Evolution of the yeast protein interaction network

Proceedings of the National Academy of Sciences of the United States of America

Volumn 100, Issue 22, 2003, Pages 12820-12824

  Qint, Hong ^a   Lu, Henry H S ^b   Wu, Wei B ^a   Li, Wen Hsiung ^a  

^a UNIVERSITY OF CHICAGO   (United States)

^b NATIONAL CHIAO TUNG UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL PROTEIN;

ARTICLE; CELL FUNCTION; GENOME; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN PROTEIN INTERACTION; STATISTICAL ANALYSIS; YEAST;

DATABASES, GENETIC; EVOLUTION; FUNGI; GENOME, FUNGAL; MODELS, BIOLOGICAL; NEURAL NETWORKS (COMPUTER); PHYLOGENY; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 0242300098     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.2235584100     Document Type: Article

References (52)

1. Hartwell, L. H., Hopfield, J. J., Leibler, S. & Murray, A. W. (1999) Nature 402, C47-C52.
2. Davidson, E. H., McClay, D. R. & Hood, L. (2003) Proc. Natl. Acad. Sci. USA 100, 1475-1480.
3. Barabasi, A. L. (2002) Linked: The New Science of Networks (Perseus Publishing, Cambridge, MA).
4. Shen-Orr, S. S., Milo, R., Mangan, S. & Alon, U. (2002) Nat. Genet. 31, 64-68.
5. Podani, J., Oltvai, Z. N., Jeong, H., Tombor, B., Barabasi, A. L. & Szathmary, E. (2001) Nat. Genet. 29, 54-56.
6. Milo, R., Shen-Orr, S., Itzkovitz, S., Kashtan, N., Chklovskii, D. & Alon, U. (2002) Science 298, 824-827.
7. Ravasz, E., Somera, A. L., Mongru, D. A., Oltvai, Z. N. & Barabasi, A. L. (2002) Science 297, 1551-1555.
8. Wolf, Y. I., Karev, G. & Koonin, E. V. (2002) BioEssays 24, 105-109.
9. Wagner, A. (2001) Mol. Biol. Evol. 18, 1283-1292.
10. Fraser, H. B., Hirsh, A. E., Steinmetz, L. M., Scharfe, C. & Feldman, M. W. (2002) Science 296, 750-752.
11. Rzhetsky, A. & Gomez, S. M. (2001) Bioinformatics 17, 988-996.
12. Wagner, A. (2003) Proc. R. Soc. London Ser. B 270, 457-466.
13. Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., et al. (2000) Nature 403, 623-627.
14. Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M. & Sakaki, Y. (2001) Proc. Natl. Acad. Sci. USA 98, 4569-4574.
15. Ito, T., Tashiro, K., Muta, S., Ozawa, R., Chiba, T., Nishizawa, M., Yamamoto, K., Kuhara, S. & Sakaki, Y. (2000) Proc. Natl. Acad. Sci. USA 97, 1143-1147.
16. Tong, A. H., Drees, B., Nardelli, G., Bader, G. D., Brannetti, B., Castagnoli, L., Evangelista, M., Ferracuti, S., Nelson, B., Paoluzi, S., et al. (2002) Science 295, 321-324.
17. Tong, A. H., Evangelista, M., Parsons, A. B., Xu, H., Bader, G. D., Page, N., Robinson, M., Raghibizadeh, S., Hogue, C. W., Bussey, H., et al. (2001) Science 294, 2364-2368.
18. Woese, C. R. (2002) Proc. Natl. Acad. Sci. USA 99, 8742-8747.
19. Brown, J. R. & Doolittle, W. F. (1997) Microbiol. Mol. Biol. Rev. 61, 456-502.
20. Martin, W. & Russell, M. J. (2003) Philos. Trans. R. Soc. London B 358, 59-85.
21. Maynard Smith, J. & Szathmáry, E. (1995) The Major Transitions in Evolution (W. H. Freeman Spektrum, Oxford).
