Odom:Publications

Odom laboratory

Home        Members        Research        Pubs        Protocols        Pix        Contact       

Selected Publications

PDF reprints are provided below within the context of fair use. Please obtain copies from the publisher if appropriate.

Control of Pancreas and Liver Gene Expression by HNF Transcription Factors
Science, 27 February 2004
D.T. Odom, N. Zizlsperger, D. Gordon, G. W. Bell, N.J. Rinaldi, H. Murray, T. Volkert, J. Schreiber, A. Rolfe, D. Gifford, E. Fraenkel, G.I. Bell, R.A. Young
URL, Comment, PDF reprint

Genome-wide analysis of CREB occupancy, phosphorylation, and target gene activation in human tissues
Proceedings of the National Academy of Sciences USA, 22 March 2005
X. Zhang, D.T. Odom, S.H. Koo, M. Conkright, G. Canettieri, J. Best, H. Chen, R. Jenner, E. Herbolsheimer, E. Jacobsen, S. Kadam, J. Ecker, B. Emerson, J. Hogenesch, T. Unterman, R. Young, M. Montminy
URL, PDF reprint

Core Transcriptional Regulatory Circuitry in Human Hepatocytes
Molecular Systems Biology, 2 May 2006
D.T. Odom, R. Dowell, E. Jacobsen, L. Nekludova, P. Rolfe, T. Danford, D. Gifford, E. Fraenkel, G. Bell, R. A. Young
URL, PDF reprint

Tissue-Specific Transcriptional Regulation has Diverged Significantly between Human and Mouse
Submitted
D.T. Odom, R. D. Dowell, E. S. Jacobsen, W. M. Gordon, T. W. Danford, K. MacIsaac, P. A. Rolfe, C. M. Conboy, D. K. Gifford, E. Fraenkel

COMPLETE PUBLICATION LIST:

D. T. Odom†, R. Dowell†, E. Jacobsen, W. Gordon, T. Danford, K. MacIsaac, P. Rolfe, C. Conboy, D. Gifford, E. Fraenkel. “Tissue-Specific Transcriptional Regulation has Diverged Significantly between Human and Mouse,” Manuscript Submitted. †Co-first

T. Palomero, W. Lim, D. T. Odom, M. Sulis, P. Real, A. Margolin, K. Barnes, J. O’Neil, D. Neuberg, A. Weng, J. Aster, F. Sigaux, J. Soulier, A. Look, R. Young, A. Califano, A. Ferrando. “NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth,” Proceedings of the National Academy of Sciences USA 103 (2006) 18261-18266.

F. C. Wardle, D. T. Odom, G. Bell, B. Yuan, T. Danford, E. Wiellette, E. Herbolsheimer, H. Sive, R. Young, J. Smith. “Zebrafish promoter microarrays identify actively transcribed embryonic genes,” Genome Biology 7 (2006) R71.

T. Palomero, D. T. Odom, J. O’Neil, A. Ferrando, A. Margolin, D. Neuberg, S. Winter, R. Larson, R. Young, A. Look. “Transcriptional Regulatory Networks Downstream of TAL1/SCL in T-cell Acute Lymphoblastic Leukemia,” Blood 108 (2006) 986-992.

D. T. Odom, R. Dowell, E. Jacobsen, L. Nekludova, P. Rolfe, T. Danford, D. Gifford, E. Fraenkel, G. Bell, R. A. Young. “Core Transcriptional Regulatory Circuitry in Human Hepatocytes,” Mol. Syst. Biol. (2006) E1.

T. Lee, R. Jenner, L. Boyer, M. Guenther, S. Levine, R. Kumar, B. Chevalier, S. Johnstone, M. Cole, K. Isono, H. Koseki, T. Fuchikami, K. Abe, H. Murray, J. Zucker, B. Yuan, G. Bell, E. Herbolsheimer, N. Hannett, K. Sun, D. T. Odom, A. Otte, T. Volkert, D. Bartel1, D. Melton, D. Gifford, R. Jaenisch R. Young. “Control of Developmental Regulators by Polycomb in Human Embryonic Stem Cells,” Cell 125 (2006) 301.

