Related papers: Viral Hitchhikers and Macroevolution: A Novel Hypo…
Mutational escape from vaccine induced immune responses has thwarted the development of a successful vaccine against AIDS, whose causative agent is HIV, a highly mutable virus. Knowing the virus' fitness as a function of its proteomic…
Branching processes are widely used to model the viral epidemic evolution. For more adequate investigation of viral epidemic modelling, we suggest to apply branching processes with transport of particles usually called branching random…
The de novo generation of drug-like molecules capable of inducing desirable phenotypic changes is receiving increasing attention. However, previous methods predominantly rely on expression profiles to guide molecule generation, but overlook…
Chromosomal rearrangements, particularly those mediated by transposable elements (TEs), can drive adaptive evolution by creating chimeric genes, inducing de novo gene formation, or altering gene expression. Here, we investigate…
Pangenome variation graphs (PVGs) allow for the representation of genetic diversity in a more nuanced way than traditional reference-based approaches. Here we focus on how PVGs are a powerful tool for studying genetic variation in viruses,…
Infection dynamics have been studied extensively on complex networks, yielding insight into the effects of heterogeneity in contact patterns on disease spread. Somewhat separately, metapopulations have provided a paradigm for modeling…
RNA viruses are a widely used tool to study evolution experimentally. Many standard protocols of virus propagation and competition are done at nominally low multiplicity of infection (m.o.i.), but lead during one passage to two or more…
A system-level genetic code is a hypothetical genetic code that exclusively or preferentially codes systems of interacting coadapted parts. System-level genetic codes differ from part-level genetic codes in which each discrete part is coded…
We present an SI epidemic model whereby a continuous variable captures variability in proliferative potential and resistance to infection among susceptibles. The occurrence of heritable, spontaneous changes in these phenotype and the…
The endogenous adaptation of agents, that may adjust their local contact network in response to the risk of being infected, can have the perverse effect of increasing the overall systemic infectiveness of a disease. We study a dynamical…
The relationship between traits that influence pathogen virulence and transmission is part of the central canon of the evolution and ecology of infectious disease. However, identifying directional and mechanistic relationships among traits…
We propose a minimal model to simulate long waiting times followed by evolutionary bursts on rugged landscapes. It combines point and inversions-like mutations as sources of genetic variation. The inversions are intended to simulate one of…
Epidemic modelling on complex networks has been studied intensively all the time. The majority of relative research assumes that the time scale of the underlying network evolution is much larger compared to the propagation dynamics on it,…
Living systems can be understood as organized entities that capture, transform, and reproduce information. Classical gene-centered models explain adaptation through frequency changes driven by differential fitness, yet they often overlook…
In this work, a hepatitis B virus infection dynamics model is proposed including the spatial dependence of viruses. The existence of traveling waves for the proposed model is established through the application of the celebrated Gersgorin…
We propose a physical theory underlying the temporal evolution of competing virus variants that relies on the existence of (quasi) fixed points capturing the large time scale invariance of the dynamics. To motivate our result we first…
During evolution of microorganisms genomes underwork have different changes in their lengths, gene orders, and gene contents. Investigating these structural rearrangements helps to understand how genomes have been modified over time. Some…
Models of human motion commonly focus either on trajectory prediction or action classification but rarely both. The marked heterogeneity and intricate compositionality of human motion render each task vulnerable to the data degradation and…
Human pathogens transmitted through environmental pathways are subject to stress and pressures outside of the host. These pressures may cause pathogen pathovars to diverge in their environmental persistence and their infectivity on an…
This theory seeks to define species and to explore evolutionary forces and genetic elements in speciation and species maintenance. The theory explains how speciation and species maintenance are caused by natural selection acting on…