Related papers: The Structure and Dynamics of Gene Regulation Netw…
Genetic regulation is a key component in development, but a clear understanding of the structure and dynamics of genetic networks is not yet at hand. In this work we investigate these properties within an artificial genome model originally…
The behavior of complex systems is determined not only by the topological organization of their interconnections but also by the dynamical processes taking place among their constituents. A faithful modeling of the dynamics is essential…
Exploring the structural topology of genome-based large-scale metabolic network is essential for investigating possible relations between structure and functionality. Visualization would be helpful for obtaining immediate information about…
The Unfolded Protein Response is the cell mechanism for maintaining the balance of properly folded proteins in the endoplasmic reticulum , the specialized cellular compartment. Although it is largely studied from a biological point of view,…
Natural systems are remarkably robust and resilient, maintaining essential functions despite variability, uncertainty, and hostile conditions. Understanding these nonlinear, dynamic behaviours is challenging because such systems involve…
Understanding why some cellular components are conserved across species, while others evolve rapidly is a key question of modern biology. Here we demonstrate that in S. cerevisiae proteins organized in cohesive patterns of interactions are…
MOTIVATION: A central goal of postgenomic biology is the elucidation of the regulatory relationships among all cellular constituents that together comprise the 'genetic network' of a cell or microorganism. Experimental manipulation of gene…
Determining mechanistic models of gene regulation, especially underlying phenotypic variation, is a central goal of both mathematical biology and modern evolutionary biology. However, several challenges, involving both common…
Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. This makes phylogenetic networks a more comprehensive…
We introduce simple models of genetic regulatory networks and we proceed to the mathematical analysis of their dynamics. The models are discrete time dynamical systems generated by piecewise affine contracting mappings whose variables…
Robustness to mutations and noise has been shown to evolve through stabilizing selection for optimal phenotypes in model gene regulatory networks. The ability to evolve robust mutants is known to depend on the network architecture. How do…
Modularity structures are common in various social and biological networks. However, its dynamical origin remains an open question. In this work, we set up a dynamical model describing the evolution of a social network. Based on the…
This paper presents the foundation for a decomposition theory for Boolean networks, a type of discrete dynamical system that has found a wide range of applications in the life sciences, engineering, and physics. Given a Boolean network…
The importance of studying properties of networks is manifest in diverse fields ranging from biology, engineering, physics, chemistry, neuroscience, and medicine. The functionality of networks with regard to performance, throughput,…
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…
Impact of an intruder on granular matter leads to formation of mesoscopic force networks seen particularly clearly in the recent experiments carried out with photoelastic particles, e.g., Clark et al., Phys. Rev. Lett., 114 144502 (2015).…
Constraints placed upon the phenotypes of organisms result from their interactions with the environment. Over evolutionary timescales, these constraints feed back onto smaller molecular subnetworks comprising the organism. The evolution of…
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…
In systems biology, attractor landscape analysis of gene regulatory networks is recognized as a powerful computational tool for studying various cellular states from proliferation and differentiation to senescence and apoptosis. Therefore,…
The concept of robustness of regulatory networks has been closely related to the nature of the interactions among genes, and the capability of pattern maintenance or reproducibility. Defining this robustness property is a challenging task,…