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We introduce a graph generating model aimed at representing the evolution of protein interaction networks. The model is based on the hypotesis of evolution by duplications and divergence of the genes which produce proteins. The obtained graphs shows multifractal properties recovering the absence of a characteristic connectivity as found in real data of(More)
Many biological processes, from cellular metabolism to population dynamics, are characterized by allometric scaling (power-law) relationships between size and rate. An outstanding question is whether typical allometric scaling relationships--the power-law dependence of a biological rate on body mass--can be understood by considering the general features of(More)
Determining protein function is one of the most challenging problems of the post-genomic era. The availability of entire genome sequences and of high-throughput capabilities to determine gene coexpression patterns has shifted the research focus from the study of single proteins or small complexes to that of the entire proteome. In this context, the search(More)
Introduced in its contemporary form in 1946 (ref. 1), but with roots that go back to the eighteenth century, the gravity law is the prevailing framework with which to predict population movement, cargo shipping volume and inter-city phone calls, as well as bilateral trade flows between nations. Despite its widespread use, it relies on adjustable parameters(More)
The theory of island biogeography asserts that an island or a local community approaches an equilibrium species richness as a result of the interplay between the immigration of species from the much larger metacommunity source area and local extinction of species on the island (local community). Hubbell generalized this neutral theory to explore the(More)
Analysis of previously published sets of DNA microarray gene expression data by singular value decomposition has uncovered underlying patterns or "characteristic modes" in their temporal profiles. These patterns contribute unequally to the structure of the expression profiles. Moreover, the essential features of a given set of expression profiles are(More)
The recurrent patterns in the commonness and rarity of species in ecological communities--the relative species abundance--have puzzled ecologists for more than half a century. Here we show that the framework of the current neutral theory in ecology can easily be generalized to incorporate symmetric density dependence. We can calculate precisely the strength(More)
It is widely accepted that metabolic rates scale across species approximately as the 3/4 power of mass in most if not all groups of organisms. Metabolic demand per unit mass thus decreases as body mass increases. Metabolic rates reflect both the ability of the organism's transport system to deliver metabolites to the tissues and the rate at which the(More)
We describe the time evolution of gene expression levels by using a time translational matrix to predict future expression levels of genes based on their expression levels at some initial time. We deduce the time translational matrix for previously published DNA microarray gene expression data sets by modeling them within a linear framework by using the(More)
The conversion from soluble states into cross-beta fibrillar aggregates is a property shared by many different proteins and peptides and was hence conjectured to be a generic feature of polypeptide chains. Increasing evidence is now accumulating that such fibrillar assemblies are generally characterized by a parallel in-register alignment of beta-strands(More)