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Single virus epidemics over complete networks are widely explored in the literature as the fraction of infected nodes is, under appropriate microscopic modeling of the virus infection, a Markov process. With non-complete networks, this…
Specific HPV DNA sequences are associated with more than 90% of invasive carcinomas of the uterine cervix. Viral E6 and E7 oncogenes are key mediators in cell transformation by disrupting TP53 and RB pathways. To investigate molecular…
Although lessons have been learned from previous severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) outbreaks, the rapid evolution of the viruses means that future outbreaks of a much larger scale are…
This work illustrates potentials for recognition within {\em ad hoc} sensor networks if their nodes possess individual inter-related biologically inspired genetic codes. The work takes ideas from natural immune systems protecting organisms…
Evolutionary transitions occur when previously-independent replicating entities unite to form more complex individuals. Such transitions have profoundly shaped natural evolutionary history and occur in two forms: fraternal transitions…
Introduction. Can the infection due to the human immunodeficiency virus type 1 induce a change in the differentiation status or process in T cells?. Methods. We will consider two stochastic Markov chain models, one which will describe the…
Mathematical disease modelling has long operated under the assumption that any one infectious disease is caused by one transmissible pathogen spreading among a population. This paradigm has been useful in simplifying the biological reality…
Epidemic disease spreading is conventionally often modelled and analyzed by means of rate and diffusion equations, following the paradigms of well-controlled chemical reactions and diffusive dynamics in a test tube. Yet, serious worries…
Variational Autoencoders (VAEs) are expressive latent variable models that can be used to learn complex probability distributions from training data. However, the quality of the resulting model crucially relies on the expressiveness of the…
Population dynamics and evolutionary genetics underly the structure of ecosystems, changing on the same timescale for interacting species with rapid turnover, such as virus (e.g. HIV) and immune response. Thus, an important problem in…
Eigen's quasi-species model describes viruses as ensembles of different mutants of a high fitness "master" genotype. Mutants are assumed to have lower fitness than the master type, yet they coexist with it forming the quasi-species. When…
Bacteria and their bacteriophages are the most abundant, widespread and diverse groups of biological entities on the planet. In an attempt to understand how the interactions between bacteria, virulent phages and temperate phages might…
The structure of heterogeneous networks and human mobility patterns profoundly influence the spreading of endemic diseases. In small-scale communities, individuals engage in social interactions within confined environments, such as homes…
We study an abstract model for the co-evolution between mutating viruses and the adaptive immune system. In sequence space, these two populations are localized around transiently dominant strains. Delocalization or error thresholds exhibit…
Variational autoencoders (VAEs) and generative adversarial networks (GANs) enjoy an intuitive connection to manifold learning: in training the decoder/generator is optimized to approximate a homeomorphism between the data distribution and…
The viral load is known to be a chief predictor of the risk of transmission of infectious diseases. In this work, we investigate the role of the individuals' viral load in the disease transmission by proposing a new…
Virus entry is a multistep process that triggers a variety of cellular pathways interconnecting into a complex network, yet the molecular complexity of this network remains largely unsolved. Here, by employing systems biology approach, we…
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…
The design of protocols to suppress the propagation of viral infections is an enduring enterprise, especially hindered by limited knowledge of the mechanisms through which extinction of infection propagation comes about. We here report on a…
A fundamental feature of collective cell migration is phenotypic heterogeneity which, for example, influences tumour progression and relapse. While current mathematical models often consider discrete phenotypic structuring of the cell…