2005

Benevolenskaya, E.V., Murray, H.L., Branton, P., Young, R.A., Kaelin W.G. Jr.
Binding of pRB to the PHD protein RBP2 promotes cellular differentiation. Mol Cell. 18:623-35 (2005).
[ABSTRACT] [FULL TEXT]

Boyer, L.A., Lee, T.I., Cole, M.F., Johnstone, S.E., Levine, S.S., Zucker, J.P., Guenther, M.G., Kumar, R.M., Murray, H.L., Jenner, R.G., Melton, D.A., Gifford, D.K., Jaenisch, R. and Young, R.A.
Core Transcriptional Regulatory Circuitry in Human Embryonic Stem Cells. Cell 122: 947-956 (2005).
[ABSTRACT] [FULL TEXT] [WEBSITE]

Guenther, M. G., Jenner, R. G., Chevalier, B., Nakamura, T., Croce, C. M., Canaani, E., and Young, R. A.
Global and Hox-specific roles for the MLL1 methyltransferase. Proc Natl Acad Sci U S A 102, 8603-8608 (2005).
[ABSTRACT] [FULL TEXT] [WEBSITE]

Jenner, R.G. and Young, R.A.
Insights into host responses against pathogens from transcriptional profiling. Nature Rev. Microbiol. 3:281-94 (2005).
[ABSTRACT] [FULL TEXT] [WEBSITE]

Kiburz, B.M., Reynolds, D.B., Megee, P.C., Marston, A.L., Lee, B.H., Lee, T.I., Levine, S.S., Young, R.A. and Amon, A.
The core centromere and Sgo1 establish a 50-kb cohesin-protected domain around centromeres during meiosis I. Genes & Dev. 19: 3017-3030 (2005).
[ABSTRACT] [FULL TEXT]

Macisaac KD, Gordon DB, Nekludova L, Odom DT, Schreiber J, Gifford DK, Young RA, Fraenkel E.
A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data. Bioinformatics (2005).
[ABSTRACT] [FULL TEXT]

Pokholok, D.K., Harbison, C.T., Levine, S., Cole, M., Hannett, N.M., Lee, T.I., Walker, K., Lewitter, F., Rolfe, P.A., Herbolsheimer, E., Bell, G.W., Zeitlinger, J., Gifford, D.K., Young, R.A.
Genome-wide Map of Nucleosome Acetylation and Methylation in Yeast. Cell. 122(4):517-27. (2005).
[ABSTRACT] [FULL TEXT] [WEBSITE]

Zhang, X., Odom, DT, Koo, SH, Conkright, MD, Canettieri, G., Best, J., Chen, H., Jenner, R., Herbolsheimer, E., Jacobsen, E., Kadam, S., Ecker, JR., Emerson, B., Hogenesch, JB., Unterman, T., Young, RA., and Montminy, M.
Genome-Wide Analysis of CREB Occupancy, Phosphorylation, and Target Gene Activation in Human Tissues Proc. Natl. Acad. Sci. USA. 102:4459-64 (2005).
[ABSTRACT] [FULL TEXT]

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2004

Cam, H., Balciunaite, E., Blais, A., Spektor, A., Scarpulla, RC., Young, R., Kluger, Y., and Dynlacht, BD.
A Common Set of Gene Regulatory Networks Links Metabolism and Growth Inhibition
Mol Cell 16: 399-411 (2004).
[ABSTRACT] [FULL TEXT]

Harbison, C.T., Gordon, D.B., Lee, T.I., Rinaldi, N., Macisaac, K.D., Danford, T.D., Hannett, N.M., Tagne, J.-B., Reynolds, D.B., Yoo, J., Jennings, E.G., Zeitlinger, J., Pokholok, D.K., Kellis, M., Rolfe, P.A., Takusagawa, K.T., Lander, E.S., Gifford, D.K., Fraenkel, E. and Young, R.A.
Transcriptional Regulatory Code of a Eukaryotic Genome.
Nature 431: 99-104 (2004).
[ABSTRACT] [FULL TEXT] [WEBSITE]

Mukherjee S, Berger MF, Jona G, Wang XS, Muzzey D, Snyder M, Young RA, Bulyk ML.
Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays.
Nat Genet. 36:1331-1339 (2004).
[ABSTRACT] [FULL TEXT]

Odom D.T., Zizlsperger, N., Gordon D.B., Bell G.W., Rinaldi N.J., Murray H.L., Volkert T.L., Schreiber J., Rolfe P.A., Gifford D.K., Fraenkel E., Bell G.I., Young R.A.
Control of Pancreas and Liver Gene Expression by HNF Transcription Factors.
Science 303: 1378-81 (2004).
[ABSTRACT] [FULL TEXT] [WEBSITE]

