Related papers: From viral evolution to spatial contagion: a biolo…
Infectious diseases are caused by pathogenic microorganisms and can spread through different ways. Mathematical models and computational simulation have been used extensively to investigate the transmission and spread of infectious…
We investigate the effects of cooperativity between contagion processes that spread and persist in a host population. We propose and analyze a dynamical model in which individuals that are affected by one transmissible agent $A$ exhibit a…
The surprisingly mercurial Covid-19 pandemic has highlighted the need to not only accelerate research on infectious disease, but to also study them using novel techniques and perspectives. A major contributor to the difficulty of containing…
When modelling HIV epidemics, it is important to incorporate set-point viral load and its heritability. As set-point viral load distributions can differ significantly amongst epidemics, it is imperative to account for the observed local…
Network--based epidemic models that account for heterogeneous contact patterns are extensively used to predict and control the diffusion of infectious diseases. We use census and survey data to reconstruct a geo--referenced and…
Two crucial elements facilitate the understanding and control of communicable disease spread within a social setting. These components are, the underlying contact structure among individuals that determines the pattern of disease…
The emergence of novel infectious agents presents challenges to statistical models of disease transmission. These challenges arise from limited, poor-quality data and an incomplete understanding of the agent. Moreover, outbreaks manifest…
The massive employment of computational models in network epidemiology calls for the development of improved inference methods for epidemic forecast. For simple compartment models, such as the Susceptible-Infected-Recovered model, Belief…
Current epidemics in the biological and social domains are challenging the standard assumptions of mathematical contagion models. Chief among them are the complex patterns of transmission caused by heterogeneous group sizes and infection…
Epidemic outbreaks of new pathogens, or known pathogens in new populations, cause a great deal of fear because they are hard to predict. For theoretical models of disease spreading, on the other hand, quantities characterizing the outbreak…
We present a thorough inspection of the dynamical behavior of epidemic phenomena in populations with complex and heterogeneous connectivity patterns. We show that the growth of the epidemic prevalence is virtually instantaneous in all…
Learning latent expression themes that best express complex patterns in a sample is a central problem in data mining and scientific research. For example, in computational biology we seek a set of salient gene expression themes that explain…
We present a stochastic epidemic model to study the effect of various preventive measures, such as uniform reduction of contacts and transmission, vaccination, isolation, screening and contact tracing, on a disease outbreak in a…
The Ebola virus is currently one of the most virulent pathogens for humans. The latest major outbreak occurred in Guinea, Sierra Leonne and Liberia in 2014. With the aim of understanding the spread of infection in the affected countries, it…
We consider a flexible Bayesian evidence synthesis approach to model the age-specific transmission dynamics of COVID-19 based on daily mortality counts. The temporal evolution of transmission rates in populations containing multiple types…
Pathogen genome data offers valuable structure for spatial models, but its utility is limited by incomplete sequencing coverage. We propose a probabilistic framework for inferring genetic distances between unsequenced cases and known…
We investigate a time-dependent spatial vector-host epidemic model with non-coincident domains for the vector and host populations. The host population resides in small non-overlapping sub-regions, while the vector population resides…
The seasonal human influenza virus undergoes rapid evolution, leading to significant changes in circulating viral strains from year to year. These changes are typically driven by adaptive mutations, particularly in the antigenic epitopes,…
Reconstructing pathogen dynamics from genetic data as they become available during an outbreak or epidemic represents an important statistical scenario in which observations arrive sequentially in time and one is interested in performing…
We develop a new structured compartmental model for the coevolutionary dynamics between susceptible and infectious individuals in heterogeneous SI epidemiological systems. In this model, the susceptible compartment is structured by a…