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Inferring dependencies between complex biological traits while accounting for evolutionary relationships between specimens is of great scientific interest yet remains infeasible when trait and specimen counts grow large. The…

Recorded history shows the long coexistence of humans and animals, suggesting it began much earlier. Despite some beneficial interdependence, many animals carry viral diseases that can spread to humans. These diseases are known as zoonotic…

CRISPR is a newly discovered prokaryotic immune system. Bacteria and archaea with this system incorporate genetic material from invading viruses into their genomes, providing protection against future infection by similar viruses. The…

Multitasking optimization is an emerging research field which has attracted lot of attention in the scientific community. The main purpose of this paradigm is how to solve multiple optimization problems or tasks simultaneously by conducting…

Coinfection phenomena are common in nature, yet there is a lack of analytical approaches for coinfection systems with a high number of circulating and interacting strains. In this paper, we investigated a coinfection SIS framework applied…

The paper studies multi-competitive continuous-time epidemic processes in the presence of a shared resource. We consider the setting where multiple viruses are simultaneously prevalent in the population, and the spread occurs due to not…

One unfortunate consequence of the success story of wireless sensor networks (WSNs) in separate research communities is an ever-growing gap between theory and practice. Even though there is a increasing number of algorithmic methods for…

This research proposes a novel indicator-based hybrid evolutionary approach that combines approximate and exact algorithms. We apply it to a new bi-criteria formulation of the travelling thief problem, which is known to the Evolutionary…

Worm origin identification and propagation path reconstruction are essential problems in digital forensics. However, a small number of studies have specifically investigated these problems so far. In this paper, we extend a distributed…

Discrete-time models are the traditional approach for capturing population dynamics of a host-parasitoid system. Recent work has introduced a semi-discrete framework for obtaining model update functions that connect host-parasitoid…

The vertebrate adaptive immune system provides a flexible and diverse set of molecules to neutralize pathogens. Yet, viruses such as HIV can cause chronic infections by evolving as quickly as the adaptive immune system, forming an…

Emerging marine infectious diseases pose a substantial threat to marine ecosystems and the conservation of their biodiversity. Compartmental models of epidemic transmission in marine sessile organisms, available only recently, are based on…

In this paper, we extend a model of host-parasite co-evolution to incorporate the semi-conservative nature of DNA replication for both the host and the parasite. We find that the optimal mutation rate for the semi-conservative and…

Co-evolution is a powerful problem-solving approach. However, fitness evaluation in co-evolutionary algorithms can be computationally expensive, as the quality of an individual in one population is defined by its interactions with many (or…

Between-species coevolution, and in particular antagonistic host-parasite coevolution, is a major process shaping within-species diversity. In this paper we investigate the role of various stochastic processes affecting the outcome of the…

Inferring concerted changes among biological traits along an evolutionary history remains an important yet challenging problem. Besides adjusting for spurious correlation induced from the shared history, the task also requires sufficient…

Computing diverse sets of high quality solutions for a given optimization problem has become an important topic in recent years. In this paper, we introduce a coevolutionary Pareto Diversity Optimization approach which builds on the success…

We study a minimal stochastic individual-based model for a microbial population challenged by a persistent (lytic) virus epidemic. We focus on the situation in which the resident microbial host population and the virus population are in…

Interacting populations often create complicated spatiotemporal behavior, and understanding it is a basic problem in the dynamics of spatial systems. We study the two-species case by simulations of a host--parasitoid model. In the case of…

Encounter-based network is a frequently-disconnected wireless ad-hoc network requiring immediate neighbors to store and forward aggregated data for information disseminations. Using traditional approaches such as gateways or firewalls for…