1. Bulyk, M. (2003) Computational prediction of transcription-factor binding site locations. Genome Biol. 5, 201.

2. Mukheijee, S., Berger, M. F., Jona, G., et al. (2004) Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat. Genet. 36, 1331-1339.

3. Sambrook, J., Fritsch, E., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

4. Liu, X., Brutlag, D., and Liu, J. (2001) BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac. Symp. Biocomput. 127-138.

5. 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, 1205-1214.

6. Bulyk, M. L., Huang, X., Choo, Y., and Church, G. M. (2001) Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc. Natl. Acad. Sci. USA 98, 7158-7163.

7. Dudley, A., Aach, J., Steffen, M., and Church, G. (2002) Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range. Proc. Natl. Acad. Sci. USA 99, 7554-7559.

8. Cleveland, W. and Devlin, S. (1988) Locally weighted regression: An approach to regression analysis by local fitting. J. Am. Stat. Assoc. 83, 596-610.

9. Taylor, J. (1997) An Introduction to Error Analysis, 2nd ed., University Science Books, Sausalito, CA.

10. Bulyk, M., Johnson, P., and Church, G. (2002) Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res. 30, 1255-1261.

11. Sokal, R. and Rohlf, R. (1995) Biometry: The Principles and Practice of Statistics in Biological Research, 3rd ed., W. H. Freeman and Company, New York.

12. Huber, B. R. and Bulyk, M. L. (in review) Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data.

13. Roth, F. P., Hughes, J. D., Estep, P. W., and Church, G. M. (1998) Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat. Biotechnol. 16, 939-945.

14. Bailey, T. and Elkan, C. (1995) The value of prior knowledge in discovering motifs with MEME. Proc. Int. Conf. Intell. Syst. Mol. Biol. 3, 21-29.

15. Liu, X., Brutlag, D., and Liu, J. (2002) An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat. Biotechnol. 20, 835-839.

16. Schneider, T. D. and Stephens, R. M. (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 18, 6097-6100.

0 0

Post a comment