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

Advancing metabolic models with kinetic information

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

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

(2014) Christopher P Long et al.   CURRENT OPINION IN BIOTECHNOLOGY

Kinetic models in industrial biotechnology – Improving cell factory performance

(2014) Joachim Almquist et al.   METABOLIC ENGINEERING

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

(2014) Dong-Feng Liu et al.   Microbial Cell Factories

Phenotypic bistability in Escherichia coli's central carbon metabolism

(2014) O. Kotte et al.   Molecular Systems Biology

Optimizing genome-scale network reconstructions

(2014) Jonathan Monk et al.   NATURE BIOTECHNOLOGY

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

Coordination of microbial metabolism

(2014) Victor Chubukov et al.   NATURE REVIEWS MICROBIOLOGY

Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism

(2014) Daniel Machado et al.   PLoS Computational Biology

Contribution of Network Connectivity in Determining the Relationship between Gene Expression and Metabolite Concentration Changes

(2014) Aleksej Zelezniak et al.   PLoS Computational Biology

k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design

(2014) Anupam Chowdhury et al.   PLoS Computational Biology

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

(2013) Ali R. Zomorrodi et al.   Biotechnology Journal

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

(2013) Anirikh Chakrabarti et al.   Biotechnology Journal

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

(2013) J. P. Faria et al.   BRIEFINGS IN BIOINFORMATICS

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

(2013) Lan K Nguyen et al.   Cell Communication and Signaling

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

(2013) Yun Chen et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

(2013) Katja Tummler et al.   FEBS Journal

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

(2013) Tobias Maier et al.   Molecular BioSystems

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

(2013) D. McCloskey et al.   Molecular Systems Biology

Systematic Construction of Kinetic Models from Genome-Scale Metabolic Networks

(2013) Natalie J. Stanford et al.   PLoS One

Evolutionary Tradeoffs between Economy and Effectiveness in Biological Homeostasis Systems

(2013) Pablo Szekely et al.   PLoS Computational Biology

Multiscale modeling for emergent behavior, complexity, and combinatorial explosion

(2012) Dionisios G. Vlachos   AICHE JOURNAL

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

(2012) Daniel Machado et al.   BIOINFORMATICS

Metabolic shifts: a fitness perspective for microbial cell factories

(2012) Anisha Goel et al.   BIOTECHNOLOGY LETTERS

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

(2012) Clemens Kreutz et al.   BMC Systems Biology

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

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

(2012) Judith Becker et al.   CURRENT OPINION IN BIOTECHNOLOGY

Kinetic modelling of central carbon metabolism inEscherichia coli

(2012) Kirill Peskov et al.   FEBS Journal

Sustained glycolytic oscillations in individual isolated yeast cells

(2012) Anna-Karin Gustavsson et al.   FEBS Journal

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

(2012) Daniel Machado et al.   METABOLIC ENGINEERING

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

(2012) Jörg Schaber et al.   Molecular Systems Biology

Microbial engineering for the production of advanced biofuels

(2012) Pamela P. Peralta-Yahya et al.   NATURE

Multidimensional Optimality of Microbial Metabolism

(2012) R. Schuetz et al.   SCIENCE

Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters

(2012) Roi Adadi et al.   PLoS Computational Biology

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

(2011) Bouke de Jong et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

(2011) Tae Yong Kim et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

(2011) R. L. Chang et al.   Molecular Systems Biology

Modeling formalisms in Systems Biology

(2011) Daniel Machado et al.   AMB Express

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

(2010) Wolfram Liebermeister et al.   BIOINFORMATICS

Mass Action Stoichiometric Simulation Models: Incorporating Kinetics and Regulation into Stoichiometric Models

(2010) Neema Jamshidi et al.   BIOPHYSICAL JOURNAL

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

(2010) Rafael S. Costa et al.   BIOSYSTEMS

Modeling of uncertainties in biochemical reactions

(2010) Ljubiša Mišković et al.   BIOTECHNOLOGY AND BIOENGINEERING

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

(2010) Chen Li et al.   BMC Systems Biology

Towards a genome-scale kinetic model of cellular metabolism

(2010) Kieran Smallbone et al.   BMC Systems Biology

A probabilistic approach to identify putative drug targets in biochemical networks

(2010) E. Murabito et al.   Journal of the Royal Society Interface

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

(2010) Yikun Tan et al.   METABOLIC ENGINEERING

Bacterial adaptation through distributed sensing of metabolic fluxes

(2010) Oliver Kotte et al.   Molecular Systems Biology

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

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Towards genome-scale signalling-network reconstructions

(2010) Daniel R. Hyduke et al.   NATURE REVIEWS GENETICS

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

(2009) A. Raue et al.   BIOINFORMATICS

Cancer systems biology: a network modeling perspective

(2009) P. K. Kreeger et al.   CARCINOGENESIS

Systems analysis of cellular networks under uncertainty

(2009) Hans-Michael Kaltenbach et al.   FEBS LETTERS

Ensemble modeling and related mathematical modeling of metabolic networks

(2009) Matthew L. Rizk et al.   Journal of the Taiwan Institute of Chemical Engineers

Ensemble Modeling of Metabolic Networks

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

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

(2008) Markus J Herrgård et al.   NATURE BIOTECHNOLOGY

Top-Down Analysis of Temporal Hierarchy in Biochemical Reaction Networks

(2008) Neema Jamshidi et al.   PLoS Computational Biology