Empirical fitness landscapes and the predictability of evolution

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

(2014) Hsin-Hung Chou et al.   PLoS Genetics

Predicting C4 Photosynthesis Evolution: Modular, Individually Adaptive Steps on a Mount Fuji Fitness Landscape

(2013) David Heckmann et al.   CELL

Should evolutionary geneticists worry about higher-order epistasis?

(2013) Daniel M Weinreich et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

SELECTION BIASES THE PREVALENCE AND TYPE OF EPISTASIS ALONG ADAPTIVE TRAJECTORIES

(2013) Jeremy A. Draghi et al.   EVOLUTION

Translating HIV Sequences into Quantitative Fitness Landscapes Predicts Viral Vulnerabilities for Rational Immunogen Design

(2013) Andrew L. Ferguson et al.   IMMUNITY

Evolutionary Accessibility of Modular Fitness Landscapes

(2013) B. Schmiegelt et al.   JOURNAL OF STATISTICAL PHYSICS

Long-term evolution is surprisingly predictable in lattice proteins

(2013) M. E. Palmer et al.   Journal of the Royal Society Interface

Exact results for amplitude spectra of fitness landscapes

(2013) Johannes Neidhart et al.   JOURNAL OF THEORETICAL BIOLOGY

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

Genotype to phenotype: lessons from model organisms for human genetics

(2013) Ben Lehner   NATURE REVIEWS GENETICS

Evolutionary biochemistry: revealing the historical and physical causes of protein properties

(2013) Michael J. Harms et al.   NATURE REVIEWS GENETICS

Understanding, predicting and manipulating the genotypic evolution of antibiotic resistance

(2013) Adam C. Palmer et al.   NATURE REVIEWS GENETICS

Genome dynamics during experimental evolution

(2013) Jeffrey E. Barrick et al.   NATURE REVIEWS GENETICS

Designing Antibiotic Cycling Strategies by Determining and Understanding Local Adaptive Landscapes

(2013) Christiane P. Goulart et al.   PLoS One

Genotype to Phenotype Mapping and the Fitness Landscape of the E. coli lac Promoter

(2013) Jakub Otwinowski et al.   PLoS One

Comprehensive experimental fitness landscape and evolutionary network for small RNA

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

Environmental Dependence of Genetic Constraint

(2013) Marjon G. J. de Vos et al.   PLoS Genetics

Stability-mediated epistasis constrains the evolution of an influenza protein

(2013) Lizhi Ian Gong et al.   eLife

A Comparison of Genotype-Phenotype Maps for RNA and Proteins

(2012) Evandro Ferrada et al.   BIOPHYSICAL JOURNAL

Real time forecasting of near-future evolution

(2012) P. J. Gerrish et al.   Journal of the Royal Society Interface

The peaks and geometry of fitness landscapes

(2012) Kristina Crona et al.   JOURNAL OF THEORETICAL BIOLOGY

Genomic analysis of a key innovation in an experimental Escherichia coli population

(2012) Zachary D. Blount et al.   NATURE

The Consistency of Beneficial Fitness Effects of Mutations across Diverse Genetic Backgrounds

(2012) Victoria M. Pearson 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

The Molecular Diversity of Adaptive Convergence

(2012) O. Tenaillon et al.   SCIENCE

The Potential for Respiratory Droplet-Transmissible A/H5N1 Influenza Virus to Evolve in a Mammalian Host

(2012) C. A. Russell et al.   SCIENCE

Exploring the Complexity of the HIV-1 Fitness Landscape

(2012) Roger D. Kouyos et al.   PLoS Genetics

Replaying the Tape of Life: Quantification of the Predictability of Evolution

(2012) Alexander E. Lobkovsky et al.   Frontiers in Genetics

EVOLUTIONARY ADVANTAGE OF SMALL POPULATIONS ON COMPLEX FITNESS LANDSCAPES

(2011) Kavita Jain et al.   EVOLUTION

A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase

(2011) Trevor Hinkley et al.   NATURE GENETICS

The pleiotropic structure of the genotype–phenotype map: the evolvability of complex organisms

