相关论文: Uncovering the hidden geometry behind metabolic ne…

Metabolic networks perform some of the most fundamental functions in living cells, including energy transduction and building block biosynthesis. While these are the best characterized networks in living systems, understanding their…

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…

Accurately determining and classifying the structure of complex networks is the focus of much current research. One class of network of particular interest are metabolic pathways, which have previously been studied from a graph theoretical…

High-throughput techniques are leading to an explosive growth in the size of biological databases and creating the opportunity to revolutionize our understanding of life and disease. Interpretation of these data remains, however, a major…

The topology of many real complex networks has been conjectured to be embedded in hidden metric spaces, where distances between nodes encode their likelihood of being connected. Besides of providing a natural geometrical interpretation of…

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…

Metabolism plays a central role in cell physiology because it provides the molecular machinery for growth. At the genome-scale, metabolism is made up of thousands of reactions interacting with one another. Untangling this complexity is key…

In this thesis, we have studied the large scale structure and system level dynamics of certain biological networks using tools from graph theory, computational biology and dynamical systems. We study the structure and dynamics of large…

Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which…

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…

The exploration of the structural topology and the organizing principles of genome-based large-scale metabolic networks is essential for studying possible relations between structure and functionality of metabolic networks. Topological…

The architecture of biological networks has been reported to exhibit high level of modularity, and to some extent, topological modules of networks overlap with known functional modules. However, how the modular topology of the molecular…

To understand the system-wide organization of metabolism, different lines of study have devised different categorizations of metabolites. The relationship and difference between categories can provide new insights for a more detailed…

Spatially or chemically isolated functional modules composed of several cellular components and carrying discrete functions are considered fundamental building blocks of cellular organization, but their presence in highly integrated…

Many methods have been developed for finding the commonalities between different organisms to study their phylogeny. The structure of metabolic networks also reveal valuable insights into metabolic capacity of species as well as into the…

Cellular metabolism, the integrated interconversion of thousands of metabolic substrates through enzyme-catalyzed biochemical reactions, is the most investigated complex intercellular web of molecular interactions. While the topological…

This article is addressing a recurrent problem in biology: mining newly built large scale networks. Our approach consists in comparing these new networks to well known ones. The visual backbone of this comparative analysis is provided by a…

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…

Representation of cities as organisms with metabolic processes is a useful analogy for urban design, development and sustainability. Urban metabolism can be modeled by representing urban systems as networks. The various networks included in…

Network self-similarity or fractality are widely accepted as an important topological property of metabolic networks; however, recent studies cast doubt on the reality of self-similarity in the networks. Therefore, we perform a…