相关论文: The interdependent network of gene regulation and …
This paper (parts I and II) provides an expository introduction to monotone and near-monotone dynamical systems associated to biochemical networks, those whose graphs are consistent or near-consistent. Many conclusions can be drawn from…
Aspects of cell metabolism are modeled by ordinary differential equations describing the change of intracellular chemical concentrations. There is a correspondence between this dynamical system and a complex network. As in the classic…
Systems of dynamical interactions between competing species can be used to model many complex systems, and can be mathematically described by {\em random} networks. Understanding how patterns of activity arise in such systems is important…
Stochastic reaction network models are widely utilized in biology and chemistry to describe the probabilistic dynamics of biochemical systems in general, and gene interaction networks in particular. Most often, statistical analysis and…
From critical infrastructure, to physiology and the human brain, complex systems rarely occur in isolation. Instead, the functioning of nodes in one system often promotes or suppresses the functioning of nodes in another. Despite advances…
In unicellular organisms such as bacteria the same acquired mutations beneficial in one environment can be restrictive in another. However, evolving Escherichia coli populations demonstrate remarkable flexibility in adaptation. The…
Understanding design principles of complex cellular organization is one of the major challenges in biology. Recent analysis of the large-scale cellular organization has revealed the scale-free nature and robustness of metabolic and protein…
Diverse biological networks exhibit universal features distinguished from those of random networks, calling much attention to their origins and implications. Here we propose a minimal evolution model of Boolean regulatory networks, which…
The recent discovery of universal principles underlying many complex networks occurring across a wide range of length scales in the biological world has spurred physicists in trying to understand such features using techniques from…
In a cell or microorganism the processes that generate mass, energy, information transfer, and cell fate specification are seamlessly integrated through a complex network of various cellular constituents and reactions. However, despite the…
Modern biological tools have made it possible to unequivocally demonstrate the deep relationship among species in terms of genes and basic molecular mechanisms. In addition, results from genetic, physical and physiological approaches…
Structural and dynamical fingerprints of evolutionary optimization in biological networks are still unclear. We here analyze the dynamics of genetic regulatory networks responsible for the regulation of cell cycle and cell differentiation…
This paper (parts I and II) provides an expository introduction to monotone and near-monotone dynamical systems associated to biochemical networks, those whose graphs are consistent or near-consistent. Many conclusions can be drawn from…
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…
Biological networks such as gene regulatory networks possess desirable properties. They are more robust and controllable than random networks. This motivates the search for structural and dynamical features that evolution has incorporated…
Evolving biomolecular networks have to combine the stability against perturbations with flexibility allowing their constituents to assume new roles in the cell. Gene duplication followed by functional divergence of associated proteins is a…
The genetic regulatory network (GRN) plays a key role in controlling the response of the cell to changes in the environment. Although the structure of GRNs has been the subject of many studies, their large scale structure in the light of…
Cellular ingredient concentrations can be stabilized by adjusting generation and consumption rates through multiple pathways. To explore the portion of cellular metabolism equipped with multiple pathways, we categorize individual metabolic…
Metabolic networks are probably among the most challenging and important biological networks. Their study provides insight into how biological pathways work and how robust a specific organism is against an environment or therapy. Here we…
Stochasticity is a key characteristic of intracellular processes such as gene regulation and chemical signalling. Therefore, characterising stochastic effects in biochemical systems is essential to understand the complex dynamics of living…