Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitrokcatmeasurements

Posttranslational regulation of microbial metabolism

(2015) Karl Kochanowski et al.   CURRENT OPINION IN MICROBIOLOGY

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

The quantitative and condition-dependent Escherichia coli proteome

(2015) Alexander Schmidt et al.   NATURE BIOTECHNOLOGY

Programmed Evolution for Optimization of Orthogonal Metabolic Output in Bacteria

(2015) Todd T. Eckdahl et al.   PLoS One

Computational protein design enables a novel one-carbon assimilation pathway

(2015) Justin B. Siegel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantification and Mass Isotopomer Profiling of α-Keto Acids in Central Carbon Metabolism

(2014) Michael Zimmermann et al.   ANALYTICAL CHEMISTRY

Coordination of microbial metabolism

(2014) Victor Chubukov et al.   NATURE REVIEWS MICROBIOLOGY

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

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

(2014) Daniel Machado et al.   PLoS Computational Biology

Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism

(2014) Elad Noor et al.   PLoS Computational Biology

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

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

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

(2013) Kaspar Valgepea et al.   Molecular BioSystems

Transcriptional regulation is insufficient to explain substrate-induced flux changes in Bacillus subtilis

(2013) V. Chubukov et al.   Molecular Systems Biology

The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes

(2013) Nicholas Furnham et al.   NUCLEIC ACIDS RESEARCH

Heterogeneity in protein expression induces metabolic variability in a modeledEscherichia colipopulation

(2013) Piyush Labhsetwar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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 Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Whyin vivomay not equalin vitro- new effectors revealed by measurement of enzymatic activities under the samein vivo-like assay conditions

(2012) Rodolfo García-Contreras et al.   FEBS Journal

EcoCyc: fusing model organism databases with systems biology

(2012) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

RELATCH: relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations

(2012) Joonhoon Kim et al.   GENOME BIOLOGY

Standardized Assay Medium To Measure Lactococcus lactis Enzyme Activities while Mimicking Intracellular Conditions

(2011) Anisha Goel et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UDP-N-acetylglucosamine enolpyruvyl transferase as a potential target for antibacterial chemotherapy: recent developments

(2011) Ankur Gautam et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

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

(2011) Arren Bar-Even et al.   BIOCHEMISTRY

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

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

Physical limits of cells and proteomes

(2011) K. A. Dill et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An overview of enzymatic reagents for the removal of affinity tags

(2011) David S. Waugh   PROTEIN EXPRESSION AND PURIFICATION

Genome-Scale Metabolic Modeling Elucidates the Role of Proliferative Adaptation in Causing the Warburg Effect

(2011) Tomer Shlomi et al.   PLoS Computational Biology

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

(2010) Wolfram Liebermeister et al.   BIOINFORMATICS

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

(2010) Karen van Eunen et al.   FEBS Journal

Kinetic and Thermodynamic Aspects of Enzyme Control and Regulation†

(2010) Johann M. Rohwer et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Parameter Balancing in Kinetic Models of Cell Metabolism†

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

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

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

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

Symmetrical Refolding of Protein Domains and Subunits: Example of the Dimeric Two-Domain 3-Isopropylmalate Dehydrogenases†

(2009) Éva Gráczer et al.   BIOCHEMISTRY

Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli

(2009) Bryson D Bennett et al.   Nature Chemical Biology

BioNumbers—the database of key numbers in molecular and cell biology

(2009) Ron Milo et al.   NUCLEIC ACIDS RESEARCH

Allosteric regulation and catalysis emerge via a common route

(2008) Nina M Goodey et al.   Nature Chemical Biology

Untangling the glutamate dehydrogenase allosteric nightmare

(2008) Thomas J. Smith et al.   TRENDS IN BIOCHEMICAL SCIENCES