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A Divide and Conquer Approach for Construction of LargeScale Signaling Networks from PPI and RNAi Data Using Linear Programming
JulyAug. 2013 (vol. 10 no. 4)
pp. 869883
ASCII Text  x  
Oyku Eren Ozsoy, Tolga Can, "A Divide and Conquer Approach for Construction of LargeScale Signaling Networks from PPI and RNAi Data Using Linear Programming," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 10, no. 4, pp. 869883, JulyAug., 2013.  
BibTex  x  
@article{ 10.1109/TCBB.2013.80, author = {Oyku Eren Ozsoy and Tolga Can}, title = {A Divide and Conquer Approach for Construction of LargeScale Signaling Networks from PPI and RNAi Data Using Linear Programming}, journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {10}, number = {4}, issn = {15455963}, year = {2013}, pages = {869883}, doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2013.80}, 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  A Divide and Conquer Approach for Construction of LargeScale Signaling Networks from PPI and RNAi Data Using Linear Programming IS  4 SN  15455963 SP869 EP883 EPD  869883 A1  Oyku Eren Ozsoy, A1  Tolga Can, PY  2013 KW  RNA KW  bioinformatics KW  computational complexity KW  genetics KW  heuristic programming KW  linear programming KW  molecular biophysics KW  optimisation KW  proteins KW  biological accuracy KW  largescale signaling network construction KW  PPI data KW  RNAi data KW  linear programming KW  signaling network topology inference KW  perturbation experiment KW  inference problem KW  reference network editing problem KW  minimum edit operation number KW  NPcomplete problem KW  integer linear optimization model KW  ILP model KW  small signaling network size KW  gene KW  computational complexity KW  large signaling network KW  heuristic programming KW  reference network division KW  reference subnetwork solution merging KW  Network topology KW  Proteins KW  Topology KW  Linear programming KW  Data models KW  Optimization KW  linear optimization KW  Signaling network topology KW  proteinprotein interactions KW  RNA interference VL  10 JA  IEEE/ACM Transactions on Computational Biology and Bioinformatics ER   
DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/TCBB.2013.80
Web Extra: View Supplemental Material(PDF)
Inference of topology of signaling networks from perturbation experiments is a challenging problem. Recently, the inference problem has been formulated as a reference network editing problem and it has been shown that finding the minimum number of edit operations on a reference network to comply with perturbation experiments is an NPcomplete problem. In this paper, we propose an integer linear optimization (ILP) model for reconstruction of signaling networks from RNAi data and a reference network. The ILP model guarantees the optimal solution; however, is practical only for small signaling networks of size 1015 genes due to computational complexity. To scale for large signaling networks, we propose a divide and conquerbased heuristic, in which a given reference network is divided into smaller subnetworks that are solved separately and the solutions are merged together to form the solution for the large network. We validate our proposed approach on real and synthetic data sets, and comparison with the state of the art shows that our proposed approach is able to scale better for large networks while attaining similar or better biological accuracy.
Index Terms:
RNA,bioinformatics,computational complexity,genetics,heuristic programming,linear programming,molecular biophysics,optimisation,proteins,biological accuracy,largescale signaling network construction,PPI data,RNAi data,linear programming,signaling network topology inference,perturbation experiment,inference problem,reference network editing problem,minimum edit operation number,NPcomplete problem,integer linear optimization model,ILP model,small signaling network size,gene,computational complexity,large signaling network,heuristic programming,reference network division,reference subnetwork solution merging,Network topology,Proteins,Topology,Linear programming,Data models,Optimization,linear optimization,Signaling network topology,proteinprotein interactions,RNA interference
Citation:
Oyku Eren Ozsoy, Tolga Can, "A Divide and Conquer Approach for Construction of LargeScale Signaling Networks from PPI and RNAi Data Using Linear Programming," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 10, no. 4, pp. 869883, JulyAug. 2013, doi:10.1109/TCBB.2013.80
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