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Items: 1 to 20 of 101

1.

Bootstrapping the interactome: unsupervised identification of protein complexes in yeast.

Friedel CC, Krumsiek J, Zimmer R.

J Comput Biol. 2009 Aug;16(8):971-87. doi: 10.1089/cmb.2009.0023.

PMID:
19630542
2.
3.

PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs.

Pitre S, Dehne F, Chan A, Cheetham J, Duong A, Emili A, Gebbia M, Greenblatt J, Jessulat M, Krogan N, Luo X, Golshani A.

BMC Bioinformatics. 2006 Jul 27;7:365.

4.

MCL-CAw: a refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure.

Srihari S, Ning K, Leong HW.

BMC Bioinformatics. 2010 Oct 12;11:504. doi: 10.1186/1471-2105-11-504.

5.

Identifying functional modules in the physical interactome of Saccharomyces cerevisiae.

Pu S, Vlasblom J, Emili A, Greenblatt J, Wodak SJ.

Proteomics. 2007 Mar;7(6):944-60.

PMID:
17370254
6.

Discover protein complexes in protein-protein interaction networks using parametric local modularity.

Kim J, Tan K.

BMC Bioinformatics. 2010 Oct 19;11:521. doi: 10.1186/1471-2105-11-521.

7.

Assessment of high-confidence protein-protein interactome in yeast.

Karagoz K, Arga KY.

Comput Biol Chem. 2013 Aug;45:1-8. doi: 10.1016/j.compbiolchem.2013.03.002. Epub 2013 Mar 26.

PMID:
23608186
8.

Pushing structural information into the yeast interactome by high-throughput protein docking experiments.

Mosca R, Pons C, Fernández-Recio J, Aloy P.

PLoS Comput Biol. 2009 Aug;5(8):e1000490. doi: 10.1371/journal.pcbi.1000490. Epub 2009 Aug 28.

9.

Protein-protein interactions.

Williamson MP, Sutcliffe MJ.

Biochem Soc Trans. 2010 Aug;38(4):875-8. doi: 10.1042/BST0380875. Review.

PMID:
20658969
10.

Structure-based prediction of protein-protein interactions on a genome-wide scale.

Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, Thu CA, Bisikirska B, Lefebvre C, Accili D, Hunter T, Maniatis T, Califano A, Honig B.

Nature. 2012 Oct 25;490(7421):556-60. doi: 10.1038/nature11503. Epub 2012 Sep 30. Erratum in: Nature. 2013 Mar 7;495(7439):127.

11.

Determining protein complex connectivity using a probabilistic deletion network derived from quantitative proteomics.

Sardiu ME, Gilmore JM, Carrozza MJ, Li B, Workman JL, Florens L, Washburn MP.

PLoS One. 2009 Oct 6;4(10):e7310. doi: 10.1371/journal.pone.0007310.

12.

Characterization and prediction of protein-protein interactions within and between complexes.

Sprinzak E, Altuvia Y, Margalit H.

Proc Natl Acad Sci U S A. 2006 Oct 3;103(40):14718-23. Epub 2006 Sep 26.

13.

A Bayesian networks approach for predicting protein-protein interactions from genomic data.

Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M.

Science. 2003 Oct 17;302(5644):449-53.

14.

High-quality binary protein interaction map of the yeast interactome network.

Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, Sahalie J, Hirozane-Kishikawa T, Gebreab F, Li N, Simonis N, Hao T, Rual JF, Dricot A, Vazquez A, Murray RR, Simon C, Tardivo L, Tam S, Svrzikapa N, Fan C, de Smet AS, Motyl A, Hudson ME, Park J, Xin X, Cusick ME, Moore T, Boone C, Snyder M, Roth FP, Barabási AL, Tavernier J, Hill DE, Vidal M.

Science. 2008 Oct 3;322(5898):104-10. doi: 10.1126/science.1158684. Epub 2008 Aug 21.

15.

Large-scale identification of yeast integral membrane protein interactions.

Miller JP, Lo RS, Ben-Hur A, Desmarais C, Stagljar I, Noble WS, Fields S.

Proc Natl Acad Sci U S A. 2005 Aug 23;102(34):12123-8. Epub 2005 Aug 10.

16.

Inferring physical protein contacts from large-scale purification data of protein complexes.

Schelhorn SE, Mestre J, Albrecht M, Zotenko E.

Mol Cell Proteomics. 2011 Jun;10(6):M110.004929. doi: 10.1074/mcp.M110.004929. Epub 2011 Mar 30.

17.

Systematic characterization of the protein interaction network and protein complexes in Saccharomyces cerevisiae using tandem affinity purification and mass spectrometry.

Babu M, Krogan NJ, Awrey DE, Emili A, Greenblatt JF.

Methods Mol Biol. 2009;548:187-207. doi: 10.1007/978-1-59745-540-4_11.

PMID:
19521826
18.

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.

Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrín-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, St Onge P, Ghanny S, Lam MH, Butland G, Altaf-Ul AM, Kanaya S, Shilatifard A, O'Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, Greenblatt JF.

Nature. 2006 Mar 30;440(7084):637-43. Epub 2006 Mar 22.

PMID:
16554755
19.

Functional organization of the yeast proteome by a yeast interactome map.

Valente AX, Roberts SB, Buck GA, Gao Y.

Proc Natl Acad Sci U S A. 2009 Feb 3;106(5):1490-5. doi: 10.1073/pnas.0808624106. Epub 2009 Jan 21.

20.

New insights into protein-protein interaction data lead to increased estimates of the S. cerevisiae interactome size.

Sambourg L, Thierry-Mieg N.

BMC Bioinformatics. 2010 Dec 21;11:605. doi: 10.1186/1471-2105-11-605.

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