De novo signaling pathway predictions based on protein-protein interaction, targeted therapy and protein microarray analysis

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 4532 LNBI, Issue , 2007, Pages 108-118

  Ruths, Derek ^a   Tseng, Jen Te ^b   Nakhleh, Luay ^a   Ram, Prahlad T ^b  

^a Rice University   (United States)

^b UNIVERSITY OF TEXAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL METHODS; DISEASES; GROWTH KINETICS; MICROARRAYS; PROTEINS;

EPIDERMAL GROWTH FACTOR RECEPTOR (EGFR); INTRA-CELLULAR SIGNALING NETWORKS; PHARMACOLOGICAL INHIBITION; PROTEIN-PROTEIN INTERACTION;

SIGNAL TRANSDUCTION;

EID: 38049132878     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-73060-6_8     Document Type: Conference Paper

References (22)

1. Ahuja, R., Mehlhorn, K., Tarjan, B.: Faster Algorithms for the Shortest Path Problem. Journal of Association of Computing Machinery 37, 213-223 (1990)
2. Bader, J., Chaudhuri, A., Rothberg, J., Chant, J.: Gaining confidence in high-throughput protein interaction networks. Nature Biotechnology 22(1), 78-85 (2004)
3. Belloni, E., Muenke, M., Roessier, E., Traverse, G., Siegel-Bartelt, J., Frumkin, A., Mitchell, H.F., Donis-Keller, H., Helms, C., Hing, A.V., Heng, H.H.Q., Koop, B., Martindale, D., Rommens, J.M., Tsui, L.-C., Scherer, S.W.: Identification of Sonic hedgehog as a candidate gene responsible for holopro-sencephaly. Nature Genetics 14, 353-356 (1996)
4. Deng, M., Sun, F., Chen, T.: Assessment of the reliability of protein-protein interactions and protein function prediction. In: Proceedings of the Eight Pacific Symposium on Biocomputing, pp. 140-151 (2003)
5. Eppstein, D.: Finding the k shortest paths. SIAM Journal of Computing 28(2), 652-673 (1998)
6. Feldman, D.S., Carnes, C.A., Abraham, W.T., Bristow, M.R.: Mechanisms of Disease: β-adrenergic receptors alterations in signal transduction and pharmacogenomics in heart failure. Nature Clinical Practice Cardiovascular Medicine 2, 475-483 (2005)
7. Hennessy, B.T., Smith, D.L., Ram, P.T., Lu, Y., Mills, G.B.: Exploiting the PI3K-AKT pathway for cancer drug discovery. Nature Review Drug Discovery 4, 988-1004 (2005)
8. Hunter, T.: Signaling - 2000 and beyond. Cell 100(1), 113-127 (2000)
9. Hwang, D., Rust, A.G., Ramsey, S., Smith, J.J., Leslie, D.M., Weston, A.D., Atauri, P., Aitchison, J.D., Hood, L., Siegel, A.F., Bolouri, H.: A data integration methodology for systems biology. PNAS 102(48), 17296-17301 (2005)
10. Johnson, G.L., Lapadat, R.: Mitogen-activated protein kinase pathways mediated by ERK, JNK, and protein kinases. Science 1912, 38 (2002)
11. Oda, K., Matsuoka, Y., Funahashi, A., Kitano, H.: A comprehensive pathway map of epidermal growth factor signaling. Molecular Systems Biology, msb41000014-El-E17 (2005)
12. Pagel, P., Kovac, S., Oesterheld, M., Brauner, B., Dunger-Kalthenbach, I., Frishman, G., Montrone, C., Mark, P., Stumpflen, V., Mewes, H., Reupp, A., Frishman, D.: The MIPS mammalian protein-protein interaction database. Bioinformatics 21(6), 832-834 (2005)
13. Pascoal, M., Martins, E.: A new implementation of Yen's ranking loopless paths algorithm. Quarterly Journal of the Belgian, French, and Italian Operations Research Societies 1(2), 121-134 (2003)
14. Ruths, D., Nakhleh, L., Iyengar, M.S., Reddy, S.A.G., Ram, P.T.: Graph-theoretic Hypothesis Generation in Biological Signaling Networks. Journal of Computational Biology 13(9), 1546-1557 (2006)
15. Scott, J., Ideker, T., Karp, R.M., Sharan, R.: Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks. In: McLysaght, A., Huson, D.H. (eds.) RECOMB 2005. LNCS (LNBI), vol. 3678, pp. 1-13. Springer, Heidelberg (2005)
16. Sharan, R., Suthram, S., Kelly, R.M., Kuhn, T., McCuine, S., Uetz, P., Sittler, T., Karp, R.M., Ideker, T.: Conserved patterns of protein interaction in multiple species. PNAS 102(6), 1974-1979 (2005)
17. Uhlik, M.T., Abell, A.N., Cuevas, B.D., Nakamura, K., Johnson, G.L.: Wiring diagrams of MAPK regulation by MEKK1, 2, and 3. Biochem. Cell Biol. 82(6), 658-663 (2004)
18. von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S.G., Fields, S., Bork, P.: Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417, 399-403 (2002)
19. von Mering, C., Heynen, M., Jaeggi, D., Schmidt, S., Bork, P., Snel, B.: STRING: a database of predicted functional associations between proteins. Nucleic Acids Research 31(1), 258-261 (2003)
20. Yeang, C.H., Ideker, T., Jaakkola, T.: Physical network models. Journal of Computational Biology 11, 243-262 (2004)
21. Yeang, C.H., Mak, H.C., McCuine, S., Workman, C., Jaakkola, T., Ideker, T.: Validation and refinement of gene regulatory pathways on a network of physical interactions. Genome Biology 6(7), R62 (2005)
22. Yen, J. Y.: Finding the K Shortest Loopless Paths in a Network. Management Science 17(11), 712-716 (1971)