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Stable Caenorhabditis elegans chromatin domains separate broadly expressed and developmentally regulated genes.

Evans KJ, Huang N, Stempor P, Chesney MA, Down TA, Ahringer J.

Proc Natl Acad Sci U S A. 2016 Nov 8;113(45):E7020-E7029. doi: 10.1073/pnas.1608162113. Epub 2016 Oct 25.


WormBase 2016: expanding to enable helminth genomic research.

Howe KL, Bolt BJ, Cain S, Chan J, Chen WJ, Davis P, Done J, Down T, Gao S, Grove C, Harris TW, Kishore R, Lee R, Lomax J, Li Y, Muller HM, Nakamura C, Nuin P, Paulini M, Raciti D, Schindelman G, Stanley E, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Wright A, Yook K, Berriman M, Kersey P, Schedl T, Stein L, Sternberg PW.

Nucleic Acids Res. 2016 Jan 4;44(D1):D774-80. doi: 10.1093/nar/gkv1217. Epub 2015 Nov 17.


An interactive genome browser of association results from the UK10K cohorts project.

Geihs M, Yan Y, Walter K, Huang J, Memari Y, Min JL, Mead D; UK10K Consortium, Hubbard TJ, Timpson NJ, Down TA, Soranzo N.

Bioinformatics. 2015 Dec 15;31(24):4029-31. doi: 10.1093/bioinformatics/btv491. Epub 2015 Aug 26.


A comparison of peak callers used for DNase-Seq data.

Koohy H, Down TA, Spivakov M, Hubbard T.

PLoS One. 2014 May 8;9(5):e96303. doi: 10.1371/journal.pone.0096303. eCollection 2014. Erratum in: PLoS One. 2014;9(8):e105136.


Extreme HOT regions are CpG-dense promoters in C. elegans and humans.

Chen RA, Stempor P, Down TA, Zeiser E, Feuer SK, Ahringer J.

Genome Res. 2014 Jul;24(7):1138-46. doi: 10.1101/gr.161992.113. Epub 2014 Mar 20.


Synergistic mechanisms of DNA demethylation during transition to ground-state pluripotency.

Hackett JA, Dietmann S, Murakami K, Down TA, Leitch HG, Surani MA.

Stem Cell Reports. 2013 Dec 17;1(6):518-31. doi: 10.1016/j.stemcr.2013.11.010. eCollection 2013.


Binding of TFIIIC to sine elements controls the relocation of activity-dependent neuronal genes to transcription factories.

Crepaldi L, Policarpi C, Coatti A, Sherlock WT, Jongbloets BC, Down TA, Riccio A.

PLoS Genet. 2013;9(8):e1003699. doi: 10.1371/journal.pgen.1003699. Epub 2013 Aug 15.


Chromatin accessibility data sets show bias due to sequence specificity of the DNase I enzyme.

Koohy H, Down TA, Hubbard TJ.

PLoS One. 2013 Jul 26;8(7):e69853. doi: 10.1371/journal.pone.0069853. Print 2013.


The epigenetic regulator PLZF represses L1 retrotransposition in germ and progenitor cells.

Puszyk W, Down T, Grimwade D, Chomienne C, Oakey RJ, Solomon E, Guidez F.

EMBO J. 2013 Jul 3;32(13):1941-52. doi: 10.1038/emboj.2013.118. Epub 2013 May 31.


Inactive or moderately active human promoters are enriched for inter-individual epialleles.

Gemma C, Ramagopalan SV, Down TA, Beyan H, Hawa MI, Holland ML, Hurd PJ, Giovannoni G, Leslie RD, Ebers GC, Rakyan VK.

Genome Biol. 2013 May 25;14(5):R43. doi: 10.1186/gb-2013-14-5-r43.


The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures.

Chen RA, Down TA, Stempor P, Chen QB, Egelhofer TA, Hillier LW, Jeffers TE, Ahringer J.

Genome Res. 2013 Aug;23(8):1339-47. doi: 10.1101/gr.153668.112. Epub 2013 Apr 2.


Germline DNA demethylation dynamics and imprint erasure through 5-hydroxymethylcytosine.

Hackett JA, Sengupta R, Zylicz JJ, Murakami K, Lee C, Down TA, Surani MA.

Science. 2013 Jan 25;339(6118):448-52. doi: 10.1126/science.1229277. Epub 2012 Dec 6.


Guthrie card methylomics identifies temporally stable epialleles that are present at birth in humans.