Palliser D, Huang Q, Hacohen N, Lamontagne SP, Guillen E, Young RA, Eisen HN.
A role for toll-like receptor 4 in dendritic cell activation and cytolytic CD8+ T cell differentiation in response to a recombinant heat shock fusion protein.
J Immunol. 2004 Mar 1;172(5):2885-93.
[ABSTRACT] [FULL TEXT]

Robert, F., Pokholok D.K., Hannett, N.M., Rinaldi, N.J., Chandy, M., Rolfe, A., Workman, J., Gifford, D.K., and Young, R.A.
Global Position and Recruitment of HATs and HDACs in the Yeast Genome
Mol Cell. 2004 Oct 22;16(2):199-209.
[ABSTRACT] [FULL TEXT] [WEBSITE]

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2003

Bar-Joseph, Z., Gerber, G.K., Lee, T.I., Yoo, J., Rinaldi, N., Robert, F., Gordon, D.B., Fraenkerl, E., Tagne, J.B., Jaakkola, T., Young, R.A., and Gifford, D.K.
Computational Discovery of Gene Modules and Regulatory Networks.
Nature Biotech. 21: 1337-1342 (2003).
[ABSTRACT] [FULL TEXT]

Dror RO, Murnick JG, Rinaldi NJ, Marinescu VD, Rifkin RM, Young RA.
Bayesian estimation of transcript levels using a general model of array measurement noise.
J Comput Biol. 10: 433-52 (2003).
[ABSTRACT] [FULL TEXT]

Izmailova E., Bertley F.M., Huang Q., Makori N., Miller C.J., Young R.A., Aldovini A.
HIV-1 Tat reprograms immature dendritic cells to express chemoattractants for activated T cells and macrophages.
Nat Med. 2003 Feb;9(2):163-4.
[ABSTRACT] [FULL TEXT]

Nau GJ, Schlesinger A, Richmond JF, and Young RA
Cumulative Toll-like receptor activation in human macrophages treated with whole bacteria.
J Immunol. 170: 5203-9 (2003).
[ABSTRACT] [FULL TEXT]

Ng H.H., Robert F., Young R.A., Struhl K.
Targeted Recruitment of Set1 Histone Methylase by Elongating Pol II Provides a Localized Mark and Memory of Recent Transcriptional Activity.
Mol. Cell 11(3):709-19 (2003).
[ABSTRACT] [FULL TEXT] [WEBSITE]

Shen WC, Bhaumik SR, Causton HC, Simon I, Zhu X, Jennings EG, Wang TH, Young RA, Green MR.
Systematic analysis of essential yeast TAFs in genome-wide transcription and preinitiation complex assembly.
EMBO J. 22: 3395-402 (2003)
[ABSTRACT] [FULL TEXT]

Zeitlinger, J., Simon, I., Harbison, C.T., Hannett, N.M., Volkert,T.L., Fink, G.F. and Young, R.A.
Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling.
Cell 113:395-404 (2003).
[ABSTRACT] [FULL TEXT] [WEBSITE]

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2002


Ansari, A.Z., Koh, S.S., Zaman, Z., Bongards, C., Lehming, N., Young, R. and Ptashne, M.
Transcriptional activating regions target a cyclin-dependent kinase
Proc. Natl. Acad. Sci. USA 99:14706-14709 (2002).
[ABSTRACT] [FREE FULL TEXT]

Damelin, M., Simon, I., Moy, T.I., Wilson, B., Komili, S., Tempst, P., Roth, F.P., Young, R.A., Cairns, B.R., and Silver, P.A.
The Genome-Wide Localization of Rsc9, a Component of the RSC Chromatin-Remodeling Complex, Changes in Response to Stress.
Mol. Cell 9:563-73 (2002).
[ABSTRACT] [FULL TEXT]

Hartemink, A.J., Gifford, D.K., Jaakkola, T.S., and Young, R.A.
Combining Location and Expression Data for Principled Discovery of Genetic Regulatory Network Models.
Pac. Symp. Biocomput. 6:437-449 (2002).
[ABSTRACT]

