Inventories to insights

Journal of Cell Biology

Volumn 161, Issue 3, 2003, Pages 465-469

  Aitchison, John D ^a   Galitski, Timothy ^a  

^a INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL CYCLE; CYTOLOGY; GENE EXPRESSION REGULATION; GENOME; PHENOTYPE; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN LOCALIZATION; SHORT SURVEY;

ANIMALS; CELL COMPARTMENTATION; COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION; HUMANS; MODELS, BIOLOGICAL; MOLECULAR BIOLOGY; NEURAL NETWORKS (COMPUTER); OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEINS;

EID: 0038273912     PISSN: 00219525     EISSN: None     Source Type: Journal    
DOI: 10.1083/jcb.200302041     Document Type: Short Survey

References (29)

1. Aebersold, R., and M. Mann. 2003. Mass spectrometry-based proteomics. Nature. 422:198-207.
2. Arkin, A.P. 2001. Synthetic cell biology. Curr. Opin. Biotechnol. 12:638-644.
3. Bell, A.W., M.A. Ward, W.P. Blackstock, H.N. Freeman, J.S. Choudhary, A.P. Lewis, D. Chotai, A. Fazel, J.N. Gushue, J. Paiement, et al. 2001. Proteomics characterization of abundant Golgi membrane proteins. J. Biol. Chem. 276:5152-5165.
4. Davidson, E.H., J.P. Rast, P. Oliveri, A. Ransick, C. Calestani, C.H. Yuh, T. Minokawa, G. Amore, V. Hinman, C. Arenas-Mena, et al. 2002. A genomic regulatory network for development. Science. 295:1669-1678.
5. Ficarro, S.B., M.L. McCleland, P.T. Stukenberg, D.J. Burke, M.M. Ross, J. Shabanowirz, D.F. Hunt, and F.M. White. 2002. Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat. Biotechnol. 20:301-305.
6. Garin, J., R. Diez, S. Kieffer, J.F. Dermine, S. Duclos, E. Gagnon, R. Sadoul, C. Rondeau, and M. Desjardins. 2001. The phagosome proteome: insight into phagosome functions. J. Cell Biol. 152:165-180.
7. Gavin, A.C., M. Bosche, R. Krause, P. Grandi, M. Marzioch, A. Bauer, J. Schultz, J.M. Rick, A.M. Michon, C.M. Cruciat, et al. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature. 415:141-147.
8. Ge, H., Z. Liu, G.M. Church, and M. Vidal. 2001. Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat. Genet. 29:482-486.
9. Griffin, T.J., S.P. Gygi, T. Ideker, B. Rist, J. Eng, L. Hood, and R. Aebersold. 2002. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol Cell. Proteomics. 1:323-333.
10. Guet, C.C., M.B. Elowitz, W. Hsing, and S. Leibler. 2002. Combinatorial synthesis of genetic networks. Science. 296:1466-1470.
11. Gygi, S.P., and R. Aebersold. 2000. Mass spectrometry and proteomics. Curr. Opin. Chem. Biol. 4:489-494.
12. Gygi, S.P., B. Rist, S.A. Gerber, F. Turecek, M.H. Gelb, and R. Aebersold. 1999. Quantitative analysis of complex protein mixtures using isotope-coded affiniry tags. Nat. Biotechnol. 17:994-999.
13. Hartwell, L.H., J.J. Hopfield, S. Leibler, and A.W. Murray. 1999. From molecular to modular cell biology. Nature. 402:C47-C52.
14. Hirabayashi, J., T. Hashidate, Y. Arata, N. Nishi, T. Nakamura, M. Hirashima, T. Urashima, T. Oka, M. Futai, W.E. Muller, et al. 2002. Oligosaccharide specificity of galectins: a search by frontal affinity chromatography. Biochim. Biophys. Acta. 1572:232-254.
15. Ho, Y., A. Gruhler, A. Heilbut, G.D. Bader, L. Moore, S.L. Adams, A. Millar, P. Taylor, K. Bennett, K. Boutilier, et al. 2002. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature. 415:180-183.
16. Ideker, T., V. Thorsson, J.A. Ranish, R. Christmas, J. Buhler, J.K. Eng, R. Bumgarner, D.R. Goodlett, R. Aebersold, and L. Hood. 2001. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science. 292:929-934.
17. Ideker, T., O. Ozier, B. Schwikowski, and A.F. Siegel. 2002. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformarics. 18(Suppl. 1):S233-S240.
18. Ito, T., T. Chiba, R. Ozawa, M. Yoshida, M. Hattori, and Y. Sakaki. 2001. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA. 98:4569-4574.
19. Kumar, A., and M. Snyder. 2001. Emerging technologies in yeast genomics. Nat. Rev. Genet. 2:302-312.
20. Kumar, A., S. Agarwal, J.A. Heyman, S. Matson, M. Heidtman, S. Piccirillo, L. Umansky, A. Drawid, R. Jansen, Y. Liu, et al. 2002. Subcellular localization of the yeast proteome. Genes Dev. 16:707-719.
21. Lee, T.I., N.J. Rinaldi, F. Robert, D.T. Odom, Z. Bar-Joseph, G.K. Gerber, N.M. Hannett, C.T. Harbison, C.M. Thompson, I. Simon, et al. 2002. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science. 298:799-804.
22. McLachlin, D.T., and B.T. Chait. 2001. Analysis of phosphorylated proteins and peptides by mass spectrometry. Curr. Opin. Chem. Biol. 5:591-602.
23. Neubauer, G., A. Gottschalk, P. Fabrizio, B. Seraphin, R. Luhrmann, and M. Mann. 1997. Identification of the proteins of the yeast U1 small nuclear ribonucleoprotein complex by mass spectrometry. Proc. Natl. Acad. Sci. USA. 94:385-390.
24. Rives, A.W., and T. Galitski. 2003. Modular organization of cellular networks. Proc. Natl. Acad. Sci. USA. 100:1128-1133.
25. Rout, M.P., J.D. Aitchison, A. Suprapto, K. Hjertaas, Y. Zhao, and B.T. Chait. 2000. The yeast nuclear pore complex: composition, architecture, and transport mechanism. J. Cell Biol. 148:635-651.
26. Shoemaker, D.D., D.A. Lashkari, D. Morris, M. Mittmann, and R.W. Davis. 1996. Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy. Nat. Genet. 14:450-456.
27. Smith, J.J., M. Marelli, R.H. Christmas, F.J. Vizeacoumar, D.J. Dilworth, T. Ideker, T. Galitski, K. Dimitrov, R.A. Rachubinski, and J.D. Aitchison. 2002. Transcriptome profiling to identify genes involved in peroxisome assembly and function. J. Cell Biol. 158:259-271.
28. Tong, A.H., M. Evangelista, A.B. Parsons, H. Xu, G.D. Bader, N. Page, M. Robinson, S. Raghibizadeh, C.W. Hogue, H. Bussey, et al. 2001. Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science. 294: 2364-2368.
29. Uetz, P., L. Giot, G. Cagney, T.A. Mansfield, R.S. Judson, J.R. Knight, D. Lockshon, V. Narayan, M. Srinivasan, P. Pochart, et al. 2000. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature. 403:623-627.