Related papers: Functional principal variance component testing fo…
The ability to manipulate complex systems, such as the brain, to modify specific outcomes has far-reaching implications, particularly in the treatment of psychiatric disorders. One approach to designing appropriate manipulations is to…
Principal component regression (PCR) is a simple, but powerful and ubiquitously utilized method. Its effectiveness is well established when the covariates exhibit low-rank structure. However, its ability to handle settings with noisy,…
Matrix-covariate is now frequently encountered in many biomedical researches. It is common to fit conventional statistical models by vectorizing matrix-covariate. This strategy, however, results in a large number of parameters, while the…
Respondent-driven sampling is a form of link-tracing network sampling, which is widely used to study hard-to-reach populations, often to estimate population proportions. Previous treatments of this process have used a with-replacement…
Protein function and dynamics are closely related to its sequence and structure. However prediction of protein function and dynamics from its sequence and structure is still a fundamental challenge in molecular biology. Protein…
Certain retroviruses, including HIV, insert their DNA in a non-random fraction of the host genome via poorly understood selection mechanisms. Here, we develop a biophysical model for retroviral integrations as stochastic and…
In this paper, a mathematical analysis of the global dynamics of a partial differential equation viral infection cellular model is carried out. We study the dynamics of a hepatitis C virus (HCV) model, under therapy, that considers both…
This study presents the development of multivariate functional Moran's I, along with a novel approach termed multivariate functional areal spatial principal component analysis (mfasPCA), specifically designed for analyzing functional areal…
In this paper we review existing methods for robust functional principal component analysis (FPCA) and propose a new method for FPCA that can be applied to longitudinal data where only a few observations per trajectory are available. This…
Principal component analysis (PCA) is commonly used in genetics to infer and visualize population structure and admixture between populations. PCA is often interpreted in a way similar to inferred admixture proportions, where it is assumed…
Motivation: Genome-wide association studies (GWASs), which assay more than a million single nucleotide polymorphisms (SNPs) in thousands of individuals, have been widely used to identify genetic risk variants for complex diseases. However,…
Predictive or treatment selection biomarkers are usually evaluated in a subgroup or regression analysis with focus on the treatment-by-marker interaction. Under a potential outcome framework (Huang, Gilbert and Janes [Biometrics 68 (2012)…
Broadly neutralizing antibodies are promising candidates for treatment and prevention of HIV-1 infections. Such antibodies can temporarily suppress viral load in infected individuals; however, the virus often rebounds by escape mutants that…
An increasing number of control techniques are introduced to HIV infection problem to explore the options of helping clinical testing, optimizing drug treatments and to study the drug resistance situations. In such cases, complete/accurate…
An exactly solvable model based on the topology of a protein native state is applied to identify bottlenecks and key-sites for the folding of HIV-1 Protease. The predicted sites are found to correlate well with clinical data on resistance…
Predicting how protein mutations affect drug binding remains a major challenge, particularly when the mutations are distal from the binding site. In this study, we introduce a coupled simulation workflow that combines long-time-scale…
Background: Highly effective direct-acting antiviral (DAA) regimens (90% efficacy) are becoming available for hepatitis C virus (HCV) treatment. This therapeutic revolution leads us to consider possibility of eradicating the virus. However,…
Cervical cancer is one of the most common types of cancer found in females. It contributes to 6-29% of all cancers in women. It is caused by the Human Papilloma Virus (HPV). The 5-year survival chances of cervical cancer range from 17%-92%…
While most studies emphasize on certain aspects of Pathogen-Host Interactions (PHI), such as the preferential attachment of bacteria or virus to its human receptor homolog, studies have attempted to methodically classify interactions among…
We consider a spatially-heterogeneous generalization of a well-established model for the dynamics of the Human Immunodeficiency Virus-type 1 (HIV) within a susceptible host. The model consists of a nonlinear system of three coupled…