• Corpus ID: 15290433

Modularity "for free" in genome architecture?

@article{Sol2003ModularityF,
  title={Modularity "for free" in genome architecture?},
  author={Ricard V. Sol{\'e} and Pau Fern{\'a}ndez},
  journal={arXiv: Genomics},
  year={2003}
}
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 consequences of such evolution is the emergence of a small world architecture together with a scale-free distribution of interactions. Here we show that the domain of parameter space were such structure emerges is related to a phase transition phenomenon. At this… 

Figures and Tables from this paper

Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis
TLDR
A biphasic (bow-tie) theory of module emergence is proposed that predicts the rise of hierarchical modularity in evolving networks at different timescales and complexity levels.
Evolution of sparsity and modularity in a model of protein allostery.
TLDR
A simple but physical model of protein evolution where selection targets allostery, the functional coupling of distal sites on protein surfaces shows how the geometrical organization of couplings between amino acids within a protein structure can depend crucially on its evolutionary history.
In Search of the Biological Significance of Modular Structures in Protein Networks
TLDR
Using computer simulation, it is demonstrated that a higher-than-expected modularity can arise during network growth through a simple model of gene duplication, without natural selection for modularity.
Dynamics of and on Complex Networks
TLDR
This thesis addresses current challenges regarding the dynamics of and dynamical processes on complex networks and proposes stochastic growth models inspired by the duplication-divergence mechanism to generate epistatic interaction networks that exhibit the property of monochromaticity as a result of their dynamical evolution.
The Generalized Topological Overlap Matrix for Detecting Modules in Gene Networks
TLDR
This work introduces a general class of node dissimilarity measures based on the notion of ‘topological’ overlap, which has been found to be biologically meaningful in several applications and provides empirical evidence that they are useful in the context of gene co-expression network analysis.
The road to modularity
TLDR
Although there is an emerging agreement that organisms have a modular organization, the main open problem is the question of whether modules arise through the action of natural selection or because of biased mutational mechanisms.
Can computational efficiency alone drive the evolution of modularity in neural networks?
  • C. Tosh
  • Biology
    Scientific reports
  • 2016
TLDR
It is indicated that computational efficiency alone does not drive the evolution of modularity, even in large biological networks, but it may still be a viable mechanism when networks evolve by non-gradualistic means.
Complex networks: The key to systems biology
TLDR
This article is an up-to-date review of the major developments related to the application of complex networks in biology, with special attention focused on the more recent literature.
Systems Biology Approaches to Evaluate Disease Modularity
TLDR
The hypothesis is enunciated, mathematical modelling based on kinetic law formalism for studying the functional modularity of the metabolism and the development of a workflow to integrate metabolic and kinetic data from different databases for metabolic modelling are declared.
Modularity and the evolution of software evolvability
TLDR
This dissertation contributes to the further understanding of modularity as a means of improving software evolvability by adding the dimension of time to the analysis.
...
...

References

SHOWING 1-10 OF 49 REFERENCES
A natural class of robust networks
  • M. Aldana, P. Cluzel
  • Biology, Computer Science
    Proceedings of the National Academy of Sciences of the United States of America
  • 2003
TLDR
This work presents a prototype for the study of dynamical systems to predict the functional robustness of intracellular networks against variations of their internal parameters, and demonstrates that the dynamical robustity of these complex networks is a direct consequence of their scale-free topology.
A Model of Large-Scale proteome Evolution
TLDR
This work presents a simple model of proteome evolution that is able to reproduce many of the observed statistical regularities reported from the analysis of the yeast proteome, and suggests that the observed patterns can be explained by a process of gene duplication and diversification that would evolve proteome networks under a selection pressure.
Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome
TLDR
This work suggests a stochastic model capable of describing the evolutionary growth of metabolic or signal-transduction networks and generates networks that share important statistical properties with real molecular networks.
The yeast coexpression network has a small‐world, scale‐free architecture and can be explained by a simple model
TLDR
A new model is derived based on the observation that there is a positive correlation between the sequence similarity of paralogues and their probability of coexpression or sharing of transcription factor binding sites (TFBSs) that reproduces the scale‐free, small‐world architecture of the coregulation network and the homology relations between coregulated genes without the need for selection.
How the global structure of protein interaction networks evolves
  • A. Wagner
  • Biology
    Proceedings of the Royal Society of London. Series B: Biological Sciences
  • 2003
TLDR
From these observations one can explain the evolutionary sustenance of the most prominent network feature, the distribution of the frequency P(d) of proteins with d neighbours, which is broad-tailed and consistent with a power law, that is: P( d) α d -γ.
Evolution of networks
TLDR
The recent rapid progress in the statistical physics of evolving networks is reviewed, and how growing networks self-organize into scale-free structures is discussed, and the role of the mechanism of preferential linking is investigated.
The topology of the possible: formal spaces underlying patterns of evolutionary change.
TLDR
This paper proposes to extend the explanatory level for phenotypic evolution from fitness considerations alone to include the topological structure of phenotype space as induced by the genotype-phenotype map, and introduces the mathematical concepts and tools necessary to formalize the notion of accessibility pre-topology relative to which the authors can speak of continuity in the genotypes-phenotypes map and in evolutionary trajectories.
Plasticity, evolvability, and modularity in RNA.
TLDR
Analytical models of neutral confinement, made tractable by the assumption of perfect plastogenetic congruence, formally connect mutation rate, the topography of phenotype space, and evolvability to suggest a possible evolutionary origin of modularity as a side effect of environmental canalization.
The structure of the protein universe and genome evolution
TLDR
These findings suggest that genome evolution is driven by extremely general mechanisms based on the preferential attachment principle, and that protein folds and families encoded in diverse genomes show similar size distributions with notable mathematical properties.
...
...