Evolutionary interplay between structure, energy and epistasis in the coat protein of theϕX174 phage family

Causes of evolutionary rate variation among protein sites

(2016) Julian Echave et al.   NATURE REVIEWS GENETICS

Biophysics of protein evolution and evolutionary protein biophysics

(2014) T. Sikosek et al.   Journal of the Royal Society Interface

IFN-γ signaling maintains skin pigmentation homeostasis through regulation of melanosome maturation

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

Strong evidence for protein epistasis, weak evidence against it

(2014) D. D. Pollock et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Selection bias at the heterosexual HIV-1 transmission bottleneck

(2014) J. M. Carlson et al.   SCIENCE

Local Packing Density Is the Main Structural Determinant of the Rate of Protein Sequence Evolution at Site Level

(2014) So-Wei Yeh et al.   Biomed Research International

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Should evolutionary geneticists worry about higher-order epistasis?

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

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

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

Biophysical mechanisms for large-effect mutations in the evolution of steroid hormone receptors

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

Mutational effects on stability are largely conserved during protein evolution

(2013) O. Ashenberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Five Years of GWAS Discovery

(2012) Peter M. Visscher et al.   AMERICAN JOURNAL OF HUMAN GENETICS

THE DISTRIBUTION OF MUTATIONAL FITNESS EFFECTS OF PHAGE φX174 ON DIFFERENT HOSTS

(2012) Pedro F. Vale et al.   EVOLUTION

The spatial architecture of protein function and adaptation

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

Epistasis as the primary factor in molecular evolution

(2012) Michael S. Breen et al.   NATURE

Assessing Predictors of Changes in Protein Stability upon Mutation Using Self-Consistency

(2012) Grant Thiltgen et al.   PLoS One

Amino acid coevolution induces an evolutionary Stokes shift

(2012) D. D. Pollock et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Agrobacterium tumefaciens recognizes its host environment using ChvE to bind diverse plant sugars as virulence signals

(2012) X. Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Bringing Molecules Back into Molecular Evolution

(2012) Claus O. Wilke   PLoS Computational Biology

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Super folds, networks, and barriers

(2011) Sean Burke et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

On epistasis: why it is unimportant in polygenic directional selection

(2010) J. F. Crow   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Role of conformational sampling in computing mutation-induced changes in protein structure and stability

(2010) Elizabeth H. Kellogg et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improved side-chain torsion potentials for the Amber ff99SB protein force field

(2010) Kresten Lindorff-Larsen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Mutation Bias Favors Protein Folding Stability in the Evolution of Small Populations

(2010) Raul Mendez et al.   PLoS Computational Biology

Fitness and its role in evolutionary genetics

(2009) H. Allen Orr   NATURE REVIEWS GENETICS

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inferring Stabilizing Mutations from Protein Phylogenies: Application to Influenza Hemagglutinin

(2009) Jesse D. Bloom et al.   PLoS Computational Biology

How Protein Stability and New Functions Trade Off

(2008) Nobuhiko Tokuriki et al.   PLoS Computational Biology