P. Scacheri, S. Davis, D. T. Odom, G.. Crawford, S. Perkins, M. Halawi, S. Agarwal, S. Marx, A. Spiegel, P. Meltzer, F.. Collins. “Genome-Wide Analysis of Menin Binding Provides Insights to MEN1 Tumorigenesis,” PLoS-Genetics 2 (2006) e51.

K. MacIsaac, D. Gordon, L. Nekludova, D. T. Odom, D. Gifford, R. Young, E. Fraenkel, “A Hypothesis Based Approach for Identifying the Binding Specificity of Regulatory Proteins from Chromatin Immunoprecipitation Data,” Bioinformatics, 22 (2006) 423-429.

X. Zhang, D. T. Odom, S.-H. Koo, M. Conkright, G. Canettieri, J. Best, H. Chen, R. Jenner, E. Herbolsheimer, E. Jacobsen, S. Kadam, J. Ecker, B. Emerson, J. Hogenesch, T. Unterman, R. Young, M. Montminy. “Genome-wide analysis of CREB occupancy, phosphorylation, and target gene activation in human tissues,” Proceedings of the National Academy of Sciences USA 102 (2005) 4459-4464.

D. T. Odom, N. Zizlsperger, D. Gordon, G. W. Bell, N. J. Rinaldi, H. Murray, T. Volkert, J. Schreiber, A. Rolfe, D. Gifford, E. Fraenkel, G. I. Bell, R. A. Young. “Control of Pancreas and Liver Gene Expression by HNF Transcription Factors,” Science 303 (2004) 1378-1381.

T. I. Lee†, N. J. Rinaldi†, F. Robert†, D. T. Odom, Z. Bar-Joseph, G. Gerber, N. Hannett, C. Harbison, C. Thompson, I. Simon, J. Zeitlinger, E. Jennings, H. Murray, D. Gordon, B. Ren, J. Wyrick, J. Tagne, T. Volkert, E. Fraenkel, D. Gifford, R. A. Young. "Transcriptional Regulatory Networks in Saccharomyces cerevisiae," Science 298 (2002) 799-805. †Co-first

D. T. Odom, J. K. Barton. "Long Range Oxidation of Guanines in RNA/DNA Hybrid Duplexes," Biochemistry 40 (2001) 8727-8737.

D. T. Odom, E. A. Dill, J. K. Barton. "Charge Transport Through DNA Four-Way Junctions," Nucleic Acids Research 29 (2001) 2026-2033.

T. T. Williams, D. T. Odom, J. K. Barton. "Variations in DNA Charge Transport with Nucleotide Composition and Sequence,” J. Am. Chem. Soc. 122 (2000) 9048-9049.

D. A. Vicic, D. T. Odom, M. E. Nunez, D. A. Gianolio, L. W. McLaughlin, J. K. Barton. "Oxidative Repair of a Thymine Dimer in DNA from a Distance by a Covalently Linked Organic Intercalator," J. Am. Chem. Soc. 122 (2000) 8603-8611.

D. T. Odom, E. A. Dill, J. K. Barton. "Robust Charge Transport in DNA Double Crossover Assemblies," Chemistry & Biology 7 (2000) 475-481.

D. T. Odom, C. J. Gramer, S. A. Hildebrand, S. E. Sherman. "Synthesis and Characterization of Magnesium and Zinc Complexes of 1,4,7-Triazacyclononane-N-Acetate. Potential Models for the Active Site of RuBisCo," Inorganica Chimica Acta 247 (2000) 404-411.

K. E. Erkkila, D. T. Odom, J. K. Barton. "Recognition and Reaction of Metallointercalators with DNA," Chemical Reviews 99 (1999) 2777-2796.

D. T. Odom, C. S. Parker, J. K. Barton. "Site-Specific Inhibition of Transcription Factor Binding to DNA by a Metallointercalator," Biochemistry 38 (1999) 5155-5163.

