Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods

Linking the Investigations of Character Evolution and Species Diversification

(2012) Karen Magnuson-Ford et al.   AMERICAN NATURALIST

TEMPO AND MODE IN PLANT BREEDING SYSTEM EVOLUTION

(2012) Emma E. Goldberg et al.   EVOLUTION

Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV)

(2012) T. Stadler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Agent-based and phylogenetic analyses reveal how HIV-1 moves between risk groups: Injecting drug users sustain the heterosexual epidemic in Latvia

(2012) Frederik Graw et al.   Epidemics

Inferring Epidemic Contact Structure from Phylogenetic Trees

(2012) Gabriel E. Leventhal et al.   PLoS Computational Biology

Phylogenetic Analysis of the Latvian HIV-1 Epidemic

(2011) Dace Balode et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

Complex Population Dynamics and the Coalescent Under Neutrality

(2011) Erik M. Volz   GENETICS

Estimating the Basic Reproductive Number from Viral Sequence Data

(2011) Tanja Stadler et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mammalian phylogeny reveals recent diversification rate shifts

(2011) T. Stadler   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record

(2011) R. S. Etienne et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Simulating Trees with a Fixed Number of Extant Species

(2011) Tanja Stadler   SYSTEMATIC BIOLOGY

Inference for Nonlinear Epidemiological Models Using Genealogies and Time Series

(2011) David A. Rasmussen et al.   PLoS Computational Biology

Endemic Dengue Associated with the Co-Circulation of Multiple Viral Lineages and Localized Density-Dependent Transmission

(2011) Jayna Raghwani et al.   PLoS Pathogens

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

Sampling-through-time in birth–death trees

(2010) Tanja Stadler   JOURNAL OF THEORETICAL BIOLOGY

Phylogeography Takes a Relaxed Random Walk in Continuous Space and Time

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

Phylodynamic Reconstruction Reveals Norovirus GII.4 Epidemic Expansions and their Molecular Determinants

(2010) J. Joukje Siebenga et al.   PLoS Pathogens

Phylodynamics of Infectious Disease Epidemics

(2009) Erik M. Volz et al.   GENETICS

Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic

(2009) Gavin J. D. Smith et al.   NATURE

Estimating Trait-Dependent Speciation and Extinction Rates from Incompletely Resolved Phylogenies

(2009) Richard G. FitzJohn et al.   SYSTEMATIC BIOLOGY

Bayesian Phylogeography Finds Its Roots

(2009) Philippe Lemey et al.   PLoS Computational Biology

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS