Related papers: Recombination rate and selection strength in HIV i…
We consider a general mathematical model of a within-host viral infection with $n$ virus strains and explicit age-since-infection structure for infected cells. In the model, multiple virus strains compete for a population of target cells.…
Inferring concerted changes among biological traits along an evolutionary history remains an important yet challenging problem. Besides adjusting for spurious correlation induced from the shared history, the task also requires sufficient…
HIV-1 can disseminate between susceptible cells by two mechanisms: cell-free infection following fluid-phase diffusion of virions and by highly-efficient direct cell-to-cell transmission at immune cell contacts. The contribution of this…
In this paper, we propose a mathematical model for HIV-1 infection with intracellular delay. The model examines a viral-therapy for controlling infections through recombining HIV-1 virus with a genetically modified virus. For this model,…
This research gives a thorough examination of an HIV infection model that includes quiescent cells and immune response dynamics in the host. The model, represented by a system of ordinary differential equations, captures the complex…
Stronger selection implies faster evolution---that is, the greater the force, the faster the change. This apparently self-evident proposition, however, is derived under the assumption that genetic variation within a population is primarily…
Intrapatient HIV-1 evolution is dominated by selection on the protein level in the arms race with the adaptive immune system. When cytotoxic CD8+ T-cells or neutralizing antibodies target a new epitope, the virus often escapes via…
Horizontal gene transfer is an important factor in bacterial evolution that can act across species boundaries. Yet, we know little about rate and genomic targets of cross-lineage gene transfer, and about its effects on the recipient…
One way in which the human immunodeficiency virus (HIV-1) replicates within a host is by infecting activated CD4+ T-cells, which then produce additional copies of the virus. Even with the introduction of antiretroviral drug therapy, which…
Evolutionary analyses of large populations commonly incorporate stochasticity through temporal variation in selection while treating genetic transmission as fixed. Much less attention has been given to stochasticity in transmission itself.…
In the human genomes, recombination frequency between homologous chromosomes during meiosis is highly correlated with their physical length while it differs significantly when their coding density is considered. Furthermore, it has been…
We study the influence of the rate of the attainment of herd immunity (HI), in the absence of an approved vaccine, on the vulnerable population. We essentially ask the question: how hard the evolution towards the desired herd immunity could…
The evolution of antimicrobial resistance generally occurs in an environment where antimicrobial concentration is variable, which has dramatic consequences on the microorganisms' fitness landscape, and thus on the evolution of resistance.…
Estimating new HIV infections is significant yet challenging due to the difficulty in distinguishing between recent and long-term infections. We demonstrate that HIV recency status (recent v.s. long-term) could be determined from the…
Background: High HIV transmission persists in many U.S. jurisdictions despite prevention efforts. HIV self-testing offers a means to overcome barriers associated with routine laboratory-based testing but carries a risk of increasing…
One of the cornerstones in combating the HIV pandemic is being able to assess the current state and evolution of local HIV epidemics. This remains a complex problem, as many HIV infected individuals remain unaware of their infection status,…
We use a cellular automata model to study the evolution of HIV infection and the onset of AIDS. The model takes into account the global features of the immune response to any pathogen, the fast mutation rate of the HIV and a fair amount of…
The antibody repertoire of each individual is continuously updated by the evolutionary process of B cell receptor mutation and selection. It has recently become possible to gain detailed information concerning this process through…
We study minimal mean-field models of viral drug resistance development in which the efficacy of a therapy is described by a one-dimensional stochastic resetting process with mixed reflecting-absorbing boundary conditions. We derive…
We have used the Monte Carlo based computer models to show that selection pressure could affect the distribution of recombination hotspots along the chromosome. Close to critical crossover rate, where genomes may switch between the…