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Items: 1 to 50 of 89

1.

Bookmarking by Non-pioneer Transcription Factors during Liver Development Establishes Competence for Future Gene Activation.

Karagianni P, Moulos P, Schmidt D, Odom DT, Talianidis I.

Cell Rep. 2020 Feb 4;30(5):1319-1328.e6. doi: 10.1016/j.celrep.2020.01.006.

2.

Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains.

Kentepozidou E, Aitken SJ, Feig C, Stefflova K, Ibarra-Soria X, Odom DT, Roller M, Flicek P.

Genome Biol. 2020 Jan 7;21(1):5. doi: 10.1186/s13059-019-1894-x.

3.

IL-7-dependent compositional changes within the γδ T cell pool in lymph nodes during ageing lead to an unbalanced anti-tumour response.

Chen HC, Eling N, Martinez-Jimenez CP, O'Brien LM, Carbonaro V, Marioni JC, Odom DT, de la Roche M.

EMBO Rep. 2019 Aug;20(8):e47379. doi: 10.15252/embr.201847379. Epub 2019 Jul 8.

4.

Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia.

Yang M, Vesterlund M, Siavelis I, Moura-Castro LH, Castor A, Fioretos T, Jafari R, Lilljebjörn H, Odom DT, Olsson L, Ravi N, Woodward EL, Harewood L, Lehtiö J, Paulsson K.

Nat Commun. 2019 Apr 3;10(1):1519. doi: 10.1038/s41467-019-09469-3.

5.

Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis.

Ernst C, Eling N, Martinez-Jimenez CP, Marioni JC, Odom DT.

Nat Commun. 2019 Mar 19;10(1):1251. doi: 10.1038/s41467-019-09182-1.

6.

Crisflash: open-source software to generate CRISPR guide RNAs against genomes annotated with individual variation.

Jacquin ALS, Odom DT, Lukk M.

Bioinformatics. 2019 Sep 1;35(17):3146-3147. doi: 10.1093/bioinformatics/btz019.

7.

Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci.

Lilue J, Doran AG, Fiddes IT, Abrudan M, Armstrong J, Bennett R, Chow W, Collins J, Collins S, Czechanski A, Danecek P, Diekhans M, Dolle DD, Dunn M, Durbin R, Earl D, Ferguson-Smith A, Flicek P, Flint J, Frankish A, Fu B, Gerstein M, Gilbert J, Goodstadt L, Harrow J, Howe K, Ibarra-Soria X, Kolmogorov M, Lelliott CJ, Logan DW, Loveland J, Mathews CE, Mott R, Muir P, Nachtweide S, Navarro FCP, Odom DT, Park N, Pelan S, Pham SK, Quail M, Reinholdt L, Romoth L, Shirley L, Sisu C, Sjoberg-Herrera M, Stanke M, Steward C, Thomas M, Threadgold G, Thybert D, Torrance J, Wong K, Wood J, Yalcin B, Yang F, Adams DJ, Paten B, Keane TM.

Nat Genet. 2018 Nov;50(11):1574-1583. doi: 10.1038/s41588-018-0223-8. Epub 2018 Oct 1.

8.

Integrative detection and analysis of structural variation in cancer genomes.

Dixon JR, Xu J, Dileep V, Zhan Y, Song F, Le VT, Yardımcı GG, Chakraborty A, Bann DV, Wang Y, Clark R, Zhang L, Yang H, Liu T, Iyyanki S, An L, Pool C, Sasaki T, Rivera-Mulia JC, Ozadam H, Lajoie BR, Kaul R, Buckley M, Lee K, Diegel M, Pezic D, Ernst C, Hadjur S, Odom DT, Stamatoyannopoulos JA, Broach JR, Hardison RC, Ay F, Noble WS, Dekker J, Gilbert DM, Yue F.

Nat Genet. 2018 Oct;50(10):1388-1398. doi: 10.1038/s41588-018-0195-8. Epub 2018 Sep 10.

9.

CTCF maintains regulatory homeostasis of cancer pathways.

Aitken SJ, Ibarra-Soria X, Kentepozidou E, Flicek P, Feig C, Marioni JC, Odom DT.

Genome Biol. 2018 Aug 7;19(1):106. doi: 10.1186/s13059-018-1484-3.

10.

Mutational landscape of a chemically-induced mouse model of liver cancer.

Connor F, Rayner TF, Aitken SJ, Feig C, Lukk M, Santoyo-Lopez J, Odom DT.

J Hepatol. 2018 Oct;69(4):840-850. doi: 10.1016/j.jhep.2018.06.009. Epub 2018 Jun 26.

