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

Using Genome-scale Models to Predict Biological Capabilities

(2015) Edward J. O’Brien et al.   CELL

Computing the functional proteome: recent progress and future prospects for genome-scale models

(2015) Edward J O’Brien et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

Hierarchy of non-glucose sugars in Escherichia coli

(2014) Guy Aidelberg et al.   BMC Systems Biology

Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources

(2014) Gene-Wei Li et al.   CELL

Coordination of microbial metabolism

(2014) Victor Chubukov et al.   NATURE REVIEWS MICROBIOLOGY

Maximal Sum of Metabolic Exchange Fluxes Outperforms Biomass Yield as a Predictor of Growth Rate of Microorganisms

(2014) Raphy Zarecki et al.   PLoS One

The Interrelationship between Promoter Strength, Gene Expression, and Growth Rate

(2014) Matthew S. Bienick et al.   PLoS One

Different Levels of Catabolite Repression Optimize Growth in Stable and Variable Environments

(2014) Aaron M. New et al.   PLOS BIOLOGY

Specific Growth Rate Determines the Sensitivity ofEscherichia colito Lactic Acid Stress: Implications for Predictive Microbiology

(2014) Roland Lindqvist et al.   Biomed Research International

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

(2013) Kaspar Valgepea et al.   Molecular BioSystems

Coordination of bacterial proteome with metabolism by cyclic AMP signalling

(2013) Conghui You et al.   NATURE

Molecular crowding limits translation and cell growth

(2013) S. Klumpp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

EcoCyc: fusing model organism databases with systems biology

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

Stress responses as determinants of antimicrobial resistance in Gram-negative bacteria

(2012) Keith Poole   TRENDS IN MICROBIOLOGY

Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters

(2012) Roi Adadi et al.   PLoS Computational Biology

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

(2011) Arren Bar-Even et al.   BIOCHEMISTRY

Functional and Metabolic Effects of Adaptive Glycerol Kinase (GLPK) Mutants inEscherichia coli

(2011) M. Kenyon Applebee et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Microbial laboratory evolution in the era of genome-scale science

(2011) T. M. Conrad et al.   Molecular Systems Biology

Novel Roles of cAMP Receptor Protein (CRP) in Regulation of Transport and Metabolism of Carbon Sources

(2011) Tomohiro Shimada et al.   PLoS One

Condition-Dependent Cell Volume and Concentration of Escherichia coli to Facilitate Data Conversion for Systems Biology Modeling

(2011) Benjamin Volkmer et al.   PLoS One

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

(2010) Irit Shachrai et al.   MOLECULAR CELL

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

(2010) M. Scott et al.   SCIENCE

Strategies for cellular decision-making

(2009) Theodore J Perkins et al.   Molecular Systems Biology

Adaptive prediction of environmental changes by microorganisms

(2009) Amir Mitchell et al.   NATURE

Predictive Behavior Within Microbial Genetic Networks

(2008) I. Tagkopoulos et al.   SCIENCE