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Biological evolution can be conceptualized as a search process in the space of gene sequences guided by the fitness landscape, a mapping that assigns a measure of reproductive value to each genotype. Here we discuss probabilistic models of…
Genetic regulatory networks with adaptive responses are widely studied in biology. Usually, models consisting only of a few nodes have been considered. They present one input receptor for activation and one output node where the adaptive…
Distribution networks -- from vasculature to urban transportation systems -- are prevalent in both the natural and consumer worlds. These systems are intrinsically physical in composition and are embedded into real space, properties that…
Understanding causal relationships within Gene Regulatory Networks (GRNs) is essential for unraveling the gene interactions in cellular processes. However, causal discovery in GRNs is a challenging problem for multiple reasons including the…
Structural changes in a network representation of a system (e.g.,different experimental conditions, time evolution), can provide insight on its organization, function and on how it responds to external perturbations. The deeper…
Motivated by a recently introduced network growth mechanism that rely on the ranking of node prestige measures [S. Fortunato \emph{et al}., Phys. Rev. Lett. \textbf{96}, 218701 (2006)], a rank-based model for weighted network evolution is…
Biological neural networks are characterized by their high degree of plasticity, a core property that enables the remarkable adaptability of natural organisms. Importantly, this ability affects both the synaptic strength and the topology of…
Modelling gene regulatory networks not only requires a thorough understanding of the biological system depicted but also the ability to accurately represent this system from a mathematical perspective. Throughout this chapter, we aim to…
We investigate a model of evolving random network, introduced by us previously {[}{\it Phys. Rev. Lett.} {\bf 83}, 5587 (1999){]} . The model is a generalization of the Bak-Sneppen model of biological evolution, with the modification that…
Networks are widely used to represent interaction pattern among the components in complex systems. Structures of real networks from differ- ent domains may vary quite significantly. Since there is an interplay be- tween network architecture…
Models of growing networks are a central topic in network science. In these models, vertices are usually labeled by their arrival time, distinguishing even those node pairs whose structural roles are identical. In contrast, unlabeled…
In biological evolution complex neural structures grow from a handful of cellular ingredients. As genomes in nature are bounded in size, this complexity is achieved by a growth process where cells communicate locally to decide whether to…
Gene duplication is a fundamental evolutionary mechanism that contributes to biological complexity and diversity (Fortna et al., 2004). Traditionally, research has focused on the duplication of gene sequences (Zhang, 1914). However,…
With the evolution of social networks, the network structure shows dynamic nature in which nodes and edges appear as well as disappear for various reasons. The role of a node in the network is presented as the number of interactions it has…
A central and long-standing issue in evolutionary theory is the origin of the biological variation upon which natural selection acts1. Some hypotheses suggest that evolutionary change represents an adaptation to the surrounding environment…
Evolving Neural Networks (NNs) has recently seen an increasing interest as an alternative path that might be more successful. It has many advantages compared to other approaches, such as learning the architecture of the NNs. However, the…
We build networks of genetic similarity in which the nodes are organisms sampled from biological populations. The procedure is illustrated by constructing networks from genetic data of a marine clonal plant. An important feature in the…
Development combines three basic processes asymmetric --- cell division, signaling and gene regulation --- in a multitude of ways to create an overwhelming diversity of multicellular life-forms. Here, we attempt to chart this diversity…
In many complex systems, the dynamic processes that take place on a network and the changes in the network topology are intertwined. Here, we propose a model of coevolutionary dynamics of information spreading which is accompanied with link…
Epidemics on complex networks is a widely investigated topic in the last few years, mainly due to the last pandemic events. Usually, real contact networks are dynamic, hence much effort has been invested in studying epidemics on evolving…