Related papers: Dynamic Epistasis under Varying Environmental Pert…
The skin microbiome plays an important role in the maintenance of a healthy skin. It is an ecosystem, composed of several species, competing for resources and interacting with the skin cells. Imbalance in the cutaneous microbiome, also…
In many complex systems, the dynamical evolution of the different components can result in adaptation of the connections between them. We consider the problem of how a fully connected network of discrete-state dynamical elements which can…
Many physical and natural systems, including the population of species, evolve in habitats with spatial stochastic variations of the individuals' motility. We study here the effect of those fluctuations on invasion and genetic loss. A…
Inferring functional relationships within complex networks from static snapshots of a subset of variables is a ubiquitous problem in science. For example, a key challenge of systems biology is to translate cellular heterogeneity data…
How do networks of relationships evolve over time? We analyse a dataset tracking the social interactions of 900 individuals over four years. Despite continuous shifts in individual relationships, the macroscopic structural properties of the…
Many biological activities are induced by cellular chemical reactions of diffusing reactants. The dynamics of such systems can be captured by stochastic reaction networks. A recent numerical study has shown that diffusion can significantly…
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…
The nature of epistasis has important consequences for the evolutionary significance of sex and recombination. Recent efforts to find negative epistasis as source of negative linkage disequilibrium and associated long-term sex advantage…
The basic mechanics of evolution have been understood since Darwin. But debate continues over whether macroevolutionary phenomena are driven primary by the fitness structure of genotype space or by ecological interaction. In this paper we…
Living organisms must respond to environmental changes. Generally, accurate and rapid responses are provided by simple, unidirectional networks that connect inputs with outputs. Besides accuracy and speed, biological responses should also…
Stochastic systems often exhibit multiple viable metastable states that are long-lived. Over very long timescales, fluctuations may push the system to transition between them, drastically changing its macroscopic configuration. In realistic…
We propose a new procedure to monitor and forecast the onset of transitions in high dimensional complex systems. We describe our procedure by an application to the Tangled Nature model of evolutionary ecology. The quasi-stable…
We investigate the formation of stable ecological networks where many species share the same resource. We show that such stable ecosystem naturally occurs as a result of extinctions. We obtain an analytical relation for the number of…
In this paper, a non-autonomous stochastic logistic system is considered. An interesting result on the effect of stochastically perturbation for the dynamic behavior are obtained. That is, under certain conditions the stochastic system have…
The persistence of biodiversity of species is a challenging proposition in ecological communities in the face of Darwinian selection. The present article investigates beyond the pairwise competitive interactions and provides a novel…
Ecosystems display a complex spatial organization. Ecologists have long tried to characterize them by looking at how different measures of biodiversity change across spatial scales. Ecological neutral theory has provided simple predictions…
Exponential family Random Graph Models (ERGMs) can be viewed as expressing a probability distribution on graphs arising from the action of competing social forces that make ties more or less likely, depending on the state of the rest of the…
Due to inherent noise in intracellular networks cellular decisions can be random, so genetically identical cells can display different phenotypic behavior even in identical environments. Most previous work in understanding the…
As the amount and complexity of genetic information increases it is necessary that we explore some efficient ways of handling these data. This study takes the "divide and conquer" approach for analyzing high dimensional genomic data. Our…
Genetically identical cells in the same population can take on phenotypically variable states, leading to differentiated responses to external signals, such as nutrients and drug-induced stress. Many models and experiments have focused on a…