Nonadaptive Amino Acid Convergence Rates Decrease over Time

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

Genome-wide signatures of convergent evolution in echolocating mammals

(2013) Joe Parker et al.   NATURE

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

Phylogenetics, likelihood, evolution and complexity

(2012) A.P. Jason de Koning et al.   BIOINFORMATICS

SP Transcription Factor Paralogs and DNA-Binding Sites Coevolve and Adaptively Converge in Mammals and Birds

(2012) Ken Daigoro Yokoyama et al.   Genome Biology and Evolution

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

Parallel Evolution of Auditory Genes for Echolocation in Bats and Toothed Whales

(2012) Yong-Yi Shen et al.   PLoS Genetics

Estimating the Distribution of Selection Coefficients from Phylogenetic Data Using Sitewise Mutation-Selection Models

(2011) A. U. Tamuri et al.   GENETICS

Convergent sequence evolution between echolocating bats and dolphins

(2010) Yang Liu et al.   CURRENT BIOLOGY

Statistical Potentials for Improved Structurally Constrained Evolutionary Models

(2010) Claudia L. Kleinman et al.   MOLECULAR BIOLOGY AND EVOLUTION

The evolution and evolutionary consequences of marginal thermostability in proteins

(2010) Richard A. Goldstein   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Evidence for an ancient adaptive episode of convergent molecular evolution

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

Identifying Changes in Selective Constraints: Host Shifts in Influenza

(2009) Asif U. Tamuri et al.   PLoS Computational Biology

Empirical profile mixture models for phylogenetic reconstruction

(2008) Le Si Quang et al.   BIOINFORMATICS

Frequent and Widespread Parallel Evolution of Protein Sequences

(2008) A. Rokas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Adaptive Evolution and Functional Redesign of Core Metabolic Proteins in Snakes

(2008) Todd A. Castoe et al.   PLoS One

Changing Selective Pressure during Antigenic Changes in Human Influenza H3

(2008) Benjamin P. Blackburne et al.   PLoS Pathogens