11.

Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis.

Stojic L, Lun ATL, Mangei J, Mascalchi P, Quarantotti V, Barr AR, Bakal C, Marioni JC, Gergely F, Odom DT.

Nucleic Acids Res. 2018 Jul 6;46(12):5950-5966. doi: 10.1093/nar/gky437.

12.

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes.

Thybert D, Roller M, Navarro FCP, Fiddes I, Streeter I, Feig C, Martin-Galvez D, Kolmogorov M, Janoušek V, Akanni W, Aken B, Aldridge S, Chakrapani V, Chow W, Clarke L, Cummins C, Doran A, Dunn M, Goodstadt L, Howe K, Howell M, Josselin AA, Karn RC, Laukaitis CM, Jingtao L, Martin F, Muffato M, Nachtweide S, Quail MA, Sisu C, Stanke M, Stefflova K, Van Oosterhout C, Veyrunes F, Ward B, Yang F, Yazdanifar G, Zadissa A, Adams DJ, Brazma A, Gerstein M, Paten B, Pham S, Keane TM, Odom DT, Flicek P.

Genome Res. 2018 Apr;28(4):448-459. doi: 10.1101/gr.234096.117. Epub 2018 Mar 21.

13.

Ageing-associated DNA methylation dynamics are a molecular readout of lifespan variation among mammalian species.

Lowe R, Barton C, Jenkins CA, Ernst C, Forman O, Fernandez-Twinn DS, Bock C, Rossiter SJ, Faulkes CG, Ozanne SE, Walter L, Odom DT, Mellersh C, Rakyan VK.

Genome Biol. 2018 Feb 16;19(1):22. doi: 10.1186/s13059-018-1397-1.

14.

Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression.

Berthelot C, Villar D, Horvath JE, Odom DT, Flicek P.

Nat Ecol Evol. 2018 Jan;2(1):152-163. doi: 10.1038/s41559-017-0377-2. Epub 2017 Nov 27.

15.

The emergence of piRNAs against transposon invasion to preserve mammalian genome integrity.

Ernst C, Odom DT, Kutter C.

Nat Commun. 2017 Nov 10;8(1):1411. doi: 10.1038/s41467-017-01049-7. Review.

16.

Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution.

Wong ES, Schmitt BM, Kazachenka A, Thybert D, Redmond A, Connor F, Rayner TF, Feig C, Ferguson-Smith AC, Marioni JC, Odom DT, Flicek P.

Nat Commun. 2017 Oct 23;8(1):1092. doi: 10.1038/s41467-017-01037-x.

17.

Charting the transcriptional regulatory changes in mouse liver during fasting.

Thierion E, Odom DT.

Hepatology. 2018 Jan;67(1):436-438. doi: 10.1002/hep.29474. No abstract available.

PMID:
28833286
18.

Aging increases cell-to-cell transcriptional variability upon immune stimulation.

Martinez-Jimenez CP, Eling N, Chen HC, Vallejos CA, Kolodziejczyk AA, Connor F, Stojic L, Rayner TF, Stubbington MJT, Teichmann SA, de la Roche M, Marioni JC, Odom DT.

Science. 2017 Mar 31;355(6332):1433-1436. doi: 10.1126/science.aah4115. Erratum in: Science. 2019 Dec 20;366(6472):.

19.

Successful transmission and transcriptional deployment of a human chromosome via mouse male meiosis.

Ernst C, Pike J, Aitken SJ, Long HK, Eling N, Stojic L, Ward MC, Connor F, Rayner TF, Lukk M, Klose RJ, Kutter C, Odom DT.

Elife. 2016 Nov 18;5. pii: e20235. doi: 10.7554/eLife.20235.

20.

Unwinding Limb Development.

Villar D, Odom DT.

Cell. 2016 Oct 20;167(3):598-600. doi: 10.1016/j.cell.2016.10.007.

21.

The Evolutionary Fates of a Large Segmental Duplication in Mouse.

Morgan AP, Holt JM, McMullan RC, Bell TA, Clayshulte AM, Didion JP, Yadgary L, Thybert D, Odom DT, Flicek P, McMillan L, de Villena FP.

Genetics. 2016 Sep;204(1):267-85. doi: 10.1534/genetics.116.191007. Epub 2016 Jul 2.

22.

Mitochondrial heteroplasmy in vertebrates using ChIP-sequencing data.

Rensch T, Villar D, Horvath J, Odom DT, Flicek P.

Genome Biol. 2016 Jun 27;17(1):139. doi: 10.1186/s13059-016-0996-y.

23.

Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States.

