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

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

Constrained Allocation Flux Balance Analysis

(2016) Matteo Mori et al.   PLoS Computational Biology

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

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

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

Visual account of protein investment in cellular functions

(2014) W. Liebermeister et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism

(2014) Elad Noor et al.   PLoS Computational Biology

What is the total number of protein molecules per cell volume? A call to rethink some published values

(2013) Ron Milo   BIOESSAYS

Non-stationary13C-metabolic flux ratio analysis

(2013) Manuel Hörl et al.   BIOTECHNOLOGY AND BIOENGINEERING

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

(2013) Elad Noor et al.   FEBS LETTERS

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

(2013) Kieran Smallbone et al.   FEBS LETTERS

A generic rate equation for catalysed, template-directed polymerisation

(2013) Jan-Hendrik S. Hofmeyr et al.   FEBS LETTERS

Expression-level optimization of a multi-enzyme pathway in the absence of a high-throughput assay

(2013) Michael E. Lee et al.   NUCLEIC ACIDS RESEARCH

Spanning high-dimensional expression space using ribosome-binding site combinatorics

(2013) Lior Zelcbuch et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Naama Tepper et al.   PLoS One

Systematic Construction of Kinetic Models from Genome-Scale Metabolic Networks

(2013) Natalie J. Stanford 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

Consistent Estimation of Gibbs Energy Using Component Contributions

(2013) Elad Noor et al.   PLoS Computational Biology

A proof for loop-law constraints in stoichiometric metabolic networks

(2012) Elad Noor et al.   BMC Systems Biology

Comparison and applications of label-free absolute proteome quantification methods on Escherichia coli

(2012) L. Arike et al.   Journal of Proteomics

Multidimensional Optimality of Microbial Metabolism

(2012) R. Schuetz et al.   SCIENCE

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

(2011) Arren Bar-Even et al.   BIOCHEMISTRY

Enzyme maintenance effort as criterion for the characterization of alternative pathways and length distribution of isofunctional enzymes

(2011) Andreas Hoppe et al.   BIOSYSTEMS

A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks

(2011) R.M.T. Fleming et al.   JOURNAL OF THEORETICAL BIOLOGY

Economics of membrane occupancy and respiro-fermentation

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

eQuilibrator--the biochemical thermodynamics calculator

(2011) A. Flamholz et al.   NUCLEIC ACIDS RESEARCH

Hydrophobicity and Charge Shape Cellular Metabolite Concentrations

(2011) Arren Bar-Even et al.   PLoS Computational Biology

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

(2010) Wolfram Liebermeister et al.   BIOINFORMATICS

Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model

(2010) K. Yizhak et al.   BIOINFORMATICS

Measuring enzyme activities under standardized in vivo-like conditions for systems biology

(2010) Karen van Eunen et al.   FEBS Journal

Parameter Balancing in Kinetic Models of Cell Metabolism†

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

Cost of Unneeded Proteins in E. coli Is Reduced after Several Generations in Exponential Growth

(2010) Irit Shachrai et al.   MOLECULAR CELL

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

(2010) Nathan E Lewis et al.   Molecular Systems Biology

Design and analysis of synthetic carbon fixation pathways

(2010) A. Bar-Even et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational framework for predictive biodegradation

(2009) Stacey D. Finley et al.   BIOTECHNOLOGY AND BIOENGINEERING

Shifts in growth strategies reflect tradeoffs in cellular economics

(2009) Douwe Molenaar et al.   Molecular Systems Biology

Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks

(2008) Matthew D. Jankowski et al.   BIOPHYSICAL JOURNAL

Network-based prediction of human tissue-specific metabolism

(2008) Tomer Shlomi et al.   NATURE BIOTECHNOLOGY