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One of the main obstacles of adopting digital pathology is the challenge of efficient processing of hyperdimensional digitized biopsy samples, called whole slide images (WSIs). Exploiting deep learning and introducing compact WSI…
Mathematical models of infectious disease transmission typically neglect within-host dynamics. Yet within-host dynamics - including pathogen replication, host immune responses, and interactions with microbiota - are crucial not only for…
Evolving one-dimensional cellular automata (CAs) with genetic algorithms has provided insight into how improved performance on a task requiring global coordination emerges when only local interactions are possible. Two approaches that can…
When an infectious disease outbreak is of a relatively small size, describing the ancestry of a sample of infected individuals is difficult because most ancestral models assume large population sizes. Given a set of infected individuals, we…
Males are often the "sicker" sex with male biased parasitism found in a taxonomically diverse range of species. There is considerable interest in the processes that could underlie the evolution of sex-biased parasitism. Mating system…
Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of…
The spread of infectious disease and the evolution of antigenically distinct strains are often modeled separately, despite strong feedbacks mediated by host immune memory and heterogeneous contacts. To tackle this challenging problem, we…
The adaptive immune system engages in an arms race with evolving viruses, trying to generate new responses to viral strains that continually move away from the set of variants that have already elicited a functional immune response. In…
General laws in ecological parasitology are scarce. Here we evaluate data published by over 100 authors to determine whether the number of hosts in a life cycle is associated with the degree of aggregation of fish parasites at different…
Host-parasitoid population dynamics is often probed using a semi-discrete/hybrid modeling framework. Here, the update functions in the discrete-time model connecting year-to-year changes in the population densities are obtained by solving…
Most infectious diseases including more than half of known human pathogens are not restricted to just one host, yet much of the mathematical modeling of infections has been limited to a single species. We investigate consequences of a…
Recently different evolutionary computation approaches have been developed that generate sets of high quality diverse solutions for a given optimisation problem. Many studies have considered diversity 1) as a mean to explore niches in…
We numerically study disease dynamics that lead to the disease switching from one host species to another, resulting in diseases gaining the ability to infect, e.g., humans. Unlike previous studies that focused on branching processes…
One strategy for winning a coevolutionary struggle is to evolve rapidly. Most of the literature on host-pathogen coevolution focuses on this phenomenon, and looks for consequent evidence of coevolutionary arms races. An alternative…
We introduce a hybrid metaphor for the visualization of the reconciliations of co-phylogenetic trees, that are mappings among the nodes of two trees. The typical application is the visualization of the co-evolution of hosts and parasites in…
Phylogenetic tree reconciliation is employed for the examination of coevolution between host and symbiont species. An important concern is the requirement for dependable cost values when selecting event-based parsimonious reconciliation.…
Graph-based machine learning methods are useful tools in the identification and prediction of variation in genetic data. In particular, the comprehension of phenotypic effects at the cellular level is an accelerating research area in…
Motivated by observations in sequence data of herpesviruses, we introduce a multi-locus model for the joint evolution of different genotypes in a virus population that is distributed across a population of hosts. In the model, virus…
Reconstructing pathogen dynamics from genetic data as they become available during an outbreak or epidemic represents an important statistical scenario in which observations arrive sequentially in time and one is interested in performing…
We introduce a model of parasite infection in a cell population, where cells can be infected, either at birth through maternal transmission, from a contact with the parasites reservoir, or because of the parasites released in the cell…