Simultaneously estimating evolutionary history and repeated traits phylogenetic signal: applications to viral and host phenotypic evolution

Virulence and Pathogenesis of HIV-1 Infection: An Evolutionary Perspective

(2014) C. Fraser et al.   SCIENCE

Clinical applications of pathogen phylogenies

(2014) Matthew Hartfield et al.   TRENDS IN MOLECULAR MEDICINE

The Contribution of Viral Genotype to Plasma Viral Set-Point in HIV Infection

(2014) Emma Hodcroft et al.   PLoS Pathogens

Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H3N2

(2014) Philippe Lemey et al.   PLoS Pathogens

Integrating influenza antigenic dynamics with molecular evolution

(2014) Trevor Bedford et al.   eLife

Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution

(2013) B. F. Koel et al.   SCIENCE

Virus-induced target cell activation reconciles set-point viral load heritability and within-host evolution

(2013) Anna Hool et al.   Epidemics

Evidence for a Continuous Drift of the HIV-1 Species towards Higher Resistance to Neutralizing Antibodies over the Course of the Epidemic

(2013) Mélanie Bouvin-Pley et al.   PLoS Pathogens

Bayesian models for comparative analysis integrating phylogenetic uncertainty

(2012) Pierre de Villemereuil et al.   BMC EVOLUTIONARY BIOLOGY

A NEW BAYESIAN METHOD FOR FITTING EVOLUTIONARY MODELS TO COMPARATIVE DATA WITH INTRASPECIFIC VARIATION

(2012) Liam J. Revell et al.   EVOLUTION

Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Unifying the spatial epidemiology and molecular evolution of emerging epidemics

(2012) O. G. Pybus et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How to measure and test phylogenetic signal

(2012) Tamara Münkemüller et al.   Methods in Ecology and Evolution

SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics

(2011) F. Bielejec et al.   BIOINFORMATICS

A NEW PHYLOGENETIC METHOD FOR IDENTIFYING EXCEPTIONAL PHENOTYPIC DIVERSIFICATION

(2011) Liam J. Revell et al.   EVOLUTION

Activity of Broadly Neutralizing Antibodies, Including PG9, PG16, and VRC01, against Recently Transmitted Subtype B HIV-1 Variants from Early and Late in the Epidemic

(2011) Z. Euler et al.   JOURNAL OF VIROLOGY

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

Host Phylogeny Determines Viral Persistence and Replication in Novel Hosts

(2011) Ben Longdon et al.   PLoS Pathogens

HIV RNA levels in transmission sources only weakly predict plasma viral load in recipients

(2010) Antoinette C van der Kuyl et al.   AIDS

Molecular Epidemiology Reveals Long‐Term Changes in HIV Type 1 Subtype B Transmission in Switzerland

(2010) Roger D. Kouyos et al.   JOURNAL OF INFECTIOUS DISEASES

Phylogeography Takes a Relaxed Random Walk in Continuous Space and Time

(2010) P. Lemey et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Bayesian Phylogenetic Method to Estimate Unknown Sequence Ages

(2010) B. Shapiro et al.   MOLECULAR BIOLOGY AND EVOLUTION

Adaptation of HIV-1 envelope gp120 to humoral immunity at a population level

(2010) Evelien M Bunnik et al.   NATURE MEDICINE

Structural Basis for Broad and Potent Neutralization of HIV-1 by Antibody VRC01

(2010) T. Zhou et al.   SCIENCE

HIV-1 Transmitting Couples Have Similar Viral Load Set-Points in Rakai, Uganda

(2010) T. Déirdre Hollingsworth et al.   PLoS Pathogens

Phylogenetic Approach Reveals That Virus Genotype Largely Determines HIV Set-Point Viral Load

(2010) Samuel Alizon et al.   PLoS Pathogens

PHYLOGENETIC ANALYSIS OF THE EVOLUTIONARY CORRELATION USING LIKELIHOOD

(2009) Liam J. Revell et al.   EVOLUTION

Cohort Profile: The Swiss HIV Cohort Study

(2009) et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Adaptation of HIV-1 to human leukocyte antigen class I

(2009) Yuka Kawashima et al.   NATURE

Broad and Potent Neutralizing Antibodies from an African Donor Reveal a New HIV-1 Vaccine Target

(2009) L. M. Walker et al.   SCIENCE

Bayesian Phylogeography Finds Its Roots

(2009) Philippe Lemey et al.   PLoS Computational Biology

Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species

(2008) Jonathan B. Losos   ECOLOGY LETTERS

Smooth Skyride through a Rough Skyline: Bayesian Coalescent-Based Inference of Population Dynamics

(2008) V. N. Minin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Morphometrics of the Avian Small Intestine Compared with That of Nonflying Mammals: A Phylogenetic Approach

(2008) Shana R. Lavin et al.   PHYSIOLOGICAL AND BIOCHEMICAL ZOOLOGY

The Global Circulation of Seasonal Influenza A (H3N2) Viruses

(2008) C. A. Russell et al.   SCIENCE