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34
Complex Detection in Protein-Protein Interaction Networks: A Compact Overview for Researchers and Practitioners
- Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics
, 2012
"... Abstract. The availability of large volumes of protein-protein interaction data has allowed the study of biological networks to unveil the complex structure and organization in the cell. It has been recognized by biologists that proteins interacting with each other often participate in the same bio ..."
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Cited by 4 (0 self)
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biological processes, and that protein modules may be often associated with specific biological functions. Thus the detection of protein complexes is an important research problem in systems biology. In this review, recent graph-based approaches to clustering protein interaction networks are described
Identification of functional modules in a PPI network by clique percolation clustering
, 2006
"... Large-scale experiments and data integration have provided the opportunity to systematically analyze and comprehensively understand the topology of biological networks and biochemical processes in cells. Modular architecture which encompasses groups of genes/proteins involved in elementary biologica ..."
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Cited by 5 (0 self)
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biological functional units is a basic form of the organization of interacting proteins. Here we apply a graph clustering algorithm based on clique percolation clustering to detect overlapping network modules of a protein–protein interaction (PPI) network. Our analysis of the yeast Sacchromyces cerevisiae
ABC and IFC: Modules Detection Method for PPI Network
"... Many clustering algorithms are unable to solve the clustering problem of protein-protein interaction (PPI) networks effectively. A novel clustering model which combines the optimization mechanism of artificial bee colony (ABC) with the fuzzy membership matrix is proposed in this paper. The proposed ..."
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Many clustering algorithms are unable to solve the clustering problem of protein-protein interaction (PPI) networks effectively. A novel clustering model which combines the optimization mechanism of artificial bee colony (ABC) with the fuzzy membership matrix is proposed in this paper
Multi-functional Protein Clustering in PPI Networks
"... Abstract. Protein-Protein Interaction (PPI) networks contain valuable information for the isolation of groups of proteins that participate in the same biological function. Many proteins play different roles in the cell by taking part in several processes, but isolating the different processes in whi ..."
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Cited by 4 (3 self)
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in which a protein is involved is often a difficult task. In this paper we present a method based on a greedy local search technique to detect functional modules in PPI graphs. The approach is conceived as a generalization of the algorithm PINCoC to generate overlapping clusters of the interaction graph
Pattern Discovery in Breast Cancer Specific Protein Interaction Network
"... The interest in indentifying novel biomarkers for early stage breast cancer (BRCA) detection has become grown significantly in recent years. From a view of network biology, one of the emerging themes today is to re-characterize a protein’s biological functions in its molecular network. Although many ..."
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many methods have been presented, including network-based gene ranking for molecular biomarker discovery, and graph clustering for functional module discovery, it is still hard to find systems-level properties hidden in disease specific molecular networks. We reconstructed BRCA-related protein
Research Article ABC and IFC: Modules Detection Method for PPI Network
"... Copyright © 2014 Xiujuan Lei et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Many clustering algorithms are unable to solve th ..."
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the clustering problem of protein-protein interaction (PPI) networks effectively. A novel clustering model which combines the optimization mechanism of artificial bee colony (ABC) with the fuzzy membership matrix is proposed in this paper. The proposed ABC-IFC clustering model contains two parts: searching
A Graph-Theoretic Method for Mining Functional Modules in Large Sparse Protein Interaction Networks
"... With ever increasing amount of available data on protein-protein interaction (PPI) networks, understanding the topology of the networks and then biochemical processes in cells has become a key problem. Modular architecture which encompasses groups of genes/proteins involved in elementary biological ..."
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functional units is a basic form of the organization of interacting proteins. Here we propose a method that combines the line graph transformation and clique percolation clustering algorithm to detect network modules which may overlap each other in large sparse protein-protein interaction (PPI) networks
Comparing protein interaction networks via a graph match-and-split algorithm
- J of Comput Biol
"... 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 between two graphs. Unlike previous network comparison methods, o ..."
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Cited by 21 (1 self)
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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 between two graphs. Unlike previous network comparison methods
BinTree Seeking: A Novel Approach to Mine Both Bi- Sparse and Cohesive Modules in Protein Interaction Networks
, 2011
"... Modern science of networks has brought significant advances to our understanding of complex systems biology. As a representative model of systems biology, Protein Interaction Networks (PINs) are characterized by a remarkable modular structures, reflecting functional associations between their compon ..."
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Cited by 1 (0 self)
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Modern science of networks has brought significant advances to our understanding of complex systems biology. As a representative model of systems biology, Protein Interaction Networks (PINs) are characterized by a remarkable modular structures, reflecting functional associations between
RESEARCH ARTICLE Molecular Architecture of Spinal Cord Injury Protein Interaction Network
"... Spinal cord injury (SCI) is associated with complex pathophysiological processes that follow the primary traumatic event and determine the extent of secondary damage and functional recovery. Numerous reports have used global and hypothesis-driven approaches to identify protein changes that contribut ..."
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of the SCI interactome revealed the presence of a rich-club organization corresponding to a “powerhouse ” of highly interacting hub-proteins. Studying the modular organization of the network have shown that rich-club proteins cluster into modules that are specifically enriched for biological processes
Results 1 - 10
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34
