Mapping the Fitness Landscape of Gene Expression Uncovers the Cause of Antagonism and Sign Epistasis between Adaptive Mutations

EPISTATIC INTERACTIONS DETERMINE THE MUTATIONAL PATHWAYS AND COEXISTENCE OF LINEAGES IN CLONALESCHERICHIA COLIPOPULATIONS

(2013) Ram Prasad Maharjan et al.   EVOLUTION

Synchronous Waves of Failed Soft Sweeps in the Laboratory: Remarkably Rampant Clonal Interference of Alleles at a Single Locus

(2013) M.-C. Lee et al.   GENETICS

Patterns of Epistasis between Beneficial Mutations in an Antibiotic Resistance Gene

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

Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations

(2013) Gregory I. Lang et al.   NATURE

Bounded population sizes, fluctuating selection and the tempo and mode of coexistence

(2013) X. Yi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

(2013) Sean Michael Carroll et al.   PLoS Genetics

FREQ-Seq: A Rapid, Cost-Effective, Sequencing-Based Method to Determine Allele Frequencies Directly from Mixed Populations

(2012) Lon M. Chubiz et al.   PLoS One

Predictability of evolution depends nonmonotonically on population size

(2012) I. G. Szendro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epistasis from functional dependence of fitness on underlying traits

(2012) H.-C. Chiu et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Molecular Diversity of Adaptive Convergence

(2012) O. Tenaillon et al.   SCIENCE

Optimization of Gene Expression through Divergent Mutational Paths

(2012) Hsin-Hung Chou et al.   Cell Reports

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

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

Tradeoffs and Optimality in the Evolution of Gene Regulation

(2011) Frank J. Poelwijk et al.   CELL

Epistasis Increases the Rate of Conditionally Neutral Substitution in an Adapting Population

(2011) J. A. Draghi et al.   GENETICS

Genetic Variation and the Fate of Beneficial Mutations in Asexual Populations

(2011) Gregory I. Lang et al.   GENETICS

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

Second-Order Selection for Evolvability in a Large Escherichia coli Population

(2011) R. J. Woods et al.   SCIENCE

Evolutionary Accessibility of Mutational Pathways

(2011) Jasper Franke et al.   PLoS Computational Biology

Reciprocal Sign Epistasis between Frequently Experimentally Evolved Adaptive Mutations Causes a Rugged Fitness Landscape

(2011) Daniel J. Kvitek et al.   PLoS Genetics

Epistasis between Beneficial Mutations and the Phenotype-to-Fitness Map for a ssDNA Virus

(2011) Darin R. Rokyta et al.   PLoS Genetics

Exploring the Effect of Sex on Empirical Fitness Landscapes

(2009) J. Arjan G. M. de Visser et al.   AMERICAN NATURALIST

ASYMMETRIC, BIMODAL TRADE-OFFS DURING ADAPTATION OFMETHYLOBACTERIUMTO DISTINCT GROWTH SUBSTRATES

(2009) Ming-Chun Lee et al.   EVOLUTION

The Evolution of Epistasis and Its Links With Genetic Robustness, Complexity and Drift in a Phenotypic Model of Adaptation

(2009) P.-A. Gros et al.   GENETICS

Optimization of gene expression by natural selection

(2009) T. Bedford et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The dynamics of adaptation on correlated fitness landscapes

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

Fast Growth Increases the Selective Advantage of a Mutation Arising Recurrently during Evolution under Metal Limitation

(2009) Hsin-Hung Chou et al.   PLoS Genetics

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

Formate as the Main Branch Point for Methylotrophic Metabolism in Methylobacterium extorquens AM1

(2008) G. J. Crowther et al.   JOURNAL OF BACTERIOLOGY

Epistasis — the essential role of gene interactions in the structure and evolution of genetic systems

(2008) Patrick C. Phillips   NATURE REVIEWS GENETICS