Rudolph KL, Schmitt BM, Villar D, White RJ, Marioni JC, Kutter C, Odom DT.

PLoS Genet. 2016 May 11;12(5):e1006024. doi: 10.1371/journal.pgen.1006024. eCollection 2016 May.

24.

Protection of CpG islands from DNA methylation is DNA-encoded and evolutionarily conserved.

Long HK, King HW, Patient RK, Odom DT, Klose RJ.

Nucleic Acids Res. 2016 Aug 19;44(14):6693-706. doi: 10.1093/nar/gkw258. Epub 2016 Apr 15.

25.

Comparative Genomics: One for all.

Odom DT.

Elife. 2016 Feb 11;5. pii: e14150. doi: 10.7554/eLife.14150.

26.

Transcriptional silencing of long noncoding RNA GNG12-AS1 uncouples its transcriptional and product-related functions.

Stojic L, Niemczyk M, Orjalo A, Ito Y, Ruijter AE, Uribe-Lewis S, Joseph N, Weston S, Menon S, Odom DT, Rinn J, Gergely F, Murrell A.

Nat Commun. 2016 Feb 2;7:10406. doi: 10.1038/ncomms10406.

27.

The mechanisms shaping the single-cell transcriptional landscape.

Martinez-Jimenez CP, Odom DT.

Curr Opin Genet Dev. 2016 Apr;37:27-35. doi: 10.1016/j.gde.2015.11.004. Epub 2016 Jan 22. Review.

PMID:
26803530
28.

When the Snake Lost Its Limbs, What Did the Mouse and Lizard Say?

Villar D, Odom DT.

Dev Cell. 2015 Oct 12;35(1):3-4. doi: 10.1016/j.devcel.2015.09.022.

29.

Regulatory Divergence of Transcript Isoforms in a Mammalian Model System.

Leigh-Brown S, Goncalves A, Thybert D, Stefflova K, Watt S, Flicek P, Brazma A, Marioni JC, Odom DT.

PLoS One. 2015 Sep 4;10(9):e0137367. doi: 10.1371/journal.pone.0137367. eCollection 2015.

30.

Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture.

Vietri Rudan M, Barrington C, Henderson S, Ernst C, Odom DT, Tanay A, Hadjur S.

Cell Rep. 2015 Mar 3;10(8):1297-309. doi: 10.1016/j.celrep.2015.02.004. Epub 2015 Feb 26.

31.

Enhancer evolution across 20 mammalian species.

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.

Cell. 2015 Jan 29;160(3):554-66. doi: 10.1016/j.cell.2015.01.006.

32.

Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals.

Wong ES, Thybert D, Schmitt BM, Stefflova K, Odom DT, Flicek P.

Genome Res. 2015 Feb;25(2):167-78. doi: 10.1101/gr.177840.114. Epub 2014 Nov 13.

33.

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways.

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, Watt S, Weirauch MT, Crossley M, Marioni JC, Odom DT, Flicek P, Wilson MD.

Elife. 2014 Oct 3;3:e02626. doi: 10.7554/eLife.02626.

34.

Gibbon genome and the fast karyotype evolution of small apes.

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, Beal K, Blancher A, Bohrson CL, Brameier M, Campbell MS, Capozzi O, Casola C, Chiatante G, Cree A, Damert A, de Jong PJ, Dumas L, Fernandez-Callejo M, Flicek P, Fuchs NV, Gut I, Gut M, Hahn MW, Hernandez-Rodriguez J, Hillier LW, Hubley R, Ianc B, Izsvák Z, Jablonski NG, Johnstone LM, Karimpour-Fard A, Konkel MK, Kostka D, Lazar NH, Lee SL, Lewis LR, Liu Y, Locke DP, Mallick S, Mendez FL, Muffato M, Nazareth LV, Nevonen KA, O'Bleness M, Ochis C, Odom DT, Pollard KS, Quilez J, Reich D, Rocchi M, Schumann GG, Searle S, Sikela JM, Skollar G, Smit A, Sonmez K, ten Hallers B, Terhune E, Thomas GW, Ullmer B, Ventura M, Walker JA, Wall JD, Walter L, Ward MC, Wheelan SJ, Whelan CW, White S, Wilhelm LJ, Woerner AE, Yandell M, Zhu B, Hammer MF, Marques-Bonet T, Eichler EE, Fulton L, Fronick C, Muzny DM, Warren WC, Worley KC, Rogers J, Wilson RK, Gibbs RA.

Nature. 2014 Sep 11;513(7517):195-201. doi: 10.1038/nature13679.

35.

High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface.

