Search results for "Network analysis"

Scientometric portrait of biochemist Santiago Grisolia: publication productivity, collaboration patterns, and citation analysis

2014

Santiago Grisolía has made numerous scientific discoveries and contributions of great relevance to the advancement of biochemistry and molecular biology, particularly in the field of enzymology in the metabolism of nitrogen related to the urea cycle and the impoverishment of pyrimidines. This article analyses, by means of bibliometrics indicators and social network analysis, his professional career, comparing the results obtained with the patterns of scientific activity of other distinguished researchers. The main findings of the study carried out are as follows: the evolution of his scientific productivity shows an initial period in which the growth is slow or moderate, followed by a fast …

Singling out functional similarities in graph databases

2008

A technique to search functional similarities in PPI networks

2009

We describe a method to search for similarities across protein-protein interaction networks of different organisms. The technique core consists in computing a maximum weight matching of bipartite graphs resulting from comparing the neighbourhoods of proteins belonging to different networks. Both quantitative and reliability information are exploited. We tested the method on the networks of S. cerevisiae, D. melanogaster and C. elegans. The experiments showed that the technique is able to detect functional orthologs when the sole sequence similarity does not prove itself sufficient. They also demonstrated the capability of our approach in discovering common biological processes involving unc…

Bi-GRAPPIN: Bipartite graph based protein-protein interaction networks similarity search

2007

Discovering meaningful protein-protein interaction modules by a co-clustering based approach

2008

Asymmetric Global Alignment of Protein-Protein Interaction Graph Databases

2010

Discovering Protein Complexes in Protein Interaction Networks

2009

New Trends in Graph Mining

2010

Searching for repeated features characterizing biological data is fundamental in computational biology. When biological networks are under analysis, the presence of repeated modules across the same network (or several distinct ones) is shown to be very relevant. Indeed, several studies prove that biological networks can be often understood in terms of coalitions of basic repeated building blocks, often referred to as network motifs.This work provides a review of the main techniques proposed for motif extraction from biological networks. In particular, main intrinsic difficulties related to the problem are pointed out, along with solutions proposed in the literature to overcome them. Open ch…

Protein-protein interaction network querying by a "focus and zoom" approach

2008

We propose an approach to network querying in protein-protein interaction networks based on bipartite graph weighted matching. An algorithm is presented that first “focuses” the potentially relevant portion of the target graph by performing a global alignment of this one with the query graph, and then “zooms” on the actual matching nodes by considering their topological arrangement, hereby obtaining a (possibly) approximated occurrence of the query graph within the target graph. Approximation is related to node insertions, node deletions and edge deletions possibly intervening in the query graph. The technique manages networks of arbitrary topology. Moreover, edge labels are used to represe…

A Coclustering Approach for Mining Large Protein-Protein Interaction Networks

2012

Several approaches have been presented in the literature to cluster Protein-Protein Interaction (PPI) networks. They can be grouped in two main categories: those allowing a protein to participate in different clusters and those generating only nonoverlapping clusters. In both cases, a challenging task is to find a suitable compromise between the biological relevance of the results and a comprehensive coverage of the analyzed networks. Indeed, methods returning high accurate results are often able to cover only small parts of the input PPI network, especially when low-characterized networks are considered. We present a coclustering-based technique able to generate both overlapping and nonove…