Bibliography

1
Barrett, T. and Edgar, R. (2006) Gene expression omnibus: microarray data storage, submission, retrieval, and analysis.. Methods Enzymol, 411, 352-369.

2
Friedlander, G., Joseph-Strauss, D., Carmi, M., Zenvirth, D., Simchen, G., and Barkai, N. (2006) Modulation of the transcription regulatory program in yeast cells committed to sporulation.. Genome Biol, 7(3), R20.

3
Foat, B. C., Morozov, A. V., and Bussemaker, H. J. (Jul, 2006) Statistical mechanical modeling of genome-wide transcription factor occupancy data by matrixreduce.. Bioinformatics, 22(14), e141-e149.

4
Cherry, J. M., Adler, C., Ball, C., Chervitz, S. A., Dwight, S. S., Hester, E. T., Jia, Y., Juvik, G., Roe, T., Schroeder, M., Weng, S., and Botstein, D. (Jan, 1998) Sgd: Saccharomyces genome database.. Nucleic Acids Res, 26(1), 73-79.

5
MacIsaac, K. D., Wang, T., Gordon, D. B., Gifford, D. K., Stormo, G. D., and Fraenkel, E. (2006) An improved map of conserved regulatory sites for saccharomyces cerevisiae.. BMC Bioinformatics, 7, 113.

6
Matys, V., Kel-Margoulis, O. V., Fricke, E., Liebich, I., Land, S., Barre-Dirrie, A., Reuter, I., Chekmenev, D., Krull, M., Hornischer, K., Voss, N., Stegmaier, P., Lewicki-Potapov, B., Saxel, H., Kel, A. E., and Wingender, E. (Jan, 2006) Transfac and its module transcompel: transcriptional gene regulation in eukaryotes.. Nucleic Acids Res, 34(Database issue), D108-D110.

7
Stark, C., Breitkreutz, B.-J., Reguly, T., Boucher, L., Breitkreutz, A., and Tyers, M. (Jan, 2006) Biogrid: a general repository for interaction datasets.. Nucleic Acids Res, 34(Database issue), D535-D539.

8
Eisen, M. B., Spellman, P. T., Brown, P. O., and Botstein, D. (Dec, 1998) Cluster analysis and display of genome-wide expression patterns.. Proc Natl Acad Sci U S A, 95(25), 14863-14868.

9
Foat, B. C., Houshmandi, S. S., Olivas, W. M., and Bussemaker, H. J. (Dec, 2005) Profiling condition-specific, genome-wide regulation of mrna stability in yeast.. Proc Natl Acad Sci U S A, 102(49), 17675-17680.

10
deHoon, M. J. L., Imoto, S., Nolan, J., and Miyano, S. (Jun, 2004) Open source clustering software.. Bioinformatics, 20(9), 1453-1454.

11
Carrozza, M. J., Florens, L., Swanson, S. K., Shia, W.-J., Anderson, S., Yates, J., Washburn, M. P., and Workman, J. L. (Nov, 2005) Stable incorporation of sequence specific repressors ash1 and ume6 into the rpd3l complex.. Biochim Biophys Acta, 1731(2), 77-87; discussion 75-6.

12
Vershon, A. K. and Pierce, M. (Jun, 2000) Transcriptional regulation of meiosis in yeast.. Curr Opin Cell Biol, 12(3), 334-339.

13
Steber, C. M. and Esposito, R. E. (Dec, 1995) Ume6 is a central component of a developmental regulatory switch controlling meiosis-specific gene expression.. Proc Natl Acad Sci U S A, 92(26), 12490-12494.

14
Strich, R., Surosky, R. T., Steber, C., Dubois, E., Messenguy, F., and Esposito, R. E. (Apr, 1994) Ume6 is a key regulator of nitrogen repression and meiotic development.. Genes Dev, 8(7), 796-810.

15
Brem, R. B. and Kruglyak, L. (Feb, 2005) The landscape of genetic complexity across 5,700 gene expression traits in yeast.. Proc Natl Acad Sci U S A, 102(5), 1572-1577.

16
Dion, M. F., Altschuler, S. J., Wu, L. F., and Rando, O. J. (Apr, 2005) Genomic characterization reveals a simple histone h4 acetylation code.. Proc Natl Acad Sci U S A, 102(15), 5501-5506.

17
Kadosh, D. and Struhl, K. (Sep, 1998) Targeted recruitment of the sin3-rpd3 histone deacetylase complex generates a highly localized domain of repressed chromatin in vivo.. Mol Cell Biol, 18(9), 5121-5127.

18
Mukherjee, S., Berger, M. F., Jona, G., Wang, X. S., Muzzey, D., Snyder, M., Young, R. A., and Bulyk, M. L. (Dec, 2004) Rapid analysis of the dna-binding specificities of transcription factors with dna microarrays.. Nat Genet, 36(12), 1331-1339.

19
Liu, X., Noll, D. M., Lieb, J. D., and Clarke, N. D. (Mar, 2005) Dip-chip: rapid and accurate determination of dna-binding specificity.. Genome Res, 15(3), 421-427.

20
Warren, C. L., Kratochvil, N. C. S., Hauschild, K. E., Foister, S., Brezinski, M. L., Dervan, P. B., Phillips, G. N., and Ansari, A. Z. (Jan, 2006) Defining the sequence-recognition profile of dna-binding molecules.. Proc Natl Acad Sci U S A, 103(4), 867-872.

21
Berger, M. F., Philippakis, A. A., Qureshi, A. M., He, F. S., Estep, P. W., and Bulyk, M. L. (Nov, 2006) Compact, universal dna microarrays to comprehensively determine transcription-factor binding site specificities.. Nat Biotechnol, 24(11), 1429-1435.



Barrett C. Foat 2007-09-17