Beyan H, Down TA, Ramagopalan SV, Uvebrant K, Nilsson A, Holland ML, Gemma C, Giovannoni G, Boehm BO, Ebers GC, Lernmark Å, Cilio CM, Leslie RD, Rakyan VK.

Genome Res. 2012 Nov;22(11):2138-45. doi: 10.1101/gr.134304.111. Epub 2012 Aug 23.


A functional methylome map of ulcerative colitis.

Häsler R, Feng Z, Bäckdahl L, Spehlmann ME, Franke A, Teschendorff A, Rakyan VK, Down TA, Wilson GA, Feber A, Beck S, Schreiber S, Rosenstiel P.

Genome Res. 2012 Nov;22(11):2130-7. doi: 10.1101/gr.138347.112. Epub 2012 Jul 23.


Genomic targets of Brachyury (T) in differentiating mouse embryonic stem cells.

Evans AL, Faial T, Gilchrist MJ, Down T, Vallier L, Pedersen RA, Wardle FC, Smith JC.

PLoS One. 2012;7(3):e33346. doi: 10.1371/journal.pone.0033346. Epub 2012 Mar 30.


Genome wide analysis of acute myeloid leukemia reveal leukemia specific methylome and subtype specific hypomethylation of repeats.

Saied MH, Marzec J, Khalid S, Smith P, Down TA, Rakyan VK, Molloy G, Raghavan M, Debernardi S, Young BD.

PLoS One. 2012;7(3):e33213. doi: 10.1371/journal.pone.0033213. Epub 2012 Mar 29.


Distinct epigenomic features in end-stage failing human hearts.

Movassagh M, Choy MK, Knowles DA, Cordeddu L, Haider S, Down T, Siggens L, Vujic A, Simeoni I, Penkett C, Goddard M, Lio P, Bennett MR, Foo RS.

Circulation. 2011 Nov 29;124(22):2411-22. doi: 10.1161/CIRCULATIONAHA.111.040071. Epub 2011 Oct 24.


Identification of type 1 diabetes-associated DNA methylation variable positions that precede disease diagnosis.

Rakyan VK, Beyan H, Down TA, Hawa MI, Maslau S, Aden D, Daunay A, Busato F, Mein CA, Manfras B, Dias KR, Bell CG, Tost J, Boehm BO, Beck S, Leslie RD.

PLoS Genet. 2011 Sep;7(9):e1002300. doi: 10.1371/journal.pgen.1002300. Epub 2011 Sep 29.


Comparative methylomics reveals gene-body H3K36me3 in Drosophila predicts DNA methylation and CpG landscapes in other invertebrates.

Nanty L, Carbajosa G, Heap GA, Ratnieks F, van Heel DA, Down TA, Rakyan VK.

Genome Res. 2011 Nov;21(11):1841-50. doi: 10.1101/gr.121640.111. Epub 2011 Sep 22.


Epigenome-wide association studies for common human diseases.

Rakyan VK, Down TA, Balding DJ, Beck S.

Nat Rev Genet. 2011 Jul 12;12(8):529-41. doi: 10.1038/nrg3000. Review.


Systematic bias in high-throughput sequencing data and its correction by BEADS.

Cheung MS, Down TA, Latorre I, Ahringer J.

Nucleic Acids Res. 2011 Aug;39(15):e103. doi: 10.1093/nar/gkr425. Epub 2011 Jun 6.


Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors.

Feber A, Wilson GA, Zhang L, Presneau N, Idowu B, Down TA, Rakyan VK, Noon LA, Lloyd AC, Stupka E, Schiza V, Teschendorff AE, Schroth GP, Flanagan A, Beck S.

Genome Res. 2011 Apr;21(4):515-24. doi: 10.1101/gr.109678.110. Epub 2011 Feb 1.


Dalliance: interactive genome viewing on the web.

Down TA, Piipari M, Hubbard TJ.

Bioinformatics. 2011 Mar 15;27(6):889-90. doi: 10.1093/bioinformatics/btr020. Epub 2011 Jan 19.


Assessing computational methods of cis-regulatory module prediction.

Su J, Teichmann SA, Down TA.

PLoS Comput Biol. 2010 Dec 2;6(12):e1001020. doi: 10.1371/journal.pcbi.1001020.


Integrated genetic and epigenetic analysis identifies haplotype-specific methylation in the FTO type 2 diabetes and obesity susceptibility locus.

Bell CG, Finer S, Lindgren CM, Wilson GA, Rakyan VK, Teschendorff AE, Akan P, Stupka E, Down TA, Prokopenko I, Morison IM, Mill J, Pidsley R; International Type 2 Diabetes 1q Consortium, Deloukas P, Frayling TM, Hattersley AT, McCarthy MI, Beck S, Hitman GA.

