Cellular Growth Arrest and Persistence from Enzyme Saturation

Phenotypic bistability in Escherichia coli's central carbon metabolism

(2014) O. Kotte et al.   Molecular Systems Biology

Lost in Transition: Start-Up of Glycolysis Yields Subpopulations of Nongrowing Cells

(2014) J. H. van Heerden et al.   SCIENCE

The role of metabolism in bacterial persistence

(2014) Stephanie M. Amato et al.   Frontiers in Microbiology

Metabolic Control of Persister Formation in Escherichia coli

(2013) Stephanie M. Amato et al.   MOLECULAR CELL

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Evolution after Introduction of a Novel Metabolic Pathway Consistently Leads to Restoration of Wild-Type Physiology

(2013) Sean Michael Carroll et al.   PLoS Genetics

Signaling-mediated bacterial persister formation

(2012) Nicole M Vega et al.   Nature Chemical Biology

EcoCyc: fusing model organism databases with systems biology

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

Regulatory architecture determines optimal regulation of gene expression in metabolic pathways

(2012) V. Chubukov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cost-Benefit Tradeoffs in Engineered lac Operons

(2012) M. Eames et al.   SCIENCE

Global Network Reorganization During Dynamic Adaptations of Bacillus subtilis Metabolism

(2012) J. M. Buescher et al.   SCIENCE

Interplay of Gene Expression Noise and Ultrasensitive Dynamics Affects Bacterial Operon Organization

(2012) J. Christian J Ray et al.   PLoS Computational Biology

Mapping the Environmental Fitness Landscape of a Synthetic Gene Circuit

(2012) Dmitry Nevozhay et al.   PLoS Computational Biology

Adaptive Evolution of the Lactose Utilization Network in Experimentally Evolved Populations of Escherichia coli

(2012) Selwyn Quan et al.   PLoS Genetics

StochKit2: software for discrete stochastic simulation of biochemical systems with events

(2011) K. R. Sanft et al.   BIOINFORMATICS

Growth, metabolic partitioning, and the size of microorganisms

(2011) C. P. Kempes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nonlinear Fitness Landscape of a Molecular Pathway

(2011) Lilia Perfeito et al.   PLoS Genetics

Persister Cells

(2010) Kim Lewis   Annual Review of Microbiology

Fundamental limits on the suppression of molecular fluctuations

(2010) Ioannis Lestas et al.   NATURE

RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media

(2010) T. M. Conrad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution under Fluctuating Environments Explains Observed Robustness in Metabolic Networks

(2010) Orkun S. Soyer et al.   PLoS Computational Biology

Achieving Optimal Growth through Product Feedback Inhibition in Metabolism

(2010) Sidhartha Goyal et al.   PLoS Computational Biology

The Chromosomal Toxin Gene yafQ Is a Determinant of Multidrug Tolerance for Escherichia coli Growing in a Biofilm

(2009) J. J. Harrison et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Cells need safety valves

(2009) Antoine Danchin   BIOESSAYS

Growth Rate-Dependent Global Effects on Gene Expression in Bacteria

(2009) Stefan Klumpp et al.   CELL

Genome Sequences of Escherichia coli B strains REL606 and BL21(DE3)

(2009) Haeyoung Jeong et al.   JOURNAL OF MOLECULAR BIOLOGY

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

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

Cellular stress created by intermediary metabolite imbalances

(2009) S. J. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stochasticity in Protein Levels Drives Colinearity of Gene Order in Metabolic Operons of Escherichia coli

(2009) Károly Kovács et al.   PLOS BIOLOGY

On the Accessibility of Adaptive Phenotypes of a Bacterial Metabolic Network

(2009) Wilfred Ndifon et al.   PLoS Computational Biology

The Cost of Expression of Escherichia coli lac Operon Proteins Is in the Process, Not in the Products

(2008) D. M. Stoebel et al.   GENETICS

Molecular Titration and Ultrasensitivity in Regulatory Networks

(2008) Nicolas E. Buchler et al.   JOURNAL OF MOLECULAR BIOLOGY

Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network

(2008) Gal Chechik et al.   NATURE BIOTECHNOLOGY

Single-cell protein induction dynamics reveals a period of vulnerability to antibiotics in persister bacteria

(2008) O. Gefen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spontaneous Reaction Silencing in Metabolic Optimization

(2008) Takashi Nishikawa et al.   PLoS Computational Biology