Protein evolution along phylogenetic histories under structurally constrained substitution models

Protein Conformational Diversity Correlates with Evolutionary Rate

(2013) Diego Javier Zea et al.   MOLECULAR BIOLOGY AND EVOLUTION

Frustration in the energy landscapes of multidomain protein misfolding

(2013) W. Zheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detecting selection for negative design in proteins through an improved model of the misfolded state

(2013) Jonas Minning et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Computer Programs and Methodologies for the Simulation of DNA Sequence Data with Recombination

(2013) Miguel Arenas   Frontiers in Genetics

Protein Conformational Diversity Modulates Sequence Divergence

(2012) Ezequiel Juritz et al.   MOLECULAR 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

The interface of protein structure, protein biophysics, and molecular evolution

(2012) David A. Liberles et al.   PROTEIN SCIENCE

Accurate Estimation of Substitution Rates with Neighbor-Dependent Models in a Phylogenetic Context

(2012) Jean Bérard et al.   SYSTEMATIC BIOLOGY

Simulation of Molecular Data under Diverse Evolutionary Scenarios

(2012) Miguel Arenas   PLoS Computational Biology

Bringing Molecules Back into Molecular Evolution

(2012) Claus O. Wilke   PLoS Computational Biology

Biophysical and structural considerations for protein sequence evolution

(2011) Johan A Grahnen et al.   BMC EVOLUTIONARY BIOLOGY

The Effect of Recombination on the Reconstruction of Ancestral Sequences

(2010) M. Arenas et al.   GENETICS

The evolution and evolutionary consequences of marginal thermostability in proteins

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

Quantifying the Impact of Dependent Evolution among Sites in Phylogenetic Inference

(2010) Chris A. Nasrallah et al.   SYSTEMATIC BIOLOGY

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

(2010) Raul Mendez et al.   PLoS Computational Biology

Coalescent Simulation of Intracodon Recombination

(2009) M. Arenas et al.   GENETICS

Trade-off between Positive and Negative Design of Protein Stability: From Lattice Models to Real Proteins

(2009) Orly Noivirt-Brik et al.   PLoS Computational Biology

Molecular Mechanisms of Recombination Restriction in the Envelope Gene of the Human Immunodeficiency Virus

(2009) Etienne Simon-Loriere et al.   PLoS Pathogens

Estimating selection pressures on HIV-1 using phylogenetic likelihood models

(2008) S. L. Kosakovsky Pond et al.   STATISTICS IN MEDICINE

Identifying the Important HIV-1 Recombination Breakpoints

(2008) John Archer et al.   PLoS Computational Biology