Related papers: Some protein interaction data do not exhibit power…
In this paper we show how The Free Energy Principle (FEP) can provide an explanation for why real-world networks deviate from scale-free behaviour, and how these characteristic deviations can emerge from constraints on information…
In this paper we present the first mathematical analysis of the protein interaction network found in the yeast, S. cerevisiae. We show that, (a) the identified protein network display a characteristic scale-free topology that demonstrate…
Protein-protein interaction (PPI) networks provide valuable insights into the function of biological systems, and aligning multiple PPI networks can reveal important functional relationships between different species. However, assessing the…
In this paper we study a model of synchronization process on scale free networks with degree-degree correlations. This model was already studied on this kind of networks without correlations by Pastore y Piontti {\it et al.}, Phys. Rev. E…
Complex networks are now being studied in a wide range of disciplines across science and technology. In this paper we propose a method by which one can probe the properties of experimentally obtained network data. Rather than just measuring…
Protein-Protein Interactions (PPIs) perform essential roles in biological functions. Although some experimental techniques have been developed to detect PPIs, they suffer from high false positive and high false negative rates. Consequently,…
The information regarding the structure of a single protein is encoded in the network of interacting amino acids. Considering each protein as a weighted and unweighted network of amino acids we have analyzed a total of forty nine protein…
We study the contact process on a class of evolving scale-free networks, where each node updates its connections at independent random times. We give a rigorous mathematical proof that there is a transition between a phase where for all…
Scale-free networks constitute a fast-developing field that has already provided us with important tools to understand natural and social phenomena. From biological systems to environmental modifications, from quantum fields to high energy…
Proteins are essential macromolecules of life and thus understanding their function is of great importance. The number of functionally unclassified proteins is large even for simple and well studied organisms such as baker's yeast. Methods…
Combinations of random and preferential growth for both on-growing and stationary networks are studied and a hierarchical topology is observed. Thus for real world scale-free networks which do not exhibit hierarchical features preferential…
Scaling behavior of scale-free evolving networks arising in communications, citations, collaborations, etc. areas is studied. We derive universal scaling relations describing properties of such networks and indicate limits of their…
We discuss three related models of scale-free networks with the same degree distribution but different correlation properties. Starting from the Barabasi-Albert construction based on growth and preferential attachment we discuss two other…
Many naturally occurring networks have a power-law degree distribution as well as a non-zero degree correlation. Despite this, most studies analyzing the robustness to random node-deletion and vulnerability to targeted node-deletion have…
Spanning trees are an important quantity characterizing the reliability of a network, however, explicitly determining the number of spanning trees in networks is a theoretical challenge. In this paper, we study the number of spanning trees…
We introduce Bi-GNN for modeling biological link prediction tasks such as drug-drug interaction (DDI) and protein-protein interaction (PPI). Taking drug-drug interaction as an example, existing methods using machine learning either only…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino…
Proteins interact with other proteins within biological pathways, forming connected subgraphs in the protein-protein interactome (PPI). Proteins are often involved in multiple biological pathways which complicates interpretation of…
Contrary to many recent models of growing networks, we present a model with fixed number of nodes and links, where it is introduced a dynamics favoring the formation of links between nodes with degree of connectivity as different as…
Degree distribution of nodes, especially a power law degree distribution, has been regarded as one of the most significant structural characteristics of social and information networks. Node degree, however, only discloses the first-order…