Related papers: Towards a phylogenetic measure to quantify HIV inc…
The goal of these lectures is to review some mathematical aspects of random tree models used in evolutionary biology to model gene trees or species trees. We start with stochastic models of tree shapes (finite trees without edge lengths),…
We present a new joint longitudinal and survival model aimed at estimating the association between the risk of an event and the change in and history of a biomarker that is repeatedly measured over time. We use cubic B-splines models for…
Intuitively, sampling is likely to be more efficient for prevalence estimation, if the cases (or positives) have a relatively higher representation in the sample than in the population. In case the virus is transmitted via personal…
We study the epidemic source detection problem in contact tracing networks modeled as a graph-constrained maximum likelihood estimation problem using the susceptible-infected model in epidemiology. Based on a snapshot observation of the…
We formulate and analyze a novel hypothesis testing problem for inferring the edge structure of an infection graph. In our model, a disease spreads over a network via contagion or random infection, where the random variables governing the…
Stochasticity and spatial heterogeneity are of great interest recently in studying the spread of an infectious disease. The presented method solves an inverse problem to discover the effectively decisive topology of a heterogeneous network…
An individual detected as HIV positive in Cuba is asked to provide a list of his/her sexual contacts for the previous 2 years. This allows one to gather detailed information on the spread of the HIV epidemic. Here we study the evolution of…
By providing a framework of accounting for the shared ancestry inherent to all life, phylogenetics is becoming the statistical foundation of biology. The importance of model choice continues to grow as phylogenetic models continue to…
We study the problem of estimating the parameters (i.e., infection rate and recovery rate) governing the spread of epidemics in networks. Such parameters are typically estimated by measuring various characteristics (such as the number of…
We study the problem of estimating the origin of an epidemic outbreak -- given a contact network and a snapshot of epidemic spread at a certain time, determine the infection source. Finding the source is important in different contexts of…
Traditionally, heritability has been estimated using family-based methods such as twin studies. Advancements in molecular genomics have facilitated the development of alternative methods that utilise large samples of unrelated or related…
Approximate Bayesian Computation (ABC) is a popular inference method when likelihoods are hard to come by. Practical bottlenecks of ABC applications include selecting statistics that summarize the data without losing too much information or…
Modeling viral dynamics in HIV/AIDS studies has resulted in a deep understanding of pathogenesis of HIV infection from which novel antiviral treatment guidance and strategies have been derived. Viral dynamics models based on nonlinear…
Modelling epidemics using contact networks provides a significant improvement over classical compartmental models by explicitly incorporating the network of contacts. However, while network-based models describe disease spread on a given…
We use a cellular automata model to study the evolution of HIV infection and the onset of AIDS. The model takes into account the global features of the immune response to any pathogen, the fast mutation rate of the HIV and a fair amount of…
Incidence estimation of HIV infection can be performed using recent infection testing algorithm (RITA) results from a cross-sectional sample. This allows practitioners to understand population trends in the HIV epidemic without having to…
Recent outbreaks of monkeypox and Ebola, and worrying waves of COVID-19, influenza and respiratory syncytial virus, have all led to a sharp increase in the use of epidemiological models to estimate key epidemiological parameters. The…
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…
Capturing the structured mixing within a population is key to the reliable projection of infectious disease dynamics and hence informed control. Both heterogeneity in the number of contacts and age-structured mixing have been repeatedly…
Like many chronic diseases, human immunodeficiency virus (HIV) is managed over time at regular clinic visits. At each visit, patient features are assessed, treatments are prescribed, and a subsequent visit is scheduled. There is a need for…