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1.) O'Connor, T.R. and Wyrick, J.J. (2007) ChromatinDB: a database of genome-wide histone modification patterns for Saccharomyces cerevisiae. Bioinformatics (in press).2.) Wood, A., Shukla, A., Schneider, J., Lee, J.S., Stanton, J.D., Dzuiba, T., Swanson, S.K., Florens, L., Washburn, M.P., Wyrick, J., Bhaumik, S.R., Shilatifard, A (2006) Ctk complex mediated regulation of histone methylation by COMPASS. Mol Cell Biol 27:709-720.
3.) Parra, M.A., Kerr, D., Fahy, D., Pouchnik, D.J., and Wyrick, J.J. (2006) Deciphering the Roles of the Histone H2B N-terminal domain in Genome-wide Transcription. Mol Cell Biol 26:3842-3852..
4.) O'Connor, T.R., Dyreson, C., and Wyrick, J.J. (2005) Athena: a resource for rapid visualization and systematic analysis of Arabidopsis promoter sequences. Bioinformatics 21:4411-4413.
5.) Martin, A.M., Pouchnik, D.J., Walker, J.L., and Wyrick, J.J. (2004) Redundant Roles for Histone H3 N-Terminal Lysine Residues in Subtelomeric Gene Repression in Saccharomyces cerevisiae. Genetics 167:1123-1132.
6.) Lee, T.I., Rinaldi, N.J., Robert, F., Odom, D.T., Bar-Joseph, Z., Gerger, G.K., Hannett, N.M., Harbison, C.T., Thompson, C.M., Simon, I., Zeitlinger, J., Jennings, E.G., Murray, H.L., Gordon, D.B., Ren, B., Wyrick, J.J., Tagne, J.B., Volkert, T.L., Fraenkel, E., Gifford, D.K., Young, R.A. (2002) Transcriptional Regulatory Networks in Saccharomyces cerevisiae. Science 298: 799-804.
7.) Wyrick, J.J. and Young, R.A. (2002) Deciphering Gene Expression Regulatory Networks. Curr Opin Genet Dev 12: 130-6.
8.) Wyrick, J.J., Aparicio, J.G., Chen, T., Barnett, J.D., Jennings, E.G., Young, R.A., Bell, S.P., and Aparicio, O.M. (2001) Genome-Wide Distribution of ORC and MCM proteins in S. cerevisiae: High-Resolution Mapping of Replication Origins. Science 294: 2357-2360.
9.) Simon, I., Barnett, J., Hannett, N., Harbison, C.T., Rinaldi, N.J., Volkert, T.L., Wyrick, J.J., Zeitlinger, J., Gifford, D.K., Jaakkola, T.S., and Young, R.A. (2001) Serial Regulation of Transcriptional Regulators in the Yeast Cell Cycle. Cell 106: 697-708.
10.) Ren, B.*, Robert, F.*, Wyrick, J.J.*, Aparicio, O., Jennings, E.J., Simon, I., Zeitlinger, J., Schreiber, J., Hannett, N., Kanin, E., Volkert, T.L., Wilson, C.J., Bell, S.P., and Young, R.A. (2000) Genome-wide Location and Function of DNA-binding Proteins. Science 290: 2306-2309.
*Authors made equal contributions.
11.) Wyrick, J.J., Holstege, F.C.P., Jennings, E.G., Causton, H.C., Shore, D., Grunstein, M., Lander, E.S., Young, R.A., (1999) Chromosomal Landscape of Nucleosome-dependent Gene Expression and Silencing in Yeast. Nature 402:418-421.
12.) Holstege, F.C.P., Jennings, E.G., Wyrick, J.J., Lee T., Hengartner, C.J., Green, M.R., Golub, T.R., Lander, E.S., and Young, R.A. (1998) Dissecting the Regulatory Circuitry of a Eukaryotic Genome. Cell 95: 717-728.
13.) Lee, T., Wyrick, J.J., Koh, S.S., Jennings, E.G., Gadbois, E.L., and Young, R.A. (1998) Interplay of Positive and Negative Regulators in Transcription Initiation by RNA Polymerase II Holoenzyme. Mol. Cell. Biol. 18: 4455-4462.