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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
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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
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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
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Tissue-Specific Transcriptional Regulation has Diverged Significantly between Human and Mouse
Nature Genetics, June 2007
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
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Cell cycle genes are the evolutionarily conserved targets of the E2F4 transcription factor
PLoS-ONE, October 2007
C. M. Conboy, C. Spyrou, N. P. Thorne, E. J. Wade, N. L. Barbosa-Morais, M. D. Wilson, A. Bhattacharjee, R. A. Young, S. Tavare, J. A. Lees, D.T. Odom
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Complete list of Duncan Odom

Schmidt D, Stark R, Wilson MD, Brown GD, and Odom DT. Genome-scale validation of deep-sequencing libraries. PLoS One. 2008;3(11):e3713. DOI:10.1371/journal.pone.0003713 | Wilson MD, Barbosa-Morais NL, Schmidt D, Conboy CM, Vanes L, Tybulewicz VL, Fisher EM, Tavaré S, and Odom DT. Species-specific transcription in mice carrying human chromosome 21. Science. 2008 Oct 17;322(5900):434-8. DOI:10.1126/science.1160930 | Conboy CM, Spyrou C, Thorne NP, Wade EJ, Barbosa-Morais NL, Wilson MD, Bhattacharjee A, Young RA, Tavaré S, Lees JA, and Odom DT. Cell cycle genes are the evolutionarily conserved targets of the E2F4 transcription factor. PLoS One. 2007 Oct 24;2(10):e1061. DOI:10.1371/journal.pone.0001061 | Odom DT, Dowell RD, Jacobsen ES, Gordon W, Danford TW, MacIsaac KD, Rolfe PA, Conboy CM, Gifford DK, and Fraenkel E. Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat Genet. 2007 Jun;39(6):730-2. DOI:10.1038/ng2047 | 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 |