PLoS One. 2010 Nov 18;5(11):e14040. doi: 10.1371/journal.pone.0014040.


Genome-wide identification of targets and function of individual MicroRNAs in mouse embryonic stem cells.

Hanina SA, Mifsud W, Down TA, Hayashi K, O'Carroll D, Lao K, Miska EA, Surani MA.

PLoS Genet. 2010 Oct 21;6(10):e1001163. doi: 10.1371/journal.pgen.1001163.


Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated.

Choy MK, Movassagh M, Goh HG, Bennett MR, Down TA, Foo RS.

BMC Genomics. 2010 Sep 27;11:519. doi: 10.1186/1471-2164-11-519.


Metamotifs--a generative model for building families of nucleotide position weight matrices.

Piipari M, Down TA, Hubbard TJ.

BMC Bioinformatics. 2010 Jun 25;11:348. doi: 10.1186/1471-2105-11-348.


Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains.

Rakyan VK, Down TA, Maslau S, Andrew T, Yang TP, Beyan H, Whittaker P, McCann OT, Finer S, Valdes AM, Leslie RD, Deloukas P, Spector TD.

Genome Res. 2010 Apr;20(4):434-9. doi: 10.1101/gr.103101.109. Epub 2010 Mar 10.


iMotifs: an integrated sequence motif visualization and analysis environment.

Piipari M, Down TA, Saini H, Enright A, Hubbard TJ.

Bioinformatics. 2010 Mar 15;26(6):843-4. doi: 10.1093/bioinformatics/btq026. Epub 2010 Jan 26.


Differential DNA methylation correlates with differential expression of angiogenic factors in human heart failure.

Movassagh M, Choy MK, Goddard M, Bennett MR, Down TA, Foo RS.

PLoS One. 2010 Jan 13;5(1):e8564. doi: 10.1371/journal.pone.0008564.


DNA methylation-mediated down-regulation of DNA methyltransferase-1 (DNMT1) is coincident with, but not essential for, global hypomethylation in human placenta.

Novakovic B, Wong NC, Sibson M, Ng HK, Morley R, Manuelpillai U, Down T, Rakyan VK, Beck S, Hiendleder S, Roberts CT, Craig JM, Saffery R.

J Biol Chem. 2010 Mar 26;285(13):9583-93. doi: 10.1074/jbc.M109.064956. Epub 2010 Jan 13.


Smicl is required for phosphorylation of RNA polymerase II and affects 3'-end processing of RNA at the midblastula transition in Xenopus.

Collart C, Ramis JM, Down TA, Smith JC.

Development. 2009 Oct;136(20):3451-61. doi: 10.1242/dev.027714.


Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level.

Bruce AW, López-Contreras AJ, Flicek P, Down TA, Dhami P, Dillon SC, Koch CM, Langford CF, Dunham I, Andrews RM, Vetrie D.

Genome Res. 2009 Jun;19(6):994-1005. doi: 10.1101/gr.089086.108. Epub 2009 Apr 28.


Placenta-specific methylation of the vitamin D 24-hydroxylase gene: implications for feedback autoregulation of active vitamin D levels at the fetomaternal interface.

Novakovic B, Sibson M, Ng HK, Manuelpillai U, Rakyan V, Down T, Beck S, Fournier T, Evain-Brion D, Dimitriadis E, Craig JM, Morley R, Saffery R.

J Biol Chem. 2009 May 29;284(22):14838-48. doi: 10.1074/jbc.M809542200. Epub 2009 Feb 23.


Differential chromatin marking of introns and expressed exons by H3K36me3.

Kolasinska-Zwierz P, Down T, Latorre I, Liu T, Liu XS, Ahringer J.

Nat Genet. 2009 Mar;41(3):376-81. doi: 10.1038/ng.322. Epub 2009 Feb 1.


Specific tumour-associated methylation in normal human term placenta and first-trimester cytotrophoblasts.

Novakovic B, Rakyan V, Ng HK, Manuelpillai U, Dewi C, Wong NC, Morley R, Down T, Beck S, Craig JM, Saffery R.

Mol Hum Reprod. 2008 Sep;14(9):547-54. doi: 10.1093/molehr/gan046. Epub 2008 Aug 16.


BioJava: an open-source framework for bioinformatics.

Holland RC, Down TA, Pocock M, Prlić A, Huen D, James K, Foisy S, Dräger A, Yates A, Heuer M, Schreiber MJ.

