Related papers: Accounting for reporting delays in real-time phylo…
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…
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…
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…
Phylodynamics focuses on the problem of reconstructing past population size dynamics from current genetic samples taken from the population of interest. This technique has been extensively used in many areas of biology, but is particularly…
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…
COVID-19 pandemic has reshaped our world in a timescale much shorter than what we can understand. Particularities of SARS-CoV-2, such as its persistence in surfaces and the lack of a curative treatment or vaccine against COVID-19, have…
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…
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…
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…
Because of the rapid spread of COVID-19 to almost every part of the globe, huge volumes of data and case studies have been made available, providing researchers with a unique opportunity to find trends and make discoveries like never…
Delay differential equations form the underpinning of many complex dynamical systems. The forward problem of solving random differential equations with delay has received increasing attention in recent years. Motivated by the challenge to…
Genomic surveillance of infectious diseases allows monitoring circulating and emerging variants and quantifying their epidemic potential. However, due to the high costs associated with genomic sequencing, only a limited number of samples…
To study population dynamics, ecologists and wildlife biologists use relative abundance data, which are often subject to temporal preferential sampling. Temporal preferential sampling occurs when sampling effort varies across time. To…
The new corona virus disease -- COVID-2019 -- is rapidly spreading through the world. The availability of unbiased timely statistics of trends in disease events are a key to effective responses. But due to reporting delays, the most…
COVID-19 data released by public health authorities features the presence of notable time-delays, corresponding to the difference between actual time of infection and identification of infection. These delays have several causes, including…
The spread of COVID-19 makes it essential to investigate its prevalence. In such investigation research, as far as we know, the widely-used sampling methods didn't use the information sufficiently about the numbers of the previously…
COVID-19 pandemic is severely impacting the lives of billions across the globe. Even after taking massive protective measures like nation-wide lockdowns, discontinuation of international flight services, rigorous testing etc., the infection…
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…
Phylogeographic methods aim to infer migration trends and the history of sampled lineages from genetic data. Applications of phylogeography are broad, and in the context of pathogens include the reconstruction of transmission histories and…
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…