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Multicellular organisms comprise a diverse collection of stable tissues built from different cell types. It remains unclear how large numbers of interacting cells can precisely coordinate their gene expression during tissue…
The rapidly developing theory of complex networks indicates that real networks are not random, but have a highly robust large-scale architecture, governed by strict organizational principles. Here, we focus on the properties of biological…
Virtually all real-world networks are dynamical entities. In social networks, the propensity of nodes to engage in social interactions (activity) and their chances to be selected by active nodes (attractiveness) are heterogeneously…
Traditional works on community detection from observations of information cascade assume that a single adjacency matrix parametrizes all the observed cascades. However, in reality the connection structure usually does not stay the same…
Simple nonlinear dynamical systems with multiple stable stationary states are often taken as models for switchlike biological systems. This paper considers the interaction of multiple such simple multistable systems when they are embedded…
A complex network is said to show topological isotropy if the topological structure around a particular node looks the same in all directions of the whole network. Topologically anisotropic networks are those where the local neighborhood…
We study the emerging large-scale structures in networks subject to selective pressures that simultaneously drive towards higher modularity and robustness against random failures. We construct maximum-entropy null models that isolate the…
Contacts between individuals serve as pathways where infections may propagate. These contact patterns can be represented by network structures. Static structures have been the common modeling paradigm but recent results suggest that…
This paper presents a real-time simulation involving ''protozoan-like'' cells that evolve by natural selection in a physical 2D ecosystem. Selection pressure is exerted via the requirements to collect mass and energy from the surroundings…
This paper considers generalised network, intended as networks where (a) the edges connecting the nodes are nonlinear, and (b) stochastic processes are continuously indexed over both vertices and edges. Such topological structures are…
A model of bit-strings, that uses the technique of multi-spin coding, was previously used to study the time evolution of B-cell clone repertoire, in a paper by Lagreca, Almeida and Santos. In this work we extend that simplified model to…
Networks play a central role in modern data analysis, enabling us to reason about systems by studying the relationships between their parts. Most often in network analysis, the edges are given. However, in many systems it is difficult or…
We investigate the evolutionary dynamics of an idealised model for the robust self-assembly of two-dimensional structures called polyominoes. The model includes rules that encode interactions between sets of square tiles that drive the…
As a model of temporally evolving networks, we consider a globally coupled logistic map with variable connection weights. The model exhibits self-organization of network structure, reflected by the collective behavior of units. Structural…
Biomimetics has played a key role in the evolution of artificial neural networks. Thus far, in silico metaphors have been dominated by concepts from neuroscience and cognitive psychology. In this paper we introduce a different type of…
In this article, we proposed a susceptible-infected model with identical infectivity, in which, at every time step, each node can only contact a constant number of neighbors. We implemented this model on scale-free networks, and found that…
Homophily, the tendency of individuals who are alike to form ties with one another, is an important concept in the study of social networks. Yet accounting for homophily effects is complicated in the context of bipartite networks where ties…
Recent progress in experimental techniques has enabled us to quantitatively study stochastic and flexible behavior of biological systems. For example, gene regulatory networks perform stochastic information processing and their…
We study the properties of discrete-time random walks on networks formed by randomly interconnected cliques, namely, random networks of cliques. Our purpose is to derive the parameters that define the network structure -- specifically, the…
A host-parasite model is considered for a population of cells that can be of two types, A or B, and exhibits unilateral reproduction: while a B-cell always splits into two cells of the same type, the two daughter cells of an A-cell can be…