Related papers: Graph animals, subgraph sampling and motif search …
A new heuristic based on vertex invariants is developed to rapidly distinguish non-isomorphic graphs to a desired level of accuracy. The method is applied to sample subgraphs from an E.coli protein interaction network, and as a probe for…
The identification of motifs--subgraphs that appear significantly more often in a particular network than in an ensemble of randomized networks--has become a ubiquitous method for uncovering potentially important subunits within networks…
We employed the random graph theory approach to analyze the protein-protein interaction database DIP (Feb. 2004), for seven species (S. cerevisiae, H. pylori, E. coli, C. elegans, H. sapiens, M. musculus and D. melanogaster). Several global…
Interaction networks are of central importance in post-genomic molecular biology, with increasing amounts of data becoming available by high-throughput methods. Examples are gene regulatory networks or protein interaction maps. The main…
We propose a biologically motivated quantity, twinness, to evaluate local similarity between nodes in a network. The twinness of a pair of nodes is the number of connected, labeled subgraphs of size n in which the two nodes possess…
A deluge of new data on social, technological and biological networked systems suggests that a large number of interactions among system units are not limited to pairs, but rather involve a higher number of nodes. To properly encode such…
Here we introduce simple structures for the analysis of complex hypergraphs, hypergraph animals. These structures are designed to describe the local node neighbourhoods of nodes in hypergraphs. We establish their relationships to lattice…
We introduce a new method for finding network motifs: interesting or informative subgraph patterns in a network. Subgraphs are motifs when their frequency in the data is high compared to the expected frequency under a null model. To compute…
Exploring statistics of locally connected subgraph patterns (also known as network motifs) has helped researchers better understand the structure and function of biological and online social networks (OSNs). Nowadays the massive size of…
Network motifs are recurrent, small-scale patterns of interactions observed frequently in a system. They shed light on the interplay between the topology and the dynamics of complex networks across various domains. In this work, we focus on…
One of the most important concepts in biological network analysis is that of network motifs, which are patterns of interconnections that occur in a given network at a frequency higher than expected in a random network. In this work we are…
We present a method that compares the protein interaction networks of two species to detect functionally similar (conserved) protein modules between them. The method is based on an algorithm we developed to identify matching subgraphs…
Motifs are the fundamental components of complex systems. The topological structure of networks representing complex systems and the frequency and distribution of motifs in these networks are intertwined. The complexities associated with…
Many real-world networks describe systems in which interactions decay with the distance between nodes. Examples include systems constrained in real space such as transportation and communication networks, as well as systems constrained in…
In this paper, we study the large-scale protein interaction network of yeast uti lizing a stochastic method based upon percolation of random graphs. In order to find the global features of connectivities in the network, we introduce numeric…
Physical and functional constraints on biological networks lead to complex topological patterns across multiple scales in their organization. A particular type of higher-order network feature that has received considerable interest is…
Network motif provides a way to uncover the basic building blocks of most complex networks. This task usually demands high computer processing, specially for motif with 5 or more vertices. This paper presents an extended methodology with…
Motif discovery is a powerful and insightful method to quantify network structures and explore their function. As a case study, we present a comprehensive analysis of regulatory motifs in the connectome of the model organism Caenorhabditis…
Detecting strong ties among users in social and information networks is a fundamental operation that can improve performance on a multitude of personalization and ranking tasks. Strong-tie edges are often readily obtained from the social…
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…