Related papers: Inferring HIV escape rates from multi-locus genoty…
In this article we suggest a new statistical approach considering survival heterogeneity as a breakpoint model in an ordered sequence of time to event variables. The survival responses need to be ordered according to a numerical covariate.…
Applying a ML approach to the temporal variability of the Spike protein sequence enables us to identify, classify and track emerging virus variants. Our analysis is unbiased, in the sense that it does not require any prior knowledge of the…
Key populations at high risk of HIV infection are critical for understanding and monitoring HIV epidemics, but global estimation is hampered by sparse, uneven data. We analyze data from 199 countries for female sex workers (FSW), men who…
Due to the heterogeneity of the randomized controlled trial (RCT) and external target populations, the estimated treatment effect from the RCT is not directly applicable to the target population. For example, the patient characteristics of…
In this work, we present two defective regression models for the analysis of interval-censored competing risk data in the presence of cured individuals, viz., defective Gompertz and defective inverse Gaussian regression models. The proposed…
Throughout the course of an epidemic, the rate at which disease spreads varies with behavioral changes, the emergence of new disease variants, and the introduction of mitigation policies. Estimating such changes in transmission rates can…
Ending the HIV/AIDS pandemic is among the Sustainable Development Goals for the next decade. In order to overcome the gap between the need for care and the available resources, better understanding of HIV epidemics is needed to guide policy…
HTTP-based Trojan is extremely threatening, and it is difficult to be effectively detected because of its concealment and confusion. Previous detection methods usually are with poor generalization ability due to outdated datasets and…
We consider the problem of verifying stochastic models of biochemical networks against behavioral properties expressed in temporal logic terms. Exact probabilistic verification approaches such as, for example, CSL/PCTL model checking, are…
Detection and differentiation of circulating tumor cells (CTCs) and non-CTCs in blood draws of cancer patients pose multiple challenges. While the gold standard relies on tedious manual evaluation of an automatically generated selection of…
Mutation testing was proposed to identify weaknesses in test suites by repeatedly generating artificially faulty versions of the software (mutants) and determining if the test suite is sufficient to detect them (kill them). When the tests…
High throughput sequencing (HTS)-based technology enables identifying and quantifying non-culturable microbial organisms in all environments. Microbial sequences have enhanced our understanding of the human microbiome, the soil and plant…
Heterogeneity in characteristics from one region (sub-population) to another, commonly observed in complex systems, such as glasses and a collection of cells, is hard to describe theoretically. In the context of cancer, intra-tumor…
We analyze a within-host model of virus infection with antibody and CD8+ cytotoxic T lymphocyte (CTL) responses proposed by Schwartz et al. (2013). The goal of this work is to gain an overview of the stability of the biologically-relevant…
Recent clinical studies have shown that HIV disease pathogenesis can depend strongly on many factors at the time of transmission, including the strength of the initial viral load and the local availability of CD4+ T-cells. In this article,…
In stopping the spread of infectious diseases, pathogen genomic data can be used to reconstruct transmission events and characterize population-level sources of infection. Most approaches for identifying transmission pairs do not account…
We consider the directed evolution of a population after an intervention that has significantly altered the underlying fitness landscape. We model the space of genotypes as a distributive lattice; the fitness landscape is a real-valued…
Infectious disease dynamics operate across multiple biological scales, with within-host viral dynamics being a key driver of between-host transmission. However, while models that explicitly link these scales exist, none have been developed…
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…
With the advent of effective pre-exposure prophylaxis agents, active-controlled HIV prevention trials have become a common study design. Nevertheless, estimating absolute efficacy relative to a placebo remains important. In this paper, we…