Related papers: Inferring HIV escape rates from multi-locus genoty…

Methods are lacking to handle the problem of survival analysis in the presence of an interval-censored covariate, specifically the case in which the conditional hazard of the primary event of interest depends on the occurrence of a…

In vaccine development, the temporal profiles of relative abundance of subtypes of immune cells (T-cells) is key to understanding vaccine efficacy. Complex and expensive experimental studies generate very sparse time series data on this…

Batch effects represent a major confounder in genomic diagnostics. In copy number variant (CNV) detection from NGS, many algorithms compare read depth between test samples and a reference sample, assuming they are process-matched. When this…

Causal inference across multiple data sources offers a promising avenue to enhance the generalizability and replicability of scientific findings. However, data integration methods for time-to-event outcomes, common in biomedical research,…

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…

Objective: The reservoir of human immunodeficiency virus (HIV) latently infected cells is the major obstacle for eradication of acquired immunodeficiency syndrome (AIDS). Due to the noisy environment and multiple influencing factors in the…

The proliferation of malware variants poses a significant challenges to traditional malware detection approaches, such as signature-based methods, necessitating the development of advanced machine learning techniques. In this research, we…

Retaining persons living with HIV (PLWH) in medical care is paramount to preventing new transmissions of the virus and allowing PLWH to live normal and healthy lifespans. Maintaining regular appointments with an HIV provider and taking…

For time-to-event data with finitely many competing risks, the proportional hazards model has been a popular tool for relating the cause-specific outcomes to covariates [Prentice et al. Biometrics 34 (1978) 541--554]. This article studies…

Mathematical modeling of biological systems is crucial to effectively and efficiently developing treatments for medical conditions that plague humanity. Often, systems of ordinary differential equations are a traditional tool used to…

The human body is able to generate a diverse set of high affinity antibodies, the soluble form of B cell receptors (BCRs), that bind to and neutralize invading pathogens. The natural development of BCRs must be understood in order to design…

Assessment of circulating CD4 count change over time in HIV-infected subjects on antiretroviral therapy (ART) is a central component of disease monitoring. The increasing number of HIV-infected subjects starting therapy and the limited…

With the launch of second line anti-retroviral therapy for HIV infected individuals, there has been an increased expectation on surviving period of people with HIV. We consider previously well-known models in HIV epidemiology where the…

A number of statistical models have been successfully developed for the analysis of high-throughput data from a single source, but few methods are available for integrating data from different sources. Here we focus on integrating gene…

HIV dynamical models are often based on non-linear systems of ordinary differential equations (ODE), which do not have analytical solution. Introducing random effects in such models leads to very challenging non-linear mixed-effects models.…

In two harmonized efficacy studies to prevent HIV infection through multiple infusions of the monoclonal antibody VRC01, a key objective is to evaluate whether the serum concentration of VRC01, which changes cyclically over time along with…

We have developed a mathematical model for in-host virus dynamics that includes spatial chemotaxis and diffusion across a two dimensional surface representing the vaginal or rectal epithelium at primary HIV infection. A linear stability…

Survival is a key metric for evaluating standards of care for people living with HIV. In resource-limited settings, high rates of loss to follow-up (LTFU) often result in underestimation of mortality when only observed deaths are…

HIV transmission within serodiscordant couples remains a significant public health challenge, particularly in sub-Saharan Africa. Estimating the rate of such infection, alongside the rates of introduction of infection from outside the…

Efficient screening and early diagnosis of HIV are critical for reducing onward transmission. Although large scale laboratory testing is not feasible, the widespread adoption of Electronic Health Records (EHRs) offers new opportunities to…