Related papers: Towards a phylogenetic measure to quantify HIV inc…
Understanding age-group dynamics of infectious diseases is a fundamental issue for both scientific study and policymaking. Age-structure epidemic models were developed in order to study and improve our understanding of these dynamics. By…
We propose a framework for Bayesian non-parametric estimation of the rate at which new infections occur assuming that the epidemic is partially observed. The developed methodology relies on modelling the rate at which new infections occur…
The diversity of virus populations within single infected hosts presents a major difficulty for the natural immune response as well as for vaccine design and antiviral drug therapy. Recently developed pyrophosphate based sequencing…
We develop a stochastic epidemic model progressing over dynamic networks, where infection rates are heterogeneous and may vary with individual-level covariates. The joint dynamics are modeled as a continuous-time Markov chain such that…
An increasing amount of geo-referenced mobile phone data enables the identification of behavioral patterns, habits and movements of people. With this data, we can extract the knowledge potentially useful for many applications including the…
Genetic data are often used to infer demographic history and changes or detect genes under selection. Inferential methods are commonly based on models making various strong assumptions: demography and population structures are supposed…
Rooted and ranked binary trees are mathematical objects of great importance used to model hierarchical data and evolutionary relationships with applications in many fields including evolutionary biology and genetic epidemiology. Bayesian…
While probabilistic projection methods for projecting life expectancy exist, few account for covariates related to life expectancy. Generalized HIV/AIDS epidemics have a large, immediate negative impact on the life expectancy in a country,…
A social (sexual) network is modeled by an extension of the configuration model to the situation where edges have weights, e.g. reflecting the number of sex-contacts between the individuals. An epidemic model is defined on the network such…
Background. Several studies have used phylogenetics to investigate Human Immunodeficiency Virus (HIV) transmission among Men who have Sex with Men (MSMs) in Montreal, Quebec, Canada, revealing many transmission clusters. The Quebec HIV…
Phylogenetic comparative methods correct for shared evolutionary history among a set of non-independent organisms by modeling sample traits as arising from a diffusion process along on the branches of a possibly unknown history. To…
Infectious diseases remain one of the major causes of human mortality and suffering. Mathematical models have been established as an important tool for capturing the features that drive the spread of the disease, predicting the progression…
Nowcasting and forecasting of epidemic spreading rely on incidence series of reported cases to derive the fundamental epidemiological parameters for a given pathogen. Two relevant drawbacks for predictions are the unknown fractions of…
Recent work has focused attention on statistical inference for the population distribution of the number of sexual partners based on survey data. The characteristics of these distributions are of interest as components of mathematical…
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
We will study a mathematical model of the human immunodeficiency virus (HIV) infection in the presence of combination therapy that includes within-host infectious dynamics. The deterministic model requires us to analyze asymptotic stability…
We consider the standard three-component differential equation model for the growth of an HIV virion population in an infected host in the absence of drug therapy. The dynamical properties of the model are determined by the set of values of…
We consider the problem of identifying the source of an epidemic, spreading through a network, from a complete observation of the infected nodes in a snapshot of the network. Previous work on the problem has often employed geometric,…
Evaluation of HIV large scale interventions programme is becoming increasingly important, but impact estimates frequently hinge on knowledge of changes in behaviour such as the frequency of condom use (CU) over time, or other self-reported…
Throughout the course of an epidemic, the rate at which disease spreads varies with behavioral changes, the emergence of new disease variants, and the introduction of mitigation policies. Estimating such changes in transmission rates can…