Selecting Genotyping Oligo Probes Via Logical Analysis of Data

1. Stears, R., Martinsky, T., Schena, M.: Trends in microarray analysis. Nature Medicine 9(1), 140–145 (2003)

   Article  Google Scholar 

2. Eom, J.H., Park, S.B., Zhang, B.T.: Genetic mining of dna sequence structures for effective classification of the risk types of human papillomavirus (hpv). In: Pal, N.R., Kasabov, N., Mudi, R.K., Pal, S., Parui, S.K. (eds.) ICONIP 2004. LNCS, vol. 3316, pp. 1334–1343. Springer, Heidelberg (2004)

   Google Scholar 

3. Heller, R., Schena, M., Chai, A., Shalon, D., Bedilion, T., Gilmore, J., Woolley, D., Davis, R.: Discovery and analysis of inflammatory disease-related genes using cdna microarrays. Proceedings of the National Academy of Sciences 94, 2150–2155 (1997)

   Article  Google Scholar 

4. Liu, C.H., Ma, W.L., Shi, R., Ou, Y.Q., Zhang, B., Zheng, W.L.: Possibility of using dna chip technology for diagnosis of human papillomavirus. Journal of Biochemistry and Molecular Biology 36(4), 349–353 (2003)

   Google Scholar 

5. Lee, Y., Lee, C.K.: Classification of multiple cancer types by multicategory support vector machines using gene expression data. Bioinformatics 19(9), 1132–1139 (2003)

   Article  Google Scholar 

6. Sengupta, S., Onodera, K., Lai, A., Melcher, U.: Molecular detection and identification of influenza viruses by oligonucleotide microarray hybridization. Journal of Clinical Microbiology 41(10), 4542–4550 (2003)

   Article  Google Scholar 

7. Vernet, G.: Dna-chip technology and infectious diseases. Virus Research 82, 65–71 (2002)

   Article  Google Scholar 

8. Wang, D., Coscoy, L., Zylberberg, M., Avila, P., Boushey, H., Ganem, D., DeRisi, J.: Microarray-based detection and genotyping of viral pathogens. PNAS 99(24), 15687–15692 (2002)

   Article  Google Scholar 

9. Li, F., Stormo, G.: Selection of optimal dna oligos for gene expression arrays. Bioinformatics 17(11), 1067–1076 (2001)

   Article  Google Scholar 

10. Borneman, J., Chrobak, M., Vedova, G., Figueroa, A., Jiang, T.: Probe selection algorithms with applications in the analysis of microbial communities. Bioinformatics 17(Suppl. 1), S39–S48 (2001)

    Google Scholar 

11. Rahmann, S.: Fast large scale oligonucleotide selection using the longest common factor approach. Journal of Bioinformatics and Computational Biology 1(2), 343–361 (2003)

    Article  Google Scholar 

12. Klau, G., Rahmann, S., Schliep, A., Vingron, M., Reinert, K.: Optimal robust non-unique probe selection using integer linear programming. Bioinformatics 20 (Suppl. 1), i186–i193 (2004)

    Google Scholar 

13. Boros, E., Hammer, P., Ibaraki, T., Kogan, A., Mayoraz, E., Muchnik, I.: An implementation of logical analysis of data. IEEE Transactions on Knowledge and Data Engineering 12, 292–306 (2000)

    Article  Google Scholar 

14. Megiddo, N.: On the complexity of polyhedral separability. Discrete and Computational Geometry 3, 325–337 (1988)

    Article  MathSciNet  MATH  Google Scholar 

15. Ryoo, H., Jang, I.Y.: Milp approach to pattern generation in logical analysis of data. Machine Learning, submitted (2005)

    Google Scholar 

16. Altschul, S., Gish, W., Miller, W., Myers, E., Lipman, D.: Basic local alignment search tool. Journal of Molecular Biology 215, 403–410 (1990)

    Google Scholar 

17. Wang, X., Seed, B.: Selection of oligonucleotide probes for protein coding sequences. Bioinformatics 19(7), 796–802 (2003)

    Article  Google Scholar 

18. Cortes, C., Vapnik, V.: Support vector networks. Machine Learning 20, 273–297 (1995)

    MATH  Google Scholar 

19. Ullman, J.: Pattern Recognition Techniques. Crane, London (1973)

    Google Scholar 

20. Vapnik, V.: Statistical Learning Theory. Wiley Interscience, Hoboken (1998)

    MATH  Google Scholar 

21. Hammer, P.: Partially defined boolean functions and cause-effect relationships. In: Proceedings of the International Conference on Multi-Attribute Decision Making Via OR-Based Expert Systems (1986)

    Google Scholar 

22. Caprara, A., Fischetti, M., Toth, P.: A heuristic method for the set covering problem. Operations Research 47(5), 730–743 (1999)

    Article  MathSciNet  MATH  Google Scholar 

23. Nemhauser, G.L., Wolsey, L.A.: Integer and Combinatorial Optimization. Wiley-Interscience Series I Discrete Mathematics and Optimization. Wiley, New York (1988)

    MATH  Google Scholar 

24. Muñoz, N., Bosch, F., de Sanjosé, S., Herrero, R., Castellsagué, X., Shah, K., Snijders, P., Meijer, C.J.L.M., for the International Agency for Research on Cancer Multicenter Cervical Cancer Study Group: Epidemiologic classification of human papillomavirus types associated with cervical cancer. The New England Journal of Medicine 348(6), 518–527 (2003)

    Article  Google Scholar 

25. Bosch, F., Lorincz, A., Muñoz, N., Meijer, C., Shah, K.: The causal relation between human papillomavirus and cervical cancer. Journal of Clinical Pathology 55, 244–265 (2002)

    Google Scholar 

26. McFadden, S., Schumann, L.: The role of human papillomavirus in screening for cervical cancer. Journal of the American Academy of Nurse Practitioners 13, 116–125 (2001)

    Article  Google Scholar 

27. Park, S.B., Hwang, S.H., Zhang, B.T.: Classification of the risk types of human papillomavirus by decision trees. In: Liu, J., Cheung, Y.-m., Yin, H. (eds.) IDEAL 2003. LNCS, vol. 2690, pp. 540–544. Springer, Heidelberg (2003)

    Google Scholar 

28. Snijder, E., Bredenbeek, P., Dobbe, J., Thiel, V., Ziebuhr, J., Poon, L., Guan, Y., Rozanov, M., Spaan, W., Gorbalenya, A.: Unique and conserved features of genome and proteome of sars-coronavirus, an early split-off from the coronavirus group 2 lineage. Journal of Molecular Biology 331, 991–1004 (2003)

    Article  Google Scholar 

29. Koopmans, M., Wilbrink, B., Conyn, M., Natrop, G., van der Nat, H., Vennema, H., Meijer, A., van Steenbergen, J., Fouchier, R., Osterhaus, A., Bosman, A.: Transmission of h7n7 avian influenza a virus to human beings during a large outbreak in commercial poultry farms in the netherlands. Lancet 363, 587–593 (2004), http://www.thelancet.com

    Article  Google Scholar 

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