Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data

How well can the exponential-growth coalescent approximate constant-rate birth-death population dynamics?

(2015) T. Stadler et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Model Inadequacy and Mistaken Inferences of Trait-Dependent Speciation

(2015) Daniel L. Rabosky et al.   SYSTEMATIC BIOLOGY

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

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

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration

(2014) Alexandra Gavryushkina et al.   PLoS Computational Biology

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

(2014) Philippe Lemey et al.   PLoS Pathogens

Exploring power and parameter estimation of the BiSSE method for analyzing species diversification

(2013) Matthew P Davis et al.   BMC EVOLUTIONARY BIOLOGY

A Stochastic Simulator of Birth-Death Master Equations with Application to Phylodynamics

(2013) T. G. Vaughan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints

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

Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods

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

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

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

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

Unified Framework to Evaluate Panmixia and Migration Direction Among Multiple Sampling Locations

(2010) P. Beerli et al.   GENETICS

Calculations for multi-type age-dependent binary branching processes

(2010) Graham Jones   JOURNAL OF MATHEMATICAL BIOLOGY

Three roads diverged? Routes to phylogeographic inference

(2010) Erik W. Bloomquist et al.   TRENDS IN ECOLOGY & EVOLUTION

Global Migration Dynamics Underlie Evolution and Persistence of Human Influenza A (H3N2)

(2010) Trevor Bedford et al.   PLoS Pathogens

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

The genomic and epidemiological dynamics of human influenza A virus

(2008) Andrew Rambaut et al.   NATURE