Fusing time series expression data through hybrid aggregation and hierarchical merge

Bioinformatics

Volumn 24, Issue 16, 2008, Pages

  Tsiporkova, Elena ^a   Boeva, Veselka ^b  

^a House of Economy   (Belgium)

^b TECHNICAL UNIVERSITY OF SOFIA   (Bulgaria)

Author keywords

[No Author keywords available]

Indexed keywords

CELL CYCLE PROTEIN; CELL CYCLE PROTEIN 22; CELL CYCLE PROTEIN 6; CYCLINE; FUNGAL DNA; HISTONE; KINESIN; PROTEIN KINASE INHIBITOR; REPLICATION LICENSING FACTOR CDT2; TRANSCRIPTION FACTOR;

CELL CYCLE REGULATION; CELL SYNCHRONIZATION; CLUSTER ANALYSIS; CONFERENCE PAPER; CONTROLLED STUDY; DNA REPLICATION; DOWN REGULATION; FALSE POSITIVE RESULT; GENE CLUSTER; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC ALGORITHM; MATHEMATICAL COMPUTING; NONHUMAN; PRIORITY JOURNAL; RETROPOSON; SCHIZOSACCHAROMYCES POMBE; SEQUENCE ALIGNMENT; TIME SERIES ANALYSIS; TRANSPOSON; UPREGULATION;

EID: 49549089568     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn264     Document Type: Conference Paper

References (20)

1. Aach,J. and Church,G.M. (2001) Aligning gene expression time series with time warping algorithms. Bioinformatics, 17, 495-508.
2. Choi,J.K., et al. (2003) Combining multiple microarray studies and modeling interstudy variation. Bioinformatics, 19 (Suppl. 1), i84-i90.
3. Choi,H. et al. (2007) A latent variable approach for meta-analysis of gene expression data from multiple microarray experiments. BMC Bioinformatics, 8, 364.
4. Conlon,E.M. et al. (2006) Bayesian models for pooling microarray studies with multiple sources of replications. BMC Bioinformatics, 7, 247.
5. Criel,J. and Tsiporkova,E. (2006) Gene Time Expression Warper: A tool for alignment, template matching and visualization of gene expression time series. Bioinformatics, 22, 251-252.
6. de Lichtenberg,U. et al. (2004) Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics, 21, 1164-1171.
7. Fodor,J.C. and Roubens,M. (1994) Fuzzy Preference Modelling and Multicriteria Decision Support. Kluwer Academic Publishers, Dordrecht.
8. Gilks,W.R. et al. (2005) Fusing microarray experiments with multivariate regression. Bioinformatics, 21, ii137-ii143.
9. Hermans,F. and Tsiporkova,E. (2007) Merging microarray cell synchronization experiments through curve alignment. Bioinformatics 23, e64-e70.
10. Oliva,A. et al. (2005) The cell cycle-regulated genes of Schizosaccharomyces pombe. PLOS, 3, 1239-1260.
11. Peng,X. et al. (2005) Identification of cell cycle-regulated genes in fission yeast. Mol. Biol. Cell 16, 1026-1042.
12. Rustici,G. et al. (2004) Periodic gene expression program of the fission yeast cell cycle. Nat. Genet., 36, 809-817.
13. Sakoe,H. and Chiba,S. (1978) Dynamic programming algorithm optimization for spoken word recognition. IEEE Trans. Acoust., ASSP-26, 43-49.
14. Sankoff,D. and Kruskal,J. (1983) Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison. Addison Wesley, Reading, MA.
15. Thompson,J.D. et al. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
16. Tsiporkova,E. and Boeva,V. (2004) Nonparametric recursive aggregation process, Kybernetika. J. Czech Soc. Cybern. Inf. Sci., 40, 51-70.
17. Tsiporkova,E. and Boeva,V. (2006) Multi-step ranking of alternatives in a multi-criteria and multi-expert decision making environment. Inf. Sci., 176, 2673-2697.
18. Tsiporkova,E. and Boeva,V. (2007a) Modelling and simulation of the genetic phenomena of additivity and dominance via gene networks of parallel aggregation processes. In Hochreiter,S. and Wagner,R. (eds.) Bioinformatics Research and Development. Lecture Notes in Bioinformatics. Springer-Verlag, Vol. 4414, pp. 199-211.
19. Tsiporkova,E. and Boeva,V. (2007b) Two-pass imputation algorithm for missing value estimation in gene expression time series. J. Bioinform. Comput. Biol., 5, 1005-1022.
20. Zaykin,D.V. et al. (2007) Combining p-values in large-scale genomics experiments. Pharm. Stat., 6, 217-226.