Lee, T.I., Rinaldi, N.J., Robert, F., Odom, D.T., Bar-Joseph, Z., Gerber, G.K., Hannett, N.M., Harbison, C.R., Thompson, C.M., Simon I., Zeitlinger J., Jennings, E.G., Murray, H.L., Gordon, D.B., Ren, B., Wyrick, J.J., Tagne, J., Volkert T.L., Fraenkel, E., Gifford D.K., and Young, R.A.
Transcriptional Regulatory Networks in Saccharomyces cerevisiae. Science 298: 799-804 (2002).
[ABSTRACT] [FREE FULL TEXT] [WEBSITE]

Nau, G.J., Richmond, J.F.L., Schlesinger, A., Jennings, E.G., Lander, E.S., and Young, R.A.
Human Macrophage Activation Programs Induced by Bacterial Pathogens.
Proc. Natl. Acad. Sci. USA 99:1503-1508 (2002).
[ABSTRACT] [FREE FULL TEXT] [WEBSITE]

Ng, H.H., Robert, F., Young, R.A., and Struhl, K.
Genome-wide Location and Regulated Recruitment of the RSC Nucleosome-remodeling complex.
Genes Dev. 16:806-819(2002).
[ABSTRACT] [FREE FULL TEXT] [WEBSITE]

Pokholok, D.K., Hannett, N.M., and Young, R.A.
Exchange of RNA Polymerase II Initiation and Elongation Factors during Gene Expression In Vivo.
Mol. Cell 9:799-809 (2002).
[ABSTRACT] [FULL TEXT]

Ren, B., Cam, H., Takahashi, Y., Volkert, T., Terragni, J., Young, R.A., and Dynlacht, B.D.
E2F Integrates Cell Cycle Progression with DNA Repair, Replication, and G2/M Checkpoints.
Genes Dev. 16:245-256 (2002).
[ABSTRACT] [FREE FULL TEXT]

Stanojevic, D. and Young, R.A.
A highly potent artificial transcription factor.
Biochemistry 41: 7209-7216 (2002).
[ABSTRACT] [FULL TEXT]

Wyrick, J.J. and Young, R.A.
Deciphering Gene Expression Regulatory Networks.
Curr. Opin. Genet. Dev. 12:130-136(2002).
[ABSTRACT] [FULL TEXT]

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2001

Causton, H.C., Ren, B., Koh, S.S., Harbison, C.T., Kanin, E., Jennings, E.G., Lee, T., True, H.L., Lander, E.S., and Young, R.A.
Remodeling of Yeast Genome Expression in Response to Environmental Changes.
Mol. Biol. Cell 12:323-337 (2001).
[ABSTRACT] [FREE FULL TEXT] [WEBSITE]

Chi, Y., Huddleston, M.J., Zhang, X., Young, R.A., Annan, R.S., Carr, S.A., and Deshaies, R.J.
Negative Regulation of Gcn4 and Msn2 Transcription Factors by Srb10 Cyclin-Dependent Kinase.
Genes Dev. 15:1078-10 92 (2001).
[ABSTRACT] [FREE FULL TEXT]

Geisberg, J.V., Holstege, F.C., Young, R.A., and Struhl, K.
Yeast NC2 Associates with the RNA Polymerase II Preinitiation Complex and Selectively Affects Transcription In Vivo.
Mol. Cell. Biol. 21:2736-2742 (2001).
[ABSTRACT] [FREE FULL TEXT] [WEBSITE]

Hartemink, A.J., Gifford, D.K., Jaakkola, T.S., and Young, R.A.
Using Graphical Models and Genomic Expression Data to Statistically Validate Models of Genetic Regulatory Networks.
Pac. Symp. Biocomput. 6:422-433 (2001).>
[ABSTRACT]

Huang, Q., Liu, D., Majewski, P., Schulte, L.C., Korn, J.M., Young, R.A., Lander, E.S. and Hacohen, N.
The plasticity of dendritic cell responses to pathogens and their components.
Science 294: 870-875 (2001).
[ABSTRACT] [FULL TEXT]

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.
Serial Regulation of Transcriptional Regulators in the Yeast Cell Cycle.
Cell 106:697-708 (2001).
[ABSTRACT] [FULL TEXT] [WEBSITE]

Virbasius, C.A., Holstege, F.C., Young, R.A., and Green, M.R.
Promoter-specific Activation Defects by a Novel Yeast TBP Mutant Compromised for TFIIB Interaction.
Curr. Biol. 11:1794-1798 (2001).
[ABSTRACT] [FULL TEXT]

Wilson, C.J., Guglielmo, C., Moua, N.D., Tudor, M., Grosveld, G., Young, R.A. and Murray, P.J.
Yeast artificial chromosome targeting technology: an approach for the deletion of genes in the c57bl/6 mouse.
Anal Biochem. 296:270-8.(2001).
[ABSTRACT] [FULL TEXT]

