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A central goal in ecology is to understand how biodiversity is maintained. Previous theoretical works have employed the rock-paper-scissors (RPS) game as a toy model, demonstrating that population mobility is crucial in determining the…
The relationship between network topology and system dynamics has significant implications for unifying our understanding of the interplay among metabolic, gene-regulatory, and ecosystem network architecures. Here we analyze the stability…
Homeostasis of protein concentrations in cells is crucial for their proper functioning, and this requires concentrations (at their steady-state levels) to be stable to fluctuations. Since gene expression is regulated by proteins such as…
The main goal of Systems Biology research is to reconstruct biological networks for its topological analysis so that reconstructed networks can be used for the identification of various kinds of disease. The availability of high-throughput…
Gene Regulatory Networks are networks of interactions in biological organisms responsible for determining the production levels of proteins and peptides. Proteins are workers of a cell factory, and their production defines the goal of a…
Based on a non-equilibrium mechanism for spatial pattern formation we study how position information can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of cells in a developing…
Coevolutionary dynamics is investigated in chemical catalysis, biological evolution, social and economic systems. The dynamics of these systems can be analyzed within the unifying framework of evolutionary game theory. In this Letter, we…
The dynamics of gene regulatory networks is governed by the interaction between deterministic biochemical reactions and molecular noise. To understand how gene regulatory networks process information during cell state transitions, we study…
Recent genomic and bioinformatic advances have motivated the development of numerous random network models purporting to describe graphs of biological, technological, and sociological origin. The success of a model has been evaluated by how…
Understanding cooperation in social dilemmas requires models that capture the complexity of real-world interactions. While network frameworks have provided valuable insights to model the evolution of cooperation, they are unable to encode…
The two most fundamental processes describing change in biology, development and evolu-tion, occur over drastically different timescales, difficult to reconcile within a unified framework. Development involves temporal sequences of cell…
Regulatory gene networks contain generic modules like those involving feedback loops, which are essential for the regulation of many biological functions. We consider a class of self-regulated genes which are the building blocks of many…
Cellular phenotypes are determined by the dynamical activity of networks of co-regulated genes. Elucidating such networks is crucial for the understanding of normal cell physiology as well as for the dissection of complex pathologic…
Spatial environmental variation can either amplify or suppress the fixation of beneficial mutants in structured populations, yet the interplay of ecological factors and spatial structure in determining which outcome occurs remains…
In a complex system, the individual components are neither so tightly coupled or correlated that they can all be treated as a single unit, nor so uncorrelated that they can be approximated as independent entities. Instead, patterns of…
Cell fate decisions emerge as a consequence of a complex set of gene regulatory networks. Models of these networks are known to have more parameters than data can determine. Recent work, inspired by Waddington's metaphor of a landscape, has…
Ecological systems are emergent features of ecological and adaptive dynamics of a community of interacting species. By natural selection through the abiotic environment and by co-adaptation within the community, species evolve, thereby…
The biological processes of cellular decision making and differentiation involve a plethora of signalling pathways and gene regulatory circuits. These networks, in their turn, exhibit a multitude of motifs playing crucial parts in…
We study the evolution of the network properties of a populated network embedded in a genotype space characterised by either a low or a high number of potential links, with particular emphasis on the connectivity and clustering. Evolution…
Multicellular organisms contain a wide variety of highly specialized cell types. The consistency and robustness of developmental trajectories suggest that complex gene regulatory networks effectively act as low-dimensional cell fate…