Bayesian phylodynamic inference with complex models

Infectious Disease Dynamics Inferred from Genetic Data via Sequential Monte Carlo

(2017) R.A. Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Structured Coalescent and Its Approximations

(2017) Nicola F. Müller et al.   MOLECULAR BIOLOGY AND EVOLUTION

Virus genomes reveal factors that spread and sustained the Ebola epidemic

(2017) Gytis Dudas et al.   NATURE

Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison

(2016) Oliver Ratmann et al.   MOLECULAR BIOLOGY AND EVOLUTION

Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference

(2016) Michael D. Karcher et al.   PLoS Computational Biology

Phylodynamic Inference with Kernel ABC and Its Application to HIV Epidemiology

(2015) Art F.Y. Poon   MOLECULAR BIOLOGY AND EVOLUTION

New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation

(2015) Nicola De Maio et al.   PLoS Genetics

Efficient Bayesian inference under the structured coalescent

(2014) Timothy G. Vaughan et al.   BIOINFORMATICS

Estimates of the reproduction number for seasonal, pandemic, and zoonotic influenza: a systematic review of the literature

(2014) Matthew Biggerstaff et al.   BMC INFECTIOUS DISEASES

Sampling through time and phylodynamic inference with coalescent and birth-death models

(2014) E. M. Volz et al.   Journal of the Royal Society Interface

Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death SIR model

(2014) D. Kuhnert et al.   Journal of the Royal Society Interface

Phylodynamic Inference for Structured Epidemiological Models

(2014) David A. Rasmussen et al.   PLoS Computational Biology

Reconciling Phylodynamics with Epidemiology: The Case of Dengue Virus in Southern Vietnam

(2013) David A. Rasmussen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Coalescent inference for infectious disease: meta-analysis of hepatitis C

(2013) B. Dearlove et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Viral Phylodynamics

(2013) Erik M. Volz et al.   PLoS Computational Biology

HIV-1 Transmission during Early Infection in Men Who Have Sex with Men: A Phylodynamic Analysis

(2013) Erik M. Volz et al.   PLOS MEDICINE

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

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

Estimating influenza latency and infectious period durations using viral excretion data

(2012) A. Cori et al.   Epidemics

Complex Population Dynamics and the Coalescent Under Neutrality

(2011) Erik M. Volz   GENETICS

Rates of coalescence for common epidemiological models at equilibrium

(2011) K. Koelle et al.   Journal of the Royal Society Interface

Phylogeography Takes a Relaxed Random Walk in Continuous Space and Time

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

Viral phylodynamics and the search for an 'effective number of infections'

(2010) S. D. W. Frost et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phylodynamics of Infectious Disease Epidemics

(2009) Erik M. Volz et al.   GENETICS

Bayesian Phylogeography Finds Its Roots

(2009) Philippe Lemey et al.   PLoS Computational Biology

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

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

The genomic and epidemiological dynamics of human influenza A virus

(2008) Andrew Rambaut et al.   NATURE

Real Time Bayesian Estimation of the Epidemic Potential of Emerging Infectious Diseases

(2008) Luís M. A. Bettencourt et al.   PLoS One