References

Bailey, T. L., & Elkan, C. (1995). The value of prior knowledge in discovering motifs with MEME. Proceedings of the Third International conference in Intelligent systems for molecular biology, 21-29.

Berg, O. G. & von Hippel, P. H. (1987). Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J. Mol. Biol. 193, 723-750.

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.

Grundy, W. N., Bailey, T. L., & Elkan, C. P. (1996). ParaMEME: A parallel implementation and a web interface for a DNA and protein motif discovery tool. Comput. Appl. Biosci. 12, 303-310.

Hartigan, J. A. (1975). Clustering Algorithms. Wiley, New York.

Hughes, J. D., Estep, P. W., Tavazoie, S., & Church, G.M. (1999). Computational identification of cis-regulatory elements associated with groups of functionally related genes in S. cerevisiae. in preparation.

Lawrence, C. E., Altschul, S. F., Boguski, M. S., Liu, J. S., Neuwald, A. F. & Wootton, J. C. (1993). Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science, 262, 208-214.

Liu, S. J., Neuwald, A. F., & Lawrence, C. E. (1995). Bayesian models for multiple local sequence alignment and gibbs sampling strategies. Journal of the American Statistical Association, 90, 1156-1170.

Mannhaupt, G. Schnall, R., Karpov, V., Vetter, I., & Feldmann, H. (1999). Rpn4 acts as a transcription factor by binding to PACE, a nonamer box found upstream of 26S proteasomal and other genes in yeast. FEBS Lett. 450, 27-34.

McGuire, A. M., Hughes, J. D., Church, G. M. (1999). Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes. submitted to JMB. (abstract)

Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G., & Maltsev, N. (1999). The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. USA, 96, 2896-2901.

Ross Overbeek, Michael Fonstein, Mark D'Souza, Gordon D. Pusch and Natalia Maltsev. Use of Contiguity on the Chromosome to Predict Functional Coupling. (1998) In Silico Biol. 1, 0009. (Full text)

Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., & Kanehisa, M. (1999). KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucl. Acids Res. 27: 29-34.

Pellegrini, M., Marcotte, E. M., Thompson, M. J., Eisenberg, D., & Yeates, T. O. (1999). Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles. Proc. Natl. Acad. Sci USA, 96, 4285-4289.

Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D. (1999). Detecting protein function and protein-protein interactions from genome sequences. Science Jul 30;285(5428):751-3.

Pietrokovski, S. (1996). Searching databases of conserved sequence regions by aligning protein multiple-alignments. Nucl. Acids Res. 24, 3836-3845.

Robison, K., McGuire, A. M., & Church, G. A. (1998). Comprehensive Library of DNA-Binding Site Matrices for 55 Proteins Applied to the Complete Escherichia coli K-12 Genome. J. Mol. Biol. 284, 241-254.

Roth, F. P., Hughes, J. D., Estep, P. W. & Church, G. M. (1998). Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nature Biotechnol. 16, 939-45.

Schneider, T. D. & Stephens, R. M. (1990). Sequence logos: a new way to display consensus sequence. Nucl. Acids Res. 18, 6097-6100.

Schuler, G. D., Altschul, S. F., & Lipman, D. J. (1991). A workbench for multiple alignment construction and analysis. Proteins: Struct. Funct. Genet. 9, 180-190.

Tamayo, P., Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES, Golub TR. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci U S A 1999 Mar 16;96(6):2907-12.

Tavazoie, S., Hughes, J. D., Campbell, M. J., Cho, R. J., & Church, G.M. (1999). Systematic determination of genetic network architecture. Nature Genetics 22(3):281-5.

Van Helden, J., Andre, B., & Collado-Vides, J. (1998). Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Mol. Biol. 281, 827-842.

Wen X, Fuhrman S, Michaels GS, Carr DB, Smith S, Barker JL, Somogyi R. Large-scale temporal gene expression mapping of central nervous system development. Proc Natl Acad Sci U S A 1998 Jan 6;95(1):334-9.


Abigail Manson McGuire
Harvard Medical School
Genetics Dept., Church Lab
Alpert Bldg. 512
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