Related papers: Global Snapshot of Protein Interaction Network -- …

Proteins are the workhorse molecules of the cell and perform their biological functions by binding to other molecules through physical contact. Protein function is then regulated through coupling of bindings on the protein (allosteric…

We review the main tools which allow for the statistical characterization of weighted networks. We then present two case studies, the airline connection network and the scientific collaboration network, which are representative of critical…

The structure and dynamics of a typical biological system are complex due to strong and inhomogeneous interactions between its constituents. The investigation of such systems with classical mathematical tools, such as differential equations…

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…

Deviations from the average can provide valuable insights about the organization of natural systems. The present article extends this important principle to the systematic identification and analysis of singular motifs in complex networks.…

Dynamic graphs are rife with higher-order interactions, such as co-authorship relationships and protein-protein interactions in biological networks, that naturally arise between more than two nodes at once. In spite of the ubiquitous…

Proteins, essential to biological systems, perform functions intricately linked to their three-dimensional structures. Understanding the relationship between protein structures and their amino acid sequences remains a core challenge in…

Graphical models are widely used to make inferences concerning interplay in multivariate systems. In many applications, data are collected from multiple related but nonidentical units whose underlying networks may differ but are likely to…

Complex interactions between genes or proteins contribute a substantial part to phenotypic evolution. Here we develop an evolutionarily grounded method for the cross-species analysis of interaction networks by {\em alignment}, which maps…

Interpreting neural networks is a crucial and challenging task in machine learning. In this paper, we develop a novel framework for detecting statistical interactions captured by a feedforward multilayer neural network by directly…

A detailed analysis of three species-rich ecosystem food webs has shown that they display scale-free distributions of connections. Such graphs of interaction are in fact shared by a number of biological and technological networks, which…

A wireless communication network is considered where any two nodes are connected if the signal-to-interference ratio (SIR) between them is greater than a threshold. Assuming that the nodes of the wireless network are distributed as a…

Despite its high and direct impact on nearly all biological processes, the underlying structure of gene-gene interaction networks is investigated so far according to pair connections. To address this, we explore the gene interaction…

Background: Representing biological networks as graphs is a powerful approach to reveal underlying patterns, signatures, and critical components from high-throughput biomolecular data. However, graphs do not natively capture the multi-way…

Comparative graph and network analysis play an important role in both systems biology and pattern recognition, but existing surveys on the topic have historically ignored or underserved one or the other of these fields. We present an…

We propose a method for characterizing large complex networks by introducing a new matrix structure, unique for a given network, which encodes structural information; provides useful visualization, even for very large networks; and allows…

Focusing on a small set of proteins that i) fold in a concerted, all-or-none fashion and ii) do not contain knots or slipknots, we show that the Gauss linking integral, the torsion and the number of sequence-distant contacts provide…

The robustness of an ecological network quantifies the resilience of the ecosystem it represents to species loss. It corresponds to the proportion of species that are disconnected from the rest of the network when extinctions occur…

Data-driven analysis of large social networks has attracted a great deal of research interest. In this paper, we investigate 120 real social networks and their measurement-calibrated synthetic counterparts generated by four well-known…

Polymerization and formation of crosslinked polymer networks are important processes in manufacturing, materials fabrication, and in the case of hydrated polymer networks, synthesis of biomedical materials, drug delivery, and tissue…