Related papers: Topological network alignment uncovers biological …
The rich and varied ways that genetic material can be passed between species has motivated extensive research into the theory of phylogenetic networks. Features that align with biological processes, or with desirable mathematical…
Sequencing large number of candidate disease genes which cause diseases in order to identify the relationship between them is an expensive and time-consuming task. To handle these challenges, different computational approaches have been…
Systematic relations between multiple objects that occur in various fields can be represented as networks. Real-world networks typically exhibit complex topologies whose structural properties are key factors in characterizing and further…
Most social, technological and biological networks are embedded in a finite dimensional space, and the distance between two nodes influences the likelihood that they link to each other. Indeed, in social systems, the chance that two…
Rooted phylogenetic networks provide a more complete representation of the ancestral relationship between species than phylogenetic trees when reticulate evolutionary processes are at play. One way to reconstruct a phylogenetic network is…
We review a recent trend in computational systems biology which aims at using pattern recognition algorithms to infer the structure of large-scale biological networks from heterogeneous genomic data. We present several strategies that have…
The importance of the use of networks to model and analyse biological data and the interplay of bio-molecules is widely recognised. Consequently, many algorithms for the analysis and the comparison of networks (such as alignment algorithms)…
Network representations of systems from various scientific and societal domains are neither completely random nor fully regular, but instead appear to contain recurring structural building blocks. These features tend to be shared by…
Normal networks are an important class of phylogenetic networks that have compelling mathematical properties which align with intuition about inference from genetic data. While tools enabling widespread use of phylogenetic networks in the…
Characterization of the differences between biological and random networks can reveal the design principles that enable the robust realization of crucial biological functions including the establishment of different cell types. Previous…
An important part of the analysis of bio-molecular networks is to detect different functional units. Different functions are reflected in a different evolutionary dynamics, and hence in different statistical characteristics of network…
Although deep learning approaches have had tremendous success in image, video and audio processing, computer vision, and speech recognition, their applications to three-dimensional (3D) biomolecular structural data sets have been hindered…
Social network alignment, aligning different social networks on their common users, is receiving dramatic attention from both academic and industry. All existing studies consider the social network to be static and neglect its inherent…
Learning the structure of a network from time series data, in particular cyclostationary data, is of significant interest in many disciplines such as power grids, biology and finance. In this article, an algorithm is presented for…
The structure of a protein is crucial in determining its functionality, and is much more conserved than sequence during evolution. A key task in structural biology is to compare protein structures in order to determine evolutionary…
Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations…
Dendrograms are a way to represent evolutionary relationships between organisms. Nowadays, these are inferred based on the comparison of genes or protein sequences by taking into account their differences and similarities. The genetic…
Syntax connects words to each other in very specific ways. Two words are syntactically connected if they depend directly on each other. Syntactic connections usually happen within a sentence. Gathering all those connection across several…
Several approaches to cognition and intelligence research rely on statistics-based models testing, namely factor analysis. In the present work we exploit the emerging dynamical systems perspective putting the focus on the role of the…
We review the recent fast progress in statistical physics of evolving networks. Interest has focused mainly on the structural properties of random complex networks in communications, biology, social sciences and economics. A number of giant…