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Items: 1 to 20 of 26

1.

Systematic discovery of in vivo phosphorylation networks.

Linding R, Jensen LJ, Ostheimer GJ, van Vugt MA, Jørgensen C, Miron IM, Diella F, Colwill K, Taylor L, Elder K, Metalnikov P, Nguyen V, Pasculescu A, Jin J, Park JG, Samson LD, Woodgett JR, Russell RB, Bork P, Yaffe MB, Pawson T.

Cell. 2007 Jun 29;129(7):1415-26. Epub 2007 Jun 14.

2.

Reactome: a knowledge base of biologic pathways and processes.

Vastrik I, D'Eustachio P, Schmidt E, Gopinath G, Croft D, de Bono B, Gillespie M, Jassal B, Lewis S, Matthews L, Wu G, Birney E, Stein L.

Genome Biol. 2007;8(3):R39. Erratum in: Genome Biol. 2009 Feb 4;10(2):402. Joshi-Tope, Geeta [removed].

3.

Large-scale phosphorylation analysis of mouse liver.

Villén J, Beausoleil SA, Gerber SA, Gygi SP.

Proc Natl Acad Sci U S A. 2007 Jan 30;104(5):1488-93. Epub 2007 Jan 22.

4.

Phospho3D: a database of three-dimensional structures of protein phosphorylation sites.

Zanzoni A, Ausiello G, Via A, Gherardini PF, Helmer-Citterich M.

Nucleic Acids Res. 2007 Jan;35(Database issue):D229-31. Epub 2006 Nov 16.

5.

MINT: the Molecular INTeraction database.

Chatr-aryamontri A, Ceol A, Palazzi LM, Nardelli G, Schneider MV, Castagnoli L, Cesareni G.

Nucleic Acids Res. 2007 Jan;35(Database issue):D572-4. Epub 2006 Nov 29.

6.

STRING 7--recent developments in the integration and prediction of protein interactions.

von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Krüger B, Snel B, Bork P.

Nucleic Acids Res. 2007 Jan;35(Database issue):D358-62. Epub 2006 Nov 10.

7.

Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.

Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M.

Cell. 2006 Nov 3;127(3):635-48.

8.

Phosphoproteome analysis of the human mitotic spindle.

Nousiainen M, Silljé HH, Sauer G, Nigg EA, Körner R.

Proc Natl Acad Sci U S A. 2006 Apr 4;103(14):5391-6. Epub 2006 Mar 24.

9.

PhosphoregDB: the tissue and sub-cellular distribution of mammalian protein kinases and phosphatases.

Forrest AR, Taylor DF, Fink JL, Gongora MM, Flegg C, Teasdale RD, Suzuki H, Kanamori M, Kai C, Hayashizaki Y, Grimmond SM.

BMC Bioinformatics. 2006 Feb 20;7:82.

10.

From genomics to chemical genomics: new developments in KEGG.

Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D354-7.

11.

Literature mining and database annotation of protein phosphorylation using a rule-based system.

Hu ZZ, Narayanaswamy M, Ravikumar KE, Vijay-Shanker K, Wu CH.

Bioinformatics. 2005 Jun 1;21(11):2759-65. Epub 2005 Apr 6.

PMID:
15814565
12.

Kinomics: methods for deciphering the kinome.

Johnson SA, Hunter T.

Nat Methods. 2005 Jan;2(1):17-25. Review.

PMID:
15789031
13.

Immunoaffinity profiling of tyrosine phosphorylation in cancer cells.

Rush J, Moritz A, Lee KA, Guo A, Goss VL, Spek EJ, Zhang H, Zha XM, Polakiewicz RD, Comb MJ.

Nat Biotechnol. 2005 Jan;23(1):94-101. Epub 2004 Dec 12.

PMID:
15592455
14.

GPS: a novel group-based phosphorylation predicting and scoring method.

Zhou FF, Xue Y, Chen GL, Yao X.

Biochem Biophys Res Commun. 2004 Dec 24;325(4):1443-8.

PMID:
15555589
15.

Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents.

Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S, Juhasz P, Martin S, Bartlet-Jones M, He F, Jacobson A, Pappin DJ.

Mol Cell Proteomics. 2004 Dec;3(12):1154-69. Epub 2004 Sep 22.

16.

Large-scale characterization of HeLa cell nuclear phosphoproteins.

Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villén J, Li J, Cohn MA, Cantley LC, Gygi SP.

Proc Natl Acad Sci U S A. 2004 Aug 17;101(33):12130-5. Epub 2004 Aug 9.

17.

Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins.

Diella F, Cameron S, Gemünd C, Linding R, Via A, Kuster B, Sicheritz-Pontén T, Blom N, Gibson TJ.

BMC Bioinformatics. 2004 Jun 22;5:79.

18.

Robust phosphoproteomic profiling of tyrosine phosphorylation sites from human T cells using immobilized metal affinity chromatography and tandem mass spectrometry.

Brill LM, Salomon AR, Ficarro SB, Mukherji M, Stettler-Gill M, Peters EC.

Anal Chem. 2004 May 15;76(10):2763-72.

PMID:
15144186
19.

The Gene Ontology (GO) database and informatics resource.

Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R; Gene Ontology Consortium.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D258-61.

20.

ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins.

Puntervoll P, Linding R, Gemünd C, Chabanis-Davidson S, Mattingsdal M, Cameron S, Martin DM, Ausiello G, Brannetti B, Costantini A, Ferrè F, Maselli V, Via A, Cesareni G, Diella F, Superti-Furga G, Wyrwicz L, Ramu C, McGuigan C, Gudavalli R, Letunic I, Bork P, Rychlewski L, Küster B, Helmer-Citterich M, Hunter WN, Aasland R, Gibson TJ.

Nucleic Acids Res. 2003 Jul 1;31(13):3625-30.

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