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Items: 19

1.

CD-Based Indices for Link Prediction in Complex Network.

Wang T, Wang H, Wang X.

PLoS One. 2016 Jan 11;11(1):e0146727. doi: 10.1371/journal.pone.0146727. eCollection 2016.

2.

Mining protein interactomes to improve their reliability and support the advancement of network medicine.

Alanis-Lobato G.

Front Genet. 2015 Sep 23;6:296. doi: 10.3389/fgene.2015.00296. eCollection 2015. Review.

3.

Protein-protein interaction detection: methods and analysis.

Rao VS, Srinivas K, Sujini GN, Kumar GN.

Int J Proteomics. 2014;2014:147648. doi: 10.1155/2014/147648. Epub 2014 Feb 17. Review.

4.

Detecting overlapping protein complexes in PPI networks based on robustness.

Wang S, Wu F.

Proteome Sci. 2013 Nov 7;11(Suppl 1):S18. doi: 10.1186/1477-5956-11-S1-S18. Epub 2013 Nov 7.

5.

Computational Prediction of Protein-Protein Interaction Networks: Algo-rithms and Resources.

Zahiri J, Bozorgmehr JH, Masoudi-Nejad A.

Curr Genomics. 2013 Sep;14(6):397-414. doi: 10.2174/1389202911314060004.

6.

Minimum curvilinearity to enhance topological prediction of protein interactions by network embedding.

Cannistraci CV, Alanis-Lobato G, Ravasi T.

Bioinformatics. 2013 Jul 1;29(13):i199-209. doi: 10.1093/bioinformatics/btt208.

7.

t-LSE: a novel robust geometric approach for modeling protein-protein interaction networks.

Zhu L, You ZH, Huang DS, Wang B.

PLoS One. 2013;8(4):e58368. doi: 10.1371/journal.pone.0058368. Epub 2013 Apr 1.

8.

Cluster-based assessment of protein-protein interaction confidence.

Kamburov A, Grossmann A, Herwig R, Stelzl U.

BMC Bioinformatics. 2012 Oct 10;13:262. doi: 10.1186/1471-2105-13-262.

9.

Assessing and predicting protein interactions by combining manifold embedding with multiple information integration.

Lei YK, You ZH, Ji Z, Zhu L, Huang DS.

BMC Bioinformatics. 2012 May 8;13 Suppl 7:S3. doi: 10.1186/1471-2105-13-S7-S3.

10.

Improving the prediction of yeast protein function using weighted protein-protein interactions.

Ahmed KS, Saloma NH, Kadah YM.

Theor Biol Med Model. 2011 Apr 27;8:11. doi: 10.1186/1742-4682-8-11.

11.

Integrating diverse biological and computational sources for reliable protein-protein interactions.

Wu M, Li X, Chua HN, Kwoh CK, Ng SK.

BMC Bioinformatics. 2010 Oct 15;11 Suppl 7:S8. doi: 10.1186/1471-2105-11-S7-S8.

12.

Predicting direct protein interactions from affinity purification mass spectrometry data.

Kim ED, Sabharwal A, Vetta AR, Blanchette M.

Algorithms Mol Biol. 2010 Oct 29;5:34. doi: 10.1186/1748-7188-5-34.

13.

HitPredict: a database of quality assessed protein-protein interactions in nine species.

Patil A, Nakai K, Nakamura H.

Nucleic Acids Res. 2011 Jan;39(Database issue):D744-9. doi: 10.1093/nar/gkq897. Epub 2010 Oct 14.

14.

Using manifold embedding for assessing and predicting protein interactions from high-throughput experimental data.

You ZH, Lei YK, Gui J, Huang DS, Zhou X.

Bioinformatics. 2010 Nov 1;26(21):2744-51. doi: 10.1093/bioinformatics/btq510. Epub 2010 Sep 3.

15.

A core-attachment based method to detect protein complexes in PPI networks.

Wu M, Li X, Kwoh CK, Ng SK.

BMC Bioinformatics. 2009 Jun 2;10:169. doi: 10.1186/1471-2105-10-169.

16.

Biomedical discovery acceleration, with applications to craniofacial development.

Leach SM, Tipney H, Feng W, Baumgartner WA, Kasliwal P, Schuyler RP, Williams T, Spritz RA, Hunter L.

PLoS Comput Biol. 2009 Mar;5(3):e1000215. doi: 10.1371/journal.pcbi.1000215. Epub 2009 Mar 27.

17.

Improved homology-driven computational validation of protein-protein interactions motivated by the evolutionary gene duplication and divergence hypothesis.

Frech C, Kommenda M, Dorfer V, Kern T, Hintner H, Bauer JW, Onder K.

BMC Bioinformatics. 2009 Jan 19;10:21. doi: 10.1186/1471-2105-10-21.

18.
19.

Inferring network mechanisms: the Drosophila melanogaster protein interaction network.

Middendorf M, Ziv E, Wiggins CH.

Proc Natl Acad Sci U S A. 2005 Mar 1;102(9):3192-7. Epub 2005 Feb 22.

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