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Results: 1 to 20 of 22

1.

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. 2014 Aug 8. pii: S1574-7891(14)00174-4. doi: 10.1016/j.molonc.2014.07.019. [Epub ahead of print]

PMID:
25169931
[PubMed - as supplied by publisher]
Free Article
2.

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.

PMID:
25164602
[PubMed - in process]
Free PMC Article
3.

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.

PMID:
24952744
[PubMed - in process]
4.

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.

PMID:
23484797
[PubMed - indexed for MEDLINE]
Free Article
5.

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.

PMID:
23100629
[PubMed - indexed for MEDLINE]
Free Article
6.

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.

PMID:
22912679
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
22522925
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
22217937
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
22144879
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
21337521
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
20925945
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
20688273
[PubMed - indexed for MEDLINE]
13.

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.

PMID:
20423502
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
19995423
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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.

PMID:
19923232
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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.

PMID:
19153169
[PubMed - indexed for MEDLINE]
17.

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.

PMID:
18953044
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Spike-in validation of an Illumina-specific variance-stabilizing transformation.

Dunning MJ, Ritchie ME, Barbosa-Morais NL, Tavaré S, Lynch AG.

BMC Res Notes. 2008 Jun 4;1:18. doi: 10.1186/1756-0500-1-18.

PMID:
18710543
[PubMed]
Free PMC Article
19.

PMC42, a breast progenitor cancer cell line, has normal-like mRNA and microRNA transcriptomes.

Git A, Spiteri I, Blenkiron C, Dunning MJ, Pole JC, Chin SF, Wang Y, Smith J, Livesey FJ, Caldas C.

Breast Cancer Res. 2008;10(3):R54. doi: 10.1186/bcr2109. Epub 2008 Jun 27.

PMID:
18588681
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Statistical issues in the analysis of Illumina data.

Dunning MJ, Barbosa-Morais NL, Lynch AG, Tavaré S, Ritchie ME.

BMC Bioinformatics. 2008 Feb 6;9:85. doi: 10.1186/1471-2105-9-85.

PMID:
18254947
[PubMed - indexed for MEDLINE]
Free PMC Article

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