Strong Selection Significantly Increases Epistatic Interactions in the Long-Term Evolution of a Protein

A tortoise–hare pattern seen in adapting structured and unstructured populations suggests a rugged fitness landscape in bacteria

(2015) Joshua R. Nahum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Valley-of-Death: Reciprocal sign epistasis constrains adaptive trajectories in a constant, nutrient limiting environment

(2014) Kami E. Chiotti et al.   GENOMICS

A Systematic Survey of an Intragenic Epistatic Landscape

(2014) Claudia Bank et al.   MOLECULAR BIOLOGY AND EVOLUTION

Historical contingency and its biophysical basis in glucocorticoid receptor evolution

(2014) Michael J. Harms et al.   NATURE

Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses

(2014) M. Lagator et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Global epistasis makes adaptation predictable despite sequence-level stochasticity

(2014) S. Kryazhimskiy et al.   SCIENCE

The Genomic Landscape of Compensatory Evolution

(2014) Béla Szamecz et al.   PLOS BIOLOGY

Epistatically Interacting Substitutions Are Enriched during Adaptive Protein Evolution

(2014) Lizhi Ian Gong et al.   PLoS Genetics

Loss and Recovery of Genetic Diversity in Adapting Populations of HIV

(2014) Pleuni S. Pennings et al.   PLoS Genetics

Enhanced Stability of Monomer Fold Correlates with Extreme Drug Resistance of HIV-1 Protease

(2013) John M. Louis et al.   BIOCHEMISTRY

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

Recursive genomewide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation inEscherichia coli

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

Mechanisms of Protein Sequence Divergence and Incompatibility

(2013) Alon Wellner et al.   PLoS Genetics

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

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

The use of information theory in evolutionary biology

(2012) Christoph Adami   Annals of the New York Academy of Sciences

HIV-1 Protease with 20 Mutations Exhibits Extreme Resistance to Clinical Inhibitors through Coordinated Structural Rearrangements

(2012) Johnson Agniswamy et al.   BIOCHEMISTRY

Commentary on the role of treatment-related HIV compensatory mutations on increasing virulence: new discoveries twenty years since the clinical testing of protease inhibitors to block HIV-1 replication

(2012) Eric J Arts   BMC Medicine

A Study on the Effect of Surface Lysine to Arginine Mutagenesis on Protein Stability and Structure Using Green Fluorescent Protein

(2012) Sriram Sokalingam et al.   PLoS One

A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function

(2012) C. L. Araya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Environmental change exposes beneficial epistatic interactions in a catalytic RNA

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

Treatment-associated polymorphisms in protease are significantly associated with higher viral load and lower CD4 count in newly diagnosed drug-naive HIV-1 infected patients

(2012) Kristof Theys et al.   Retrovirology

Diminishing returns and tradeoffs constrain the laboratory optimization of an enzyme

(2012) Nobuhiko Tokuriki et al.   Nature Communications

Standing Genetic Variation and the Evolution of Drug Resistance in HIV

(2012) Pleuni Simone Pennings   PLoS Computational Biology

Exploring the Complexity of the HIV-1 Fitness Landscape

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

Accessory Mutations Maintain Stability in Drug-Resistant HIV-1 Protease

(2011) Max W. Chang et al.   JOURNAL OF MOLECULAR BIOLOGY

The Value of Information for Populations in Varying Environments

(2011) Olivier Rivoire et al.   JOURNAL OF STATISTICAL PHYSICS

Evolution of Drug-Resistant Viral Populations during Interruption of Antiretroviral Therapy

(2011) D. Wang et al.   JOURNAL OF VIROLOGY

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

(2011) Trevor Hinkley et al.   NATURE GENETICS

The causes of epistasis

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

Impact of epistasis and pleiotropy on evolutionary adaptation

(2011) B. Ostman et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

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

Transmission of HIV‐1 Drug‐Resistant Variants: Prevalence and Effect on Treatment Outcome

(2010) Martin R. Jakobsen et al.   CLINICAL INFECTIOUS DISEASES

Evolutionary dynamics, epistatic interactions, and biological information

(2010) Christopher C. Strelioff et al.   JOURNAL OF THEORETICAL BIOLOGY

Mutational effects and the evolution of new protein functions

(2010) Misha Soskine et al.   NATURE REVIEWS GENETICS

Evidence that Adaptation in Drosophila Is Not Limited by Mutation at Single Sites

(2010) Talia Karasov et al.   PLoS Genetics

Pervasive Cryptic Epistasis in Molecular Evolution

(2010) Mark Lunzer et al.   PLoS Genetics

Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease

(2009) Omar Haq et al.   BMC BIOINFORMATICS

Amino Acid Covariation in a Functionally Important Human Immunodeficiency Virus Type 1 Protein Region Is Associated With Population Subdivision

(2009) J. da Silva   GENETICS

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

(2009) Jeffrey E. Barrick 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

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

Positive Epistasis Drives the Acquisition of Multidrug Resistance

(2009) Sandra Trindade et al.   PLoS Genetics

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

(2008) Patrick C. Phillips   NATURE REVIEWS GENETICS

HIV-1 reverse transcriptase inhibitor resistance mutations and fitness: A view from the clinic and ex vivo

(2008) Javier Martinez-Picado et al.   VIRUS RESEARCH

How Protein Stability and New Functions Trade Off

(2008) Nobuhiko Tokuriki et al.   PLoS Computational Biology