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5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer.

Uribe-Lewis S, Stark R, Carroll T, Dunning MJ, Bachman M, Ito Y, Stojic L, Halim S, Vowler SL, Lynch AG, Delatte B, de Bony EJ, Colin L, Defrance M, Krueger F, Silva AL, Ten Hoopen R, Ibrahim AE, Fuks F, Murrell A.

Genome Biol. 2015 Apr 1;16:69. doi: 10.1186/s13059-015-0605-5.


HES5 silencing is an early and recurrent change in prostate tumourigenesis.

Massie CE, Spiteri I, Ross-Adams H, Luxton H, Kay J, Whitaker HC, Dunning MJ, Lamb AD, Ramos-Montoya A, Brewer DS, Cooper CS, Eeles R; UK Prostate ICGC Group, Warren AY, Tavaré S, Neal DE, Lynch AG.

Endocr Relat Cancer. 2015 Apr;22(2):131-44. doi: 10.1530/ERC-14-0454. Epub 2015 Jan 5.


Tumour genomic and microenvironmental heterogeneity for integrated prediction of 5-year biochemical recurrence of prostate cancer: a retrospective cohort study.

Lalonde E, Ishkanian AS, Sykes J, Fraser M, Ross-Adams H, Erho N, Dunning MJ, Halim S, Lamb AD, Moon NC, Zafarana G, Warren AY, Meng X, Thoms J, Grzadkowski MR, Berlin A, Have CL, Ramnarine VR, Yao CQ, Malloff CA, Lam LL, Xie H, Harding NJ, Mak DY, Chu KC, Chong LC, Sendorek DH, P'ng C, Collins CC, Squire JA, Jurisica I, Cooper C, Eeles R, Pintilie M, Dal Pra A, Davicioni E, Lam WL, Milosevic M, Neal DE, van der Kwast T, Boutros PC, Bristow RG.

Lancet Oncol. 2014 Dec;15(13):1521-32. doi: 10.1016/S1470-2045(14)71021-6. Epub 2014 Nov 13.


A tumor DNA complex aberration index is an independent predictor of survival in breast and ovarian cancer.

Vollan HK, Rueda OM, Chin SF, Curtis C, Turashvili G, Shah S, Lingjærde OC, Yuan Y, Ng CK, Dunning MJ, Dicks E, Provenzano E, Sammut S, McKinney S, Ellis IO, Pinder S, Purushotham A, Murphy LC, Kristensen VN; METABRIC Group, Brenton JD, Pharoah PD, Børresen-Dale AL, Aparicio S, Caldas C.

Mol Oncol. 2015 Jan;9(1):115-27. doi: 10.1016/j.molonc.2014.07.019. Epub 2014 Aug 8.


Genome-driven integrated classification of breast cancer validated in over 7,500 samples.

Ali HR, Rueda OM, Chin SF, Curtis C, Dunning MJ, Aparicio SA, Caldas C.

Genome Biol. 2014 Aug 28;15(8):431. doi: 10.1186/s13059-014-0431-1.


Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis.

Weaver JM, Ross-Innes CS, Shannon N, Lynch AG, Forshew T, Barbera M, Murtaza M, Ong CA, Lao-Sirieix P, Dunning MJ, Smith L, Smith ML, Anderson CL, Carvalho B, O'Donovan M, Underwood TJ, May AP, Grehan N, Hardwick R, Davies J, Oloumi A, Aparicio S, Caldas C, Eldridge MD, Edwards PA, Rosenfeld N, Tavaré S, Fitzgerald RC; OCCAMS Consortium.

Nat Genet. 2014 Aug;46(8):837-43. doi: 10.1038/ng.3013. Epub 2014 Jun 22.


Analysis of circulating tumor DNA to monitor metastatic breast cancer.

Dawson SJ, Tsui DW, Murtaza M, Biggs H, Rueda OM, Chin SF, Dunning MJ, Gale D, Forshew T, Mahler-Araujo B, Rajan S, Humphray S, Becq J, Halsall D, Wallis M, Bentley D, Caldas C, Rosenfeld N.

N Engl J Med. 2013 Mar 28;368(13):1199-209. doi: 10.1056/NEJMoa1213261. Epub 2013 Mar 13.


Quantitative image analysis of cellular heterogeneity in breast tumors complements genomic profiling.

Yuan Y, Failmezger H, Rueda OM, Ali HR, Gräf S, Chin SF, Schwarz RF, Curtis C, Dunning MJ, Bardwell H, Johnson N, Doyle S, Turashvili G, Provenzano E, Aparicio S, Caldas C, Markowetz F.

