phylodyn: an R package for phylodynamic simulation and inference

Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference

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

An efficient Bayesian inference framework for coalescent-based nonparametric phylodynamics

(2015) Shiwei Lan et al.   BIOINFORMATICS

Bayesian Nonparametric Inference of Population Size Changes from Sequential Genealogies

(2015) J. A. Palacios et al.   GENETICS

Eight challenges in phylodynamic inference

(2015) Simon D.W. Frost et al.   Epidemics

Gaussian Process-Based Bayesian Nonparametric Inference of Population Size Trajectories from Gene Genealogies

(2013) Julia A. Palacios et al.   BIOMETRICS

Split Hamiltonian Monte Carlo

(2013) Babak Shahbaba et al.   STATISTICS AND COMPUTING

Improving Bayesian Population Dynamics Inference: A Coalescent-Based Model for Multiple Loci

(2012) M. S. Gill 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

Skyline-plot methods for estimating demographic history from nucleotide sequences

(2011) SIMON Y. W. HO et al.   Molecular Ecology Resources

Discovering the Phylodynamics of RNA Viruses

(2009) Edward C. Holmes 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