Related papers: Vaccine sieve analysis on deep sequencing data usi…
Viral deep-sequencing data play a crucial role toward understanding disease transmission network flows, because the higher resolution of these data compared to standard Sanger sequencing provide evidence into the direction of infectious…
Post-market safety surveillance is an integral part of mass vaccination programs. Typically relying on sequential analysis of real-world health data as they accrue, safety surveillance is challenged by the difficulty of sequential multiple…
In this paper we propose a method and discuss its computational implementation as an integrated tool for the analysis of viral genetic diversity on data generated by high-throughput sequencing. Most methods for viral diversity estimation…
Mutational escape from vaccine induced immune responses has thwarted the development of a successful vaccine against AIDS, whose causative agent is HIV, a highly mutable virus. Knowing the virus' fitness as a function of its proteomic…
Personalized neoantigen vaccines represent a promising immunotherapy approach that harnesses tumor-specific antigens to stimulate anti-tumor immune responses. However, the design of these vaccines requires sophisticated computational…
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…
Randomization inference is a powerful tool in early phase vaccine trials when estimating the causal effect of a regimen against a placebo or another regimen. Randomization-based inference often focuses on testing either Fisher's sharp null…
The rapid spread of SARS-CoV-2 caused the COVID-19 pandemic and accelerated vaccine development to prevent the spread of the virus and control the disease. Given the sustained high infectivity and evolution of SARS-CoV-2, there is an…
Background: The Cox model and its extensions assuming proportional hazards is widely used to estimate vaccine efficacy (VE). In the typical situation that VE wanes over time, the VE estimates are not only sensitive to study duration and…
While vaccines are crucial to end the COVID-19 pandemic, public confidence in vaccine safety has always been vulnerable. Many statistical methods have been applied to VAERS (Vaccine Adverse Event Reporting System) database to study the…
Within-host genetic sequencing from samples collected over time provides a dynamic view of how viruses evade host immunity. Immune-driven mutations might stimulate neutralization breadth by selecting antibodies adapted to cycles of immune…
Knowledge of the time at which an HIV-infected individual seroconverts, when the immune system starts responding to HIV infection, plays a vital role in the design and implementation of interventions to reduce the impact of the HIV…
Four randomized placebo-controlled efficacy trials of a candidate vaccine or passively infused monoclonal antibody for prevention of HIV-1 infection are underway (HVTN 702 in South African men and women; HVTN 705 in sub-Saharan African…
Epidemiologic and genetic studies in chronic obstructive pulmonary disease (COPD) and many complex diseases suggest subgroup disparities (e.g., by sex). We consider this problem from the standpoint of integrative analysis where we combine…
The test-negative design (TND) has become a standard approach to evaluate vaccine effectiveness against the risk of acquiring infectious diseases in real-world settings, such as Influenza, Rotavirus, Dengue fever, and more recently…
The advent and subsequent widespread availability of preventive vaccines has altered the course of public health over the past century. Despite this success, effective vaccines to prevent many high-burden diseases, including HIV, have been…
Studies of HPV vaccine efficacy usually record infections with vaccine targeted and nontargeted strains. Contrary to blinded randomized controlled trials, confounding bias can be a threat and risk compensation may occur in observational…
Controlling and understanding epidemic outbreaks has recently drawn great interest in a large spectrum of research communities. Vaccination is one of the most well-established and effective strategies in order to contain an epidemic. In the…
The evolutionary dynamics of HIV during the chronic phase of infection is driven by the host immune response and by selective pressures exerted through drug treatment. To understand and model the evolution of HIV quantitatively, the…
Chronic infections of the human immunodeficiency virus (HIV) create a very complex co-evolutionary process, where the virus tries to escape the continuously adapting host immune system. Quantitative details of this process are largely…