The number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates

Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield

(2018) Meike T. Wortel et al.   PLoS Computational Biology

Maintaining maximal metabolic flux by gene expression control

(2018) Robert Planqué et al.   PLoS Computational Biology

Few regulatory metabolites coordinate expression of central metabolic genes in Escherichia coli

(2017) Karl Kochanowski et al.   Molecular Systems Biology

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

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

ArcA overexpression induces fermentation and results in enhanced growth rates of E. coli

(2017) Markus Basan et al.   Scientific Reports

From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints

(2017) Steffen Klamt et al.   PLoS Computational Biology

Why Do Fast-Growing Bacteria Enter Overflow Metabolism? Testing the Membrane Real Estate Hypothesis

(2017) Mariola Szenk et al.   Cell Systems

Massively Parallel Interrogation of the Effects of Gene Expression Levels on Fitness

(2016) Leeat Keren et al.   CELL

Macromolecular crowding explains overflow metabolism in cells

(2016) Alexei Vazquez et al.   Scientific Reports

Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments

(2016) Edward J. O’Brien et al.   PLoS Computational Biology

Constrained Allocation Flux Balance Analysis

(2016) Matteo Mori et al.   PLoS Computational Biology

Reduction of translating ribosomes enables Escherichia coli to maintain elongation rates during slow growth

(2016) Xiongfeng Dai et al.   Nature Microbiology

Metabolic Trade-offs in Yeast are Caused by F1F0-ATP synthase

(2016) Avlant Nilsson et al.   Scientific Reports

How fast-growing bacteria robustly tune their ribosome concentration to approximate growth-rate maximization

(2015) Evert Bosdriesz et al.   FEBS Journal

Quantitative prediction of genome-wide resource allocation in bacteria

(2015) Anne Goelzer et al.   METABOLIC ENGINEERING

Proteome reallocation in Escherichia coli with increasing specific growth rate

(2015) Karl Peebo et al.   Molecular BioSystems

Protein costs do not explain evolution of metabolic strategies and regulation of ribosomal content: does protein investment explain an anaerobic bacterial Crabtree effect?

(2015) Anisha Goel et al.   MOLECULAR MICROBIOLOGY

A growth-rate composition formula for the growth of E. coli on co-utilized carbon substrates

(2015) R. Hermsen et al.   Molecular Systems Biology

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

Mechanistic links between cellular trade-offs, gene expression, and growth

(2015) Andrea Y. Weiße et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The concept of fitness in fluctuating environments

(2015) Bernt-Erik Sæther et al.   TRENDS IN ECOLOGY & EVOLUTION

Interplay between Constraints, Objectives, and Optimality for Genome-Scale Stoichiometric Models

(2015) Timo R. Maarleveld et al.   PLoS Computational Biology

Elucidating the adaptation and temporal coordination of metabolic pathways using in-silico evolution

(2014) Willi Gottstein et al.   BIOSYSTEMS

Hierarchy of non-glucose sugars in Escherichia coli

(2014) Guy Aidelberg et al.   BMC Systems Biology

Metabolic states with maximal specific rate carry flux through an elementary flux mode

(2014) Meike T. Wortel et al.   FEBS Journal

Emergence of robust growth laws from optimal regulation of ribosome synthesis

(2014) M. Scott et al.   Molecular Systems Biology

How Biochemical Constraints of Cellular Growth Shape Evolutionary Adaptations in Metabolism

(2013) J. Berkhout et al.   GENETICS

Enzyme allocation problems in kinetic metabolic networks: Optimal solutions are elementary flux modes

(2013) Stefan Müller et al.   JOURNAL OF THEORETICAL 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

Redox balance is key to explaining full vs. partial switching to low-yield metabolism

(2012) Milan JA van Hoek et al.   BMC Systems Biology

Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks

(2012) Steven M. Kelk et al.   Scientific Reports

The biomass objective function

(2010) Adam M Feist et al.   CURRENT OPINION IN MICROBIOLOGY

Identification of flux control in metabolic networks using non-equilibrium thermodynamics

(2010) Sergio Bordel et al.   METABOLIC ENGINEERING

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

(2010) M. Scott et al.   SCIENCE

Growth Rate-Dependent Global Effects on Gene Expression in Bacteria

(2009) Stefan Klumpp et al.   CELL

Control of specific growth rate in Saccharomyces cerevisiae

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

Impact of the solvent capacity constraint on E. coli metabolism

(2008) Alexei Vazquez et al.   BMC Systems Biology

Maintenance metabolism and carbon fluxes in Bacillus species

(2008) Simon Tännler et al.   Microbial Cell Factories