Schmitt BM, Rudolph KL, Karagianni P, Fonseca NA, White RJ, Talianidis I, Odom DT, Marioni JC, Kutter C.

Genome Res. 2014 Nov;24(11):1797-807. doi: 10.1101/gr.176784.114. Epub 2014 Aug 13.

36.

Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders.

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, Klopstock T, Fuchs H, Gailus-Durner V, Hrabĕ de Angelis M, Káradóttir RT, Helm M, Ule J, Gleeson JG, Odom DT, Frye M.

EMBO J. 2014 Sep 17;33(18):2020-39. doi: 10.15252/embj.201489282. Epub 2014 Jul 25.

37.

Survival strategies for choosing the right postdoc position.

Odom DT.

Genome Biol. 2014 Mar 10;15(3):107. doi: 10.1186/gb4163.

38.

Evolution of transcription factor binding in metazoans - mechanisms and functional implications.

Villar D, Flicek P, Odom DT.

Nat Rev Genet. 2014 Apr;15(4):221-33. doi: 10.1038/nrg3481. Epub 2014 Mar 4. Review.

39.

Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes.

Schwalie PC, Ward MC, Cain CE, Faure AJ, Gilad Y, Odom DT, Flicek P.

Genome Biol. 2013 Dec 31;14(12):R148. doi: 10.1186/gb-2013-14-12-r148.

40.

Cohesin's role as an active chromatin domain anchorage revealed.

Feig C, Odom DT.

EMBO J. 2013 Dec 11;32(24):3114-5. doi: 10.1038/emboj.2013.248. Epub 2013 Nov 22.

41.

AHT-ChIP-seq: a completely automated robotic protocol for high-throughput chromatin immunoprecipitation.

Aldridge S, Watt S, Quail MA, Rayner T, Lukk M, Bimson MF, Gaffney D, Odom DT.

Genome Biol. 2013 Nov 7;14(11):R124. doi: 10.1186/gb-2013-14-11-r124.

42.

Cooperativity and rapid evolution of cobound transcription factors in closely related mammals.

Stefflova K, Thybert D, Wilson MD, Streeter I, Aleksic J, Karagianni P, Brazma A, Adams DJ, Talianidis I, Marioni JC, Flicek P, Odom DT.

Cell. 2013 Aug 1;154(3):530-40. doi: 10.1016/j.cell.2013.07.007.

43.

NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs.

Hussain S, Sajini AA, Blanco S, Dietmann S, Lombard P, Sugimoto Y, Paramor M, Gleeson JG, Odom DT, Ule J, Frye M.

Cell Rep. 2013 Jul 25;4(2):255-61. doi: 10.1016/j.celrep.2013.06.029. Epub 2013 Jul 18.

44.

How to evaluate a graduate studentship, or choosing the right doctoral advisor.

Odom DT.

Genome Biol. 2013 Apr 29;14(4):114. doi: 10.1186/gb-2013-14-4-114. No abstract available.

45.

Global gene expression profiling reveals SPINK1 as a potential hepatocellular carcinoma marker.

Marshall A, Lukk M, Kutter C, Davies S, Alexander G, Odom DT.

PLoS One. 2013;8(3):e59459. doi: 10.1371/journal.pone.0059459. Epub 2013 Mar 18.

46.

CTCF and cohesin: linking gene regulatory elements with their targets.

Merkenschlager M, Odom DT.

Cell. 2013 Mar 14;152(6):1285-97. doi: 10.1016/j.cell.2013.02.029. Review.

47.

A CpG mutational hotspot in a ONECUT binding site accounts for the prevalent variant of hemophilia B Leyden.

Funnell AP, Wilson MD, Ballester B, Mak KS, Burdach J, Magan N, Pearson RC, Lemaigre FP, Stowell KM, Odom DT, Flicek P, Crossley M.

Am J Hum Genet. 2013 Mar 7;92(3):460-7. doi: 10.1016/j.ajhg.2013.02.003.

48.

Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates.

Long HK, Sims D, Heger A, Blackledge NP, Kutter C, Wright ML, Grützner F, Odom DT, Patient R, Ponting CP, Klose RJ.

Elife. 2013 Feb 26;2:e00348. doi: 10.7554/eLife.00348.

49.

The evolutionary landscape of alternative splicing in vertebrate species.

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, Frey BJ, Blencowe BJ.

Science. 2012 Dec 21;338(6114):1587-93. doi: 10.1126/science.1230612.

PMID:
23258890
50.

Latent regulatory potential of human-specific repetitive elements.

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.

Mol Cell. 2013 Jan 24;49(2):262-72. doi: 10.1016/j.molcel.2012.11.013. Epub 2012 Dec 13.

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