A clustering genetic algorithm for genomic data mining

Studies in Computational Intelligence

Volumn 204, Issue , 2009, Pages 249-275

  Tapia, José Juan ^a   Morett, Enrique ^a   Vallejo, Edgar E ^b  

^a SCHOOL OF ENGINEERING AND SCIENCES   (Mexico)

^b UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO   (Mexico)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 65549141611     PISSN: 1860949X     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-3-642-01088-0_11     Document Type: Article

References (40)

1. Bork, P., DandeFer, T., et al.: Predicting function: from genes to genomes and back. J. Mol. Biol. 283, 707-725 (1998)
2. Coello-Coello, C., et al.: Evolutionary Algorithms for Solving Multi Objective Problems. Kluwer Academic Publishers, Dordrecht (2002)
3. Curteanu, S., Leon, F., Galea, D.: Alternatives for Multi-objective Optimization of a Polymerization Process. J. Applied Polymer Science (2006)
4. Deb, K., Reddy, A.R.: Reliable Classification of Two-Class Cancer Data Using Evolutionary Algorithms. Biosystems 72(1-2), 111-129 (2003)
5. Duester, G., Campen, R., et al.: Nucleotide sequence of an Escherichia coli tRNA (Leu 1) operon and identification of the transcription promoter signal. Nucleic Acids Research 9, 2121-2139 (1981)
6. Eisenberg, D., Marcotte, E., et al.: Protein function in the post-genomic era. Nature 405, 823-826 (2000)
7. Facelli, K., de Souto, M.: Multi-objective Clustering Ensemble. In: Proceedings of the Sixth International Conference on Hybrid Intelligent Systems (2006)
8. Fernández, J.C., Vallejo, E.E., Morett, E.: Fuzzy-C means for inferring functional coupling of proteins from their phylogenetic profiles. In: Ashlock, D., et al. (eds.) IEEE Computational Intelligence in Bioinformatics and Computational biology. IEEE Computer Society Press, Los Alamitos (2006)
9. Goldberg, D.E., Korb, B., Deb, K.: Messy genetic algorithms: Motivation, analysis, and first results. In: Complex Systems, pp. 493-530 (1989)
10. Holland, J.H.: Adaptation in Natural and Artificial Systems. An introduction. University of Michigan Press (1975)
11. Horn, J., et al.: Fitness Sharing and Niching Methods Revisited. IEEE Transactions on Evolutionary Computation, 82-87 (1994)
12. Huynen, M., Snel, B., et al.: Predicting Protein Function by genomic context: Quantitative evaluation and qualitative inferences. Genomic Research 10(8), 1204-1210 (2000)
13. Jang, J.S.R., Sun, C.T., et al.: Neuro-fuzzy and soft-computing. Prentice Hall, Englewood Cliffs (1997)
14. Jensen, L.J., Kuhn, M., et al.: STRING 8-a global view on proteins and their functional interactions in 630 organisms. In: Ashlock, D., et al. (eds.) Pubmed (2009)
15. Lin, C., Wang, M.: Genetic-clustering algorithm for intrusion detection system. International Journal of Information and Computer Security 2(2), 218-234 (2008)
16. Marcotte, E.: CompFtational genetics: finding protein function by nonhomology methods. Current Option in Structural Biology 10, 359-365 (2000)
17. Mandal, C., Gudi, R.D., Suraishkumar, G.K.: Multi-Objective Optimization in Aspergillus Niger Fermentation for Selective Product Enhancement. Bioprocess and Biosystems Eng. 28, 149-164 (2005)
18. Marcotte, E., Xenarios, I., et al.: Localizing proteins in the cell from their phylogenetic profiles. In: PNAS, vol. 97, pp. 12115-12120 (2000)
19. von Mering, C., et al.: STRING 7-recent developments in the integration and prediction of protein interactions. Nuclear Acid Res., D358-D362 (January 2007)
20. Milano., M., et al.: A Clustering Genetic Algorithm for Actuator Optimization in Flow Control. In: Proceedings of the 2nd NASA/DoD workshop on Evolvable Hardware (2000)
21. CiGia, R., Abreu-Goodger, C., Morett, E., Merino, E.: GeConT: gene context analysis. Bioinformatics 20, 2307-2308 (2004)
22. Pellegrini, M., Marcotte, E., et al.: Assigning protein function by comparative genome analysis: Protein phylogenetic profiles. In: PNAS, vol. 96, pp. 4285-4288 (1999)
23. Sali, A.: Funtional links between proteins. Nature 402, 23-26 (1999)
24. Sareni, B., Laurent, K.: Fitness Sharing and Niching Methods Revisited. IEEE Transactions on Evolutionary Computation, 97-108 (1998)
25. Sun, J., Xu, J., et al.: Refined phylogenetic profiles method for predicting protein-protein interactions. Bioinformatics 21, 3409-3415 (2005)
26. Vert, J.F.: A tree kernel to analyze phylogenetic profiles. Bioinformatics 18, S276-S284 (2002)
27. Marcotte, E., Pellegrini, M., et al.: A combined algorithm for genomewide prediction of protein function. Nature 402, 83-86 (1999)
28. Karp, P.D., Keseler, I.M., et al.: Multidimensional annotation of the Escherichia coli K-12 genome. Nucleic Acids Research (2007)
29. Salwinski, L., Miller, C.S., et al.: The Database of Interacting Proteins: Update. NAR 32(Database issue), D449-D451 (2004)
30. Falkenaeur, E.: Genetic algorithms and grouping problems. Wiley, Chichester (c1998)
31. Sammon, J.: A Nonlinear Mapping for Data Structure Analysis. IEEE Transactions on Computers c18, 401-409 (1969)
32. Someren, E.P., et al.: Multi-Criterion Optimization for Genetic Network Modeling. Signal Processing 83, 763-775 (2003)
33. Tapia, J.J., Vallejo, E.E.: A Clustering Genetic Algorithm for Inferring Protein-Protein Functional Interactions from Phylogenetic Profiles. In: 2008 IEEE World Congress on Computational Intelligence (2008)
34. Tatusov, R.LN, Natale, D.A., et al.: The COG database: new developments in phylogenetic classification of protein from complete genomes. Nucletic Acids Research 29(1), 22-28 (2001)
35. Tatusov, R.L., Koonin, E.V., et al.: A genomic perspective on protein families. Science 278, 631-637 (1997)
36. Tatusov, R.LA, Fedorova, N.D., et al.: The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4, 41-54 (2003)
37. Watanabe, R.L.A., Morett, E., Vallejo, E.E.: Inferring modules of functionally interacting proteins using the Bond Energy Algorithm. BMC Bioinformatics 9, 285 (2008)
38. Wren, J.: The emerging in silico scientist how text-based bioinformatics is bridging biology and artificial intelligence. IEEE Engineering in Medicine and Biology Magazine, 87-93 (2004)
39. Wu, J., Kasif, S., et al.: Identification of functional links between genes using phylogenetic profiles. Bioinformatics 19, 1524-1530 (2003)
40. Wu, F.X.: Genetic weighted k-means algorithm for clustering large-scale gene expression data. BMC Bioinformatics 28(suppl. 6), S12 (2008)