Related papers: Vaccine sieve analysis on deep sequencing data usi…
Intercellular heterogeneity serves as both a confounding factor in studying individual clones and an information source in characterizing any heterogeneous tissues, such as blood, tumor systems. Due to inevitable sequencing errors and other…
Given a collection of features available for inclusion in a predictive model, it may be of interest to quantify the relative importance of a subset of features for the prediction task at hand. For example, in HIV vaccine trials, participant…
We propose a Bayesian Heterogeneity Learning approach for Susceptible-Infected-Removal-Susceptible (SIRS) model that allows underlying clustering patterns for transmission rate, recovery rate, and loss of immunity rate for the latest…
High-throughput shotgun sequence data makes it possible in principle to accurately estimate population genetic parameters without confounding by SNP ascertainment bias. One such statistic of interest is the proportion of heterozygous sites…
Vaccinations are an important tool in the prevention of disease. Vaccinations are generally voluntary for each member of a population and vaccination decisions are influenced by individual risk perceptions and contact structures within…
Recent advances in genomic sequencing technology have resulted in an abundance of genome sequence data. Despite the progress in interpreting those data, there remains a broad scope for their translation into clinical and societal benefits.…
The COVID-19 pandemic has influenced the lives of people globally. In the past year many researchers have proposed different models and approaches to explore in what ways the spread of the disease could be mitigated. One of the models that…
H1N1 influenza causes substantial seasonal illness and was the subtype of the 2009 influenza pandemic. Precise measures of antigenic distance between the vaccine and circulating virus strains help researchers design influenza vaccines with…
Patients in clinical studies often exhibit heterogeneous treatment effect (HTE). Classical subgroup analyses provide inferential tools to test for effect modification, while modern machine learning methods estimate the Conditional Average…
While the HVTN 505 trial showed no overall efficacy of the tested vaccine to prevent HIV infection over placebo, previous studies, biological theories, and the finding that immune response markers strongly correlated with infection in…
The analysis of competing risks data is often complicated by misclassification of the cause of failure. This issue can lead to seriously biased estimates and invalid conclusions. One way to deal with such misclassification is to use a…
Genetic risk prediction is an important component of individualized medicine, but prediction accuracies remain low for many complex diseases. A fundamental limitation is the sample sizes of the studies on which the prediction algorithms are…
As in many fields of medical research, survival analysis has witnessed a growing interest in the application of deep learning techniques to model complex, high-dimensional, heterogeneous, incomplete, and censored medical data. Current…
Genetic sequence data of pathogens are increasingly used to investigate transmission dynamics in both endemic diseases and disease outbreaks; such research can aid in development of appropriate interventions and in design of studies to…
In immunological studies, the characterization of small, functionally distinct cell subsets from blood and tissue is crucial to decipher system level biological changes. An increasing number of studies rely on assays that provide…
Misinformation about vaccination poses a significant public health threat by reducing vaccination rates and increasing disease burden. Understanding population heterogeneity can aid in recognizing and mitigating the effects of such…
COVID-19 vaccines are highly efficacious at preventing symptomatic infection, severe disease, and death. Most of the evidence that COVID-19 vaccines also reduce transmission of SARS-CoV-2 is based on retrospective, observational studies.…
Refined vaccine regimens containing variant-matched inserts are often authorized based on historical phase 3 efficacy trials together with immunobridging studies. Phase 3 trials are essential for establishing immune biomarkers that reliably…
We develop statistically based methods to detect single nucleotide DNA mutations in next generation sequencing data. Sequencing generates counts of the number of times each base was observed at hundreds of thousands to billions of genome…
Conducting genome-wide association studies (GWAS) in copy number variation (CNV) level is a field where few people involves and little statistical progresses have been achieved, traditional methods suffer from many problems such as batch…