Related papers: Ancestral process for infectious disease outbreaks…
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…
Despite the enormous relevance of zoonotic infections to world- wide public health, and despite much effort in modeling individual zoonoses, a fundamental understanding of the disease dynamics and the nature of outbreaks arising in such…
We analyse a model that describes the propagation of many pathogens within and between many species. A branching process approximation is used to compute the probability of disease outbreaks. Special cases of aquatic environments with two…
Uncertainty can be classified as either aleatoric (intrinsic randomness) or epistemic (imperfect knowledge of parameters). The majority of frameworks assessing infectious disease risk consider only epistemic uncertainty. We only ever…
Whole genome sequencing of pathogens from multiple hosts in an epidemic offers the potential to investigate who infected whom with unparalleled resolution, potentially yielding important insights into disease dynamics and the impact of…
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…
Traditional disease transmission models assume that the infectious period is exponentially distributed with a recovery rate fixed in time and across individuals. This assumption provides analytical and computational advantages, however it…
Several systems can be modeled as sets of interdependent networks where each network contains distinct nodes. Diffusion processes like the spreading of a disease or the propagation of information constitute fundamental phenomena occurring…
A primary quantity of interest in the study of infectious diseases is the average number of new infections that an infected person produces. This so-called reproduction number has significant implications for the disease progression. There…
Diffusion processes are governed by external triggers and internal dynamics in complex systems. Timely and cost-effective control of infectious disease spread critically relies on uncovering the underlying diffusion mechanisms, which is…
The dynamics of contact networks and epidemics of infectious diseases often occur on comparable time scales. Ignoring one of these time scales may provide an incomplete understanding of the population dynamics of the infection process. We…
In this paper we first introduce the general stochastic epidemic model for the spread of infectious diseases. Then we give methods for inferring model parameters such as the basic reproduction number $R_0$ and vaccination coverage $v_c$…
We study the problems of estimating the past and future evolutions of two diffusion processes that spread concurrently on a network. Specifically, given a known network $G=(V, \overrightarrow{E})$ and a (possibly noisy) snapshot…
Coalescents with multiple collisions (also called Lambda-coalescents or simple exchangeable coalescents) are used as models of genealogies. We study a new class of Markovian coalescent processes connected to a population model with…
We introduce and investigate an SIS-type model for the spread of an infectious disease, where the infected population is structured with respect to the different strain of the virus/bacteria they are carrying. Our aim is to capture the…
Early estimates of the transmission properties of a newly emerged pathogen are critical to an effective public health response, and are often based on limited outbreak data. Here, we use simulations to investigate a potential source of bias…
During infectious disease epidemics, pathogen transmission occurs in host populations made up of interacting subpopulations. Using stochastic simulation and analytical approximations, we examine how outbreak sizes in networked populations…
Infectious diseases are studied to understand their spreading mechanisms, to evaluate control strategies and to predict the risk and course of future outbreaks. Because people only interact with a small number of individuals, and because…
This work presents a model combining the simplest communicable and non-communicable disease models. The latter is, by far, the leading cause of sickness and death in the World, and introduces basal heterogeneity in populations where…
Early estimates of the transmission potential of emerging and re-emerging infections are increasingly used to inform public health authorities on the level of risk posed by outbreaks. Existing methods to estimate the reproduction number…