140 research outputs found
Structure and dynamics of core-periphery networks
Recent studies uncovered important core/periphery network structures
characterizing complex sets of cooperative and competitive interactions between
network nodes, be they proteins, cells, species or humans. Better
characterization of the structure, dynamics and function of core/periphery
networks is a key step of our understanding cellular functions, species
adaptation, social and market changes. Here we summarize the current knowledge
of the structure and dynamics of "traditional" core/periphery networks,
rich-clubs, nested, bow-tie and onion networks. Comparing core/periphery
structures with network modules, we discriminate between global and local
cores. The core/periphery network organization lies in the middle of several
extreme properties, such as random/condensed structures, clique/star
configurations, network symmetry/asymmetry, network
assortativity/disassortativity, as well as network hierarchy/anti-hierarchy.
These properties of high complexity together with the large degeneracy of core
pathways ensuring cooperation and providing multiple options of network flow
re-channelling greatly contribute to the high robustness of complex systems.
Core processes enable a coordinated response to various stimuli, decrease
noise, and evolve slowly. The integrative function of network cores is an
important step in the development of a large variety of complex organisms and
organizations. In addition to these important features and several decades of
research interest, studies on core/periphery networks still have a number of
unexplored areas.Comment: a comprehensive review of 41 pages, 2 figures, 1 table and 182
reference
Modular co-evolution of metabolic networks
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 network affects the evolution of its member proteins remains unclear.
In this work, the functional and evolutionary modularity of Homo sapiens (H.
sapiens) metabolic network were investigated from a topological point of view.
Network decomposition shows that the metabolic network is organized in a highly
modular core-periphery way, in which the core modules are tightly linked
together and perform basic metabolism functions, whereas the periphery modules
only interact with few modules and accomplish relatively independent and
specialized functions. Moreover, over half of the modules exhibit
co-evolutionary feature and belong to specific evolutionary ages. Peripheral
modules tend to evolve more cohesively and faster than core modules do. The
correlation between functional, evolutionary and topological modularity
suggests that the evolutionary history and functional requirements of metabolic
systems have been imprinted in the architecture of metabolic networks. Such
systems level analysis could demonstrate how the evolution of genes may be
placed in a genome-scale network context, giving a novel perspective on
molecular evolution.Comment: 26 pages, 7 figure
Model validation of simple-graph representations of metabolism
The large-scale properties of chemical reaction systems, such as the
metabolism, can be studied with graph-based methods. To do this, one needs to
reduce the information -- lists of chemical reactions -- available in
databases. Even for the simplest type of graph representation, this reduction
can be done in several ways. We investigate different simple network
representations by testing how well they encode information about one
biologically important network structure -- network modularity (the propensity
for edges to be cluster into dense groups that are sparsely connected between
each other). To reach this goal, we design a model of reaction-systems where
network modularity can be controlled and measure how well the reduction to
simple graphs capture the modular structure of the model reaction system. We
find that the network types that best capture the modular structure of the
reaction system are substrate-product networks (where substrates are linked to
products of a reaction) and substance networks (with edges between all
substances participating in a reaction). Furthermore, we argue that the
proposed model for reaction systems with tunable clustering is a general
framework for studies of how reaction-systems are affected by modularity. To
this end, we investigate statistical properties of the model and find, among
other things, that it recreate correlations between degree and mass of the
molecules.Comment: to appear in J. Roy. Soc. Intefac
Environmental variability and modularity of bacterial metabolic networks
<p>Abstract</p> <p>Background</p> <p>Biological systems are often modular: they can be decomposed into nearly-independent structural units that perform specific functions. The evolutionary origin of modularity is a subject of much current interest. Recent theory suggests that modularity can be enhanced when the environment changes over time. However, this theory has not yet been tested using biological data.</p> <p>Results</p> <p>To address this, we studied the relation between environmental variability and modularity in a natural and well-studied system, the metabolic networks of bacteria. We classified 117 bacterial species according to the degree of variability in their natural habitat. We find that metabolic networks of organisms in variable environments are significantly more modular than networks of organisms that evolved under more constant conditions.</p> <p>Conclusion</p> <p>This study supports the view that variability in the natural habitat of an organism promotes modularity in its metabolic network and perhaps in other biological systems.</p
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