Related papers: Metabolic network modularity arising from simple g…
Topology and weights are closely related in weighted complex networks and this is reflected in their modular structure. We present a simple network model where the weights are generated dynamically and they shape the developing topology. By…
Networks coming from protein-protein interactions, transcriptional regulation, signaling, or metabolism may appear to have "unusual" properties. To quantify this, it is appropriate to randomize the network and test the hypothesis that the…
Biological systems exhibit two structural features on many levels of organization: sparseness, in which only a small fraction of possible interactions between components actually occur; and modularity - the near decomposability of the…
Background: Recent models of genome-proteome evolution have shown that some of the key traits displayed by the global structure of cellular networks might be a natural result of a duplication-diversification (DD) process. One of the…
Scale-free and non-computable characteristics of natural networks are found to result from the least-time dispersal of energy. To consider a network as a thermodynamic system is motivated since ultimately everything that exists can be…
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…
Networks are fundamental building blocks for representing data, and computations. Remarkable progress in learning in structurally defined (shallow or deep) networks has recently been achieved. Here we introduce evolutionary exploratory…
In a recent paper, Marr, Muller-Linow and Hutt [Phys. Rev. E 75, 041917 (2007)] investigate an artificial dynamic system on metabolic networks. They find a less complex time evolution of this dynamic system in real networks, compared to…
A standard technique for understanding underlying dependency structures among a set of variables posits a shared conditional probability distribution for the variables measured on individuals within a group. This approach is often referred…
Given the large size and complexity of most biochemical regulation and signaling networks, there is a non-trivial relationship between the micro-level logic of component interactions and the observed macro-dynamics. Here we address this…
Understanding the origins of complexity is a fundamental challenge with implications for biological and technological systems. Network theory emerges as a powerful tool to model complex systems. Networks are an intuitive framework to…
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…
The interaction between natural selection and random mutation is frequently debated in recent years. Does similar dilemma also exist in the evolution of real networks such as biological networks? In this paper, we try to discuss this issue…
The relationship between network topology and system dynamics has significant implications for unifying our understanding of the interplay among metabolic, gene-regulatory, and ecosystem network architecures. Here we analyze the stability…
Food webs are networks describing who is eating whom in an ecological community. By now it is clear that many aspects of food-web structure are reproducible across diverse habitats, yet little is known about the driving force behind this…
Species or population that proliferate faster than others become dominant in numbers. Catalysis allows catalytic sets within a molecular reaction network to dominate the non catalytic parts of the network by processing most of the available…
Biological lifeforms can heal, grow, adapt, and reproduce -- abilities essential for sustained survival and development. In contrast, robots today are primarily monolithic machines with limited ability to self-repair, physically develop, or…
Recent work on synthetic rescues has shown that the targeted deletion of specific metabolic genes can often be used to rescue otherwise non-viable mutants. This raises a fundamental biophysical question: to what extent can the whole-cell…
One of the main tasks of post-genomic informatics is to systematically investigate all molecules and their interactions within a living cell so as to understand how these molecules and the interactions between them relate to the function of…
Efforts to catalogue the structure of metabolic networks have generated highly detailed, genome-scale atlases of biochemical reactions in the cell. Unfortunately, these atlases fall short of capturing the kinetic details of metabolic…