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

Fast growth phenotype of E. coli K-12 from adaptive laboratory evolution does not require intracellular flux rewiring

(2017) Christopher P. Long et al.   METABOLIC ENGINEERING

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

How important is thermodynamics for identifying elementary flux modes?

(2017) Sabine Peres et al.   PLoS One

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

Expression of a functional oxygen-labile nitrogenase component in the mitochondrial matrix of aerobically grown yeast

(2016) Gema López-Torrejón et al.   Nature Communications

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

(2016) Elad Noor et al.   PLoS Computational Biology

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

Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes

(2016) Jonathan M. Monk et al.   Cell Systems

Evolutionary pressures on microbial metabolic strategies in the chemostat

(2016) Meike T. Wortel et al.   Scientific Reports

Resource allocation in metabolic networks: kinetic optimization and approximations by FBA

(2015) S. Muller et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

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

Overflow metabolism in Escherichia coli results from efficient proteome allocation

(2015) Markus Basan et al.   NATURE

Metabolomics integrated elementary flux mode analysis in large metabolic networks

(2015) Matthias P. Gerstl et al.   Scientific Reports

Use of Adaptive Laboratory Evolution To Discover Key Mutations Enabling Rapid Growth of Escherichia coli K-12 MG1655 on Glucose Minimal Medium

(2014) Ryan A. LaCroix et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism

(2014) Elad Noor et al.   PLoS Computational Biology

A note on the kinetics of enzyme action: A decomposition that highlights thermodynamic effects

(2013) Elad Noor et al.   FEBS LETTERS

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

(2013) Stefan Müller et al.   JOURNAL OF THEORETICAL BIOLOGY

Escherichia coli achieves faster growth by increasing catalytic and translation rates of proteins

(2013) Kaspar Valgepea et al.   Molecular BioSystems

Steady-State Metabolite Concentrations Reflect a Balance between Maximizing Enzyme Efficiency and Minimizing Total Metabolite Load

(2013) Naama Tepper et al.   PLoS One

Glycolytic strategy as a tradeoff between energy yield and protein cost

(2013) A. Flamholz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Availability of public goods shapes the evolution of competing metabolic strategies

(2013) H. Bachmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolic shifts: a fitness perspective for microbial cell factories

(2012) Anisha Goel et al.   BIOTECHNOLOGY LETTERS

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

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

System-Level Insights into Yeast Metabolism by Thermodynamic Analysis of Elementary Flux Modes

(2012) Stefan J. Jol et al.   PLoS Computational Biology

Cell design in bacteria as a convex optimization problem

(2011) Anne Goelzer et al.   AUTOMATICA

Bacterial growth rate reflects a bottleneck in resource allocation

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

Combining Metabolic Pathway Analysis with Evolutionary Game Theory. Explaining the occurrence of low-yield pathways by an analytic optimization approach

(2011) Stefan Schuster et al.   BIOSYSTEMS

Large-scale 13C-flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli

(2011) B. R. B. Haverkorn van Rijsewijk et al.   Molecular Systems Biology

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

(2010) Wolfram Liebermeister et al.   BIOINFORMATICS

Revisiting the Thermodynamic Theory of Optimal ATP Stoichiometries by Analysis of Various ATP-Producing Metabolic Pathways

(2010) Sarah Werner et al.   JOURNAL OF MOLECULAR EVOLUTION

Parameter Balancing in Kinetic Models of Cell Metabolism†

(2010) Timo Lubitz et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

(2010) M. Scott et al.   SCIENCE

Population consequences of mutational events: effects of antibiotic resistance on the r/K trade-off

(2009) Jay M. Fitzsimmons et al.   EVOLUTIONARY ECOLOGY