Related papers: Preferential attachment in the protein network evo…
Many social, technological and biological interactions involve network relationships whose outcome intimately depends on the structure of the network and on the strengths of the connections. Yet, although much information is now available…
Preferential attachment probabilities scheme appear in the context of scale free random graphs [1],[2]. In this work we present preferential attachment probabilities scheme as a sequence of dependent Bernoulli random variables and we give…
Recent developments in complex networks have paved the way to a series of important biological insights, such as the fact that many of the essential proteins of S. cerevisae corresponds to the so-called hubs of the respective…
The preferential attachment model is a natural and popular random graph model for a growing network that contains very well-connected ``hubs''. We study the higher-order connectivity of such a network by investigating the topological…
A central and long-standing issue in evolutionary theory is the origin of the biological variation upon which natural selection acts1. Some hypotheses suggest that evolutionary change represents an adaptation to the surrounding environment…
This paper is concerned with statistical estimation of two preferential attachment models: the Buckley-Osthus model and the hierarchical preferential attachment model. We prove that the maximum likelihood estimates for both models are…
Interacting proteins coevolve at multiple but interconnected scales, from the residue-residue over the protein-protein up to the family-family level. The recent accumulation of enormous amounts of sequence data allows for the development of…
We introduce a minimal model for the evolution of functional protein-interaction networks using a sequence-based mutational algorithm, and apply the model to study neutral drift in networks that yield oscillatory dynamics. Starting with a…
We derive a general statistical model of interactions, starting from probabilistic principles and elementary requirements. Prevailing interaction models in biomedical researches diverge both mathematically and practically. In particular,…
We analyze protein-protein interaction networks for six different species under the framework of random matrix theory. Nearest neighbor spacing distribution of the eigenvalues of adjacency matrices of the largest connected part of these…
We propose a preferential attachment model for network growth where new entering nodes have a partial information about the state of the network. Our main result is that the presence of bounded information modifies the degree distribution…
A new mechanism leading to scale-free networks is proposed in this letter. It is shown that in many cases of interest, the connectivity power-law behavior is neither related to dynamical properties nor to preferential attachment. Instead,…
Preferential attachment is a widely adopted paradigm for understanding the dynamics of social networks. Formal statistical inference,for instance GLM techniques, and model verification methods will require knowing test statistics are…
Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…
One of the best-known models in network science is preferential attachment. In this model, the probability of attaching to a node depends on the degree of all nodes in the population, and thus depends on global information. In many…
Genomic duplication-divergence events, which are the primary source of new protein functions, occur stochastically at a wide range of genomic scales, from single gene to whole genome duplications. Clearly, this fundamental evolutionary…
We study a new class of preferential attachment trees with \emph{self-reinforcement}. At each time, each vertex is assigned a weight equal to the cumulative sum over past times of an affine function of its degree. A new vertex attaches…
Real complex systems are not rigidly structured; no clear rules or blueprints exist for their construction. Yet, amidst their apparent randomness, complex structural properties universally emerge. We propose that an important class of…
We extend the work of Antunovi\'{c}, Mossel and R\'{a}cz on competing types in preferential attachment models to include cases where the types have different fitnesses, which may be either multiplicative or additive. We will show that,…
High-throughput protein interaction detection methods are strongly affected by false positive and false negative results. Focused experiments are needed to complement the large-scale methods by validating previously detected interactions…