Inferring fitness landscapes by regression produces biased estimates of epistasis

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

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

(2013) Ram Prasad Maharjan et al.   EVOLUTION

Exact results for amplitude spectra of fitness landscapes

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

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

Experiments on the role of deleterious mutations as stepping stones in adaptive evolution

(2013) Arthur W. Covert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Capturing the mutational landscape of the beta-lactamase TEM-1

(2013) H. Jacquier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The spatial architecture of protein function and adaptation

(2012) Richard N. McLaughlin Jr et al.   NATURE

Environmental change exposes beneficial epistatic interactions in a catalytic RNA

(2012) E. J. Hayden et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Exploring the Complexity of the HIV-1 Fitness Landscape

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

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Distinguishing Driver and Passenger Mutations in an Evolutionary History Categorized by Interference

(2011) Christopher J. R. Illingworth et al.   GENETICS

Quantifying Selection Acting on a Complex Trait Using Allele Frequency Time Series Data

(2011) C. J. R. Illingworth et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2011) Trevor Hinkley et al.   NATURE GENETICS

Fitness Ranking of Individual Mutants Drives Patterns of Epistatic Interactions in HIV-1

(2011) Javier P. Martínez et al.   PLoS One

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

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

Deep mutational scanning: assessing protein function on a massive scale

(2011) Carlos L. Araya et al.   TRENDS IN BIOTECHNOLOGY

Predictability of Evolutionary Trajectories in Fitness Landscapes

(2011) Alexander E. Lobkovsky 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

Prevalence of Epistasis in the Evolution of Influenza A Surface Proteins

(2011) Sergey Kryazhimskiy 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

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

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

High-resolution mapping of protein sequence-function relationships

(2010) Douglas M Fowler et al.   NATURE METHODS

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

Pervasive Cryptic Epistasis in Molecular Evolution

(2010) Mark Lunzer et al.   PLoS Genetics

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

(2010) Ângela Novais et al.   PLoS Pathogens

Revealing evolutionary pathways by fitness landscape reconstruction

(2009) Manjunatha Kogenaru et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Directed enzyme evolution: climbing fitness peaks one amino acid at a time

(2009) Cara A Tracewell et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

An epistatic ratchet constrains the direction of glucocorticoid receptor evolution

(2009) Jamie T. Bridgham et al.   NATURE

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 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

In the light of directed evolution: Pathways of adaptive protein evolution

(2009) J. D. Bloom et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein Dynamism and Evolvability

(2009) N. Tokuriki et al.   SCIENCE

The rate at which asexual populations cross fitness valleys

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

Positive Epistasis Drives the Acquisition of Multidrug Resistance

(2009) Sandra Trindade et al.   PLoS Genetics

Constructing and Analyzing the Fitness Landscape of an Experimental Evolutionary Process

(2008) Manfred T. Reetz et al.   CHEMBIOCHEM

Rapid in vivo exploration of a 5S rRNA neutral network

(2008) Zhengdong D. Zhang et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Quantitative exploration of the catalytic landscape separating divergent plant sesquiterpene synthases

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

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

(2008) Patrick C. Phillips   NATURE REVIEWS GENETICS

Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli

(2008) Z. D. Blount et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA