Soft topographic map for clustering and classification of bacteria

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

Volumn 4723 LNCS, Issue , 2007, Pages 332-343

  La Rosa, Massimo ^a   Di Fatta, Giuseppe ^b   Gaglio, Salvatore ^a,c   Giammanco, Giovanni M ^c   Rizzo, Riccardo ^a   Urso, Alfonso M ^a  

^a CNR   (Italy)

^b UNIVERSITY OF READING   (United Kingdom)

^c UNIVERSITY OF PALERMO   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; DATABASE SYSTEMS; DNA; GENES; TAXONOMIES;

EVOLUTIONARY DISTANCES; HOUSEKEEPING GENE; SOFT TOPOGRAPHIC MAP;

BACTERIA;

EID: 38049022511     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-74825-0_30     Document Type: Conference Paper

References (35)

1. Garrity, G.M., Julia, B.A., Lilburn, T.: The revised road map to the manual. In: Garrity, G.M. (ed.) Bergey's manual of systematic bacteriology, pp. 159-187. Springer, New York (2004)
2. Joliffe, I.T.: Principal Component Analysis. Springer, New York (1986)
3. Clarridge III, J.E.: Impact of 16S rRNA Gene Sequence Analysis for Identification of Bacteria on Clinical Microbiology and Infectious Diseases. Clin. Microbiol. Rev. 17, 840-862 (2004)
4. Drancourt, M., Bollet, C., Carlioz, A., Martelin, R., Gayral, J.-P., Raoult, D.: 16S Ribosomal DNA Sequence Analysis of a Large Collection of Environmental and Clinical Unidentifiable Bacterial Isolates. J. Clin. Microbiol 38, 3623-3630 (2000)
5. Drancourt, M., Berger, P., Raoult, D.: Systematic 16S rRNA Gene Sequencing of Atypical Clinical Isolates Identified 27 New Bacterial Species Associated with Humans. J. Clin. Microbiol. 42, 2197-2202 (2004)
6. Drancourt, M., Raoult, D.: Sequence-Based Identification of New Bacteria: a Proposition for Creation of an Orphan Bacterium Repository. J. Clin. Microbiol. 43, 4311-4315 (2005)
7. Oja, M., Somervuo, P., Kaski, S., Kohonen, T.: Clustering of human endogenous retrovirus sequences with median self-organizing map. In: WSOM'03. Workshop on Self-Organizing Maps (9-14 September 2003)
8. Butte, A.J., Kohane, I.S.: Mutual information relevance networks: functional genomics clustering using pairwise entropy measurements. In: Proc. Pacific Symposium on Biocomputing, vol. 5, pp. 415-426 (2000)
9. Somervuo, P., Kohonen, T.: Clustering and visualization of large protein sequence databases by means of an extension of the self-organizing map. In: Discovery Science. Proceedings of the Third International Conference, pp. 76-85 (2000)
10. Kohonen, T., Somervuo, P.: How to make large self-organizing maps for nonvectcrial data. Neural Networks 15(8-9), 945-952 (2002)
11. Chen, Y., Reilly, K.D., Sprague, A.P., Guan, Z.: SEQOPTICS: A Protein Sequence Clustering Method. In: First International Multi-Symposiums on Computer and Computational Sciences. IMSCCS '06, 20-24 June 2006, vol. 1, pp. 69-75 (2006)
12. Ankerst, M., Breunig, M.M., Kriegel, H.P., Sander, J.: OPTICS: Ordering Points To Identify the Clustering Structure. In: SIGMOD 1999, Proceedings ACM SIGMOD International Conference on Management of Data, Philadelphia, Pennsylvania, USA, June 1-3, 1999, pp. 49-60 (1999)
13. Remm, M., Storm, C.E.V., Sonnhammer, E.L.L.: Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. Journal of Molecular Biology 314(5), 1041-1052 (2001)
14. Altschul, S., Gish, W., Miller, W., Myers, E., Lipman, D.: Basic local alignment search tool. J. Mol. Biol. 232, 584-599 (1993)
15. http://www.ncbi.nlm.nih.gov/blast/fasta.shtml
16. Dubnov, S., El-Yaniv, R., Gdalyahu, Y., Schneidman, E., Tishby, N., Yona, G.: A new nonparametric pairwise clustering algorithm based on iterative estimation of distance profiles. Machine Learning 47, 35-61 (2002)
17. Buhmann, J., Zoller, T.: Active Learning for Hierarchical Pairwise Data Clustering, icpr, 2186 (2000)
18. Hofmann, T., Buhmann, J.M.: Hierarchical pairwise data clustering by mean-field annealing. In: Proceedings of ICANN'95, NEURON IMES'95, vol. II, pp. 197-202. EC2 & Cie (1995)
19. Graepel, T., Herbrich, R., Bollmann-Sdorra, P., Obermayer, K.: Classification on Pairwise Proximity Data. In: NIPS
20. Hofmann, T., Buhmann, J.: Multidimensional scaling and data clustering. In: Tesauro, G., Touretzky, D.S., Leen, T.K. (eds.) Advances in Neural Information Processing Systems, vol. 7, pp. 459-466. MIT Press, Cambridge, Mass (1995)
21. Klock, H., Buhmann, J.M.: Multidimensional scaling by deterministic annealing. In: Pelillo, M., Hancock, E.R. (eds.) EMMCVPR 1997. LNCS, vol. 1223, pp. 246-260. Springer, Heidelberg (1997)
22. Torgerson, W.S.: Multidimensional scaling: I. Theory and method. Psychometrika 17, 401-419 (1952)
23. Thompson, J.D., Higgins, D.G., Gibson, T.J.: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Research 22, 4673-4680 (1994)
24. Needleman, S.B., Wunsch, C.D.: J. Mol. Biol. 48, 443-453 (1970)
25. Jukes, T.H., Cantor, C.R.: Mammalian Protein Metabolism. In: Munro, H.N. (ed.) Evolution of Protein Molecules, pp. 21-132. Academic Press, New York (1969)
26. Luttrell, S.P.: A Bayesian analysis of self-organizing maps. Neural Comput. 6, 767-794 (1994)
27. Graepel, T., Burger, M., Obermayer, K.: Self-organizing maps: generalizations and new optimization techniques. Neurocomputing 21, 173-190 (1998)
28. Graepel, T., Obermayer, K.: A stochastic self organizing map for proximity data. Neural Computation 11, 139-155 (1999)
29. Hofmann, T., Buhmann, J.M.: Pairwise data clustering by deterministic annealing. IEEE Transactions on Pattern Analysis and Machine Intelligence 19, 1-14 (1997)
30. Rose, K.: Deterministic Annealing for Clustering, Compression, Classification, Regression, and Related Optimization Problems. Proc. of the IEEE 86(11), 2210-2239 (1998)
31. Kohonen, T.: Self-organizing maps. Springer, Heidelberg (1995)
32. Ultsch, A.: U*-Matrix: a Tool to visualize Clusters in high dimensional Data, Technical Report No. 36, Dept. of Mathematics and Computer Science, University of Marburg, Germany (2003)
33. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide
34. Kumar, S., Tamura, K., Nei, M.: MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Briefings in Bioinformatics 5, 150-163 (2004)
35. Rice, P., Longden, I., Bleasby, A.: EMBOSS: The European Molecular Biology Open Software Suite. Trends in Genetics 16(6), 276-277 (2000)