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Items: 1 to 20 of 102

1.

A network synthesis model for generating protein interaction network families.

Sahraeian SM, Yoon BJ.

PLoS One. 2012;7(8):e41474. doi: 10.1371/journal.pone.0041474. Epub 2012 Aug 13.

3.

SMETANA: accurate and scalable algorithm for probabilistic alignment of large-scale biological networks.

Sahraeian SM, Yoon BJ.

PLoS One. 2013 Jul 12;8(7):e67995. doi: 10.1371/journal.pone.0067995. Print 2013.

4.

SiPAN: simultaneous prediction and alignment of protein-protein interaction networks.

Alkan F, Erten C.

Bioinformatics. 2015 Jul 15;31(14):2356-63. doi: 10.1093/bioinformatics/btv160. Epub 2015 Mar 18.

PMID:
25788620
5.

RESQUE: network reduction using semi-Markov random walk scores for efficient querying of biological networks.

Sahraeian SM, Yoon BJ.

Bioinformatics. 2012 Aug 15;28(16):2129-36. doi: 10.1093/bioinformatics/bts341. Epub 2012 Jun 23.

PMID:
22730436
6.

Bayesian coestimation of phylogeny and sequence alignment.

Lunter G, Miklós I, Drummond A, Jensen JL, Hein J.

BMC Bioinformatics. 2005 Apr 1;6:83.

7.

PROPER: global protein interaction network alignment through percolation matching.

Kazemi E, Hassani H, Grossglauser M, Pezeshgi Modarres H.

BMC Bioinformatics. 2016 Dec 12;17(1):527.

8.

SEQUOIA: significance enhanced network querying through context-sensitive random walk and minimization of network conductance.

Jeong H, Yoon BJ.

BMC Syst Biol. 2017 Mar 14;11(Suppl 3):20. doi: 10.1186/s12918-017-0404-6.

9.

Scalable global alignment for multiple biological networks.

Shih YK, Parthasarathy S.

BMC Bioinformatics. 2012 Mar 21;13 Suppl 3:S11. doi: 10.1186/1471-2105-13-S3-S11.

10.

Global alignment of protein-protein interaction networks.

Mongiovì M, Sharan R.

Methods Mol Biol. 2013;939:21-34. doi: 10.1007/978-1-62703-107-3_3.

PMID:
23192538
11.

Benchmarking regulatory network reconstruction with GRENDEL.

Haynes BC, Brent MR.

Bioinformatics. 2009 Mar 15;25(6):801-7. doi: 10.1093/bioinformatics/btp068. Epub 2009 Feb 2.

12.

The evolutionary dynamics of protein-protein interaction networks inferred from the reconstruction of ancient networks.

Jin Y, Turaev D, Weinmaier T, Rattei T, Makse HA.

PLoS One. 2013;8(3):e58134. doi: 10.1371/journal.pone.0058134. Epub 2013 Mar 20.

13.

Pairwise alignment of protein interaction networks.

Koyutürk M, Kim Y, Topkara U, Subramaniam S, Szpankowski W, Grama A.

J Comput Biol. 2006 Mar;13(2):182-99.

PMID:
16597234
14.

PicXAA: greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences.

Sahraeian SM, Yoon BJ.

Nucleic Acids Res. 2010 Aug;38(15):4917-28. doi: 10.1093/nar/gkq255. Epub 2010 Apr 22.

15.

Using PPI network autocorrelation in hierarchical multi-label classification trees for gene function prediction.

Stojanova D, Ceci M, Malerba D, Dzeroski S.

BMC Bioinformatics. 2013 Sep 26;14:285. doi: 10.1186/1471-2105-14-285.

16.

Geometric evolutionary dynamics of protein interaction networks.

Przulj N, Kuchaiev O, Stevanović A, Hayes W.

Pac Symp Biocomput. 2010:178-89.

17.

DualAligner: a dual alignment-based strategy to align protein interaction networks.

Seah BS, Bhowmick SS, Dewey CF Jr.

Bioinformatics. 2014 Sep 15;30(18):2619-26. doi: 10.1093/bioinformatics/btu358. Epub 2014 May 28.

PMID:
24872427
18.

LocalAli: an evolutionary-based local alignment approach to identify functionally conserved modules in multiple networks.

Hu J, Reinert K.

Bioinformatics. 2015 Feb 1;31(3):363-72. doi: 10.1093/bioinformatics/btu652. Epub 2014 Oct 4.

PMID:
25282642
19.

Domain-oriented edge-based alignment of protein interaction networks.

Guo X, Hartemink AJ.

Bioinformatics. 2009 Jun 15;25(12):i240-6. doi: 10.1093/bioinformatics/btp202.

20.

Evolutionary Model Selection and Parameter Estimation for Protein-Protein Interaction Network Based on Differential Evolution Algorithm.

Huang L, Liao L, Wu CH.

IEEE/ACM Trans Comput Biol Bioinform. 2015 May-Jun;12(3):622-31. doi: 10.1109/TCBB.2014.2366748.

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