Changing preferences: deformation of single position amino acid fitness landscapes and evolution of proteins

Nonadaptive Amino Acid Convergence Rates Decrease over Time

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Pervasive degeneracy and epistasis in a protein-protein interface

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Topological features of rugged fitness landscapes in sequence space

(2015) Dmitry A. Kondrashov et al.   TRENDS IN GENETICS

Combining Natural Sequence Variation with High Throughput Mutational Data to Reveal Protein Interaction Sites

(2015) Daniel Melamed et al.   PLoS Genetics

Coordinated Evolution of Influenza A Surface Proteins

(2015) Alexey D. Neverov et al.   PLoS Genetics

A structural perspective of compensatory evolution

(2014) Dmitry N Ivankov et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A Model of Substitution Trajectories in Sequence Space and Long-Term Protein Evolution

(2014) Dinara R. Usmanova et al.   MOLECULAR BIOLOGY AND EVOLUTION

Empirical fitness landscapes and the predictability of evolution

(2014) J. Arjan G.M. de Visser et al.   NATURE REVIEWS GENETICS

Fluctuating Selection Models and Mcdonald-Kreitman Type Analyses

(2014) Toni I. Gossmann et al.   PLoS One

Intrasubtype Reassortments Cause Adaptive Amino Acid Replacements in H3N2 Influenza Genes

(2014) Alexey D. Neverov et al.   PLoS Genetics

Genomic Evidence of Rapid and Stable Adaptive Oscillations over Seasonal Time Scales in Drosophila

(2014) Alan O. Bergland et al.   PLoS Genetics

Should evolutionary geneticists worry about higher-order epistasis?

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Breen et al. reply

(2013) Michael S. Breen et al.   NATURE

The role of epistasis in protein evolution

(2013) David M. McCandlish et al.   NATURE

Genome sequencing and population genomics in non-model organisms

(2013) Hans Ellegren   TRENDS IN ECOLOGY & EVOLUTION

Fitness conferred by replaced amino acids declines with time

(2012) S. A. Naumenko et al.   Biology Letters

On the Statistical Interpretation of Site-Specific Variables in Phylogeny-Based Substitution Models

(2012) N. Rodrigue   GENETICS

Estimating the Rate of Irreversibility in Protein Evolution

(2012) Onuralp Soylemez et al.   Genome Biology and Evolution

Epistasis as the primary factor in molecular evolution

(2012) Michael S. Breen et al.   NATURE

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

Insertions and deletions trigger adaptive walks in Drosophila proteins

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

Modeling the effect of changing selective pressures on polymorphism and divergence

(2012) Etam Benger et al.   THEORETICAL POPULATION BIOLOGY

Detecting Individual Sites Subject to Episodic Diversifying Selection

(2012) Ben Murrell et al.   PLoS Genetics

Site-specific time heterogeneity of the substitution process and its impact on phylogenetic inference

(2011) Béatrice Roure et al.   BMC EVOLUTIONARY BIOLOGY

Detecting Past Positive Selection through Ongoing Negative Selection

(2011) Georgii A. Bazykin et al.   Genome Biology and Evolution

High-throughput identification of genetic interactions in HIV-1

(2011) Daniel M Weinreich   NATURE GENETICS

Weighing the evidence for adaptation at the molecular level

(2011) Justin C. Fay   TRENDS IN GENETICS

Molecular mechanisms of epistasis within and between genes

(2011) Ben Lehner   TRENDS IN GENETICS

Prevalence of Epistasis in the Evolution of Influenza A Surface Proteins

(2011) Sergey Kryazhimskiy et al.   PLoS Genetics

Correlated Evolution of Nearby Residues in Drosophilid Proteins

(2011) Benjamin Callahan et al.   PLoS Genetics

Rate of sequence divergence under constant selection

(2010) Alexey S Kondrashov et al.   Biology Direct

Sequence space and the ongoing expansion of the protein universe

(2010) Inna S. Povolotskaya et al.   NATURE

Fitness flux and ubiquity of adaptive evolution

(2010) V. Mustonen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles

(2010) N. Rodrigue et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mechanistic revisions of phenomenological modeling strategies in molecular evolution

(2010) Nicolas Rodrigue et al.   TRENDS IN GENETICS

Estimating the Rate of Adaptive Molecular Evolution in the Presence of Slightly Deleterious Mutations and Population Size Change

(2009) A. Eyre-Walker et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fluctuating selection: the perpetual renewal of adaptation in variable environments

(2009) G. Bell   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

From fitness landscapes to seascapes: non-equilibrium dynamics of selection and adaptation

(2009) Ville Mustonen et al.   TRENDS IN GENETICS

Identifying Changes in Selective Constraints: Host Shifts in Influenza

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

Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series

(2008) Igor B Rogozin et al.   Biology Direct

Directionality in the evolution of influenza A haemagglutinin

(2008) S. Kryazhimskiy et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES