Related papers: Viral Hitchhikers and Macroevolution: A Novel Hypo…
It is estimated that approximately 15% of cancers worldwide can be linked to viral infections. The viruses that can cause or increase the risk of cancer include human papillomavirus, hepatitis B and C viruses, Epstein-Barr virus, and human…
Extrachromosomal DNA (ecDNA) can drive oncogene amplification, gene expression and intratumor heterogeneity, representing a major force in cancer initiation and progression. The phenomenon becomes even more intricate as distinct types of…
Epidemiological evidence suggests that simultaneous exposures to multiple environmental risk factors (Es) can increase disease risk larger than the additive effect of individual exposure acting alone. The interaction between a gene and…
We study the SIR epidemic model with infections carried by $k$ particles making independent random walks on a random regular graph. Here we assume $k\leq n^{\epsilon}$, where $n$ is the number of vertices in the random graph, and $\epsilon$…
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…
We investigate the selective forces that promote the emergence of modularity in nature. We demonstrate the spontaneous emergence of modularity in a population of individuals that evolve in a changing environment. We show that the level of…
Because of its relevance to everyday life, the spreading of viral infections has been of central interest in a variety of scientific communities involved in fighting, preventing and theoretically interpreting epidemic processes. Recent…
When a biological population expands into new territory, genetic drift develops an enormous influence on evolution at the propagating front. In such range expansion processes, fluctuations in allele frequencies occur through stochastic…
We investigate a randomly evolving process of subgraphs in an underlying host graph using the spectral theory of semigroups related to the Tsetlin library and hyperplane arrangements. Starting with some initial subgraph, at each iteration,…
Evolving systems, be it an antibody repertoire in the face of mutating pathogens or a microbial population exposed to varied antibiotics, constantly search for adaptive solutions in time-varying fitness landscapes. Generalists correspond to…
RNA viruses exist as genetically diverse populations displaying different phenotypes, including diverse degrees of virulence. The evolution of virulence in viral populations is, however, poorly understood. Based on the experimental…
Competition between random genetic drift and natural selection plays a central role in evolution: Whereas non-beneficial mutations often prevail in small populations by chance, mutations that sweep through large populations typically confer…
Hepatitis B virus (HBV) is considered as etiological agent of the lethal liver disease hepatitis B. Globally, hepatitis B is recognized as one of the prevailing infectious diseases with a significant impact on human health. In spite of…
Defective interfering particles (DIPs) are virus-like particles that occur naturally during virus infections. These particles are defective, lacking essential genetic materials for replication, but they can interact with the wild-type virus…
Early estimates of the transmission properties of a newly emerged pathogen are critical to an effective public health response, and are often based on limited outbreak data. Here, we use simulations to investigate a potential source of bias…
The incubation period of a disease is the time between an initiating pathologic event and the onset of symptoms. For typhoid fever, polio, measles, leukemia and many other diseases, the incubation period is highly variable. Some affected…
Human to human transmissible infectious diseases spread in a population using human interactions as its transmission vector. The early stages of such an outbreak can be modeled by a graph whose edges encode these interactions between…
We introduce EVE (Elemental Variational Expanse), a variational distributional neuron formulated as a local probabilistic computational unit with an explicit prior, an amortized posterior, and unit-level variational regularization. In most…
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.…
Many physical and natural systems, including the population of species, evolve in habitats with spatial stochastic variations of the individuals' motility. We study here the effect of those fluctuations on invasion and genetic loss. A…