Related papers: Inferring HIV escape rates from multi-locus genoty…
To fulfill their killing functions, cytotoxic T lymphocytes (CTLs) need to migrate to search for their target cells in complex biological microenvironments, a key component of which is extracellular matrix (ECM). The mechanisms underlying…
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…
Antibodies, an essential part of our immune system, develop through an intricate process to bind a wide array of pathogens. This process involves randomly mutating DNA sequences encoding these antibodies to find variants with improved…
Based on a recent model of evolving viruses competing with an adapting immune system [1], we study the conditions under which a viral quasispecies can maximize its growth rate. The range of mutation rates that allows viruses to thrive is…
Cancer arises from successive rounds of mutations which generate tumor cells with different genomic variation i.e. clones. For drug responsiveness and therapeutics, it is necessary to identify the clones in tumor sample accurately. Many…
The diversity of virus populations within single infected hosts presents a major difficulty for the natural immune response as well as for vaccine design and antiviral drug therapy. Recently developed pyrophosphate based sequencing…
Interval-censored competing risks data arise when each study subject may experience an event or failure from one of several causes and the failure time is not observed exactly but rather known to lie in an interval between two successive…
Missing data is a recurrent issue in epidemiology where the infection process may be partially observed. Approximate Bayesian Computation, an alternative to data imputation methods such as Markov Chain Monte Carlo integration, is proposed…
Like many chronic diseases, human immunodeficiency virus (HIV) is managed over time at regular clinic visits. At each visit, patient features are assessed, treatments are prescribed, and a subsequent visit is scheduled. There is a need for…
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…
Colorectal cancer liver metastases (CLM) are the most common type of distant metastases originating from the abdomen and are characterized by a high recurrence rate after curative resection. It has been previously reported that CLM…
Viral infections trigger complex immune responses with heterogeneous outcomes shaped by nonlinear feedbacks. An ordinary differential equation model is developed to investigate immune response dynamics during viral infection, incorporating…
Immune cells have evolved to recognize and eliminate pathogens, and the efficiency of this process can be measured in a Petri dish. Yet, even if the cells are time-lapse recorded and tracked with high resolution, it is difficult to judge…
Infection by many viruses begins with fusion of viral and cellular lipid membranes, followed by entry of viral contents into the target cell and ultimately, after many biochemical steps, integration of viral DNA into that of the host cell.…
Hepatitis C virus (HCV) coinfection has become one of the most challenging clinical situations to manage in HIV-infected patients. Recently the effect of HCV coinfection on HIV dynamics following initiation of highly active antiretroviral…
Combination Antiretroviral Therapy (cART) succeeds to control viral replication in most HIV infected patients. This is normally followed by a reconstitution of the CD4$^+$ T cells pool; however, this does not happen for a substantial…
We introduce a new version of forward stepwise regression. Our modification finds solutions to regression problems where the selected predictors appear in a structured pattern, with respect to a predefined distance measure over the…
A ternary reaction-diffusion model for early HIV infection dynamics, incorporating logistic growth of target cells, is introduced. According to in vitro and in vivo studies, random movement of target cells, infected cells, and virions and a…
In vaccine studies for infectious diseases such as human immunodeficiency virus (HIV), the frequency and type of contacts between study participants and infectious sources are among the most informative risk factors, but are often not…
In this work we introduce a differential equation model with time-delay that describes the three-stage dynamics and the two time scales observed in HIV infection. Assuming that the virus has high mutation and rapid reproduction rates that…