LESS IS MORE: SELECTIVE ADVANTAGES CAN EXPLAIN THE PREVALENT LOSS OF BIOSYNTHETIC GENES IN BACTERIA

Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria

(2013) Samay Pande et al.   ISME Journal

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

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

(2013) J. M. Monk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial Adaptation through Loss of Function

(2013) Alison K. Hottes et al.   PLoS Genetics

Ecological interactions drive evolutionary loss of traits

(2012) Jacintha Ellers et al.   ECOLOGY LETTERS

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

(2012) J. J. Morris et al.   mBio

Repeated, Selection-Driven Genome Reduction of Accessory Genes in Experimental Populations

(2012) Ming-Chun Lee et al.   PLoS Genetics

Selection-Driven Gene Loss in Bacteria

(2012) Sanna Koskiniemi et al.   PLoS Genetics

Experimental Evolution of Legionella pneumophila in Mouse Macrophages Leads to Strains with Altered Determinants of Environmental Survival

(2012) Alexander W. Ensminger et al.   PLoS Pathogens

An Interdependent Metabolic Patchwork in the Nested Symbiosis of Mealybugs

(2011) John P. McCutcheon et al.   CURRENT BIOLOGY

Synthetic Escherichia coli consortia engineered for syntrophy demonstrate enhanced biomass productivity

(2011) Hans C. Bernstein et al.   JOURNAL OF BIOTECHNOLOGY

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

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

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata

(2011) I. Pagani et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2011) R. Caspi et al.   NUCLEIC ACIDS RESEARCH

Computational Design of Auxotrophy-Dependent Microbial Biosensors for Combinatorial Metabolic Engineering Experiments

(2011) Naama Tepper et al.   PLoS One

Similarity of genes horizontally acquired by Escherichia coli and Salmonella enterica is evidence of a supraspecies pangenome

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

Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population

(2011) A. I. Khan et al.   SCIENCE

Comparison of 61 Sequenced Escherichia coli Genomes

(2010) Oksana Lukjancenko et al.   MICROBIAL ECOLOGY

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

(2010) Irit Shachrai et al.   MOLECULAR CELL

EcoCyc: a comprehensive database of Escherichia coli biology

(2010) I. M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

(2010) M. Scott et al.   SCIENCE

The consequences of genetic drift for bacterial genome complexity

(2009) C.-H. Kuo et al.   GENOME RESEARCH

Genome evolution and adaptation in a long-term experiment with Escherichia coli

(2009) Jeffrey E. Barrick et al.   NATURE

Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

(2009) Marie Touchon et al.   PLoS Genetics

Genomics and Evolution of Heritable Bacterial Symbionts

(2008) Nancy A. Moran et al.   Annual Review of Genetics

The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates

(2008) D. A. Rasko et al.   JOURNAL OF BACTERIOLOGY

A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1

(2008) Véronique de Berardinis et al.   Molecular Systems Biology