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Duncan T. Odom - Publications

Affiliations: 
University of Cambridge, Cambridge, England, United Kingdom 
 2001 California Institute of Technology, Pasadena, CA 
Website:
http://www.cruk.cam.ac.uk/research-groups/odom-group

47 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2015 Leigh-Brown S, Goncalves A, Thybert D, Stefflova K, Watt S, Flicek P, Brazma A, Marioni JC, Odom DT. Regulatory Divergence of Transcript Isoforms in a Mammalian Model System. Plos One. 10: e0137367. PMID 26339903 DOI: 10.1371/Journal.Pone.0137367  1
2015 Vietri Rudan M, Barrington C, Henderson S, Ernst C, Odom DT, Tanay A, Hadjur S. Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture. Cell Reports. 10: 1297-309. PMID 25732821 DOI: 10.1016/J.Celrep.2015.02.004  1
2015 Villar D, Berthelot C, Aldridge S, Rayner TF, Lukk M, Pignatelli M, Park TJ, Deaville R, Erichsen JT, Jasinska AJ, Turner JM, Bertelsen MF, Murchison EP, Flicek P, Odom DT. Enhancer evolution across 20 mammalian species. Cell. 160: 554-66. PMID 25635462 DOI: 10.1016/J.Cell.2015.01.006  1
2015 Wong ES, Thybert D, Schmitt BM, Stefflova K, Odom DT, Flicek P. Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals. Genome Research. 25: 167-78. PMID 25394363 DOI: 10.1101/Gr.177840.114  1
2014 Ballester B, Medina-Rivera A, Schmidt D, Gonzàlez-Porta M, Carlucci M, Chen X, Chessman K, Faure AJ, Funnell AP, Goncalves A, Kutter C, Lukk M, Menon S, McLaren WM, Stefflova K, ... ... Odom DT, et al. Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways. Elife. 3: e02626. PMID 25279814 DOI: 10.7554/Elife.02626  1
2014 Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C, Barrell D, Batzer MA, ... ... Odom DT, et al. Gibbon genome and the fast karyotype evolution of small apes. Nature. 513: 195-201. PMID 25209798 DOI: 10.1038/Nature13679  1
2014 Schmitt BM, Rudolph KL, Karagianni P, Fonseca NA, White RJ, Talianidis I, Odom DT, Marioni JC, Kutter C. High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface. Genome Research. 24: 1797-807. PMID 25122613 DOI: 10.1101/Gr.176784.114  1
2014 Blanco S, Dietmann S, Flores JV, Hussain S, Kutter C, Humphreys P, Lukk M, Lombard P, Treps L, Popis M, Kellner S, Hölter SM, Garrett L, Wurst W, Becker L, ... ... Odom DT, et al. Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders. The Embo Journal. 33: 2020-39. PMID 25063673 DOI: 10.15252/Embj.201489282  1
2014 Villar D, Flicek P, Odom DT. Evolution of transcription factor binding in metazoans - mechanisms and functional implications. Nature Reviews. Genetics. 15: 221-33. PMID 24590227 DOI: 10.1038/Nrg3481  1
2013 Schwalie PC, Ward MC, Cain CE, Faure AJ, Gilad Y, Odom DT, Flicek P. Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes. Genome Biology. 14: R148. PMID 24380390 DOI: 10.1186/Gb-2013-14-12-R148  1
2013 Aldridge S, Watt S, Quail MA, Rayner T, Lukk M, Bimson MF, Gaffney D, Odom DT. AHT-ChIP-seq: a completely automated robotic protocol for high-throughput chromatin immunoprecipitation. Genome Biology. 14: R124. PMID 24200198 DOI: 10.1186/Gb-2013-14-11-R124  1
2013 Stefflova K, Thybert D, Wilson MD, Streeter I, Aleksic J, Karagianni P, Brazma A, Adams DJ, Talianidis I, Marioni JC, Flicek P, Odom DT. Cooperativity and rapid evolution of cobound transcription factors in closely related mammals. Cell. 154: 530-40. PMID 23911320 DOI: 10.1016/J.Cell.2013.07.007  1
2013 Hussain S, Sajini AA, Blanco S, Dietmann S, Lombard P, Sugimoto Y, Paramor M, Gleeson JG, Odom DT, Ule J, Frye M. NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs. Cell Reports. 4: 255-61. PMID 23871666 DOI: 10.1016/J.Celrep.2013.06.029  1
2013 Funnell AP, Wilson MD, Ballester B, Mak KS, Burdach J, Magan N, Pearson RC, Lemaigre FP, Stowell KM, Odom DT, Flicek P, Crossley M. A CpG mutational hotspot in a ONECUT binding site accounts for the prevalent variant of hemophilia B Leyden. American Journal of Human Genetics. 92: 460-7. PMID 23472758 DOI: 10.1016/J.Ajhg.2013.02.003  1
2013 Long HK, Sims D, Heger A, Blackledge NP, Kutter C, Wright ML, Grützner F, Odom DT, Patient R, Ponting CP, Klose RJ. Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates. Elife. 2: e00348. PMID 23467541 DOI: 10.7554/Elife.00348  1
2013 Ward MC, Wilson MD, Barbosa-Morais NL, Schmidt D, Stark R, Pan Q, Schwalie PC, Menon S, Lukk M, Watt S, Thybert D, Kutter C, Kirschner K, Flicek P, Blencowe BJ, ... Odom DT, et al. Latent regulatory potential of human-specific repetitive elements. Molecular Cell. 49: 262-72. PMID 23246434 DOI: 10.1016/J.Molcel.2012.11.013  1
2012 Barbosa-Morais NL, Irimia M, Pan Q, Xiong HY, Gueroussov S, Lee LJ, Slobodeniuc V, Kutter C, Watt S, Colak R, Kim T, Misquitta-Ali CM, Wilson MD, Kim PM, Odom DT, et al. The evolutionary landscape of alternative splicing in vertebrate species. Science (New York, N.Y.). 338: 1587-93. PMID 23258890 DOI: 10.1126/Science.1230612  1
2012 Goncalves A, Leigh-Brown S, Thybert D, Stefflova K, Turro E, Flicek P, Brazma A, Odom DT, Marioni JC. Extensive compensatory cis-trans regulation in the evolution of mouse gene expression. Genome Research. 22: 2376-84. PMID 22919075 DOI: 10.1101/Gr.142281.112  1
2012 Kutter C, Watt S, Stefflova K, Wilson MD, Goncalves A, Ponting CP, Odom DT, Marques AC. Rapid turnover of long noncoding RNAs and the evolution of gene expression. Plos Genetics. 8: e1002841. PMID 22844254 DOI: 10.1371/Journal.Pgen.1002841  1
2012 Chandra T, Kirschner K, Thuret JY, Pope BD, Ryba T, Newman S, Ahmed K, Samarajiwa SA, Salama R, Carroll T, Stark R, Janky R, Narita M, Xue L, Chicas A, ... ... Odom DT, et al. Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation. Molecular Cell. 47: 203-14. PMID 22795131 DOI: 10.1016/J.Molcel.2012.06.010  1
2012 Faure AJ, Schmidt D, Watt S, Schwalie PC, Wilson MD, Xu H, Ramsay RG, Odom DT, Flicek P. Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules. Genome Research. 22: 2163-75. PMID 22780989 DOI: 10.1101/Gr.136507.111  1
2012 Pope BD, Chandra T, Buckley Q, Hoare M, Ryba T, Wiseman FK, Kuta A, Wilson MD, Odom DT, Gilbert DM. Replication-timing boundaries facilitate cell-type and species-specific regulation of a rearranged human chromosome in mouse. Human Molecular Genetics. 21: 4162-70. PMID 22736031 DOI: 10.1093/Hmg/Dds232  1
2012 Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, ... ... Odom DT, et al. Insights into hominid evolution from the gorilla genome sequence. Nature. 483: 169-75. PMID 22398555 DOI: 10.1038/Nature10842  1
2012 Schmidt D, Schwalie PC, Wilson MD, Ballester B, Gonçalves A, Kutter C, Brown GD, Marshall A, Flicek P, Odom DT. Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages. Cell. 148: 335-48. PMID 22244452 DOI: 10.1016/J.Cell.2011.11.058  1
2012 Holmes KA, Hurtado A, Brown GD, Launchbury R, Ross-Innes CS, Hadfield J, Odom DT, Carroll JS. Transducin-like enhancer protein 1 mediates estrogen receptor binding and transcriptional activity in breast cancer cells. Proceedings of the National Academy of Sciences of the United States of America. 109: 2748-53. PMID 21536917 DOI: 10.1073/Pnas.1018863108  1
2011 Nascimento EM, Cox CL, MacArthur S, Hussain S, Trotter M, Blanco S, Suraj M, Nichols J, Kübler B, Benitah SA, Hendrich B, Odom DT, Frye M. The opposing transcriptional functions of Sin3a and c-Myc are required to maintain tissue homeostasis. Nature Cell Biology. 13: 1395-405. PMID 22101514 DOI: 10.1038/Ncb2385  1
2011 Kutter C, Brown GD, Gonçalves A, Wilson MD, Watt S, Brazma A, White RJ, Odom DT. Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes. Nature Genetics. 43: 948-55. PMID 21873999 DOI: 10.1038/Ng.906  1
2011 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 Research. 21: 390-401. PMID 21163941 DOI: 10.1101/Gr.111070.110  1
2010 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 (New York, N.Y.). 328: 1036-40. PMID 20378774 DOI: 10.1126/Science.1186176  1
2010 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 Research. 20: 578-88. PMID 20219941 DOI: 10.1101/Gr.100479.109  1
2010 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, et al. Transcriptional role of cyclin D1 in development revealed by a genetic-proteomic screen. Nature. 463: 374-8. PMID 20090754 DOI: 10.1038/Nature08684  1
2009 Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. ChIP-seq: Using high-throughput sequencing to discover protein-DNA interactions Methods. 48: 240-248. PMID 19275939 DOI: 10.1016/J.Ymeth.2009.03.001  1
2007 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. 2: e1061. PMID 17957245 DOI: 10.1371/Journal.Pone.0001061  1
2006 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, et al. NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth. Proceedings of the National Academy of Sciences of the United States of America. 103: 18261-6. PMID 17114293 DOI: 10.1073/Pnas.0606108103  1
2006 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 Biology. 7: R71. PMID 16889661 DOI: 10.1186/Gb-2006-7-8-R71  1
2006 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. Molecular Systems Biology. 2: 2006.0017. PMID 16738562 DOI: 10.1038/Msb4100059  1
2006 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, ... ... Odom DT, et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell. 125: 301-13. PMID 16630818 DOI: 10.1016/J.Cell.2006.02.043  1
2006 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. 108: 986-92. PMID 16621969 DOI: 10.1182/Blood-2005-08-3482  1
2006 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 Genetics. 2: e51. PMID 16604156 DOI: 10.1371/Journal.Pgen.0020051  1
2006 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 (Oxford, England). 22: 423-9. PMID 16332710 DOI: 10.1093/Bioinformatics/Bti815  1
2004 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 (New York, N.Y.). 303: 1378-81. PMID 14988562 DOI: 10.1126/Science.1089769  1
2002 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, et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (New York, N.Y.). 298: 799-804. PMID 12399584 DOI: 10.1126/Science.1075090  1
2001 Odom DT, Barton JK. Long-range oxidative damage in DNA/RNA duplexes. Biochemistry. 40: 8727-37. PMID 11467932 DOI: 10.1021/Bi0102961  1
2001 Odom DT, Dill EA, Barton JK. Charge transport through DNA four-way junctions Nucleic Acids Research. 29: 2026-2033. PMID 11353071 DOI: 10.1093/Nar/29.10.2026  1
2000 Odom DT, Dill EA, Barton JK. Robust charge transport in DNA double crossover assemblies Chemistry and Biology. 7: 475-481. PMID 10903935 DOI: 10.1016/S1074-5521(00)00133-2  1
1999 Erkkila KE, Odom DT, Barton JK. Recognition and reaction of metallointercalators with DNA. Chemical Reviews. 99: 2777-96. PMID 11749500 DOI: 10.1021/Cr9804341  1
1999 Odom DT, Parker CS, Barton JK. Site-specific inhibition of transcription factor binding to DNA by a metallointercalator. Biochemistry. 38: 5155-63. PMID 10213621 DOI: 10.1021/Bi9827969  1
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