22. Kauffman, S. (1993) The Origins of Order: Self-organization and Selection in Evolution (Oxford Univ. Press, New York).
23. Corning, P. A. (1995) Syst. Res. 12, 89-121.
24. Thompson, D. W. (1917) On Growth and Form (Cambridge Univ. Press, Cambridge, U.K.).
25. Wolfram, S. (2002) A New Kind of Science (Wolfram Media, Champaign, IL).
26. Oltvai, Z. N. & Barabasi, A. L. (2002) Science 298, 763-764.
27. Gould, S. J. (2002) The Structure of Evolutionary Theory (Harvard Univ. Press, Cambridge, MA).
28. Mewes, H. W., Frishman, D., Guldener, U., Mannhaupt, G., Mayer, K., Mokrejs, M., Morgenstern, B., Munsterkotter, M., Rudd, S. & Weil, B. (2002) Nucleic Acids Res. 30, 31-34.
29. Mewes, H. W., Albermann, K., Heumann, K., Liebl, S. & Pfeiffer, F. (1997) Nucleic Acids Res. 25, 28-30.
30. von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S. G., Fields, S. & Bork, P. (2002) Nature 417, 399-403.
31. Tatusov, R. L., Koonin, E. V. & Lipman, D. J. (1997) Science 278, 631-637.
32. Tatusov, R. L., Natale, D. A., Garkavtsev, I. V., Tatusova, T. A., Shankavaram, U. T., Rao, B. S., Kiryutin, B., Galperin, M. Y., Fedorova, N. D. & Koonin, E. V. (2001) Nucleic Acids Res. 29, 22-28.
33. Cormen, T. H., Leiserson, C. E. & Rivest, R. L. (1990) Introduction to Algorithms (MIT Press, Cambridge, MA).
34. Batagelj, A. & Mrvar, A. (1998) Connections 21, 47-57.
35. Ripley, B. D. (2001) MSOR Connections 1, 23-25.
36. Page, R. D. M. (1996) Comput. Appl. Biosci. 12, 357-358.
37. Maslov, S. & Sneppen, K. (2002) Science 296, 910-913.
38. Woese, C. R. (1987) Microbiol. Rev. 51, 221-271.
39. Achenbach-Richter, L., Gupta, R., Stetter, K. O. & Woese, C. R. (1987) Syst. Appl. Microbiol. 9, 34-39.
40. Deckert, G., Warren, P. V., Gaasterland, T., Young, W. G., Lenox, A. L., Graham, D. E., Overbeek, R., Snead, M. A., Keller, M., Aujay, M., etal. (1998) Nature 392, 353-358.
41. Nelson, K. E., Clayton, R. A., Gill, S. R., Gwinn, M. L., Dodson, R. J., Haft, D. H., Hickey, E. K., Peterson, J. D., Nelson, W. C., Ketchum, K. A., et al. (1999) Nature 399, 323-329.
42. Saitou, N. & Nei, M. (1987) Mol. Biol. Evol. 4, 406-425.
43. Martin, W., Hoffmeister, M., Rotte, C. & Henze, K. (2001) Biol. Chem. 382, 1521-1539.
44. Anderberg, M. R. (1973) Cluster Analysis for Applications (Academic, New York).
45. Rives, A. W. & Galitski, T. (2003) Proc. Natl. Acad. Sci. USA 100, 1128-1133.
46. Deane, C. M., Salwinski, L., Xenarios, I. & Eisenberg, D. (2002) Mol. Cell Proteomics 1, 349-356.
47. Edwards, A. M., Kus, B., Jansen, R., Greenbaum, D., Greenblatt, J. & Gerstein, M. (2002) Trends Genet. 18, 529-536.
48. Bader, G. D. & Hogue, C. W. (2002) Nat. Biotechnol. 20, 991-997.
49. Aloy, P. & Russell, R. B. (2002) FEBS Lett. 530, 253-254.
50. Kemmeren, P., van Berkum, N. L., Vilo, J., Bijma, T., Donders, R., Brazma, A. & Holstege, F. C. (2002) Mol. Cell 9, 1133-1143.
51. Brenner, S. (1998) Science 282, 1411-1412.
52. Jeong, H., Tombor, B., Albert, R., Oltvai, Z. N. & Barabasi, A. L. (2000) Nature 407, 651-654.