Related papers: Towards a phylogenetic measure to quantify HIV inc…
In this paper we present a new way to understand the timing of branching events in phylogenetic trees. Our method explicitly considers the relative timing of diversification events between sister clades; as such it is complimentary to…
Up to now, the effects of having heterogeneous networks of contacts have been studied mostly for diseases which are not persistent in time, i.e., for diseases where the infectious period can be considered very small compared to the lifetime…
One of the popular dynamics on complex networks is the epidemic spreading. An epidemic model describes how infections spread throughout a network. Among the compartmental models used to describe epidemics, the…
Epidemic models currently play a central role in our attempts to understand and control infectious diseases. Here, we derive a model for the diffusion limit of stochastic susceptible-infectious-removed (SIR) epidemic dynamics on a…
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…
Estimating HIV-1 incidence using biomarker assays in cross-sectional surveys is important for understanding the HIV pandemic. However, the utility of these estimates has been limited by uncertainty about what input parameters to use for…
We consider a continuous-time Markov chain model of SIR disease dynamics with two levels of mixing. For this so-called stochastic households model, we provide two methods for inferring the model parameters---governing within-household…
To combat the HIV/AIDS pandemic effectively, targeted interventions among certain key populations play a critical role. Examples of such key populations include sex workers, people who inject drugs, and men who have sex with men. While…
Network epidemiology often assumes that the relationships defining the social network of a population are static. The dynamics of relationships is only taken indirectly into account, by assuming that the relevant information to study…
In epidemic modeling, the term infection strength indicates the ratio of infection rate and cure rate. If the infection strength is higher than a certain threshold -- which we define as the epidemic threshold - then the epidemic spreads…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
Machine learning models are increasingly used in the medical domain to study the association between risk factors and diseases to support practitioners in predicting health outcomes. In this paper, we showcase the use of machine-learned…
The epidemiology has recently witnessed great advances based on computational models. Its scope and impact are getting wider thanks to the new data sources feeding analytical frameworks and models. Besides traditional variables considered…
Cell lineage statistics is a powerful tool for inferring cellular parameters, such as division rate, death rate or the population growth rate. Yet, in practice such an analysis suffers from a basic problem: how should we treat incomplete…
Cytotoxic T lymphocytes (CTLs) are immune system cells that are thought to play an important role in controlling HIV infection. We develop a stochastic ODE model of HIV-CTL interaction that extends current deterministic ODE models. Based on…
Inferring how an epidemic will progress and what actions to take when presented with limited information is of critical importance for epidemiologists and health professionals. In real world settings, epidemiology data can be scarce or…
Mathematical and computational modeling approaches are increasingly used as quantitative tools in the analysis and forecasting of infectious disease epidemics. The growing need for realism in addressing complex public health questions is…
Human immunodeficiency virus (HIV) evolves with extraordinary rapidity. However, its evolution is constrained by interactions between mutations in its fitness landscape. Here we show that an Ising model describing these interactions,…
We describe a new and computationally efficient Bayesian methodology for inferring species trees and demographics from unlinked binary markers. Likelihood calculations are carried out using diffusion models of allele frequency dynamics…
Many models in mathematical epidemiology are developed with the aim to provide a framework for parameter estimation and then prediction. It is well-known that parameters are not always uniquely identifiable. In this paper we consider…