Related papers: Quantifying the recency of HIV infection using mul…
We propose a time-parameterized analogy between the thermodynamic behavior of a 3-level energy system and the progression of the HIV infection described by the cell population evolution generated by an appropriated cellular automata model.…
We propose and study a fully efficient method to estimate associations of an exposure with disease incidence when both, incident cases and prevalent cases, i.e. individuals who were diagnosed with the disease at some prior time point and…
The evolution of antimicrobial resistance generally occurs in an environment where antimicrobial concentration is variable, which has dramatic consequences on the microorganisms' fitness landscape, and thus on the evolution of resistance.…
Mechanisms of immunity, and of the host-pathogen interactions in general are among the most fundamental problems of medicine, ecology, and evolution studies. Here, we present a microscopic, protein-level, sequence-based model of immune…
Sexually transmitted infections (STIs) continue to present a complex and costly challenge to public health programs. The preferences and social dynamics of a population can have a large impact on the course of an outbreak as well as the…
In this paper we generalise a simple discrete time stochastic SIR type model defined by Tuckwell and Williams. The SIR model by Tuckwell and Williams assumes a homogeneous population, a fixed infectious period, and a strict transition from…
People living with HIV face a high burden of comorbidities, yet early detection is often limited by symptom-driven screening. We evaluate the potential of AI to predict multiple comorbidities from routinely collected Electronic Health…
Biomarker-guided designs are increasingly used to evaluate personalized treatments based on patients' biomarker status in Phase II and III clinical trials. With adaptive enrichment, these designs can improve the efficiency of evaluating the…
We study the problem of identifying a single infection source in a network under the susceptible-infected-recovered-infected (SIRI) model. We describe the infection model via a state-space model, and utilizing a state propagation approach,…
We study a symmetric two-disease SIR co-infection model on networks in which co-infected individuals recover at a rate distinct from that of single infections. The model explicitly represents all co-infection states and features absorbing…
We propose and study a new mathematical model of the human immunodeficiency virus (HIV). The main novelty is to consider that the antibody growth depends not only on the virus and on the antibodies concentration but also on the uninfected…
HIV pre-exposure Prophylaxis (PrEP) has become essential for global HIV control, but its implementation coincides with rising bacterial STI rates among men who have sex with men (MSM). While risk-compensation behavioral changes like reduced…
The expected number of secondary infections arising from each index case, referred to as the reproduction or $R$ number, is a vital summary statistic for understanding and managing epidemic diseases. There are many methods for estimating…
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…
Despite high vaccine coverage, pertussis has re-emerged as a public health concern in many countries. One hypothesis posed for re-emergence is the waning of immunity. In some disease systems, the process of waning immunity can be…
Within-individual variability of health indicators measured over time is becoming commonly used to inform about disease progression. Simple summary statistics (e.g. the standard deviation for each individual) are often used but they are not…
We introduce and analyze a waiting time model for the accumulation of genetic changes. The continuous time conjunctive Bayesian network is defined by a partially ordered set of mutations and by the rate of fixation of each mutation. The…
This paper describes a novel approach to modeling homphily, i.e. the tendency of nodes that share (or differ in) certain attributes to be linked; we consider dynamic networks in which nodes can be added over time but not removed. Our…
Reports from the Health Department in the Philippines show that cases of Human Immunodeficiency Virus (HIV) are increasing despite management and control efforts by the government. Worldwide, the Philippines has one of the fastest growing…
We consider a stochastic epidemic model with sideward contact tracing. We assume that infection is driven by interactions within mixing events (gatherings of two or more individuals). Once an infective is diagnosed, each individual who was…