Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection

Optimization strategies for fast detection of positive selection on phylogenetic trees

(2014) Mario Valle et al.   BIOINFORMATICS

Rapid evolution of BRCA1 and BRCA2 in humans and other primates

(2014) Dianne I Lou et al.   BMC EVOLUTIONARY BIOLOGY

Dynamics of the Emergence and Establishment of a Newly Dominant Genotype of Japanese Encephalitis Virus throughout Asia

(2014) A. J. Schuh et al.   JOURNAL OF VIROLOGY

On the Validity of Evolutionary Models with Site-Specific Parameters

(2014) Konrad Scheffler et al.   PLoS One

Rapid Evolution of PARP Genes Suggests a Broad Role for ADP-Ribosylation in Host-Virus Conflicts

(2014) Matthew D. Daugherty et al.   PLoS Genetics

A Case for the Ancient Origin of Coronaviruses

(2013) J. O. Wertheim et al.   JOURNAL OF VIROLOGY

Performance of Standard and Stochastic Branch-Site Models for Detecting Positive Selection among Coding Sequences

(2013) A. Lu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Selectome update: quality control and computational improvements to a database of positive selection

(2013) Sébastien Moretti et al.   NUCLEIC ACIDS RESEARCH

Overlapping structure of hepatitis B virus (HBV) genome and immune selection pressure are critical forces modulating HBV evolution

(2012) V. Cento et al.   JOURNAL OF GENERAL VIROLOGY

Evidence for ACE2-Utilizing Coronaviruses (CoVs) Related to Severe Acute Respiratory Syndrome CoV in Bats

(2012) A. Demogines et al.   JOURNAL OF VIROLOGY

Modeling HIV-1 Drug Resistance as Episodic Directional Selection

(2012) Ben Murrell et al.   PLoS Computational Biology

Detecting Individual Sites Subject to Episodic Diversifying Selection

(2012) Ben Murrell et al.   PLoS Genetics

The Breadth of Antiviral Activity of Apobec3DE in Chimpanzees Has Been Driven by Positive Selection

(2011) N. K. Duggal et al.   JOURNAL OF VIROLOGY

Comparative Analysis of Avian Influenza Virus Diversity in Poultry and Humans during a Highly Pathogenic Avian Influenza A (H7N7) Virus Outbreak

(2011) M. Jonges et al.   JOURNAL OF VIROLOGY

Model Averaging and Bayes Factor Calculation of Relaxed Molecular Clocks in Bayesian Phylogenetics

(2011) W. L. S. Li et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Random Effects Branch-Site Model for Detecting Episodic Diversifying Selection

(2011) Sergei L. Kosakovsky Pond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Purifying Selection Can Obscure the Ancient Age of Viral Lineages

(2011) Joel O. Wertheim et al.   MOLECULAR BIOLOGY AND EVOLUTION

Statistical Properties of the Branch-Site Test of Positive Selection

(2010) Z. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences

(2010) Wayne Delport et al.   PLoS Computational Biology

Rapidly evolving genes in pathogens: Methods for detecting positive selection and examples among fungi, bacteria, viruses and protists

(2009) Gabriela Aguileta et al.   INFECTION GENETICS AND EVOLUTION

Evolutionary Fingerprinting of Genes

(2009) S. L. Kosakovsky Pond et al.   MOLECULAR BIOLOGY AND EVOLUTION

An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1

(2009) Sergei L. Kosakovsky Pond et al.   PLoS Computational Biology

Models of coding sequence evolution

(2008) W. Delport et al.   BRIEFINGS IN BIOINFORMATICS

Positive selection in penicillin-binding proteins 1a, 2b, and 2x from Streptococcus pneumoniae and its correlation with amoxicillin resistance development

(2008) Michael J. Stanhope et al.   INFECTION GENETICS AND EVOLUTION

Evolution of drug resistance in multiple distinct lineages of H5N1 avian influenza

(2008) Andrew W. Hill et al.   INFECTION GENETICS AND EVOLUTION

Investigating Protein-Coding Sequence Evolution with Probabilistic Codon Substitution Models

(2008) M. Anisimova et al.   MOLECULAR BIOLOGY AND EVOLUTION

jModelTest: Phylogenetic Model Averaging

(2008) D. Posada   MOLECULAR BIOLOGY AND EVOLUTION