Complete list

Palomero T, Lim WK, Odom DT, Sulis ML, Real PJ, Margolin A, Barnes KC, O'Neil J, Neuberg D, Weng AP, Aster JC, Sigaux F, Soulier J, Look AT, Young RA, Califano A, and Ferrando AA. NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth. Proc Natl Acad Sci U S A. 2006 Nov 28;103(48):18261-6. DOI:10.1073/pnas.0606108103 | Wardle FC, Odom DT, Bell GW, Yuan B, Danford TW, Wiellette EL, Herbolsheimer E, Sive HL, Young RA, and Smith JC. Zebrafish promoter microarrays identify actively transcribed embryonic genes. Genome Biol. 2006;7(8):R71. DOI:10.1186/gb-2006-7-8-R71 | Odom DT, Dowell RD, Jacobsen ES, Nekludova L, Rolfe PA, Danford TW, Gifford DK, Fraenkel E, Bell GI, and Young RA. Core transcriptional regulatory circuitry in human hepatocytes. Mol Syst Biol. 2006;2:2006.0017. DOI:10.1038/msb4100059 | Lee TI, Jenner RG, Boyer LA, Guenther MG, Levine SS, Kumar RM, Chevalier B, Johnstone SE, Cole MF, Isono K, Koseki H, Fuchikami T, Abe K, Murray HL, Zucker JP, Yuan B, Bell GW, Herbolsheimer E, Hannett NM, Sun K, Odom DT, Otte AP, Volkert TL, Bartel DP, Melton DA, Gifford DK, Jaenisch R, and Young RA. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell. 2006 Apr 21;125(2):301-13. DOI:10.1016/j.cell.2006.02.043 | Palomero T, Odom DT, O'Neil J, Ferrando AA, Margolin A, Neuberg DS, Winter SS, Larson RS, Li W, Liu XS, Young RA, and Look AT. Transcriptional regulatory networks downstream of TAL1/SCL in T-cell acute lymphoblastic leukemia. Blood. 2006 Aug 1;108(3):986-92. DOI:10.1182/blood-2005-08-3482 | Scacheri PC, Davis S, Odom DT, Crawford GE, Perkins S, Halawi MJ, Agarwal SK, Marx SJ, Spiegel AM, Meltzer PS, and Collins FS. Genome-wide analysis of menin binding provides insights into MEN1 tumorigenesis. PLoS Genet. 2006 Apr;2(4):e51. DOI:10.1371/journal.pgen.0020051 | Macisaac KD, Gordon DB, Nekludova L, Odom DT, Schreiber J, Gifford DK, Young RA, and Fraenkel E. A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data. Bioinformatics. 2006 Feb 15;22(4):423-9. DOI:10.1093/bioinformatics/bti815 | 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 cAMP-response element binding protein occupancy, phosphorylation, and target gene activation in human tissues. Proc Natl Acad Sci U S A. 2005 Mar 22;102(12):4459-64. DOI:10.1073/pnas.0501076102 | Odom DT, Zizlsperger N, Gordon DB, Bell GW, Rinaldi NJ, Murray HL, Volkert TL, Schreiber J, Rolfe PA, Gifford DK, Fraenkel E, Bell GI, and Young RA. Control of pancreas and liver gene expression by HNF transcription factors. Science. 2004 Feb 27;303(5662):1378-81. DOI:10.1126/science.1089769 | Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, and Young RA. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science. 2002 Oct 25;298(5594):799-804. DOI:10.1126/science.1075090 | Erkkila KE, Odom DT, and Barton JK. Recognition and reaction of metallointercalators with DNA. Chem Rev. 1999 Sep 8;99(9):2777-96. DOI:10.1021/cr9804341 | Odom DT and Barton JK. Long-range oxidative damage in DNA/RNA duplexes. Biochemistry. 2001 Jul 31;40(30):8727-37. DOI:10.1021/bi0102961 | Odom DT, Dill EA, and Barton JK. Charge transport through DNA four-way junctions. Nucleic Acids Res. 2001 May 15;29(10):2026-33. DOI:10.1093/nar/29.10.2026 | D. T. Odom, C. J. Gramer, S. A. Hildebrand, S. E. Sherman. "Synthesis and Characterization of Magnesium and Zinc Complexes of 1,4,7-Triazacyclononane-N-Acetate. Potential Models for the Active Site of RuBisCo," Inorganica Chimica Acta 247 (2000) 404-411. Odom DT, Dill EA, and Barton JK. Robust charge transport in DNA double crossover assemblies. Chem Biol. 2000 Jul;7(7):475-81. DOI:10.1016/s1074-5521(00)00133-2 | Odom DT, Parker CS, and Barton JK. Site-specific inhibition of transcription factor binding to DNA by a metallointercalator. Biochemistry. 1999 Apr 20;38(16):5155-63. DOI:10.1021/bi9827969 |