysis and Shift of Metabolic State in Cultured Mammalian Cells

(2015) Bhanu Chandra Mulukutla et al.   PLoS One

Ki MoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems

(2014) Rafael S Costa et al.   BMC Systems Biology

Advancing metabolic models with kinetic information

(2014) Hannes Link et al.   CURRENT OPINION IN BIOTECHNOLOGY

A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data

(2014) Ali Khodayari et al.   METABOLIC ENGINEERING

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

(2013) Kieran Smallbone et al.   FEBS LETTERS

Testing Biochemistry Revisited: How In Vivo Metabolism Can Be Understood from In Vitro Enzyme Kinetics

(2012) Karen van Eunen et al.   PLoS Computational Biology

The Moderately Efficient Enzyme: Evolutionary and Physicochemical Trends Shaping Enzyme Parameters

(2011) Arren Bar-Even et al.   BIOCHEMISTRY

DBSolve Optimum: a software package for kinetic modeling which allows dynamic visualization of simulation results

(2010) Nail M Gizzatkulov et al.   BMC Systems Biology

Production of biofuels and biochemicals: in need of an ORACLE

(2010) Ljubisa Miskovic et al.   TRENDS IN BIOTECHNOLOGY

Ensemble Modeling of Metabolic Networks

(2008) Linh M. Tran et al.   BIOPHYSICAL JOURNAL