2008

Guenther M.G., Lawton L.N., Rozovskaia T., Frampton G.M., Levine S.S., Volkert T.L., Croce C.M., Nakamura T., Canaani E., Young, R.A.
Aberrant chromatin at genes encoding stem cell regulators in human mixed-lineage leukemia. Genes Dev 22(24):3403-3408 (2008)
[ABSTRACT]

Seila A.C., Calabrese J.M., Levine S.S>, Yeo G.W., Rahl P.B., Flynn R.A., Young, R.A., Sharp P.A.
Divergent transcription from active promoters. Science 322(5909):1849-1851 (2008) [ABSTRACT]

Cole M.F., Young, R.A.
Mapping key features of transcriptional regulatory circuitry in embryonic stem cells. Cold Spring Harbor Symp Quant Biol 73:183-193 (2008)
[ABSTRACT]

Creyghton M.P., Markoulaki S., Levine S.S., Hanna J., Lodato M.A., Sha K., Young, R.A., Jaenisch R., Boyer L.A.
H2AZ is enriched at polycomb complex target genes in ES cells and is necessary for lineage commitment. Cell 135(4):649-661 (2008)
[ABSTRACT]

Lopez-Bigas N., Kisiel T.A., Dewaal D.C., Holmes K.B., Volkert T.L., Gupta S., Love J., Murray H.L., Young, R.A., Benevolenskaya E.V.
Genome-wide analysis of the H3K4 histone demethylase RBP2 reveals a transcriptional program controlling differentiation. Mol Cell 31(4):520-530 (2008)
[ABSTRACT]

Mathur D., Danford T.W., Boyer L.A., Young, R.A., Gifford D.K., Jaenisch R.
Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET. Genome Biol 9(8):R126 (2008)
[ABSTRACT]

Marson A., Levine S.S., Cole M.F., Frampton G.M., Brambrink T., Johnstone S., Guenther M.G., Johnston W.K., Wernig M., Newman J., Calabrese J.M., Dennis L.M., Volkert T.L., Gupta S., Love J., Hannett N., Sharp P.A., Bartel D.P., Jaenisch R., Young, R.A.
Connecting the microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 134(3):521-533 (2008)
[ABSTRACT]

Marson A., Foreman R., Chevalier B., Bilodeau S., Kahn M., Young R.A., Jaenisch R.
Wnt Signaling promotes reprogramming of somatic cells to pluripotency. Cell Stem Cell 3(2):132-135 (2008)
[ABSTRACT]

Cole M.F., Johnstone S.J., Newman J.J., Kagey M.H., Young, R.A.
Tcf3 is an integral component of the core regulatory circuitry of embryonic stem cells. Genes Dev 22(6):746-755 (2008)
[ABSTRACT] [FREE FULL TEXT]

Jaenisch, R. and Young, R.A.
Stem Cells, the Molecular Circuitry of Pluripotency and Nuclear Reprogramming. Cell 132(4):567-582 (2008)
[ABSTRACT]

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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