An Experimentally Informed Evolutionary Model Improves Phylogenetic Fit to Divergent Lactamase Homologs

A Comprehensive, High-Resolution Map of a Gene’s Fitness Landscape

(2014) Elad Firnberg et al.   MOLECULAR BIOLOGY AND EVOLUTION

An Experimentally Determined Evolutionary Model Dramatically Improves Phylogenetic Fit

(2014) Jesse D. Bloom   MOLECULAR BIOLOGY AND EVOLUTION

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

Analyses of the Effects of All Ubiquitin Point Mutants on Yeast Growth Rate

(2013) Benjamin P. Roscoe et al.   JOURNAL OF MOLECULAR BIOLOGY

CodonPhyML: Fast Maximum Likelihood Phylogeny Estimation under Codon Substitution Models

(2013) Manuel Gil et al.   MOLECULAR BIOLOGY AND EVOLUTION

Maximum Allowed Solvent Accessibilites of Residues in Proteins

(2013) Matthew Z. Tien et al.   PLoS One

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

Activity-enhancing mutations in an E3 ubiquitin ligase identified by high-throughput mutagenesis

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

Deep mutational scanning of an RRM domain of the Saccharomyces cerevisiae poly(A)-binding protein

(2013) D. Melamed et al.   RNA

Stability-mediated epistasis constrains the evolution of an influenza protein

(2013) Lizhi Ian Gong et al.   eLife

Modeling coding-sequence evolution within the context of residue solvent accessibility

(2012) Michael P Scherrer et al.   BMC EVOLUTIONARY BIOLOGY

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

(2012) N. Rodrigue   GENETICS

Construction of a Stability Landscape of the CH3 Domain of Human IgG1 by Combining Directed Evolution with High Throughput Sequencing

(2012) Michael W. Traxlmayr et al.   JOURNAL OF MOLECULAR BIOLOGY

Bayesian Selection of Nucleotide Substitution Models and Their Site Assignments

(2012) Chieh-Hsi Wu et al.   MOLECULAR BIOLOGY AND EVOLUTION

The spatial architecture of protein function and adaptation

(2012) Richard N. McLaughlin Jr 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

Deep mutational scanning: assessing protein function on a massive scale

(2011) Carlos L. Araya et al.   TRENDS IN BIOTECHNOLOGY

Statistical Potentials for Improved Structurally Constrained Evolutionary Models

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

High-resolution mapping of protein sequence-function relationships

(2010) Douglas M Fowler et al.   NATURE METHODS

A series of PDB related databases for everyday needs

(2010) R. P. Joosten et al.   NUCLEIC ACIDS RESEARCH

Correcting the Bias of Empirical Frequency Parameter Estimators in Codon Models

(2010) Sergei Kosakovsky Pond et al.   PLoS One

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

Pervasive Cryptic Epistasis in Molecular Evolution

(2010) Mark Lunzer et al.   PLoS Genetics

Evidence That Mutation Is Universally Biased towards AT in Bacteria

(2010) Ruth Hershberg et al.   PLoS Genetics

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

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

Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details

(2009) V. Potapov et al.   PROTEIN ENGINEERING DESIGN & SELECTION

A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny

(2008) Huai-Chun Wang et al.   BMC EVOLUTIONARY BIOLOGY

Frequent and Widespread Parallel Evolution of Protein Sequences

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

Phylogenetic mixture models for proteins

(2008) S. Q. Le et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES