Plasticity and epistasis strongly affect bacterial fitness after losing multiple metabolic genes

Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes

(2014) Pere Puigbò et al.   BMC BIOLOGY

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

(2014) Glen D'Souza et al.   EVOLUTION

Biased Estimates of Diminishing-Returns Epistasis? Empirical Evidence Revisited

(2014) David Berger et al.   GENETICS

Phylogenomics and the Dynamic Genome Evolution of the Genus Streptococcus

(2014) Vincent P. Richards et al.   Genome Biology and Evolution

Epistatic interactions among metabolic genes depend upon environmental conditions

(2014) Chintan Jagdishchandra Joshi et al.   Molecular BioSystems

Syntrophic exchange in synthetic microbial communities

(2014) M. T. Mee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolic costs of amino acid and protein production inEscherichia coli

(2013) Christoph Kaleta et al.   Biotechnology Journal

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

(2013) Samay Pande et al.   ISME Journal

Patterns of Epistasis between Beneficial Mutations in an Antibiotic Resistance Gene

(2013) Martijn F. Schenk et al.   MOLECULAR BIOLOGY AND EVOLUTION

Relative Amino Acid Composition Signatures of Organisms and Environments

(2013) Alexandra Moura et al.   PLoS One

Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean

(2013) B. K. Swan 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

Evolution of Divergent Life History Strategies in Marine Alphaproteobacteria

(2013) H. Luo et al.   mBio

The Environment Affects Epistatic Interactions to Alter the Topology of an Empirical Fitness Landscape

(2013) Kenneth M. Flynn et al.   PLoS Genetics

Design and Characterization of Auxotrophy-Based Amino Acid Biosensors

(2012) Felix Bertels et al.   PLoS One

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

(2012) J. J. Morris et al.   mBio

Economics of membrane occupancy and respiro-fermentation

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

Cooperative Adaptation to Establishment of a Synthetic Bacterial Mutualism

(2011) Kazufumi Hosoda et al.   PLoS One

Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population

(2011) A. I. Khan et al.   SCIENCE

Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation

(2011) H.-H. Chou et al.   SCIENCE

Fitness Epistasis and Constraints on Adaptation in a Human Immunodeficiency Virus Type 1 Protein Region

(2010) J. da Silva et al.   GENETICS

The consequences of genetic drift for bacterial genome complexity

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

Positive Epistasis Drives the Acquisition of Multidrug Resistance

(2009) Sandra Trindade et al.   PLoS Genetics

Genomics and Evolution of Heritable Bacterial Symbionts

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

Increased Fitness of Pseudomonas fluorescens Pf0-1 Leucine Auxotrophs in Soil

(2008) W. Kim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The global, ppGpp-mediated stringent response to amino acid starvation in Escherichia coli

(2008) Matthew F. Traxler et al.   MOLECULAR MICROBIOLOGY