2007

Conboy, C.M., Spyrou C., Thorne, N.P., Wade, E.J., Barbosa-Morais, N.L., Wilson, M.D., Bhattacharjee, A., Young, R.A., Tavare, S., Lees, J.A., Odom, D.T.
Cell Cycle Genes Are the Evolutionarily Conserved Targets of the E2F4 Transcription Factor. PLoS ONE 2(10):e1061 (2007)
[ABSTRACT]

Guenther, M.G., Levine, S.S., Boyer, L.A., Jaenisch, R., Young, R.A.
A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130, 77-88 (2007).
[ABSTRACT] [FULL TEXT] [WEBSITE]

Marson, A., Kretschmer, K., Frampton, G.M., Jacobsen, E.S., Polansky, J.K., Macisaac, K.D., Levine, S.S., Fraenkel, E., von Boehmer, H., Young, R.A.
Foxp3 occupancy and regulation of key target genes during T-cell stimulation. Nature 445:931-5 (2007).
[ABSTRACT] [FULL TEXT]

Zeitlinger, J., Stark, A., Kellis, M., Hong, J.W., Nechaev, S, Adelman, K., Levine, M., Young, R.A.
RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nature Genet. 39:1512-6 (2007).
[ABSTRACT] [FULL TEXT] [WEBSITE]

Zeitlinger, J., Zinzen, R.P., Stark, A., Kellis, M., Zhang, H., Young, R.A., Levine, M.
Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning porcesses in the Drosophila embryo. Genes Dev. 21:385-90 (2007).
[ABSTRACT] [FULL TEXT] [WEBSITE]

2006

Boyer, L.A., Plath, K., Zeitlinger, J., Brambrink, T., Medeiros, L.A., Lee, T.I., Levine, S.S., Wernig, M., Tajonar, A., Ray, M.K., Otte, A.P., Vidal, M., Gifford, D.K., Young, R.A. and Jaenisch, R.
Polycomb Complexes Repress Developmental Regulators in Murine Embryonic Stem Cells. Nature 441:349-353 (2006).
[ABSTRACT] [FULL TEXT] [WEBSITE]

Cao, Y., Kumar, R.M., Penn, B.H., Berkes, C.A., Kooperberg, C., Boyer, L.A., Young, R.A., Tapscott, S.J.
Global and gene-specific analyses show distinct roles for Myod and Myog at a common set of promoters. EMBO J. 25: 502-11 (2006).
[ABSTRACT] [FULL TEXT]

Keshet, I., Schlesinger, Y., Farkash, S., Rand, E., Hecht, M., Segal, E., Pikarski, E., Young, R.A., Niveleau, A., Cedar, H., Simon, I.
Evidence for an instructive mechanism of de novo methylation in cancer cells. Nature Genetics 38: 149-153 (2006).
[ABSTRACT] [FULL TEXT]

Lee, T.I., Jenner, R.G., Boyer, L.A., Guenther, M.G., Chevalier, B., Levine, S.S., Kumar, R.M., Johnstone, S.E., Murray, H.L., Zucker, J.P., Yuan, B., Bell, G.W., Herbolsheimer, E., Hannett, N.M., Cole, M.F., Sun, K., Odom, D.T., Volkert, T.L., Bartel, D.P., Gifford, D.K., Melton, D.A., Jaenisch, R. and Young, R.A.
Control of Developmental Regulators by Polycomb in Human Embryonic Stem Cells. Cell 125: 301-313 (2006).
[ABSTRACT] [FULL TEXT] [WEBSITE]

Lee, T.I., Johnstone, S. and Young, R.A.
Chromatin Immunoprecipitation and Microarray-Based Analysis of Protein Location.Nature Protocols 1: 729-748 (2006)

Odom, D.T., Dowell, R.D., Jacobsen, E.S., Nekludova, L., Rolfe, P.A., Danford, T.W., Gifford, D.K., Fraenkel, E., Bell, G.I. and Young, R.A.
Core transcriptional regulatory circuitry in human hepatocytes. Molecular Systems Biology, 4100059-E1 - 4100059-E5 (2006).
[ABSTRACT] [FULL TEXT] [WEBSITE]

Palomero, T., Odom, D.T., O'Neil, J., Ferrando, A.A., Margolin, A., Neuberg, D.S., Winter, S.S., Larson, R.S., Li, W., Liu, X.S., Young, R.A,. and Look, A.T.
Transcriptional regulatory networks downstream of TAL1/SCL in t-cell acute lymphoblastic leukemia. Blood. 2006 Apr 18; [Epub ahead of print].
[ABSTRACT] [FULL TEXT] [WEBSITE]

Pokholok, D.K., Zeitlinger, J., Hannett, N., Reynolds, D., and Young, R.A.
Activated Signal Transduction Kinases Frequently Occupy Target Genes. Science 313: 533-536 (2006).
[ABSTRACT] [FULL TEXT] [WEBSITE]

Qi, Y., Rolfe, P.A., Macisaac, K.D., Gerber, G.K., Pokholok, D.K., Zeitlinger, J., Danford, T.W., Dowell, R.D., Fraenkel, E., Jaakkola, T.S., Young, R.A., Gifford, D.K.
High-resolution computational models of genome binding events. Nat Biotechnol. 2006 Aug;24(8):963-70.
[ABSTRACT] [FULL TEXT]

Schreiber, J., Jenner, R.G., Guenther M.G., Murray, H.L., Gerber, G.K. Gifford, D.K. Young, R.A..
Coordinated Binding of NF-kB Family Members in the Response of Human Cells to Lipopolysaccharide. Proc. Natl. Aced. Sci, USA 103: 5899-5904 (2006).
[ABSTRACT] [FREE FULL TEXT] [WEBSITE]

Wardle, F.C., Odom, D.T., Bell, G.W., Yuan, B., Danford, T.W., Wiellette, E.L., Herbolsheimer, E., Sive, H.L., Young, R.A., Smith, J.C.
Zebrafish promoter microarrays identify actively transcribed embryonic genes. Genome Biol. 2006 Aug 4;7(8):R71 [Epub ahead of print]
[ABSTRACT] [FULL TEXT]

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