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Graph embedding techniques are useful to characterize spectral signature relations for hyperspectral images. However, such images consists of disjoint classes due to spatial details that are often ignored by existing graph computing tools.…
Whether comparing networks to each other or to random expectation, measuring dissimilarity is essential to understanding the complex phenomena under study. However, determining the structural dissimilarity between networks is an ill-defined…
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…
Many data analysis problems rely on dynamic networks, such as social or communication network analyses. Providing a scalable overview of long sequences of such dynamic networks remains challenging due to the underlying large-scale data…
Nucleic acids have been regarded as stiff polymers with long-range flexibility and generally modeled using elastic rod models of polymer physics. Notwithstanding, investigations carried out over the past few years on single fragments of…
The degree distribution of many biological and technological networks has been described as a power-law distribution. While the degree distribution does not capture all aspects of a network, it has often been suggested that its functional…
Inferring topological characteristics of complex networks from observed data is critical to understand the dynamical behavior of networked systems, ranging from the Internet and the World Wide Web to biological networks and social networks.…
This works explores and illustrates recent results developed by the author in field of dynamical network analysis. The considered approach is blind, i.e., no a priori assumptions on the interconnected systems are available. Moreover, the…
Current experimental and theoretical studies on the effect of intermolecular interactions on molecular conduction appear to be in conflict with each other. In particular, some experimental results, e.g., the observation of 2-dimensional…
Thermodynamic aspects of chemical reactions have a long history in the Physical Chemistry literature. In particular, biochemical cycles - the building-blocks of biochemical systems - require a source of energy to function. However, although…
Complex networks contain various interactions among similar or different entities. These kinds of networks are called multi-relational networks, in which each layer corresponds to a special type of interaction. Multi-relational networks are…
The use of networks to integrate different genetic, proteomic, and metabolic datasets has been proposed as a viable path toward elucidating the origins of specific diseases. Here we introduce a new phenotypic database summarizing…
Single-molecule experiments in which force is applied to DNA or RNA molecules have enabled important discoveries of nucleic acid properties and nucleic acid-enzyme interactions. These experiments rely on a model of the polymer…
Predator-prey networks originating from different aqueous and terrestrial environments are compared to assess if the difference in environments of these networks produce any significant difference in the structure of such predator-prey…
In this study, we present a method of pattern mining based on network theory that enables the identification of protein structures or complexes from synthetic volume densities, without the knowledge of predefined templates or human biases…
The network paradigm is increasingly used to describe the topology and dynamics of complex systems. Here we review the results of the topological analysis of protein structures as molecular networks describing their small-world character,…
Network science has become an essential interdisciplinary tool for understanding complex biological systems. However, because these systems undergo continuous, often stimulus-driven changes in both structure and function, traditional static…
Proteins are linear molecular chains that often fold to function. The topology of folding is widely believed to define its properties and function, and knot theory has been applied to study protein structure and its implications. More that…
A dynamic logic method was developed to analyze molecular networks of cells by combining Kauffman and Thomas's logic operations with molecular interaction parameters. The logic operations characterize the discrete interactions between…
A methodology for the statistical mechanical analysis of polymeric chains under tension introduced previously is extended to include torque. The response of individual bonds between monomers or of entire groups of monomers to a combination…