Wyrick, J.J., Aparicio, J.G., Chen, T., Barnett, J.D., Jennings, E.G., Young, R.A., Bell, S.P., and Aparicio, O.M.
Genome-Wide Distribution of ORC and MCM Proteins in S. cerevisiae: High-Resolution Mapping of Replication Origins.
Science 294:2357-2360 (2001).>
[ABSTRACT] [FULL TEXT] [WEBSITE]

Zaman, Z., Ansari, A.Z., Koh, S.S., Young, R., and Ptashne M.
Interaction of a Transcriptional Repressor with the RNA Polymerase II Holoenzyme Plays a Crucial Role in Repression.
Proc. Natl. Acad. Sci. USA 98:2550-2554 (2001).
[ABSTRACT] [FREE FULL TEXT]

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2000

Chen, C-H., Wang, T-L., Hung, C-F., Yang, Y., Chen, H., Young, R.A., Pardoll, D.M. and Wu, T-C.
Enhancement of DNA vaccine potency by linkage of antigen gene to an HSP70 gene.
Cancer Research 60:1035-1042 (2000).
[ABSTRACT] [FREE FULL TEXT]

Cho, B.K., Palliser, D., Guillen, E., Wisniewski, J., Young, R.A., Chen, J. and Eisen, H.N.
Aproposed mechanism for the induction of cytotoxic T lymphocyte production by heat shock fusion proteins.
Immunity 12:263-272 (2000).
[ABSTRACT] [FULL TEXT]

Huang, Q., Richmond, J.F.L., Suzue, K., Eisen, H.N. and Young, R.A.
Elicitation of CTLs by Mycobacterial hsp70 Fusion Proteins Maps to a Discrete Domain and is CD4+ T Cell-Independent. J. Exp. Med. 191:403-408 (2000).
[ABSTRACT] [FREE FULL TEXT]

Jabbar, I.A., Fernando, G.J.P., Saunders, N., Aldovini, A., Young, R., Malcolm, K. and Frazer, I.H.
Immune responses induced by BCG recombinant for human papillomavirus L1 and E7 proteins.
Vaccine 18:2444-2453 (2000).
[ABSTRACT] [FULL TEXT]

Lee, T., Causton, H.C., Holstege, F.C.P, Shen, W.-C., Hannett, N., Jennings, E.G., Winston, F., Green, M.R. and Young, R.A.
Redundant Roles for the TFIID and SAGA Complexes in Global Transcription.
Nature 405:701-704 (2000).
[ABSTRACT] [FULL TEXT] [WEBSITE]

Lee, T. and Young, R.A.
Transcription of Eukaryotic Protein-coding Genes.
Ann. Rev. Genet. 34:77-137 (2000).
[ABSTRACT] [FULL TEXT]

Leung, N.J., Aldovini, A., Young, R., Jarvis, M.A., Smith, J.M., Meyer, D., Anderson, D.E., Carlos, M.P., Gardner, M.B. and Torres, J.V.
The Kinetics of Specific Immune Responses in Rhesus Monkeys Inoculated with Live Recombinant BCG Expressing SIV Gag, Pol, Env, and Nef Proteins.
Virology 268:94-103 (2000).
[ABSTRACT] [FULL TEXT]

Nau, G.J., Chupp, G.L., Emile, J.F., Jouanguy, E., Berman, J.S., Casanova, J.L. and Young, R.A.
Osteopontin Expression Correlates with Clinical Outcome in Patients with Mycobacterial Infection.
Am J Pathol. 157:37-42 (2000).
[ABSTRACT] [FREE FULL TEXT]

Ren, B., Robert, F., Wyrick, J.J., Aparicio, O., Jennings, E.G., Simon, I., Zeitlinger, J., Schreiber, J., Hannett, N., Kanin, E., Volkert, T.L., Wilson, C.J., Bell, S.P., and Young, R.A.
Genome-wide Location and Function of DNA Binding Proteins.
Science 290:2306-2309 (2000).
[ABSTRACT] [FULL TEXT] [WEBSITE]

Robertson, L.S., Causton, H.C., Young, R.A. and Fink, G.R.
The Yeast A Kinases Differentially Regulate Iron Uptake and Respiratory Function.
Proc. Natl. Acad. Sci. USA 97:5984-5988 (2000).
[ABSTRACT] [FREE FULL TEXT] [WEBSITE]

Young, R.A.
Biomedical Discovery with DNA Arrays.
Cell 102:9-15 (2000).
[ABSTRACT] [FULL TEXT]

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