Local graph alignment and motif search in biological networks

The alignment of biological networks has the potential to teach us as much about biology and disease as has sequence alignment. Sequence alignment can be optimally solved in polynomial time. In contrast, network alignment is $NP$-hard, meaning optimal solutions are impossible to find, and the quality of found alignments depend strongly upon the algorithm used to create them. Every network alignment algorithm consists of two orthogonal components: first, an objective function ...

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 the following features: (i) search for motifs up to 6 vertices, (ii) multithread processing, and a (iii) new enumeration algorithm with lower complexity. The algorithm to compute motifs solve isomorphism in $O(1)$ with the use of hash table. ...

Protein-protein interaction (PPI) network alignment is a canonical operation to transfer biological knowledge among species. The alignment of PPI-networks has many applications, such as the prediction of protein function, detection of conserved network motifs, and the reconstruction of species' phylogenetic relationships. A good multiple-network alignment (MNA), by considering the data related to several species, provides a deep understanding of biological networks and system...

Biological and technological networks contain patterns, termed network motifs, which occur far more often than in randomized networks. Network motifs were suggested to be elementary building blocks that carry out key functions in the network. It is of interest to understand how network motifs combine to form larger structures. To address this, we present a systematic approach to define 'motif generalizations': families of motifs of different sizes that share a common architec...

Gene duplication is a fundamental evolutionary mechanism that contributes to biological complexity and diversity (Fortna et al., 2004). Traditionally, research has focused on the duplication of gene sequences (Zhang, 1914). However, evidence suggests that the duplication of regulatory elements may also play a significant role in the evolution of genomic functions (Teichmann and Babu, 2004; Hallin and Landry, 2019). In this work, the evolution of regulatory relationships belon...

A determinant property of the structure of a biological network is the distribution of local connectivity patterns, i.e., network motifs. In this work, a method for creating directed, unweighted networks while promoting a certain combination of motifs is presented. This motif-based network algorithm starts with an empty graph and randomly connects the nodes by advancing or discouraging the formation of chosen motifs. The in- or out-degree distribution of the generated network...

One of the most difficult problems difficult problem in systems biology is to discover protein-protein interactions as well as their associated functions. The analysis and alignment of protein-protein interaction networks (PPIN), which are the standard model to describe protein-protein interactions, has become a key ingredient to obtain functional orthologs as well as evolutionary conserved pathways and protein complexes. Several methods have been proposed to solve the PPIN a...

Biological systems and processes are networks of complex nonlinear regulatory interactions between nucleic acids, proteins, and metabolites. A natural way in which to represent these interaction networks is through the use of a graph. In this formulation, each node represents a nucleic acid, protein, or metabolite and edges represent intermolecular interactions (inhibition, regulation, promotion, coexpression, etc.). In this work, a novel algorithm for the discovery of latent...

The interaction between proteins and DNA is a key driving force in a significant number of biological processes such as transcriptional regulation, repair, recombination, splicing, and DNA modification. The identification of DNA-binding sites and the specificity of target proteins in binding to these regions are two important steps in understanding the mechanisms of these biological activities. A number of high-throughput technologies have recently emerged that try to quantif...

Understanding the structure and dynamics of biological networks is one of the important challenges in system biology. In addition, increasing amount of experimental data in biological networks necessitate the use of efficient methods to analyze these huge amounts of data. Such methods require to recognize common patterns to analyze data. As biological networks can be modeled by graphs, the problem of common patterns recognition is equivalent with frequent sub graph mining in ...