Symmetric time warping, Boltzmann pair probabilities and functional genomics

Journal of Mathematical Biology

Volumn 53, Issue 1, 2006, Pages 135-161

  Clote, Peter ^a   Straubhaar, Jürg ^b  

^a BOSTON COLLEGE   (United States)

^b UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

Author keywords

Boltzmann partition function; Gene expression data; Time series; Time warping

Indexed keywords

CELL CYCLE PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BIOLOGICAL MODEL; GENE EXPRESSION PROFILING; GENETICS; GENOMICS; HUMAN; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SACCHAROMYCES CEREVISIAE; SEQUENCE ALIGNMENT;

ALGORITHMS; AMINO ACID SEQUENCE; BASE SEQUENCE; CELL CYCLE PROTEINS; GENE EXPRESSION PROFILING; GENOMICS; HUMANS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE ALIGNMENT;

EID: 33745434025     PISSN: 03036812     EISSN: 14321416     Source Type: Journal    
DOI: 10.1007/s00285-006-0379-1     Document Type: Article

References (17)

1. Aach, J., Church, G.: Aligning gene expression time series with time warping algorithms. Bioinformatics 17 (6), 495-508 (2001)
2. Clote, P., Backofen, R.: Computational Molecular Biology: An Introduction. John Wiley & Sons, 2000 286 pages
3. Eisen, M.B., Spellman, P.T., Brown, P.O., Botstein, D.: Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95, 14863-14868 (1998)
4. Spellman, P., et al.: Comprehensive identification of cell cycle-regulated genes of the yeast saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 9, 3273-3297 (1998)
5. Cho, R., et al.: A genome-wide transcriptional analysis of the mitotic cell cycle. Molecular Cell 2, 65-73 (1998)
6. Cho, R. et al.: Transcriptional regulation and function during the human cell cycle. Nature Genetics 27, 48-54 (2001)
7. Kruskal, J.B., Liberman, M.: The symmetric time-warping problem: From continuous to discrete. In: Kruskal, J.B., Sankoff, D. (eds.), Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison, CSLI Publications,Stanford, 1999, pp. 125-161 Text originally published by Addison-Wesley in 1983
8. McCaskill, J.S.: The equilibrium partition function and base pair binding probabilities for rna secondary structure. Biopolymers 29, 1105-1119 (1990)
9. Mückstein, U., Hofacker, I., Stadler, P.: Stochastic pairwise alignments. Bioinformatics 18, S153-S160 (2002)
10. Myazawa, S.: A reliable sequence alignment method based on probabilities of residue correspondences. Protein Eng. 8, 999-1009 (1994)
11. Needleman, S.B., Wunsch, C.D.: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Bio. 48, 443-453 (1970)
12. Smith, T.F., Waterman, M.S.: Identification of common molecular subsequences. J. Mol. Biol. 147, 195-197 (1981)
13. Vingron, M., Argos, P.: Determination of reliable regions in protein sequence alignments. Protein Eng. 3 (7), 565-569 (1990)
14. Waterman, M.S.: Introduction to Computational Biology - Maps, Sequences and Genomes. Chapman & Hall, 1995
15. Xia, T., Jr., SantaLucia, J., Burkard, M.E., Kierzek, R., Schroeder, S.J., Jiao, X., Cox, C., Turner, D.H.: Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry 37, 14719-35 (1999)
16. Zuker, M.: Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31 (13), 3406-3415 (2003)
17. Zuker, M., Stiegler, P.: Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 9, 133-148 (1981)