Supervised classification for gene network reconstruction

Biochemical Society Transactions

Volumn 31, Issue 6, 2003, Pages 1497-1502

  Soinov, L A ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

Gene network; Microarray; Supervised learning

Indexed keywords

CONFERENCE PAPER; DATA ANALYSIS; DNA MICROARRAY; GENE EXPRESSION REGULATION; GENE NETWORK; GENETIC TRANSCRIPTION; LEARNING; MODEL; PREDICTION; PRIORITY JOURNAL;

EID: 0348136790     PISSN: 03005127     EISSN: None     Source Type: Journal    
DOI: 10.1042/bst0311497     Document Type: Conference Paper

References (40)

1. Nutt, C.L., Mani, D.R., Betensky, R.A., Tamayo, P., Cairncross, J.G., Ladd, C., Pohl, U., Hartmann, C., McLaughlin, M.E., Batchelor, T.T. et al. (2003) Cancer Res. 63, 1602-1607
2. Golub, T.R., Slonim, D.K., Tamayo, P., Huard, C., Gaasenbeek, M., Mesirov, J.P., Coller, H., Loh, M.L., Downing, J.R., Caligiuri, M.A. et al. (1999) Science 286, 531-537
3. Dyrskjot, L., Thykjaer, T., Kruhoffer, M., Jensen, J.L., Marcussen, N., Hamilton-Dutoit, S., Wolf, H. and Orntoft, T.F. (2003) Nat. Genet. 33, 90-96
4. Ramaswamy, S., Tamayo, P., Rifkin, R., Mukherjee, S., Yeang, C.H., Angelo, M., Ladd, C., Reich, M., Latulippe, E., Mesirov, J.P. et al. (2001) Proc. Natl. Acad. Sci. U.S.A. 98, 15149-15154
5. Shipp, M.A., Ross, K.N., Tamayo, P., Weng, A.P., Kutok, J.L., Aguiar, R.C., Gaasenbeek, M., Angelo, M., Reich, M., Pinkus, G.S. et al. (2002) Nat. Med. 8, 68-74
6. van't Veer, L.J., Dai, H., van de Vijver, M.J., He, Y.D., Hart, A.A., Mao, M., Peterse, H.L., van der Kooy, K., Marton, M.J., Witteveen, A.T. et al. (2002) Nature (London) 415; 530-536
7. Pavlidis, P., Weston, J., Cai, J. and Noble, W.S. (2002) J. Comput. Biol. 9, 401-411
8. Mateos, A., Dopazo, J., Jansen, R., Tu, Y., Gerstein, M. and Stolovitzky, G. (2002) Genome Res. 12, 1703-1715
9. Brown, M.P., Grundy, W.N., Lin, D., Cristianini, N., Sugnet, C.W., Furey, T.S., Ares, Jr, M. and Haussler, D. (2000) Proc. Natl. Acad. Sci. U.S.A. 97, 262-267
10. Hvidsten, T.R., Komorowski, J., Sandvik, A.K. and Laegreid, A. (2001) Pac. Symp. Biocomput. 2001, 299-310
11. Kohonen, T. (1992) Biol. Cybernetics 43, 59-69
12. Tamayo, P., Slonim, D., Mesirov, J., Zhu, Q., Kitareewan, S., Dritrovsky, E., Lander, E.S. and Golub, J.R. (1999) Proc. Natl. Acad. Sci. U.S.A. 96, 2907-2912
13. Mjolsness, E. and DeCoste, D. (2001) Science 293, 2051-2055
14. Kohavi, R. (1995) PhD Thesis, Stanford University
15. Brazma, A. and Vilo, J. (2000) FEBS Lett. 480, 17-24
16. Stolovitzky, G. (2003) Curr. Opin. Struct. Biol. 13, 370-376
17. Spellman, P.T., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Botstein, D. and Futcher, B, (1998) Mol Biol Cell. 9, 3273-3297
18. Cho, R.J., Campbell, M.J., Winzeler, E.A., Steinmetz, L., Conway, A., Wodicka, L., Wolfsberg, T.G., Gabrielian, A.E., Landsman, D., Lockhart, D.J. and Davis, R.W. (1998) Mol. Cell 2, 65-73
19. Brazma, A. (2001) Bioinformatics 17, 113-114
20. Lee, T.I., Rinaldi, N.J., Robert, F., Odom, D.T., Bar-Joseph, Z., Gerber, G.K., Hannett, N.M., Harbison, C.T., Thompson, C.M., Simon, I. et al. (2002) Science 298, 799-804
21. Quackenbush, J. (2002) Nat. Genet. 32 (suppl.), 496-501
22. Ihmels, J., Friedlander, G., Bergmann, S., Sarig, O., Ziv, Y. and Barkai, N. (2002) Nat. Genet. 31, 370-377
23. Maslov, S. and Sneppen, K. (2002) Science 296, 910-913
24. van Someren, E.P., Wessels, L.F., Backer, E. and Reinders, M.J. (2002) Pharmacogenomics 3, 507-525
25. Alm, E. and Arkin, A.P. (2003) Curr. Opin. Struct. Biol. 13, 193-202
26. Wuensche, A. (1998) Pac. Symp. Biocomput. 1998, 89-102
27. Kauffman, S.A. (1993) The Origins of Order: Self Organization and Selection in Evolution, Oxford University Press, Oxford
28. Cross, F.R., Archambault, V., Miller, M. and Klovstad, M. (2002) Mol. Biol. Cell 13, 52-70
29. Kerr, M.K. and Churchill, G.A. (2001) Proc. Natl. Acad. Sci. U.S.A. 98, 8961-8965
30. Nguyen, D.V. and Rocke, D.M. (2002) Bioinformatics 18, 1216-1226
31. Bilban, M., Buehler, L., Head, S., Desoye, G. and Quaranta, V. (2002) BMC Genomics 3, 19
32. Mukherjee, S., Tamayo, P., Rogers, S., Rifkin, R., Engle, A., Campbell, C., Golub, T.R. and Mesirov, J.P. (2003) J. Comput. Biol. 10, 119-142
33. Lyons-Weiler, J., Patel, S. and Bhattacharya, S. (2003) Genome Res. 13, 503-512
34. Pan, W. (2002) Bioinformatics 18, 546-554
35. Mitchell, T.M. (1997) Machine Learning, McGraw-Hill, Boston
36. Kohavi, R. (1995) in Proc. IJCAI-95, pp. 1137-1143, Montreal, 20-25 August
37. Ciuelziu, N., Bottani, S., Bowgine, P. and Kepes, F. (2002) Nat. Genet. 31, 60-63
38. Quinlan, J.R. (1993) C4.5 Programs for Machine Learning, Morgan Kaufmann Publishers, San Francisco
39. Witten, E.H. and Frank, E. (1999) Data Mining: Practical Machine Learning Tools and Techniques with Java Implementations, Morgan Kaufmann, San Francisco
40. Soinov, L.A., Krestyaninova, M.A. and Brazma, A. (2003) Genome Biol. 4, R6