An Experimentally Determined Evolutionary Model Dramatically Improves Phylogenetic Fit

A Penalized-Likelihood Method to Estimate the Distribution of Selection Coefficients from Phylogenetic Data

(2014) Asif U. Tamuri et al.   GENETICS

A rapid, efficient, and economical inverse polymerase chain reaction-based method for generating a site saturation mutant library

(2013) Pankaj C. Jain et al.   ANALYTICAL BIOCHEMISTRY

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

High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing

(2013) D. I. Lou 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

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

Estimating Empirical Codon Hidden Markov Models

(2012) Nicola De Maio et al.   MOLECULAR BIOLOGY AND EVOLUTION

PFunkel: Efficient, Expansive, User-Defined Mutagenesis

(2012) Elad Firnberg et al.   PLoS One

Detection of ultra-rare mutations by next-generation sequencing

(2012) M. W. Schmitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) A. U. Tamuri et al.   GENETICS

Deep mutational scanning: assessing protein function on a massive scale

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

FLU, an amino acid substitution model for influenza proteins

(2010) Cuong Dang et al.   BMC EVOLUTIONARY BIOLOGY

Statistical Potentials for Improved Structurally Constrained Evolutionary Models

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

Parallel, tag-directed assembly of locally derived short sequence reads

(2010) Joseph B Hiatt et al.   NATURE METHODS

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

Serious Overestimation in Quantitative PCR by Circular (Supercoiled) Plasmid Standard: Microalgal pcna as the Model Gene

(2010) Yubo Hou et al.   PLoS One

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

Permissive Secondary Mutations Enable the Evolution of Influenza Oseltamivir Resistance

(2010) J. D. Bloom et al.   SCIENCE

Pervasive Cryptic Epistasis in Molecular Evolution

(2010) Mark Lunzer et al.   PLoS Genetics

Spontaneous Mutation Accumulation Studies in Evolutionary Genetics

(2009) Daniel L. Halligan et al.   Annual Review of Ecology Evolution and Systematics

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

Anomalies in the Influenza Virus Genome Database: New Biology or Laboratory Errors?

(2008) M. Krasnitz et al.   JOURNAL OF VIROLOGY

Phylogenetic mixture models for proteins

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