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  4. PROPER: global protein interaction network alignment through percolation matching
 
research article

PROPER: global protein interaction network alignment through percolation matching

Kazemi, Ehsan
•
Hassani, Hamed
•
Grossglauser, Matthias  
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2016
BMC Bioinformatics

Background The alignment of protein-protein interaction (PPI) networks enables us to uncover the relationships between different species, which leads to a deeper understanding of biological systems. Network alignment can be used to transfer biological knowledge between species. Although different PI-network alignment algorithms were introduced during the last decade, developing an accurate and scalable algorithm that can find alignments with high biological and structural similarities among PPI networks is still challenging. Results In this paper, we introduce a new global network alignment algorithm for PPI networks called PROPER. Compared to other global network alignment methods, our algorithm shows higher accuracy and speed over real PPI datasets and synthetic networks. We show that the PROPER algorithm can detect large portions of conserved biological pathways between species. Also, using a simple parsimonious evolutionary model, we explain why PROPER performs well based on several different comparison criteria. Conclusions We highlight that PROPER has high potential in further applications such as detecting biological pathways, finding protein complexes and PPI prediction. The PROPER algorithm is available at http://proper.epfl.ch.

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Type
research article
DOI
10.1186/s12859-016-1395-9
Web of Science ID

WOS:000389958500001

Author(s)
Kazemi, Ehsan
Hassani, Hamed
Grossglauser, Matthias  
Modarres, Hassan Pezeshgi
Date Issued

2016

Published in
BMC Bioinformatics
Volume

17

Start page

527

Subjects

Global network alignment

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Protein-protein interaction

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Percolation graph matching

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Biological network

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Graph mining

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
INDY1  
Available on Infoscience
December 17, 2016
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/132051
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