Computational prediction of functional similarity of CRMs

0044 English OPEN
Koohy, Hashem;
  • Subject: QH426

Transcriptional regulation of genes is fundamental to all living organisms. The spatial, temporal and condition-specific expression levels of genes are in part determined by inherited regulatory codes in non-coding regions of the DNA. A large set of methods have been pr... View more
  • References (32)
    32 references, page 1 of 4

    [1] S. Aerts, P. Van Loo, G. Thijs, Y. Moreau, and B. De Moor. Computational detection of cis-regulatory modules. Bioinjormatics, 19 SuppI2:ii5-14, 2003. 6, 26

    [2] A. Aggarwal, M.M. Klawe, M. Shlomo, P. Shor, and R. Wilber. Geometric applications of a matrix-searching algorithm. Algorithmica, 2: 195-208, 1987. 115

    [3] S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. Basic local alignment search tool. J Mol Biol, 215(3):403-10, 1990. 6

    [4] A. N. Arslan, O. Egecioglu, and P. A. Pevzner. A new approach to sequence comparison: normalized sequence alignment. Bioinjormatics, 17(4):327-37, 2001. 111

    [5] E. Berezikov, V. Guryev, and E. Cuppen. Conreal web server: identification and visualization of conserved transcription factor binding sites. Nucleic Acids Res, 33(Web Server issue):W447-50, 2005. 109

    [6] L. Bintu, N. E. Buchler, H. G. Garcia, U. Gerland, T. Hwa, J. Kondev, T. Kuhlman, and R. Phillips. Transcriptional regulation by the numbers: applications. CUrT' Opin Genet Dev, 15(2):125-35, 2005. 12

    [7] L. Bintu, N. E. Buchler, H. G. Garcia, U. Gerland, T. Hwa, J. Kondev, and R. Phillips. Transcriptional regulation by the numbers: models. CUrT' Opin Genet Dev, 15(2):116-24, 2005. 11, 12, 13, 15

    [8] B. E. Blaisdell. A measure of the similarity of sets of sequences not requiring sequence alignment. Proc Natl Acad Sci USA, 83(14):5155-9, 1986. 6, 26 [18] B. C. Foat, A. V. Morozov, and H. J. Bussemaker. Statistical mechanical modeling of genome-wide transcription factor occupancy data by matrixreduce. Bioinjormatics, 22(14):eI41-9, 2006.

    [20] J. Gertz, E. D. Siggia, and B. A. Cohen. Analysis of combinatorial cisregulation in synthetic and genomic promoters. Nature, 457(7226):215-8, 2009. 2, 6, 12, 13

    [21] R. Gordan, L. Narlikar, and A. J. Hartemink. Finding regulatory DNA motifs using alignment-free evolutionary conservation information. Nucleic Acids Res, 38(6):e90, 2010. 8

  • Related Research Results (1)
  • Metrics
Share - Bookmark