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Querying protein-protein interaction networks
- in Proceedings of the 5th International Symposium on Bioinformatics Research and Applications
, 2009
"... Abstract. Recent techniques increase the amount of our knowledge of interactions between proteins. To filter, interpret and organize this data, many authors have provided tools for querying patterns in the shape of paths or trees in Protein-Protein Interaction networks. In this paper, we propose an ..."
Abstract
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Cited by 5 (3 self)
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Abstract. Recent techniques increase the amount of our knowledge of interactions between proteins. To filter, interpret and organize this data, many authors have provided tools for querying patterns in the shape of paths or trees in Protein-Protein Interaction networks. In this paper, we propose
the protein–protein interaction network
, 2004
"... The interactome as a tree—an attempt to visualize ..."
in protein–protein interaction networks
, 2005
"... Binding properties and evolution of homodimers ..."
Laplacian Spectrum and Protein-Protein Interaction Networks
, 2008
"... From the spectral plot of the (normalized) graph Laplacian, the essential qualitative properties of a network can be simultaneously deduced. Given a class of empirical networks, reconstruction schemes for elucidating the evolutionary dynamics leading to those particular data can then be developed. T ..."
Abstract
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Cited by 6 (2 self)
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. This method is exemplified for protein-protein interaction networks. Traces of their evolutionary history of duplication and divergence processes are identified. In particular, we can identify typical specific features that robustly distinguish protein-protein interaction networks from other classes
Protein-protein Interaction: Network Alignment ∗
, 2006
"... In the last few years the amount of available data on protein-protein interaction (PPI) networks have increased rapidly, spanning different species such as yeast, bacteria, fly, worm and Human. The rapid growth is shown in Figure 1. Besides the availability of the data, other incentives to analyze s ..."
Abstract
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Cited by 1 (0 self)
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In the last few years the amount of available data on protein-protein interaction (PPI) networks have increased rapidly, spanning different species such as yeast, bacteria, fly, worm and Human. The rapid growth is shown in Figure 1. Besides the availability of the data, other incentives to analyze
Human Protein-Protein Interaction Networks
, 2009
"... Copyright: © 2009 Gao S, et al. This is an open-access article distributed under the terms of the Creative Commons Attribu-tion License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Background Proteins directly i ..."
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interacting with each other tend to have similar functions and be involved in the same cellular processes. Mutations in genes that code for them often lead to the same family of disease phenotypes. Efforts have been made to prioritize positional candidate genes for complex diseases utilize the protein-protein
Visualization of Protein-Protein Interaction Network for Knowledge Discovery
"... Abstract- A new visualization tool, called "Visual Concept Explorer (VCE)", was developed to visualize concept relationships in bio-medical literatura VCE integrates Pathfinder Network Scaling and Kohonen Self-organizing Feature Map Algorithm for visual mapping. As a case study, VCE was ap ..."
Abstract
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Cited by 1 (0 self)
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was applied to visualize a chromatin protein-protein interaction (PPI) network The mapping results demonstrated that VCE could explore the semantic structure and latent domain knowledge hidden in protein-protein interaction data sets generatedfrom bio-medical literature. Index Terms-knowledge discovery
Identifying critical nodes in protein-protein interaction networks
- Clustering challenges in biological networks
, 2009
"... ABSTRACT. In recent years, the study of biological networks has increased dramatically. These problems have piqued the interest of researchers in many disciplines from biology to mathematics. In particular, many problems of interest to biological scientists can be modeled as combinatorial optimizati ..."
Abstract
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Cited by 2 (0 self)
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optimization problems and studied by operations researchers. In this chapter, we consider the problem of identifying the critical nodes of a network and its potential applications to protein-protein interaction networks. More specifically, we are interested in determining the smallest set of nodes whose
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