Related papers: Quantifying evolvability in small biological netwo…
In this paper, we propose an evolving network model growing fast in units of module, based on the analysis of the evolution characteristics in real complex networks. Each module is a small-world network containing several interconnected…
Boolean network models of strongly connected modules are capable of capturing the high regulatory complexity of many biological gene regulatory circuits. We study numerically the previously introduced basin entropy, a parameter for the…
Regulatory interactions between genes show a large amount of cross-species variability, even when the underlying functions are conserved: There are many ways to achieve the same function. Here we investigate the ability of regulatory…
Linking networks of molecular interactions to cellular functions and phenotypes is a key goal in systems biology. Here, we adapt concepts of spatial statistics to assess the functional content of molecular networks. Based on the…
The increasing volume of ecologically and biologically relevant data has revealed a wide collection of emergent patterns in living systems. Analyzing different datasets, ranging from metabolic gene-regulatory to species interaction…
Nature is rife with networks that are functionally optimized to propagate inputs in order to perform specific tasks. Whether via genetic evolution or dynamic adaptation, many networks create functionality by locally tuning interactions…
Living systems operate in a critical dynamical regime -- between order and chaos -- where they are both resilient to perturbation, and flexible enough to evolve. To characterize such critical dynamics, the established 'structural theory' of…
The co-authorship network of scientists represents a prototype of complex evolving networks. By mapping the electronic database containing all relevant journals in mathematics and neuro-science for an eight-year period (1991-98), we infer…
In this paper we present the application of a novel methodology to scientific citation and collaboration networks. This methodology is designed for understanding the governing dynamics of evolving networks and relies on an attachment…
We construct and investigate Boolean networks that follow a given reliable trajectory in state space, which is insensitive to fluctuations in the updating schedule, and which is also robust against noise. Robustness is quantified as the…
Inference of the network structure (e.g., routing topology) and dynamics (e.g., link performance) is an essential component in many network design and management tasks. In this paper we propose a new, general framework for analyzing and…
A recent article by Weidner et al. [2021] presents a method to extract graph properties that are predictive of the dynamical behavior of multivariate, discrete models of biochemical regulation. In other words, a method that uses only…
Topological features of gene regulatory networks can be successfully reproduced by a model population evolving under selection for short dynamical attractors. The evolved population of networks exhibit motif statistics, summarized by…
Models of biochemical networks are usually presented as connected graphs where vertices indicate proteins and edges are drawn to indicate activation or inhibition relationships. These diagrams are useful for drawing qualitative conclusions…
Given the stochastic nature of gene expression, genetically identical cells exposed to the same environmental inputs will produce different outputs. This heterogeneity has been hypothesized to have consequences for how cells are able to…
Mechanistic models can provide an intuitive and interpretable explanation of network growth by specifying a set of generative rules. These rules can be defined by domain knowledge about real-world mechanisms governing network growth or may…
Connectivity networks have recently become widely used in biology due to increasing amounts of information on the physical and functional links between individual proteins. This connectivity data provides valuable material for expanding our…
Robustness to genetic or environmental disturbances is often considered as a key property of living systems. Yet, in spite of being discussed since the 1950s, how robustness emerges from the complexity of genetic architectures and how it…
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…
Robustness and sensitivity of responses generated by cell signaling networks has been associated with survival and evolvability of organisms. However, existing methods analyzing robustness and sensitivity of signaling networks ignore the…