PCA and K-Means decipher genome

Lecture Notes in Computational Science and Engineering

Volumn 58, Issue , 2008, Pages 309-323

  Gorban, Alexander N ^a,c   Zinovyev, Andrei Y ^b,c  

^a UNIVERSITY OF LEICESTER   (United Kingdom)

^b INSTITUT CURIE   (France)

^c INSTITUTE OF COMPUTATIONAL MODELING   (Russian Federation)

Author keywords

Bioinfomatics; Clustering; Cryptography; Data visualization; Principal component analysis

Indexed keywords

BACTERIAL GENOMES; BIOINFOMATICS; CLUSTERING; GENOMIC SEQUENCE; K-MEANS; K-MEANS CLUSTERING; UNDERGRADUATE STUDENTS;

BIOINFORMATICS; CLUSTER ANALYSIS; CRYPTOGRAPHY; DATA VISUALIZATION; STUDENTS; VISUALIZATION;

PRINCIPAL COMPONENT ANALYSIS;

EID: 78651594912     PISSN: 14397358     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-3-540-73750-6_14     Document Type: Conference Paper

References (18)

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8. Zinovyev, A.: Visualizing the spatial structure of triplet distributions in genetic texts. HES Preprint, M/02/28 (2003) Online: http://www.ihes.fr/ PREPRINTS/M02/Resu/resu-M02-28.html
9. Gorban, A.N., Zinovyev, A.Yu., and Popova, T.G.: Statistical approaches to the automated gene identification without teacher, Institut des Hautes Etudes Scientiques. IHES Preprint, M/01/34 (2001) Online: http://www.ihes.fr website. (See also e-print: http://arxiv.org/abs/physics/0108016)
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11. Gorban, A., Zinovyev, A., and Popova, T.: Seven clusters in genomic triplet distributions In Silico Biology, 3, 0039 (2003) (Online: http://arxiv.org/abs/condmat/0305681 and http://cogprints.ecs.soton.ac.uk/ archive/00003077/)
12. Gorban, A.N., Popova, T.G., and Zinovyev, A.Yu.: Codon usage trajectories and 7-cluster structure of 143 complete bacterial genomic sequences. Physica A, 353, 365-387 (2005)
13. Ou, H.Y., Guo, F.B., and Zhang, C.T.: Analysis of nucleotide distribution in the genome of Streptomyces coelicolor A3(2) using the Z curve method, FEBS Lett. 540 (1-3), 188-194 (2003)
14. Cluster structures in genomic word frequency distributions. Web-site with supplementary materials. http://www.ihes.fr/̃zinovyev/7clusters/index.htm
15. Gorban, A.N., Zinovyev, A.Yu., and Popova, T.G.: Four basic symmetry types in the universal 7-cluster structure of 143 complete bacterial genomic sequences. In Silico Biology 5 (2005) 0025. On-line: http://www.bioinfo. de/isb/2005/05/0025/
16. Staden, R. and McLachlan, A.D.: Codon preference and its use in identifying protein coding regions in long DNA sequences. Nucleic Acids Res 10 (1), 141-56 (1982)
17. Gorban, A.N., Zinovyev, A.Y., and Wunsch, D.C.: Application of The Method of Elastic Maps In Analysis of Genetic Texts, In Proceedings of International Joint Conference on Neural Networks (IJCNN'03), Portland, Oregon (2003)
18. Gorban, A.N., Sumner, N.R., and Zinovyev, A.Y.: Elastic maps and nets for approximating principal manifolds and their application to microarray data visualization, In this book.