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Asymmetric Comparison and Querying of Biological Networks
July/August 2011 (vol. 8 no. 4)
pp. 876-889
ASCII Text
x 
 
Nicola Ferraro, Luigi Palopoli, Simona Panni, Simona E. Rombo, "Asymmetric Comparison and Querying of Biological Networks," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8, no. 4, pp. 876-889, July/August, 2011.
 
 
BibTex
x
 
@article{ 10.1109/TCBB.2011.29,
author = {Nicola Ferraro and Luigi Palopoli and Simona Panni and Simona E. Rombo},
title = {Asymmetric Comparison and Querying of Biological Networks},
journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
volume = {8},
number = {4},
issn = {1545-5963},
year = {2011},
pages = {876-889},
doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.29},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - JOUR
JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics
TI - Asymmetric Comparison and Querying of Biological Networks
IS - 4
SN - 1545-5963
SP876
EP889
EPD - 876-889
A1 - Nicola Ferraro,
A1 - Luigi Palopoli,
A1 - Simona Panni,
A1 - Simona E. Rombo,
PY - 2011
KW - Biological networks
KW - asymmetric alignment
KW - master-slave analysis
KW - network querying
KW - evolutive conservations.
VL - 8
JA - IEEE/ACM Transactions on Computational Biology and Bioinformatics
ER -
 
Nicola Ferraro, University of Calabria, Rende (Cosenza)
Luigi Palopoli, University of Calabria, Rende (Cosenza)
Simona Panni, University of Calabria, Rende (Cosenza)
Simona E. Rombo, University of Calabria, Rende (Cosenza)
Comparing and querying the protein-protein interaction (PPI) networks of different organisms is important to infer knowledge about conservation across species. Known methods that perform these tasks operate symmetrically, i.e., they do not assign a distinct role to the input PPI networks. However, in most cases, the input networks are indeed distinguishable on the basis of how the corresponding organism is biologically well characterized. In this paper a new idea is developed, that is, to exploit differences in the characterization of organisms at hand in order to devise methods for comparing their PPI networks. We use the PPI network (called Master) of the best characterized organism as a fingerprint to guide the alignment process to the second input network (called Slave), so that generated results preferably retain the structural characteristics of the Master network. Technically, this is obtained by generating from the Master a finite automaton, called alignment model, which is then fed with (a linearization of) the Slave for the purpose of extracting, via the Viterbi algorithm, matching subgraphs. We propose an approach able to perform global alignment and network querying, and we apply it on PPI networks. We tested our method showing that the results it returns are biologically relevant.

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Index Terms:
Biological networks, asymmetric alignment, master-slave analysis, network querying, evolutive conservations.
Citation:
Nicola Ferraro, Luigi Palopoli, Simona Panni, Simona E. Rombo, "Asymmetric Comparison and Querying of Biological Networks," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8, no. 4, pp. 876-889, July-Aug. 2011, doi:10.1109/TCBB.2011.29
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