Related papers: Motifs emerge from function in model gene regulato…
Investigating the frequency and distribution of small subgraphs with a few nodes/edges, i.e., motifs, is an effective analysis method for static networks. Motif-driven analysis is also useful for temporal networks where the spectrum of…
Biological phenomena differ significantly from physical phenomena. At the heart of this distinction is the fact that biological entities have computational abilities and thus they are inherently difficult to predict. This is the reason why…
Unraveling the complexities of Gene Regulatory Networks (GRNs) is crucial for understanding cellular processes and disease mechanisms. Traditional computational methods often struggle with the dynamic nature of these networks. This study…
Transcription networks, and other directed networks can be characterized by some topological observables such as for example subgraph occurrence (network motifs). In order to perform such kind of analysis, it is necessary to be able to…
Biological and technological networks contain patterns, termed network motifs, which occur far more often than in randomized networks. Network motifs were suggested to be elementary building blocks that carry out key functions in the…
Network motifs are patterns of over-represented node interactions in a network which have been previously used as building blocks to understand various aspects of the social networks. In this paper, we use motif patterns to characterize the…
Biological networks of interacting agents exhibit similar topological properties for a wide range of scales, from cellular to ecological levels, suggesting the existence of a common evolutionary origin. A general evolutionary mechanism…
The major biochemical networks of the living cell, the network of interacting genes and the network of biochemical reactions, are highly interdependent, however, they have been studied mostly as separate systems so far. In the last years an…
We study a genetic regulatory network model developed to demonstrate that genetic robustness can evolve through stabilizing selection for optimal phenotypes. We report preliminary results on whether such selection could result in a…
We investigate the problem of producing structured graph representations of visual scenes. Our work analyzes the role of motifs: regularly appearing substructures in scene graphs. We present new quantitative insights on such repeated…
In physics, biology and engineering, network systems abound. How does the connectivity of a network system combine with the behavior of its individual components to determine its collective function? We approach this question for networks…
Boolean networks are popular tools for the exploration of qualitative dynamical properties of biological systems. Several dynamical interpretations have been proposed based on the same logical structure that captures the interactions…
Single trial analyses of ensemble activity in alert animals demonstrate that cortical circuits dynamics evolve through temporal sequences of metastable states. Metastability has been studied for its potential role in sensory coding, memory…
Biological systems are driven by intricate interactions among the complex array of molecules that comprise the cell. Many methods have been developed to reconstruct network models of those interactions. These methods often draw on large…
We show that biological networks with serial regulation (each node regulated by at most one other node) are constrained to {\it direct functionality}, in which the sign of the effect of an environmental input on a target species depends…
Diseases involve complex processes and modifications to the cellular machinery. The gene expression profile of the affected cells contains characteristic patterns linked to a disease. Hence, biological knowledge pertaining to a disease can…
Precise temporal coordination of gene expression is crucial for many developmental processes. One central question in developmental biology is how such coordinated expression patterns are robustly controlled. During embryonic development of…
Biological systems rely on robust internal information processing: Survival depends on highly reproducible dynamics of regulatory processes. Biological information processing elements, however, are intrinsically noisy (genetic switches,…
Systems as diverse as genetic networks or the world wide web are best described as networks with complex topology. A common property of many large networks is that the vertex connectivities follow a scale-free power-law distribution. This…
We study the versatile performance of networks of coupled circuits. Each of these circuits is composed of a positive and a negative feedback loop in a motif that is frequently found in genetic and neural networks. When two of these circuits…