Bioinformatics. 2008 Sep 15;24(18):2096-7. doi: 10.1093/bioinformatics/btn397. Epub 2008 Aug 8.


Integrating biological data--the Distributed Annotation System.

Jenkinson AM, Albrecht M, Birney E, Blankenburg H, Down T, Finn RD, Hermjakob H, Hubbard TJ, Jimenez RC, Jones P, Kähäri A, Kulesha E, Macías JR, Reeves GA, Prlić A.

BMC Bioinformatics. 2008 Jul 22;9 Suppl 8:S3. doi: 10.1186/1471-2105-9-S8-S3.


A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis.

Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Bäckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavaré S, Beck S.

Nat Biotechnol. 2008 Jul;26(7):779-85. doi: 10.1038/nbt1414.


An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs).

Rakyan VK, Down TA, Thorne NP, Flicek P, Kulesha E, Gräf S, Tomazou EM, Bäckdahl L, Johnson N, Herberth M, Howe KL, Jackson DK, Miretti MM, Fiegler H, Marioni JC, Birney E, Hubbard TJ, Carter NP, Tavaré S, Beck S.

Genome Res. 2008 Sep;18(9):1518-29. doi: 10.1101/gr.077479.108. Epub 2008 Jun 24.


NestedMICA as an ab initio protein motif discovery tool.

Doğruel M, Down TA, Hubbard TJ.

BMC Bioinformatics. 2008 Jan 14;9:19. doi: 10.1186/1471-2105-9-19.


Ensembl 2008.

Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Eyre T, Fitzgerald S, Fernandez-Banet J, Gräf S, Haider S, Hammond M, Holland R, Howe KL, Howe K, Johnson N, Jenkinson A, Kähäri A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Slater G, Smedley D, Spudich G, Trevanion S, Vilella AJ, Vogel J, White S, Wood M, Birney E, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Hubbard TJ, Kasprzyk A, Proctor G, Smith J, Ureta-Vidal A, Searle S.

Nucleic Acids Res. 2008 Jan;36(Database issue):D707-14. Epub 2007 Nov 13.


Integrating sequence and structural biology with DAS.

Prlić A, Down TA, Kulesha E, Finn RD, Kähäri A, Hubbard TJ.

BMC Bioinformatics. 2007 Sep 12;8:333.


Large-scale discovery of promoter motifs in Drosophila melanogaster.

Down TA, Bergman CM, Su J, Hubbard TJ.

PLoS Comput Biol. 2007 Jan 19;3(1):e7. Epub 2006 Dec 5.


Ensembl 2007.

Hubbard TJ, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Fitzgerald S, Fernandez-Banet J, Graf S, Haider S, Hammond M, Herrero J, Holland R, Howe K, Howe K, Johnson N, Kahari A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Melsopp C, Megy K, Meidl P, Ouverdin B, Parker A, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Severin J, Slater G, Smedley D, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wood M, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Flicek P, Kasprzyk A, Proctor G, Searle S, Smith J, Ureta-Vidal A, Birney E.

Nucleic Acids Res. 2007 Jan;35(Database issue):D610-7. Epub 2006 Dec 5.


DNA methylation profiling of human chromosomes 6, 20 and 22.

Eckhardt F, Lewin J, Cortese R, Rakyan VK, Attwood J, Burger M, Burton J, Cox TV, Davies R, Down TA, Haefliger C, Horton R, Howe K, Jackson DK, Kunde J, Koenig C, Liddle J, Niblett D, Otto T, Pettett R, Seemann S, Thompson C, West T, Rogers J, Olek A, Berlin K, Beck S.

Nat Genet. 2006 Dec;38(12):1378-85. Epub 2006 Oct 29.


Multi-genome biology.

Down TA.

Genome Biol. 2006;7(2):305. Epub 2006 Feb 10.


Ensembl 2006.

Birney E, Andrews D, Caccamo M, Chen Y, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez-Suarez XM, Flicek P, Gräf S, Hammond M, Herrero J, Howe K, Iyer V, Jekosch K, Kähäri A, Kasprzyk A, Keefe D, Kokocinski F, Kulesha E, London D, Longden I, Melsopp C, Meidl P, Overduin B, Parker A, Proctor G, Prlic A, Rae M, Rios D, Redmond S, Schuster M, Sealy I, Searle S, Severin J, Slater G, Smedley D, Smith J, Stabenau A, Stalker J, Trevanion S, Ureta-Vidal A, Vogel J, White S, Woodwark C, Hubbard TJ.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D556-61.

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