Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction

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

(2013) Kaspar Valgepea et al.   Molecular BioSystems

Dissecting specific and global transcriptional regulation of bacterial gene expression

(2013) L. Gerosa et al.   Molecular Systems Biology

Shared control of gene expression in bacteria by transcription factors and global physiology of the cell

(2013) S. Berthoumieux et al.   Molecular Systems Biology

The Ability of Flux Balance Analysis to Predict Evolution of Central Metabolism Scales with the Initial Distance to the Optimum

(2013) William R. Harcombe et al.   PLoS Computational Biology

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

The anti-Shine–Dalgarno sequence drives translational pausing and codon choice in bacteria

(2012) Gene-Wei Li et al.   NATURE

EcoCyc: fusing model organism databases with systems biology

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

Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage

(2012) Ines Thiele et al.   PLoS One

Multidimensional Optimality of Microbial Metabolism

(2012) R. Schuetz et al.   SCIENCE

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

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

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

(2012) Roi Adadi et al.   PLoS Computational Biology

Economics of membrane occupancy and respiro-fermentation

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

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

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

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

The PurR regulon in Escherichia coli K-12 MG1655

(2011) Byung-Kwan Cho et al.   NUCLEIC ACIDS RESEARCH

Characterization of diverse natural variants of CYP102A1 found within a species of Bacillus megaterium

(2011) Ji-Yeon Kang et al.   AMB Express

Functional Characterization of Alternate Optimal Solutions of Escherichia coli's Transcriptional and Translational Machinery

(2010) Ines Thiele et al.   BIOPHYSICAL JOURNAL

An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation

(2010) Tamir Tuller et al.   CELL

The biomass objective function

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

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

(2010) M. Scott et al.   SCIENCE

Cooperation Between Translating Ribosomes and RNA Polymerase in Transcription Elongation

(2010) S. Proshkin et al.   SCIENCE

Growth Rate-Dependent Global Effects on Gene Expression in Bacteria

(2009) Stefan Klumpp et al.   CELL

Specific growth rate dependent transcriptome profiling of Escherichia coli K12 MG1655 in accelerostat cultures

(2009) Ranno Nahku et al.   JOURNAL OF BIOTECHNOLOGY

Growth-limiting Intracellular Metabolites in Yeast Growing under Diverse Nutrient Limitations

(2009) Viktor M. Boer et al.   MOLECULAR BIOLOGY OF THE CELL

Shifts in growth strategies reflect tradeoffs in cellular economics

(2009) Douwe Molenaar et al.   Molecular Systems Biology

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

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

Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization

(2009) Ines Thiele et al.   PLoS Computational Biology

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Growth-rate-dependent partitioning of RNA polymerases in bacteria

(2008) S. Klumpp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA