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Recent Publications

PDF reprints are provided below within the context of fair use. Please obtain copies from the publisher if appropriate. Note: †co-first, * corresponding

Global Gene Expression Profiling Reveals SPINK1 as a Potential Hepatocellular Carcinoma Marker.
PLoS-ONE, March 2013
Marshall A†, Lukk M†, Kutter C, Davies S, Alexander G, Odom D.T.
URL

CTCF and Cohesin: Linking Gene Regulatory Elements with Their Targets.
Cell, March 2013
Merkenschlager M, Odom D.T.

Latent Regulatory Potential of Human-Specific Repetitive Elements. Molecular Cell, December 2012
Ward M.C†, Wilson M.D†, Barbosa-Morais N.L, Schmidt D, Stark R, Pan Q, Schwalie P.C, Menon S, Lukk M, Watt S, Thybert D, Kutter C, Kirschner K, Flicek P, Blencowe B.J, D.T. Odom* . URL

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression.
Genome Research., 2012 December
Goncalves A†, Leigh-Brown S†, Thybert D, Stefflova K, Turro E, Flicek P, Brazma A, Odom D.T, Marioni J.C.

Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression
PLoS-Genetics, July 2012
C. Kutter†, S. Watt†, K. Stefflova, M. D. Wilson, A. Goncalves, C. P. Ponting*, D.T. Odom*, A. C. Marques*.
URL

Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules.
Genome Research., November 2012
Faure A.J†, Schmidt D†, Watt S, Schwalie P.C, Wilson M.D, Xu H, Ramsay R.G, Odom D.T, Flicek P.

Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages
Cell, January 2012
D. Schmidt†, P. C. Schwalie†, M. D. Wilson, B. Ballester, A. Goncalves, C. Kutter, G. Brown, A. Marshall, P. Flicek*, D.T. Odom*.
URL

Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes
Nature Genetics, August 2011
C. Kutter†, G. D. Brown†, A. Goncalves, M. D. Wilson, S. Watt, A. Brazma, R. J. White, D.T. Odom*.
URL

Nuclear transcription factors in mammalian mitochondria
Genome Biology, 2010
S. Leigh-Brown, J. A. Enriquez, D.T. Odom*
URL

Five vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding
Science, May 2010
D. Schmidt†, M. D. Wilson†, B. Ballester†, P. C. Schwalie, G. D. Brown, A. Marshall, C. Kutter, S. Watt, C. Martinez-Jimenez, S. Mackay, I. Talianidis, P. Flicek*, D.T. Odom*
URL

A CTCF-independent role for cohesin in tissue-specific transcription
Genome Research, April 2010
D. Schmidt†, P. C. Schwalie†, C. S. Ross-Innes, A. Hurtado, G. D. Brown, J. S. Carroll, P. Flicek, D.T. Odom*
URL † co-first

The evolution of transcriptional regulation in mammals
Current Opinion in Genetics and Development, November 2009
M. D. Wilson, D.T. Odom*
URL

Species-specific transcription in mice carrying human chromosome 21
Science, October 2008
M. D. Wilson†, N. Barbosa-Morais†, D. Schmidt, C. M. Conboy, L. Vanes, V. Tybulewicz, E. Fisher, S. Tavare, D.T. Odom*
[1] † co-first

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*
URL

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

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

Complete list of Duncan Odom

1. Laudadio I, Manfroid I, Achouri Y, Schmidt D, Wilson MD, Cordi S, Thorrez L, Knoops L, Jacquemin P, Schuit F, Pierreux CE, Odom DT, Peers B, Lemaigre FPA Feedback Loop Between The Liver-Enriched Transcription Factor Network and Mir-122 Controls Hepatocyte Differentiation. Gastroenterology. 2011 Sep 12. 2. Holmes KA, Hurtado A, Brown GD, Launchbury R, Ross-Innes CS, Hadfield J, Odom DT, Carroll JS: Breast Cancer Special Feature: Transducin-like enhancer protein 1 mediates estrogen receptor binding and transcriptional activity in breast cancer cells. Proc Natl Acad Sci USA 2011, 10.1073/pnas.1018863108. 3. Ip JY, Schmidt D, Pan Q, Ramani AK, Fraser AG, Odom DT, Blencowe BJ: Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation. Genome Res 2011, 21:390-40110.1101/gr.111070.110. 4. Odom DT: Identification of Transcription Factor-DNA Interactions In Vivo. Subcell. Biochem. 2011, 52:175-19110.1007/978-90-481-9069-0_8. 5. Schmidt D, Wilson MD, Ballester B, Schwalie PC, Brown GD, Marshall A, Kutter C, Watt S, Martinez-Jimenez CP, Mackay S, Talianidis I, Flicek P, Odom DT: Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science 2010, 328:1036-104010.1126/science.1186176. 6. Schmidt D, Schwalie PC, Ross-Innes CS, Hurtado A, Brown GD, Carroll JS, Flicek P, Odom DT: A CTCF-independent role for cohesin in tissue-specific transcription. Genome Res 2010, 20:578-58810.1101/gr.100479.109. 7. Bienvenu F, Jirawatnotai S, Elias JE, Meyer CA, Mizeracka K, Marson A, Frampton GM, Cole MF, Odom DT, Odajima J, Geng Y, Zagozdzon A, Jecrois M, Young RA, Liu XS, Cepko CL, Gygi SP, Sicinski P: Transcriptional role of cyclin D1 in development revealed by a genetic-proteomic screen. Nature 2010, 463:374-37810.1038/nature08684. 8. Leigh-Brown S, Enriquez JA, Odom DT: Nuclear transcription factors in mammalian mitochondria. Genome Biol 2010, 11:21510.1186/gb-2010-11-7-215. 9. Wilson MD, Odom DT: Evolution of transcriptional control in mammals. Curr Opin Genet Dev 2009, 19:579-58510.1016/j.gde.2009.10.003. 10. Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT: ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods 2009, 48:240-24810.1016/j.ymeth.2009.03.001. 11. Wilson MD, Barbosa-Morais NL, Schmidt D, Conboy CM, Vanes L, Tybulewicz VLJ, Fisher EMC, Tavaré S, Odom DT: Species-specific transcription in mice carrying human chromosome 21. Science 2008, 322:434-43810.1126/science.1160930. 12. Schmidt D, Stark R, Wilson MD, Brown GD, Odom DT: Genome-scale validation of deep-sequencing libraries. PLoS ONE 2008, 3:e371310.1371/journal.pone.0003713. 13. Conboy CM, Spyrou C, Thorne NP, Wade EJ, Barbosa-Morais NL, Wilson MD, Bhattacharjee A, Young RA, Tavaré S, Lees JA, Odom DT: Cell cycle genes are the evolutionarily conserved targets of the E2F4 transcription factor. PLoS ONE 2007, 2:e106110.1371/journal.pone.0001061. 14. Odom DT, Dowell RD, Jacobsen ES, Gordon W, Danford TW, MacIsaac KD, Rolfe PA, Conboy CM, Gifford DK, Fraenkel E: Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat Genet 2007, 39:730-73210.1038/ng2047. 15. 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, Ferrando AA: NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth. Proc Natl Acad Sci USA 2006, 103:18261-1826610.1073/pnas.0606108103. 16. Palomero T, Odom DT, O'Neil J, Ferrando AA, Margolin A, Neuberg DS, Winter SS, Larson RS, Li W, Liu XS, Young RA, Look AT: Transcriptional regulatory networks downstream of TAL1/SCL in T-cell acute lymphoblastic leukemia. Blood 2006, 108:986-99210.1182/blood-2005-08-3482. 17. 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, Young RA: Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 2006, 125:301-31310.1016/j.cell.2006.02.043. 18. Scacheri PC, Davis S, Odom DT, Crawford GE, Perkins S, Halawi MJ, Agarwal SK, Marx SJ, Spiegel AM, Meltzer PS, Collins FS: Genome-wide analysis of menin binding provides insights into MEN1 tumorigenesis. PLoS Genet 2006, 2:e5110.1371/journal.pgen.0020051. 19. 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 2006, 22:423-42910.1093/bioinformatics/bti815. 20. Wardle FC, Odom DT, Bell GW, Yuan B, Danford TW, Wiellette EL, Herbolsheimer E, Sive HL, Young RA, Smith JC: Zebrafish promoter microarrays identify actively transcribed embryonic genes. Genome Biol 2006, 7:R7110.1186/gb-2006-7-8-R71. 21. Odom DT, Dowell RD, Jacobsen ES, Nekludova L, Rolfe PA, Danford TW, Gifford DK, Fraenkel E, Bell GI, Young RA: Core transcriptional regulatory circuitry in human hepatocytes. Mol Syst Biol 2006, 2:2006.001710.1038/msb4100059. 22. Zhang X, Odom DT, Koo S, 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, Montminy M: Genome-wide analysis of cAMP-response element binding protein occupancy, phosphorylation, and target gene activation in human tissues. Proc Natl Acad Sci USA 2005, 102:4459-446410.1073/pnas.0501076102. 23. Odom DT, Zizlsperger N, Gordon DB, Bell GW, Rinaldi NJ, Murray HL, Volkert TL, Schreiber J, Rolfe PA, Gifford DK, Fraenkel E, Bell GI, Young RA: Control of pancreas and liver gene expression by HNF transcription factors. Science 2004, 303:1378-138110.1126/science.1089769. 24. 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 J, Volkert TL, Fraenkel E, Gifford DK, Young RA: Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 2002, 298:799-80410.1126/science.1075090. 25. Odom DT, Barton JK: Long-range oxidative damage in DNA/RNA duplexes. Biochemistry 2001, 40:8727-8737. 26. Odom DT, Dill EA, Barton JK: Charge transport through DNA four-way junctions. Nucleic Acids Res 2001, 29:2026-2033. 27. Odom DT, Dill EA, Barton JK: Robust charge transport in DNA double crossover assemblies. Chem. Biol. 2000, 7:475-481. 28. Erkkila KE, Odom DT, Barton JK: Recognition and reaction of metallointercalators with DNA. Chem. Rev. 1999, 99:2777-2796. 29. Odom DT, Parker CS, Barton JK: Site-specific inhibition of transcription factor binding to DNA by a metallointercalator. Biochemistry 1999, 38:5155-516310.1021/bi9827969.