Related papers: An Efficient Bayesian Inference Framework for Coal…
Phylodynamics seeks to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. One way to accomplish this task formulates an observed sequence data likelihood exploiting…
Phylodynamics is an area of population genetics that uses genetic sequence data to estimate past population dynamics. Modern state-of-the-art Bayesian nonparametric methods for recovering population size trajectories of unknown form use…
Changes in population size influence genetic diversity of the population and, as a result, leave a signature of these changes in individual genomes in the population. We are interested in the inverse problem of reconstructing past…
Variation in a sample of molecular sequence data informs about the past evolutionary history of the sample's population. Traditionally, Bayesian modeling coupled with the standard coalescent, is used to infer the sample's bifurcating…
Effective population size characterizes the genetic variability in a population and is a parameter of paramount importance in population genetics. Kingman's coalescent process enables inference of past population dynamics directly from…
We introduce phylodyn, an R package for phylodynamic analysis based on gene genealogies. The package main functionality is Bayesian nonparametric estimation of effective population size fluctuations over time. Our implementation includes…
Phylodynamics is a set of population genetics tools that aim at reconstructing demographic history of a population based on molecular sequences of individuals sampled from the population of interest. One important task in phylodynamics is…
The goal of phylodynamics, an area on the intersection of phylogenetics and population genetics, is to reconstruct population size dynamics from genetic data. Recently, a series of nonparametric Bayesian methods have been proposed for such…
Kingman's coalescent is one of the most popular models in population genetics. It describes the genealogy of a population whose genetic composition evolves in time according to the Wright-Fisher model, or suitable approximations of it…
Estimation of epidemiological and population parameters from molecular sequence data has become central to the understanding of infectious disease dynamics. Various models have been proposed to infer details of the dynamics that describe…
Coalescent theory combined with statistical modeling allows us to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. When sequences are sampled serially through…
Longitudinal molecular data of rapidly evolving viruses and pathogens provide information about disease spread and complement traditional surveillance approaches based on case count data. The coalescent is used to model the genealogy that…
Effective population size (Ne(t)) is a fundamental parameter in population genetics and phylodynamics that quantifies genetic diversity and reveals demographic history. Coalescent-based methods enable the inference of Ne(t) trajectories…
Many population genetic models have been developed for the purpose of inferring population size and growth rates from random samples of genetic data. We examine two popular approaches to this problem, the coalescent and the…
Coalescent models are used to study the transmission dynamics of rapidly evolving pathogens from molecular sequence data obtained from infected individuals. However coalescent parameters, such as effective population size, offer limited…
Phylogenetic comparative methods correct for shared evolutionary history among a set of non-independent organisms by modeling sample traits as arising from a diffusion process along on the branches of a possibly unknown history. To…
We consider the problem of inference for the states and parameters of a continuous-time multitype branching process from partially observed time series data. Exact inference for this class of models, typically using sequential Monte Carlo,…
Many biological studies involve inferring the evolutionary history of a sample of individuals from a large population and interpreting the reconstructed tree. Such an ascertained tree typically represents only a small part of a…
Phylodynamics is used to estimate epidemic dynamics from phylogenetic trees or genomic sequences of pathogens, but the likelihood calculations needed can be challenging for complex models. We present a neural Bayes estimator (NBE) for key…
Biological data objects often have both of the following features: (i) they are functions rather than single numbers or vectors, and (ii) they are correlated due to phylogenetic relationships. In this paper we give a flexible statistical…