An algorithmic framework for predicting side-effects of drugs

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

Volumn 6044 LNBI, Issue , 2010, Pages 1-14

  Atias, Nir ^a   Sharan, Roded ^a  

^a TEL AVIV UNIVERSITY   (Israel)

Author keywords

Canonical correclation analysis; Drug targets; Network diffusion; Prediction

Indexed keywords

ALGORITHMIC FRAMEWORK; CANONICAL CORRECLATION ANALYSIS; CANONICAL CORRELATION ANALYSIS; COMPUTATIONAL APPROACH; CROSS VALIDATION; DATA SETS; DRUG DEVELOPMENT; DRUG LEADS; DRUG TARGETS; NETWORK DIFFUSION; NETWORK-BASED; PREDICTION; SIDE EFFECT;

DIFFUSION; FORECASTING; MOLECULAR BIOLOGY; MOLECULAR STRUCTURE;

DRUG INTERACTIONS;

EID: 78650273194     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-12683-3_1     Document Type: Conference Paper

References (25)

1. Lamb, J., Crawford, E., Peck, D., Modell, J., Blat, I., Wrobel, M., Lerner, J., Brunet, J., Subramanian, A., Ross, K., Reich, M., Hieronymus, H., Wei, G., Armstrong, S., Haggarty, S., Clemons, P., Wei, R., Carr, S., Lander, E., Golub, T.: The connectivity map: using gene-expression signatures to connect small molecules, genes, and disease. Science 313(5795), 1929-1935 (2006).
2. Campillos, M., Kuhn, M., Gavin, A., Jensen, L., Bork, P.: Drug target identification using side-effect similarity. Science 321(5886), 263-266 (2008).
3. Billingsley, M.: Druggable targets and targeted drugs: enhancing the development of new therapeutics. Pharmacology 82(4), 239-244 (2008).
4. Moore, T., Cohen, M., Furberg, C.: Serious adverse drug events reported to the food and drug administration, 1998-2005. Arch. Intern. Med. 167(16), 1752-1759 (2007).
5. Xie, L., Li, J., Bourne, P.: Drug discovery using chemical systems biology: identification of the protein-ligand binding network to explain the side effects of cetp inhibitors. PLoS Comput. Biol. 5(5), e1000387 (2009).
6. Need, A., Motulsky, A., Goldstein, D.: Priorities and standards in pharmacogenetic research. Nat. Genet. 37(7), 671-681 (2005).
7. Oti, M., Snel, B., Huynen, M.A., Brunner, H.G.: Predicting disease genes using protein-protein interactions. J. Med. Genet. 43(8), 691-698 (2006).
8. Franke, L., van Bakel, H., Fokkens, L., de Jong, E.D., Egmont-Petersen, M., Wijmenga, C.: Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. Am. J. Hum. Genet. 78(6), 1011-1025 (2006).
9. Kohler, S., Bauer, S., Horn, D., Robinson, P.N.: Walking the interactome for prioritization of candidate disease genes. Am. J. Hum. Genet. 82(4), 949-958 (2008).
10. Vanunu, O., Sharan, R.: A propagation-based algorithm for inferring gene-disease assocations. In: German Conference on Bioinformatics, pp. 54-52 (2008).
11. Wu, X., Jiang, R., Zhang, M.Q., Li, S.: Network-based global inference of human disease genes. Mol. Syst. Biol. 4, 189 (2008).
12. Yildirim, M.A., Goh, K.I., Cusick, M.E., Barabasi, A.L., Vidal, M.: Drug-target network. Nat. Biotechnol. 25(10), 1119-1126 (2007).
13. Yang, L., Xu, L., He, L.: A citationrank algorithm inheriting google technology designed to highlight genes responsible for serious adverse drug reaction. Bioinformatics 25(17), 2244-2250 (2009).
14. Kutalik, Z., Beckmann, J.S., Bergmann, S.: A modular approach for integrative analysis of large-scale gene-expression and drug-response data. Nat. Biotechnol. 26(5), 531-539 (2008).
15. Leurgans, S.E., Moyeed, R.A., Silverman, B.W.: Canonical correlation analysis when the data are curves. Journal of the Royal Statistical Society, Series B (Methodological) 55(3), 725-740 (1993).
16. Wolf, L., Donner, Y.: An experimental study of employing visual appearance as a phenotype. In: IEEE Conference on Computer Vision and Pattern Recognition, CVPR 2008, pp. 1-7 (2008).
17. Zhou, D., Bousquet, O., Lal, T.N., Weston, J., Scholkopf, B.: Learning with local and global consistency. In: Advances in Neural Information Processing Systems, vol. 16, pp. 321-328. MIT Press, Cambridge (2004).
18. Lin, W.-H., Hauptmann, A.: Merging rank lists from multiple sources in video classification. In: Proc. IEEE International Conference on Multimedia and Expo ICME 2004, vol. 3, pp. 1535-1538 (2004).
19. Kuhn, M., Campillos, M., Letunic, I., Jensen, L., Bork, P.: A side effect resource to capture phenotypic effects of drugs (submitted), http://sideeffects.embl.de/.
20. Wheeler, D.L., Barrett, T., Benson, D.A., Bryant, S.H., Canese, K., Chetvernin, V., Church, D.M., Dicuccio, M., Edgar, R., Federhen, S., Feolo, M., Geer, L.Y., Helmberg, W., Kapustin, Y., Khovayko, O., Landsman, D., Lipman, D.J., Madden, T.L., Maglott, D.R., Miller, V., Ostell, J., Pruitt, K.D., Schuler, G.D., Shumway, M., Sequeira, E., Sherry, S.T., Sirotkin, K., Souvorov, A., Starchenko, G., Tatusov, R.L., Tatusova, T.A., Wagner, L., Yaschenko, E.: Database resources of the national center for biotechnology information. Nucleic Acids Res. 36(Database issue), D13-D21 (2008).
21. Steinbeck, C., Han, Y., Kuhn, S., Horlacher, O., Luttmann, E., Willighagen, E.: The chemistry development kit (cdk): an open-source java library for chemo- and bioinformatics. J. Chem. Inf. Comput. Sci. 43(2), 493-500 (2003).
22. Steinbeck, C., Hoppe, C., Kuhn, S., Floris, M., Guha, R., Willighagen, E.L.: Recent developments of the chemistry development kit (cdk) - an open-source java library for chemo- and bioinformatics. Curr. Pharm. Des. 12(17), 2111-2120 (2006).
23. Wishart, D.S., Knox, C., Guo, A.C., Cheng, D., Shrivastava, S., Tzur, D., Gautam, B., Hassanali, M.: Drugbank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res. 36(Database issue), D901-D906 (2008).
24. Wishart, D.S., Knox, C., Guo, A.C., Shrivastava, S., Hassanali, M., Stothard, P., Chang, Z., Woolsey, J.: Drugbank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res. 34(Database issue), D668-D672 (2006).
25. Wexler, P.: Toxnet: an evolving web resource for toxicology and environmental health information. Toxicology 157(1-2), 3-10 (2001).