(2011) Günter P. Wagner et al.   NATURE REVIEWS GENETICS

Systems-biology approaches for predicting genomic evolution

(2011) Balázs Papp et al.   NATURE REVIEWS GENETICS

Hidden Randomness between Fitness Landscapes Limits Reverse Evolution

(2011) Longzhi Tan et al.   PHYSICAL REVIEW LETTERS

Experimental illumination of a fitness landscape

(2011) R. T. Hietpas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A biophysical protein folding model accounts for most mutational fitness effects in viruses

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

The causes of epistasis

(2011) J. A. G. M. de Visser et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Statistical genetics and evolution of quantitative traits

(2011) Richard A. Neher et al.   REVIEWS OF MODERN PHYSICS

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

Epistasis in a Model of Molecular Signal Transduction

(2011) Alain Pumir et al.   PLoS Computational Biology

Evolutionary Accessibility of Mutational Pathways

(2011) Jasper Franke et al.   PLoS Computational Biology

Predictability of Evolutionary Trajectories in Fitness Landscapes

(2011) Alexander E. Lobkovsky et al.   PLoS Computational Biology

Nonlinear Fitness Landscape of a Molecular Pathway

(2011) Lilia Perfeito 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

Initial Mutations Direct Alternative Pathways of Protein Evolution

(2011) Merijn L. M. Salverda et al.   PLoS Genetics

GENOME STRUCTURE AND THE BENEFIT OF SEX

(2010) Richard A. Watson et al.   EVOLUTION

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

(2010) J. da Silva et al.   GENETICS

Fitness Epistasis among 6 Biosynthetic Loci in the Budding Yeast Saccharomyces cerevisiae

(2010) D. W. Hall et al.   JOURNAL OF HEREDITY

Reciprocal sign epistasis is a necessary condition for multi-peaked fitness landscapes

(2010) Frank J. Poelwijk et al.   JOURNAL OF THEORETICAL BIOLOGY

Compensatory Mutations Restore Fitness during the Evolution of Dihydrofolate Reductase

(2010) K. M. Brown et al.   MOLECULAR BIOLOGY AND EVOLUTION

Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence

(2010) J. B. Kinney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid Construction of Empirical RNA Fitness Landscapes

(2010) J. N. Pitt et al.   SCIENCE

Evolutionary Trajectories of Beta-Lactamase CTX-M-1 Cluster Enzymes: Predicting Antibiotic Resistance

(2010) Ângela Novais et al.   PLoS Pathogens

Exploring the Effect of Sex on Empirical Fitness Landscapes

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

Analysis of a complete DNA-protein affinity landscape

(2009) W. Rowe et al.   Journal of the Royal Society Interface

Probing Evolutionary Repeatability: Neutral and Double Changes and the Predictability of Evolutionary Adaptation

(2009) Scott William Roy   PLoS One

Emergence of species in evolutionary “simulated annealing”

(2009) Muyoung Heo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stepwise acquisition of pyrimethamine resistance in the malaria parasite

(2009) E. R. Lozovsky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The rate at which asexual populations cross fitness valleys

(2009) Daniel B. Weissman et al.   THEORETICAL POPULATION BIOLOGY

Quantitative exploration of the catalytic landscape separating divergent plant sesquiterpene synthases

(2008) Paul E O'Maille et al.   Nature Chemical Biology

Neutralism and selectionism: a network-based reconciliation

(2008) Andreas Wagner   NATURE REVIEWS GENETICS

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

(2008) Patrick C. Phillips   NATURE REVIEWS GENETICS

Heterogeneous Adaptive Trajectories of Small Populations on Complex Fitness Landscapes

(2008) Daniel E. Rozen et al.   PLoS One

Energy-dependent fitness: A quantitative model for the evolution of yeast transcription factor binding sites

(2008) V. Mustonen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA