SEARCH

SEARCH BY CITATION

References

  • Asai, K., Hayamizu, S. and Handa, K. (1993) Prediction of protein secondary structure by the hidden Markov model. Comput. Appl. Biosci. 9, 141146.
  • Florea, L., Hartzell, G., Zhang, Z., Rubin, G.M. and Miller, W. (1998) A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res. 8, 967974.
  • Hollander, M. and Wolfe, D.A. (1999) Nonparametric Statistical Methods, 2nd edn. John Wiley and Sons, Inc, New Jersey.
  • Kapranov, P., Cawley, S.E., Drenkow, J., Bekiranov, S., Strausberg, R.L., Fodor, S.P. and Gingeras, T.R. (2002) Large-scale transcriptional activity in chromosomes 21 and 22. Science, 296, 916919.
  • Krogh, A., Brown, M., Mian, I.S., Sjolander, K. and Haussler, D. (1994) Hidden Markov models in computational biology. Applications to protein modeling. J. Mol. Biol. 235, 15011531.
  • Lukashin, A.V. and Borodovsky, M. (1998) GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res. 26, 11071115.
  • Okazaki, Y., Furuno, M., Kasukawa, T. et al. (2002) Analysis for the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature, 420, 563573.
  • Rinn, J.L., Euskirchen, G., Bertone, P. et al. (2003) The transcriptional activity of human chromosome 22. Genes Dev. 17, 529540.
  • Schoof, H., Ernst, R., Nazarov, V., Pfeifer, L., Mewes, H.W. and Mayer, K.F. (2004) MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics. Nucleic Acids Res. 32, D373376.
  • Shoemaker, D.D., Schadt, E.E., Armour, C.D. et al. (2001) Experimental annotation of the human genome using microarray technology. Nature, 409, 922.
  • Snyder, E.E. and Stormo, G.D. (1993) Identification of coding regions in genomic DNA sequences: an application of dynamic programming and neural networks. Nucleic Acids Res. 21, 607613.
  • Stolc, V., Gauhar, Z. and Mason C. (2004) A gene expression map for the euchromatic genome of Drosophila melanogaster. Science, 306, 655660.
  • Taft, R.J. and Mattick, J.S. (2003) Increasing biological complexity is positively correlated with the relative genome-wide expansion of non-protein-coding DNA sequences. Genome Biol. 5, P1.
  • Tanaka, H., Ishikawa, M., Asai, K. and Konagaya, A. (1993) Hidden Markov models and interactive aligners: study of their equivalence and possibilities. Proc. Int. Conf. Intell. Syst. Mol. Biol. 1, 395401.
  • Toyoda, T. and Wada, A. (2004) Omic space: coordinate-based integration and analysis of genomic–phenomic interactions. Bioinformatics, 20, 17591765.
  • Uberbacher, E.C., Xu, Y. and Mural, R.J. (1996) Discovering and understanding genes in human DNA sequence using GRAIL. Methods Enzymol. 266, 259281.
  • Yamada, K., Lim, J., Dale J.M. et al. (2003) Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 302, 842845.