相关论文: On Gene Duplication Models for Evolving Regulatory…

We compare asynchronous vs. synchronous update of discrete dynamical networks and find that a simple time delay in the nodes may induce a reproducible deterministic dynamics even in the case of asynchronous update in random order. 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…

Genomic alterations lead to cancer complexity and form a major hurdle for a comprehensive understanding of the molecular mechanisms underlying oncogenesis. In this review, we describe the recent advances in studying cancer-associated genes…

Preferential attachment is often suggested to be the underlying mechanism of the growth of a network, largely due to that many real networks are, to a certain extent, scale-free. However, such attribution is usually made under debatable…

It is suggested that the degree distribution for networks of the cell-metabolism for simple organisms reflects an ubiquitous randomness. This implies that natural selection has exerted no or very little pressure on the network degree…

The parallel computational complexity or depth of growing network models is investigated. The networks considered are generated by preferential attachment rules where the probability of attaching a new node to an existing node is given by a…

In this paper we introduce a model of spatial network growth in which nodes are placed at randomly selected locations on a unit square in $\mathbb{R}^2$, forming new connections to old nodes subject to the constraint that edges do not…

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…

Gene Regulatory Networks (GRNs) consisting of combinations of transcription factors (TFs) and their cis promoters are assumed to be sufficient to direct the development of organisms. Mutations in GRNs are assumed to be the primary drivers…

Ever since the Barab\'{a}si-Albert (BA) scale-free network has been proposed, network modeling has been studied intensively in light of the network growth and the preferential attachment (PA). However, numerous real systems are featured…

Networks are mathematical structures that are universally used to describe a large variety of complex systems such as the brain or the Internet. Characterizing the geometrical properties of these networks has become increasingly relevant…

Many important real-world networks manifest "small-world" properties such as scale-free degree distributions, small diameters, and clustering. The most common model of growth for these networks is "preferential attachment", where nodes…

In this paper we investigate networks whose evolution is governed by the interaction of a random assembly process and an optimization process. In the first process, new nodes are added one at a time and form connections to randomly selected…

Large scale databases are available that contain homologous gene families constructed from hundreds of complete genome sequences from across the three domains of Life. Here we discuss approches of increasing complexity aimed at extracting…

Many real-world complex networks arise as a result of a competition between growth and rewiring processes. Usually the initial part of the evolution is dominated by growth while the later one rather by rewiring. The initial growth allows…

Cells often exhibit different and stable phenotypes from the same DNA sequence. Robustness and plasticity of such cellular states are controlled by diverse transcriptional and epigenetic mechanisms, among them the modification of…

Here we propose a generic mechanism - networked buffering - for generating robust traits in complex systems that requires two basic conditions to be satisfied: 1) agents are versatile enough to perform more than one single functional role…

We consider a simplified model for gene regulation, where gene expression is regulated by transcription factors (TFs), which are single proteins or protein complexes. Proteins are in turn synthesised from expressed genes, creating a…

Gene expression-based heterogeneity analysis has been extensively conducted. In recent studies, it has been shown that network-based analysis, which takes a system perspective and accommodates the interconnections among genes, can be more…

In the present paper we propose to describe gene networks in biological systems using probabilistic algorithms. We describe gene duplication in the process of biological evolution using introduction of the replica procedure for…