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Predator prey interactions are one of ecology's central research themes, but with many interdisciplinary implications across the social and natural sciences. Here we consider an often-overlooked species in these interactions, namely…

Measuring gene expression simultaneously in both hosts and symbionts offers a powerful approach to explore the biology underlying species interactions. Such dual or simultaneous RNAseq approaches have primarily been used to gain insight…

In order to model real ecological systems one has to consider many species that interact in complex ways. However, most of the recent theoretical studies have been restricted to few species systems with rather trivial interactions. The few…

We investigate a model of a parasite population invading spatially distributed immobile hosts on a graph, which is a modification of the frog model. Each host has an unbreakable immunity against infection with a certain probability $1-p$…

Self-propagating malware (e.g., an Internet worm) exploits security loopholes in software to infect servers and then use them to scan the Internet for more vulnerable servers. While the mechanisms of worm infection and their propagation…

Multi-population evolutionary algorithms are, by nature, highly complex and difficult to describe. Even two populations working in concert (or opposition) present a myriad of potential configurations that are often difficult to relate using…

The emergence or adaptation of pathogens may lead to epidemics, highlighting the need for a thorough understanding of pathogen evolution. The tradeoff hypothesis suggests that virulence evolves to reach an optimal transmission intensity…

In the biclustering problem, we seek to simultaneously group observations and features. While biclustering has applications in a wide array of domains, ranging from text mining to collaborative filtering, the problem of identifying…

A computationally simple genome-wide association study (GWAS) algorithm for estimating the main and epistatic effects of markers or single nucleotide polymorphisms (SNPs) is proposed. It is based on the intuitive assumption that changes of…

Spatial extent is a complicating factor in mathematical biology. The possibility that an action at point A cannot immediately affect what happens at point B creates the opportunity for spatial nonuniformity. This nonuniformity must change…

Motile organisms can form stable agglomerates such as cities or colonies. In the outbreak of a highly contagious disease, the control of large-scale epidemic spread depends on factors like the number and size of agglomerates, travel rate…

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…

The pursuit algorithms integrated in multi-layer convolutional sparse coding (ML-CSC) can interpret the convolutional neural networks (CNNs). However, many current state-of-art (SOTA) pursuit algorithms require multiple iterations to…

This paper demonstrates that simple yet important characteristics of coevolution can occur in evolutionary algorithms when only a few conditions are met. We find that interaction-based fitness measurements such as fitness (linear) ranking…

We propose a hybrid dynamical system approach to model the evolution of a pathogen that experiences different selective pressures according to a stochastic process. In every environment, the evolution of the pathogen is described by a…

We introduce and analyze a within-host dynamical model of the coevolution between rapidly mutating pathogens and the adaptive immune response. Pathogen mutation and a homeostatic constraint on lymphocytes both play a role in allowing the…

If two species exhibit different nonlinear responses to a single shared resource, and if each species modifies the resource dynamics such that this favors its competitor, they may stably coexist. This coexistence mechanism, known as…

The chance-constrained knapsack problem is a variant of the classical knapsack problem where each item has a weight distribution instead of a deterministic weight. The objective is to maximize the total profit of the selected items under…

The evolutionary persistence of symbiotic associations is a puzzle. Adaptation should eliminate cooperative traits if it is possible to enjoy the advantages of cooperation without reciprocating - a facet of cooperation known in game theory…

We have generalized our ``unified'' model of evolutionary ecology by taking into account the possible movements of the organisms from one ``patch'' to another within the same eco-system. We model the spatial extension of the eco-system…