Pervasive Cryptic Epistasis in Molecular Evolution

Functionally Compensating Coevolving Positions Are Neither Homoplasic Nor Conserved in Clades

(2010) G. B. Gloor et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sequence space and the ongoing expansion of the protein universe

(2010) Inna S. Povolotskaya et al.   NATURE

The molecular evolutionary basis of species formation

(2010) Daven C. Presgraves   NATURE REVIEWS GENETICS

PROCOV: maximum likelihood estimation of protein phylogeny under covarion models and site-specific covarion pattern analysis

(2009) Huai-Chun Wang et al.   BMC EVOLUTIONARY BIOLOGY

Retracing Evolution of Red Fluorescence in GFP-Like Proteins from Faviina Corals

(2009) S. F. Field et al.   MOLECULAR BIOLOGY AND EVOLUTION

Computational Methods for Evaluating Phylogenetic Models of Coding Sequence Evolution with Dependence between Codons

(2009) N. Rodrigue et al.   MOLECULAR BIOLOGY AND EVOLUTION

An epistatic ratchet constrains the direction of glucocorticoid receptor evolution

(2009) Jamie T. Bridgham et al.   NATURE

Detecting gene–gene interactions that underlie human diseases

(2009) Heather J Cordell   NATURE REVIEWS GENETICS

Long-Branch Attraction Bias and Inconsistency in Bayesian Phylogenetics

(2009) Bryan Kolaczkowski et al.   PLoS One

Near Neutrality

(2008) Austin L. Hughes   Annals of the New York Academy of Sciences

Overdispersion of the Molecular Clock Varies Between Yeast, Drosophila and Mammals

(2008) Trevor Bedford et al.   GENETICS

Intense Neutral Drifts Yield Robust and Evolvable Consensus Proteins

(2008) Shimon Bershtein et al.   JOURNAL OF MOLECULAR BIOLOGY

A Mixed Branch Length Model of Heterotachy Improves Phylogenetic Accuracy

(2008) Bryan Kolaczkowski et al.   MOLECULAR BIOLOGY AND EVOLUTION

Difficulties in Testing for Covarion-Like Properties of Sequences under the Confounding Influence of Changing Proportions of Variable Sites

(2008) N. Gruenheit et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genetic code can cause systematic bias in simple phylogenetic models

(2008) S. Whelan   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates

(2008) S. Yokoyama et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How Protein Stability and New Functions Trade Off

(2008) Nobuhiko Tokuriki et al.   PLoS Computational Biology