Code - Cisregul - References

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Berman, B. P., Nibu, Y., Pfeiffer, B. D., Tomancak, P., Celniker, S. E., Levine, M., Rubin, G. M., and Eisen, M. B. (2002). Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proceedings of the National Academy of Sciences of the United States of America 99, 757-762.

Hughes, J. D., Estep, P. W., Tavazoie, S., and Church, G. M. (2000). Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol 296, 1205-14.

Koranda, M., Schleiffer, A., Endler, L., and Ammerer, G. (2000). Forkhead-like transcription factors recruit Ndd1 to the chromatin of G2/M-specific promoters. Nature 406, 94-98.

Ohler, U., Liao, G., Niemann, H., and Rubin, G. (2003). Computational analysis of core promoters in the Drosophila genome. Genome Biology 3, 0087.

Spellman, P., Sherlock, G., Zhang, M., Iyer, V., Anders, K., Eisen, M., Brown, P., Botstein, D., and Futcher, B. (1998). Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Molecular Biology of the Cell 9, 3273-3297.

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Thijs, G., Marchal, K., Lescot, M., Rombauts, S., De Moor, B., Rouze, P., and Moreau, Y. (2002). A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes. Journal of Computational Biology 9, 447-464.

Wasserman, W. W., and Fickett, J. W. (1998). Identification of regulatory regions which confer muscle-specific gene expression. J Mol Biol 278, 167-81.

Wingender, E., Kel, A., Kel, O., Karas, H., Heinemeyer, T., Dietze, P., Knuppel, R., Romaschenko, A., and Kolchanov, N. (1997). TRANSFAC, TRRD and COMPEL: Towards a federated database system on transcriptional regulation. Nucleic Acid Research 25, 265-268.

Zhu, G. F., Spellman, P. T., Volpe, T., Brown, P. O., Botstein, D., Davis, T. N., and Futcher, B. (2000). Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature 406, 90-94.