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Recent studies have consistently inferred high rates of adaptive molecular evolution between Drosophila species. At the same time, the Drosophila genome evolves under different rates of recombination, which results in partial genetic…
Genomic surveillance of infectious diseases allows monitoring circulating and emerging variants and quantifying their epidemic potential. However, due to the high costs associated with genomic sequencing, only a limited number of samples…
We introduce a minimal multiscale framework that links within-host virus dynamics to population-level SIRS epidemiology through explicit, bidirectional coupling. At the microscopic layer, a two variant quasispecies (master and mutant…
Transport of dense core vesicles (DCVs) in neurons is crucial for distributing molecules like neuropeptides and growth factors. We studied the experimental trajectories of dynein-driven directed movement of DCVs in the ALA neuron C. elegans…
The human MHC transplantation loci (HLA-A, -B, -C, -DPB1, -DQB1, -DRB1) are the most polymorphic in the human genome. It is generally accepted this polymorphism reflects a role in presenting pathogen-derived peptide to the adaptive immune…
Evolving genomes increase a number of their genes by gene duplications. To escape degradation in a functionless pseudogene, any gene duplicate needs to be guarded by negative (purifying) selection from otherwise inevitable fixation of…
Co-evolution of two coupled quasispecies is studied, motivated by the competition between viral evolution and adapting immune response. In this co-adaptive model, besides the classical error catastrophe for high virus mutation rates, a…
CoV2019 has evolved to be much more dangerous than CoV2003. Experiments suggest that structural rearrangements dramatically enhance CoV2019 activity. We identify a new first stage of infection which precedes structural rearrangements by…
Morphologic diversity is observed across all families of viruses. Yet these supra-molecular assemblies are produced most of the time in a spontaneous way through complex molecular self-assembly scenarios. The modeling of these phenomena…
Sexually transmitted infections (STIs) continue to present a complex and costly challenge to public health programs. The preferences and social dynamics of a population can have a large impact on the course of an outbreak as well as the…
In this paper, the mathematical model of HIV infection for CD8+ T-cells is illustrated. The homotopy analysis method and the Laplace transformations are combined for solving this model. Also, the convergence theorem is proved to demonstrate…
Enveloped viruses enter host cells either through endocytosis, or by direct fusion of the viral membrane envelope and the membrane of the host cell. However, some viruses, such as HIV-1, HSV-1, and Epstein-Barr can enter a cell through…
When modelling HIV epidemics, it is important to incorporate set-point viral load and its heritability. As set-point viral load distributions can differ significantly amongst epidemics, it is imperative to account for the observed local…
During primary HIV infection, the kinetics of plasma virus concentrations and CD4+ cell counts is very complex. Parametric and nonparametric models have been suggested for fitting repeated measurements of these markers. Alternatively,…
An increasing amount of geo-referenced mobile phone data enables the identification of behavioral patterns, habits and movements of people. With this data, we can extract the knowledge potentially useful for many applications including the…
Foundation models refer to architectures trained on vast datasets using autoregressive pre-training from natural language processing to capture intricate patterns and motifs. They were originally developed to transfer such learned knowledge…
We investigate a discrete-time two-strain symbiotic epidemic model on complex networks with both random and long-range interactions. Our analysis examines how the co-infection recovery rate ($\mu$), the long-range decay exponent ($\alpha$),…
T-cell activation plays a critical role in the initiation and propagation of HIV-1 infection and yet transient activation of the immune system is a normal response to immunization. In this study we extend a simple of model of HIV infection…
Horizontal gene Transfer (HT) denotes the transmission of genetic material between two living organisms, while the vertical transmission refers to a DNA transfer from parents to their offspring. Consistent experimental evidence report that…
We show how the characteristics of the evolutionary algorithm influence the evolvability of candidate solutions, i.e. the propensity of evolving individuals to generate better solutions as a result of genetic variation. More specifically,…