FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection

Phylogenetics, likelihood, evolution and complexity

(2012) A.P. Jason de Koning et al.   BIOINFORMATICS

Evolution of the hepatitis E virus hypervariable region

(2012) D. B. Smith et al.   JOURNAL OF GENERAL VIROLOGY

Capsid protein evolution and comparative phylogeny of novel porcine parvoviruses

(2012) Dániel Cadar et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

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

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

Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9

(2011) Jason S. McLellan et al.   NATURE

A Neutralizing Antibody Selected from Plasma Cells That Binds to Group 1 and Group 2 Influenza A Hemagglutinins

(2011) D. Corti et al.   SCIENCE

A Potent and Broad Neutralizing Antibody Recognizes and Penetrates the HIV Glycan Shield

(2011) R. Pejchal et al.   SCIENCE

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Broadly Protective Monoclonal Antibodies against H3 Influenza Viruses following Sequential Immunization with Different Hemagglutinins

(2010) Taia T. Wang et al.   PLoS Pathogens

Structural and functional bases for broad-spectrum neutralization of avian and human influenza A viruses

(2009) Jianhua Sui et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Antibody Recognition of a Highly Conserved Influenza Virus Epitope

(2009) D. C. Ekiert et al.   SCIENCE

Hemagglutinin Receptor Binding Avidity Drives Influenza A Virus Antigenic Drift

(2009) S. E. Hensley et al.   SCIENCE

Empirical profile mixture models for phylogenetic reconstruction

(2008) Le Si Quang et al.   BIOINFORMATICS

Models of coding sequence evolution

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

Investigating Protein-Coding Sequence Evolution with Probabilistic Codon Substitution Models

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

A Maximum Likelihood Method for Detecting Directional Evolution in Protein Sequences and Its Application to Influenza A Virus

(2008) S. L. Kosakovsky Pond et al.   MOLECULAR BIOLOGY AND EVOLUTION