Sci Transl Med. 2012 Oct 24;4(157):157ra143. doi: 10.1126/scitranslmed.3004330. Erratum in: Sci Transl Med. 2012 Oct 24;4(157):161er6.


Calling sample mix-ups in cancer population studies.

Lynch AG, Chin SF, Dunning MJ, Caldas C, Tavaré S, Curtis C.

PLoS One. 2012;7(8):e41815. doi: 10.1371/journal.pone.0041815. Epub 2012 Aug 9.


The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups.

Curtis C, Shah SP, Chin SF, Turashvili G, Rueda OM, Dunning MJ, Speed D, Lynch AG, Samarajiwa S, Yuan Y, Gräf S, Ha G, Haffari G, Bashashati A, Russell R, McKinney S; METABRIC Group, Langerød A, Green A, Provenzano E, Wishart G, Pinder S, Watson P, Markowetz F, Murphy L, Ellis I, Purushotham A, Børresen-Dale AL, Brenton JD, Tavaré S, Caldas C, Aparicio S.

Nature. 2012 Apr 18;486(7403):346-52. doi: 10.1038/nature10983.


Differential oestrogen receptor binding is associated with clinical outcome in breast cancer.

Ross-Innes CS, Stark R, Teschendorff AE, Holmes KA, Ali HR, Dunning MJ, Brown GD, Gojis O, Ellis IO, Green AR, Ali S, Chin SF, Palmieri C, Caldas C, Carroll JS.

Nature. 2012 Jan 4;481(7381):389-93. doi: 10.1038/nature10730.


BeadArray expression analysis using bioconductor.

Ritchie ME, Dunning MJ, Smith ML, Shi W, Lynch AG.

PLoS Comput Biol. 2011 Dec;7(12):e1002276. doi: 10.1371/journal.pcbi.1002276. Epub 2011 Dec 1.


ZNF703 is a common Luminal B breast cancer oncogene that differentially regulates luminal and basal progenitors in human mammary epithelium.

Holland DG, Burleigh A, Git A, Goldgraben MA, Perez-Mancera PA, Chin SF, Hurtado A, Bruna A, Ali HR, Greenwood W, Dunning MJ, Samarajiwa S, Menon S, Rueda OM, Lynch AG, McKinney S, Ellis IO, Eaves CJ, Carroll JS, Curtis C, Aparicio S, Caldas C.

EMBO Mol Med. 2011 Mar;3(3):167-80. doi: 10.1002/emmm.201100122. Epub 2011 Feb 18.


The cost of reducing starting RNA quantity for Illumina BeadArrays: a bead-level dilution experiment.

Lynch AG, Hadfield J, Dunning MJ, Osborne M, Thorne NP, Tavaré S.

BMC Genomics. 2010 Oct 6;11:540. doi: 10.1186/1471-2164-11-540.


The importance of platform annotation in interpreting microarray data.

Dunning MJ, Curtis C, Barbosa-Morais NL, Caldas C, Tavaré S, Lynch AG.

Lancet Oncol. 2010 Aug;11(8):717. doi: 10.1016/S1470-2045(10)70115-7. No abstract available.


Identification and correction of previously unreported spatial phenomena using raw Illumina BeadArray data.

Smith ML, Dunning MJ, Tavaré S, Lynch AG.

BMC Bioinformatics. 2010 Apr 27;11:208. doi: 10.1186/1471-2105-11-208.


The pitfalls of platform comparison: DNA copy number array technologies assessed.

Curtis C, Lynch AG, Dunning MJ, Spiteri I, Marioni JC, Hadfield J, Chin SF, Brenton JD, Tavaré S, Caldas C.

BMC Genomics. 2009 Dec 8;10:588. doi: 10.1186/1471-2164-10-588.


A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

Barbosa-Morais NL, Dunning MJ, Samarajiwa SA, Darot JF, Ritchie ME, Lynch AG, Tavaré S.

Nucleic Acids Res. 2010 Jan;38(3):e17. doi: 10.1093/nar/gkp942. Epub 2009 Nov 18.


Considerations for the processing and analysis of GoldenGate-based two-colour Illumina platforms.

Lynch AG, Dunning MJ, Iddawela M, Barbosa-Morais NL, Ritchie ME.

Stat Methods Med Res. 2009 Oct;18(5):437-52. doi: 10.1177/0962280208099451. Epub 2009 Jan 19.


BASH: a tool for managing BeadArray spatial artefacts.

Cairns JM, Dunning MJ, Ritchie ME, Russell R, Lynch AG.

Bioinformatics. 2008 Dec 15;24(24):2921-2. doi: 10.1093/bioinformatics/btn557. Epub 2008 Oct 25.

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