Related papers: Functional principal variance component testing fo…
Mutation rates and fitness costs of deleterious mutations are difficult to measure in vivo but essential for a quantitative understanding of evolution. Using whole genome deep sequencing data from longitudinal samples during untreated HIV-1…
Inferring dependencies between complex biological traits while accounting for evolutionary relationships between specimens is of great scientific interest yet remains infeasible when trait and specimen counts grow large. The…
During the HIV infection several quasispecies of the virus arise, which are able to use different coreceptors, in particular the CCR5 and CXCR4 coreceptors (R5 and X4 phenotypes, respectively). The switch in coreceptor usage has been…
We develop a functional proportional hazards mixture cure (FPHMC) model with scalar and functional covariates measured at the baseline. The mixture cure model, useful in studying populations with a cure fraction of a particular event of…
Genome-wide association studies (GWAS) have led to the discovery of numerous single nucleotide polymorphisms (SNPs) associated with various phenotypes and complex diseases. However, the identified genetic variants do not fully explain the…
Longitudinal cohorts to determine the incidence of HIV infection are logistically challenging, so researchers have sought alternative strategies. Recency test methods use biomarker profiles of HIV-infected subjects in a cross-sectional…
Key populations at high risk of HIV infection are critical for understanding and monitoring HIV epidemics, but global estimation is hampered by sparse, uneven data. We analyze data from 199 countries for female sex workers (FSW), men who…
We develop a Bayesian statistical model and estimation methodology based on Forward Projection Adaptive Markov chain Monte Carlo in order to perform the calibration of a high-dimensional non-linear system of Ordinary Differential Equations…
Extreme enrichment of the human immunodeficiency virus (HIV-1) RNA genome for the purine A parallels the mild purine-loading of the RNAs of most organisms. This should militate against loop-loop "kissing" interactions between the structured…
Cardiovascular Disease (CVD) is considered as one of the principal causes of death in the world. Over recent years, this field of study has attracted researchers' attention to investigate heart sounds' patterns for disease diagnostics. In…
Principal component analysis (PCA) is a classical and widely used method for dimensionality reduction, with applications in data compression, computer vision, pattern recognition, and signal processing. However, PCA is designed for…
Experiments have shown that hepatitis C virus (HCV) infections in vitro disseminate both distally via the release and diffusion of cell-free virus through the medium, and locally via direct, cell-to-cell transmission. To determine the…
Gene expression and phenotype association can be affected by potential unmeasured confounders from multiple sources, leading to biased estimates of the associations. Since genetic variants largely explain gene expression variations, they…
Background: Heritability is a central measure in genetics quantifying how much of the variability observed in a trait is attributable to genetic differences. Existing methods for estimating heritability are most often based on random-effect…
We consider the problem of comparing a reference distribution with several other distributions. Given a sample from both the reference and the comparison groups, we aim to identify the comparison groups whose distributions differ from that…
HIV is a retrovirus that attacks the human immune system and can lead to death without proper treatment. In collaboration with the WHO and Wits University, we study how to improve the efficiency of HIV testing with the goal of eventual…
A set of curves or images of similar shape is an increasingly common functional data set collected in the sciences. Principal Component Analysis (PCA) is the most widely used technique to decompose variation in functional data. However, the…
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 the problem of robustly detecting changepoints in the variability of a sequence of independent multivariate functions. We develop a novel changepoint procedure, called the functional Kruskal--Wallis for covariance (FKWC)…
The search to understand how the HIV virus spreads inside the human body and how the immune response works to control it has motivated studies related to Mathematical Immunology. Actually, researches include the idea of mathematical models…