Bridging substrate intake kinetics and bacterial growth phenotypes with flux balance analysis incorporating proteome allocation

Modelling overflow metabolism in Escherichia coli with flux balance analysis incorporating differential proteomic efficiencies of energy pathways

(2019) Hong Zeng et al.   BMC Systems Biology

Quantification of proteomic and metabolic burdens predicts growth retardation and overflow metabolism in recombinant Escherichia coli

(2019) Hong Zeng et al.   BIOTECHNOLOGY AND BIOENGINEERING

Energy metabolism controls phenotypes by protein efficiency and allocation

(2019) Yu Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Optimal bioprocess design through a gene regulatory network – Growth kinetic hybrid model: Towards replacing Monod kinetics

(2018) Argyro Tsipa et al.   METABOLIC ENGINEERING

Metabolic Models of Protein Allocation Call for the Kinetome

(2017) Avlant Nilsson et al.   Cell Systems

Macromolecular crowding explains overflow metabolism in cells

(2016) Alexei Vazquez et al.   Scientific Reports

Constrained Allocation Flux Balance Analysis

(2016) Matteo Mori et al.   PLoS Computational Biology

Proteome reallocation in Escherichia coli with increasing specific growth rate

(2015) Karl Peebo et al.   Molecular BioSystems

Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria

(2015) S. Hui et al.   Molecular Systems Biology

Overflow metabolism in Escherichia coli results from efficient proteome allocation

(2015) Markus Basan et al.   NATURE

Dynamic flux balance analysis for synthetic microbial communities

(2014) Michael A. Henson et al.   IET Systems Biology

Dynamic model-based analysis of furfural and HMF detoxification by pure and mixed batch cultures ofS. cerevisiaeandS. stipitis

(2013) Timothy J. Hanly et al.   BIOTECHNOLOGY AND BIOENGINEERING

Dynamic metabolic modeling of a microaerobic yeast co-culture: predicting and optimizing ethanol production from glucose/xylose mixtures

(2013) Timothy J Hanly et al.   Biotechnology for Biofuels

The last generation of bacterial growth in limiting nutrient

(2013) Anat Bren et al.   BMC Systems Biology

Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction

(2013) E. J. O{middle dot}Brien et al.   Molecular Systems Biology

Coordination of bacterial proteome with metabolism by cyclic AMP signalling

(2013) Conghui You et al.   NATURE

Characteristics of mixed microbial culture at different sludge ages: Effect on variable kinetics for substrate utilization

(2012) Ilke Pala-Ozkok et al.   BIORESOURCE TECHNOLOGY

Glucose Transport in Escherichia coli Mutant Strains with Defects in Sugar Transport Systems

(2012) S. Steinsiek et al.   JOURNAL OF BACTERIOLOGY

Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage

(2012) Ines Thiele et al.   PLoS One

In silico method for modelling metabolism and gene product expression at genome scale

(2012) Joshua A. Lerman et al.   Nature Communications

Bacterial growth rate reflects a bottleneck in resource allocation

(2011) A. Goelzer et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

In glucose-limited continuous culture the minimum substrate concentration for growth, smin, is crucial in the competition between the enterobacterium Escherichia coli and Chelatobacter heintzii, an environmentally abundant bacterium

(2011) Hans Peter Füchslin et al.   ISME Journal

Economics of membrane occupancy and respiro-fermentation

(2011) K. Zhuang et al.   Molecular Systems Biology

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

(2010) M. Scott et al.   SCIENCE

Validity of Monod kinetics at different sludge ages – Peptone biodegradation under aerobic conditions

(2009) Derin Orhon et al.   BIORESOURCE TECHNOLOGY

Connecting extracellular metabolomic measurements to intracellular flux states in yeast

(2009) Monica L Mo et al.   BMC Systems Biology

Control of specific growth rate in Saccharomyces cerevisiae

(2009) J. L. Snoep et al.   MICROBIOLOGY-SGM

Shifts in growth strategies reflect tradeoffs in cellular economics

(2009) Douwe Molenaar et al.   Molecular Systems Biology