Indirect and suboptimal control of gene expression is widespread in bacteria

Mode of Regulation and the Insulation of Bacterial Gene Expression

(2012) Vered Sasson et al.   MOLECULAR CELL

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

Selection-Driven Gene Loss in Bacteria

(2012) Sanna Koskiniemi et al.   PLoS Genetics

Fnr (EtrA) acts as a fine-tuning regulator of anaerobic metabolism in Shewanella oneidensis MR-1

(2011) Claribel Cruz-García et al.   BMC MICROBIOLOGY

Evidence-Based Annotation of Transcripts and Proteins in the Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough

(2011) M. N. Price et al.   JOURNAL OF BACTERIOLOGY

Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs

(2011) F. Wessely et al.   Molecular Systems Biology

A mathematical model for adaptive prediction of environmental changes by microorganisms

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

Direct regulation of Escherichia coli ribosomal protein promoters by the transcription factors ppGpp and DksA

(2011) J. J. Lemke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evidence-Based Annotation of Gene Function in Shewanella oneidensis MR-1 Using Genome-Wide Fitness Profiling across 121 Conditions

(2011) Adam Deutschbauer et al.   PLoS Genetics

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

(2010) Irit Shachrai et al.   MOLECULAR CELL

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

Genomic repertoires of DNA-binding transcription factors across the tree of life

(2010) Varodom Charoensawan et al.   NUCLEIC ACIDS RESEARCH

RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)

(2010) S. Gama-Castro et al.   NUCLEIC ACIDS RESEARCH

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

(2010) Y. Taniguchi et al.   SCIENCE

Constraint-Based Model of Shewanella oneidensis MR-1 Metabolism: A Tool for Data Analysis and Hypothesis Generation

(2010) Grigoriy E. Pinchuk et al.   PLoS Computational Biology

Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants

(2009) G. C. Langridge et al.   GENOME RESEARCH

Adaptive prediction of environmental changes by microorganisms

(2009) Amir Mitchell et al.   NATURE

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

(2009) Ron Milo et al.   NUCLEIC ACIDS RESEARCH

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes

(2009) Pavel S. Novichkov et al.   NUCLEIC ACIDS RESEARCH

Transcriptome Complexity in a Genome-Reduced Bacterium

(2009) M. Guell et al.   SCIENCE

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

Principles of transcriptional regulation and evolution of the metabolic system in E. coli

(2008) A. S.N. Seshasayee et al.   GENOME RESEARCH

The Role of DNA-binding Specificity in the Evolution of Bacterial Regulatory Networks

(2008) Irma Lozada-Chávez et al.   JOURNAL OF MOLECULAR BIOLOGY

Predictive Behavior Within Microbial Genetic Networks

(2008) I. Tagkopoulos et al.   SCIENCE

Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli

(2008) Morgan N Price et al.   GENOME BIOLOGY

Integration of Horizontally Transferred Genes into Regulatory Interaction Networks Takes Many Million Years

(2007) M. J. Lercher et al.   MOLECULAR BIOLOGY AND EVOLUTION