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Results: 1 to 20 of 93

1.

A computational framework for boosting confidence in high-throughput protein-protein interaction datasets.

Hosur R, Peng J, Vinayagam A, Stelzl U, Xu J, Perrimon N, Bienkowska J, Berger B.

Genome Biol. 2012 Aug 31;13(8):R76. doi: 10.1186/gb-2012-13-8-r76.

PMID:
22937800
[PubMed - in process]
Free PMC Article
2.

Struct2net: integrating structure into protein-protein interaction prediction.

Singh R, Xu J, Berger B.

Pac Symp Biocomput. 2006:403-14.

PMID:
17094256
[PubMed - indexed for MEDLINE]
Free Article
3.

Struct2Net: a web service to predict protein-protein interactions using a structure-based approach.

Singh R, Park D, Xu J, Hosur R, Berger B.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W508-15. doi: 10.1093/nar/gkq481. Epub 2010 May 31.

PMID:
20513650
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Increasing confidence of protein interactomes using network topological metrics.

Chen J, Hsu W, Lee ML, Ng SK.

Bioinformatics. 2006 Aug 15;22(16):1998-2004. Epub 2006 Jun 20.

PMID:
16787971
[PubMed - indexed for MEDLINE]
Free Article
5.

Probabilistic prediction and ranking of human protein-protein interactions.

Scott MS, Barton GJ.

BMC Bioinformatics. 2007 Jul 5;8:239.

PMID:
17615067
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Computational large-scale mapping of protein-protein interactions using structural complexes.

Shoemaker B, Wuchty S, Panchenko AR.

Curr Protoc Protein Sci. 2013 Sep 24;73:Unit 3.9. doi: 10.1002/0471140864.ps0309s73.

PMID:
24510594
[PubMed - in process]
7.

Mycobacterium tuberculosis and Clostridium difficille interactomes: demonstration of rapid development of computational system for bacterial interactome prediction.

Ananthasubramanian S, Metri R, Khetan A, Gupta A, Handen A, Chandra N, Ganapathiraju M.

Microb Inform Exp. 2012 Mar 21;2:4. doi: 10.1186/2042-5783-2-4.

PMID:
22587966
[PubMed]
Free PMC Article
8.

High-quality binary interactome mapping.

Dreze M, Monachello D, Lurin C, Cusick ME, Hill DE, Vidal M, Braun P.

Methods Enzymol. 2010;470:281-315. doi: 10.1016/S0076-6879(10)70012-4. Epub 2010 Mar 1.

PMID:
20946815
[PubMed - indexed for MEDLINE]
9.

False positive reduction in protein-protein interaction predictions using gene ontology annotations.

Mahdavi MA, Lin YH.

BMC Bioinformatics. 2007 Jul 23;8:262.

PMID:
17645798
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

A sampling framework for incorporating quantitative mass spectrometry data in protein interaction analysis.

Tucker G, Loh PR, Berger B.

BMC Bioinformatics. 2013 Oct 4;14:299. doi: 10.1186/1471-2105-14-299.

PMID:
24093595
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Computational analysis of human protein interaction networks.

Ramírez F, Schlicker A, Assenov Y, Lengauer T, Albrecht M.

Proteomics. 2007 Aug;7(15):2541-52.

PMID:
17647236
[PubMed - indexed for MEDLINE]
12.

Large-scale mapping of human protein interactome using structural complexes.

Tyagi M, Hashimoto K, Shoemaker BA, Wuchty S, Panchenko AR.

EMBO Rep. 2012 Mar 1;13(3):266-71. doi: 10.1038/embor.2011.261.

PMID:
22261719
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Functional annotation from predicted protein interaction networks.

McDermott J, Bumgarner R, Samudrala R.

Bioinformatics. 2005 Aug 1;21(15):3217-26. Epub 2005 May 26.

PMID:
15919725
[PubMed - indexed for MEDLINE]
Free Article
14.

Predicting co-complexed protein pairs from heterogeneous data.

Qiu J, Noble WS.

PLoS Comput Biol. 2008 Apr 18;4(4):e1000054. doi: 10.1371/journal.pcbi.1000054.

PMID:
18421371
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

ROCS: a reproducibility index and confidence score for interaction proteomics studies.

Dazard JE, Saha S, Ewing RM.

BMC Bioinformatics. 2012 Jun 8;13:128. doi: 10.1186/1471-2105-13-128.

PMID:
22682516
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

HAPPI: an online database of comprehensive human annotated and predicted protein interactions.

Chen JY, Mamidipalli S, Huan T.

BMC Genomics. 2009 Jul 7;10 Suppl 1:S16. doi: 10.1186/1471-2164-10-S1-S16.

PMID:
19594875
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Prediction and analysis of the protein interactome in Pseudomonas aeruginosa to enable network-based drug target selection.

Zhang M, Su S, Bhatnagar RK, Hassett DJ, Lu LJ.

PLoS One. 2012;7(7):e41202. doi: 10.1371/journal.pone.0041202. Epub 2012 Jul 24.

PMID:
22848443
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Comparative analysis and assessment of M. tuberculosis H37Rv protein-protein interaction datasets.

Zhou H, Wong L.

BMC Genomics. 2011 Nov 30;12 Suppl 3:S20. doi: 10.1186/1471-2164-12-S3-S20. Epub 2011 Nov 30.

PMID:
22369691
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

The identification of short linear motif-mediated interfaces within the human interactome.

Weatheritt RJ, Luck K, Petsalaki E, Davey NE, Gibson TJ.

Bioinformatics. 2012 Apr 1;28(7):976-82. doi: 10.1093/bioinformatics/bts072. Epub 2012 Feb 10.

PMID:
22328783
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Identification of functional hubs and modules by converting interactome networks into hierarchical ordering of proteins.

Cho YR, Zhang A.

BMC Bioinformatics. 2010 Apr 29;11 Suppl 3:S3. doi: 10.1186/1471-2105-11-S3-S3.

PMID:
20438650
[PubMed - indexed for MEDLINE]
Free PMC Article

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