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Items: 1 to 20 of 30

1.

A global protein kinase and phosphatase interaction network in yeast.

Breitkreutz A, Choi H, Sharom JR, Boucher L, Neduva V, Larsen B, Lin ZY, Breitkreutz BJ, Stark C, Liu G, Ahn J, Dewar-Darch D, Reguly T, Tang X, Almeida R, Qin ZS, Pawson T, Gingras AC, Nesvizhskii AI, Tyers M.

Science. 2010 May 21;328(5981):1043-6. doi: 10.1126/science.1176495.

2.

Distinguishing direct versus indirect transcription factor-DNA interactions.

Gordân R, Hartemink AJ, Bulyk ML.

Genome Res. 2009 Nov;19(11):2090-100. doi: 10.1101/gr.094144.109. Epub 2009 Aug 3.

3.

High-resolution mapping of the protein interaction network for the human transcription machinery and affinity purification of RNA polymerase II-associated complexes.

Cloutier P, Al-Khoury R, Lavallée-Adam M, Faubert D, Jiang H, Poitras C, Bouchard A, Forget D, Blanchette M, Coulombe B.

Methods. 2009 Aug;48(4):381-6. doi: 10.1016/j.ymeth.2009.05.005. Epub 2009 May 18.

4.

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.

5.

A Bayesian estimator of protein-protein association probabilities.

Gilmore JM, Auberry DL, Sharp JL, White AM, Anderson KK, Daly DS.

Bioinformatics. 2008 Jul 1;24(13):1554-5. doi: 10.1093/bioinformatics/btn238. Epub 2008 May 22.

PMID:
18499697
6.

Steps towards a repertoire of comprehensive maps of human protein interaction networks: the Human Proteotheque Initiative (HuPI).

Coulombe B, Blanchette M, Jeronimo C.

Biochem Cell Biol. 2008 Apr;86(2):149-56. doi: 10.1139/O08-006. Review.

7.

From pull-down data to protein interaction networks and complexes with biological relevance.

Zhang B, Park BH, Karpinets T, Samatova NF.

Bioinformatics. 2008 Apr 1;24(7):979-86. doi: 10.1093/bioinformatics/btn036. Epub 2008 Feb 26.

PMID:
18304937
8.

Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae.

Collins SR, Kemmeren P, Zhao XC, Greenblatt JF, Spencer F, Holstege FC, Weissman JS, Krogan NJ.

Mol Cell Proteomics. 2007 Mar;6(3):439-50. Epub 2007 Jan 2.

9.

Protein identification by tandem mass spectrometry and sequence database searching.

Nesvizhskii AI.

Methods Mol Biol. 2007;367:87-119. Review.

PMID:
17185772
10.

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
11.

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
12.

A topological measurement for weighted protein interaction network.

Pei P, Zhang A.

Proc IEEE Comput Syst Bioinform Conf. 2005:268-78.

PMID:
16447984
13.

Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein.

Ishihama Y, Oda Y, Tabata T, Sato T, Nagasu T, Rappsilber J, Mann M.

Mol Cell Proteomics. 2005 Sep;4(9):1265-72. Epub 2005 Jun 14.

14.

A model for random sampling and estimation of relative protein abundance in shotgun proteomics.

Liu H, Sadygov RG, Yates JR 3rd.

Anal Chem. 2004 Jul 15;76(14):4193-201.

PMID:
15253663
15.

Predicting protein complex membership using probabilistic network reliability.

Asthana S, King OD, Gibbons FD, Roth FP.

Genome Res. 2004 Jun;14(6):1170-5. Epub 2004 May 12.

16.

Changes in the protein expression of yeast as a function of carbon source.

Gao J, Opiteck GJ, Friedrichs MS, Dongre AR, Hefta SA.

J Proteome Res. 2003 Nov-Dec;2(6):643-9.

PMID:
14692458
17.

Construction of reliable protein-protein interaction networks with a new interaction generality measure.

Saito R, Suzuki H, Hayashizaki Y.

Bioinformatics. 2003 Apr 12;19(6):756-63.

PMID:
12691988
18.

A duplication growth model of gene expression networks.

Bhan A, Galas DJ, Dewey TG.

Bioinformatics. 2002 Nov;18(11):1486-93.

PMID:
12424120
19.

A proteomic view of the Plasmodium falciparum life cycle.

Florens L, Washburn MP, Raine JD, Anthony RM, Grainger M, Haynes JD, Moch JK, Muster N, Sacci JB, Tabb DL, Witney AA, Wolters D, Wu Y, Gardner MJ, Holder AA, Sinden RE, Yates JR, Carucci DJ.

Nature. 2002 Oct 3;419(6906):520-6.

PMID:
12368866
20.

Interaction generality, a measurement to assess the reliability of a protein-protein interaction.

Saito R, Suzuki H, Hayashizaki Y.

Nucleic Acids Res. 2002 Mar 1;30(5):1163-8.

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