Related papers: Network Models of Phage-Bacteria Coevolution
We study a general set of models of social network evolution and dynamics. The models consist of both a dynamics on the network and evolution of the network. Links are formed preferentially between 'similar' nodes, where the similarity is…
One of the properties that make ecological systems so unique is the range of complex behavioural patterns that can be exhibited by even the simplest communities with only a few species. Much of this complexity is commonly attributed to…
Many social and biological systems are characterized by enduring hierarchies, including those organized around prestige in academia, dominance in animal groups, and desirability in online dating. Despite their ubiquity, the general…
We introduce an evolutionary metacommunity of multitrophic food webs on several habitats coupled by migration. In contrast to previous studies that focus either on evolutionary or on spatial aspects, we include both and investigate the…
An important part of the analysis of bio-molecular networks is to detect different functional units. Different functions are reflected in a different evolutionary dynamics, and hence in different statistical characteristics of network…
A central concern of community ecology is the interdependence between interaction strengths and the underlying structure of the network upon which species interact. In this work we present a solvable example of such a feedback mechanism in…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
Advances in next-generation sequencing technology have enabled the high-throughput profiling of metagenomes and accelerated the microbiome study. Recently, there has been a rise in quantitative studies that aim to decipher the microbiome…
Bacteria and phages have been in an ongoing arms race for billions of years. To resist phages bacteria have evolved numerous defense systems, which nevertheless are still overcome by counter-defense mechanisms of specific phages. These…
Phase separation has emerged as an essential concept for the spatial organization inside biological cells. However, despite the clear relevance to virtually all physiological functions, we understand surprisingly little about what phases…
Microbes are everywhere, including in and on our bodies, and have been shown to play key roles in a variety of prevalent human diseases. Consequently, there has been intense interest in the design of bacteriotherapies or "bugs as drugs,"…
We propose a minimal model of the dynamics of diversity -- replicator equations with extinction, invasion and mutation. We numerically study the behavior of this simple model and show that it displays completely different behavior from the…
Does an ecological community allow stable coexistence? Identifying the general principles that determine the answer to this question is a central problem of theoretical ecology. Random matrix theory approaches have uncovered the general…
We consider multiple diseases spreading in a static Configuration Model network. We make standard assumptions that infection transmits from neighbor to neighbor at a disease-specific rate and infected individuals recover at a…
The recent realization that entire communities fuse and separate (community coalescence) has led to a reappraisal of the forces determining species diversity and dynamics, especially in microbial communities where coalescence is likely…
Biological functions in living cells are controlled by protein interaction and genetic networks. These molecular networks should be dynamically stable against various fluctuations which are inevitable in the living world. In this paper, we…
The structure of molecular networks derives from dynamical processes on evolutionary time scales. For protein interaction networks, global statistical features of their structure can now be inferred consistently from several…
In this paper we study the dynamics of stochastic microorganism flocculation models. Given the strong influence of environmental and seasonal fluctuations that are present in these models, we propose a stochastic model that includes…
Microbial communities harbor extensive fine-scale diversity: closely-related strains of the same species coexist alongside many distantly-related taxa. Yet strain coexistence remains poorly understood, largely because most studies neglect…
The phage $\lambda$ infection of an \textit{E. coli} cell has become a paradigm for understanding the molecular processes involved in gene expression and cell signaling. This system provides an example of a genetic switch, as cells with…