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Items: 1 to 50 of 72

1.

Deciphering the genomic, epigenomic, and transcriptomic landscapes of pre-invasive lung cancer lesions.

Teixeira VH, Pipinikas CP, Pennycuick A, Lee-Six H, Chandrasekharan D, Beane J, Morris TJ, Karpathakis A, Feber A, Breeze CE, Ntolios P, Hynds RE, Falzon M, Capitanio A, Carroll B, Durrenberger PF, Hardavella G, Brown JM, Lynch AG, Farmery H, Paul DS, Chambers RC, McGranahan N, Navani N, Thakrar RM, Swanton C, Beck S, George PJ, Spira A, Campbell PJ, Thirlwell C, Janes SM.

Nat Med. 2019 Mar;25(3):517-525. doi: 10.1038/s41591-018-0323-0. Epub 2019 Jan 21.

PMID:
30664780
2.

Publisher Correction: Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.

Farmery JHR, Smith ML; NIHR BioResource - Rare Diseases, Lynch AG.

Sci Rep. 2018 Sep 3;8(1):13376. doi: 10.1038/s41598-018-31524-0.

3.

Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets.

Wedge DC, Gundem G, Mitchell T, Woodcock DJ, Martincorena I, Ghori M, Zamora J, Butler A, Whitaker H, Kote-Jarai Z, Alexandrov LB, Van Loo P, Massie CE, Dentro S, Warren AY, Verrill C, Berney DM, Dennis N, Merson S, Hawkins S, Howat W, Lu YJ, Lambert A, Kay J, Kremeyer B, Karaszi K, Luxton H, Camacho N, Marsden L, Edwards S, Matthews L, Bo V, Leongamornlert D, McLaren S, Ng A, Yu Y, Zhang H, Dadaev T, Thomas S, Easton DF, Ahmed M, Bancroft E, Fisher C, Livni N, Nicol D, Tavaré S, Gill P, Greenman C, Khoo V, Van As N, Kumar P, Ogden C, Cahill D, Thompson A, Mayer E, Rowe E, Dudderidge T, Gnanapragasam V, Shah NC, Raine K, Jones D, Menzies A, Stebbings L, Teague J, Hazell S, Corbishley C; CAMCAP Study Group, de Bono J, Attard G, Isaacs W, Visakorpi T, Fraser M, Boutros PC, Bristow RG, Workman P, Sander C; TCGA Consortium, Hamdy FC, Futreal A, McDermott U, Al-Lazikani B, Lynch AG, Bova GS, Foster CS, Brewer DS, Neal DE, Cooper CS, Eeles RA.

Nat Genet. 2018 May;50(5):682-692. doi: 10.1038/s41588-018-0086-z. Epub 2018 Apr 16.

4.

Timing the Landmark Events in the Evolution of Clear Cell Renal Cell Cancer: TRACERx Renal.

Mitchell TJ, Turajlic S, Rowan A, Nicol D, Farmery JHR, O'Brien T, Martincorena I, Tarpey P, Angelopoulos N, Yates LR, Butler AP, Raine K, Stewart GD, Challacombe B, Fernando A, Lopez JI, Hazell S, Chandra A, Chowdhury S, Rudman S, Soultati A, Stamp G, Fotiadis N, Pickering L, Au L, Spain L, Lynch J, Stares M, Teague J, Maura F, Wedge DC, Horswell S, Chambers T, Litchfield K, Xu H, Stewart A, Elaidi R, Oudard S, McGranahan N, Csabai I, Gore M, Futreal PA, Larkin J, Lynch AG, Szallasi Z, Swanton C, Campbell PJ; TRACERx Renal Consortium.

Cell. 2018 Apr 19;173(3):611-623.e17. doi: 10.1016/j.cell.2018.02.020. Epub 2018 Apr 12.

5.

Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.

Farmery JHR, Smith ML; NIHR BioResource - Rare Diseases, Lynch AG.

Sci Rep. 2018 Jan 22;8(1):1300. doi: 10.1038/s41598-017-14403-y. Erratum in: Sci Rep. 2018 Sep 3;8(1):13376.

6.

Corrigendum: A comparative analysis of whole genome sequencing of esophageal adenocarcinoma pre- and post-chemotherapy.

Noorani A, Bornschein J, Lynch AG, Secrier M, Achilleos A, Eldridge M, Bower L, Weaver JMJ, Crawte J, Ong CA, Shannon N, MacRae S, Grehan N, Nutzinger B, O'Donovan M, Hardwick R, Tavaré S, Fitzgerald RC; Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium.

Genome Res. 2017 Oct;27(10):1782. doi: 10.1101/gr.229153.117. No abstract available.

7.

Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data.

Camacho N, Van Loo P, Edwards S, Kay JD, Matthews L, Haase K, Clark J, Dennis N, Thomas S, Kremeyer B, Zamora J, Butler AP, Gundem G, Merson S, Luxton H, Hawkins S, Ghori M, Marsden L, Lambert A, Karaszi K, Pelvender G, Massie CE, Kote-Jarai Z, Raine K, Jones D, Howat WJ, Hazell S, Livni N, Fisher C, Ogden C, Kumar P, Thompson A, Nicol D, Mayer E, Dudderidge T, Yu Y, Zhang H, Shah NC, Gnanapragasam VJ; CRUK-ICGC Prostate Group, Isaacs W, Visakorpi T, Hamdy F, Berney D, Verrill C, Warren AY, Wedge DC, Lynch AG, Foster CS, Lu YJ, Bova GS, Whitaker HC, McDermott U, Neal DE, Eeles R, Cooper CS, Brewer DS.

PLoS Genet. 2017 Sep 25;13(9):e1007001. doi: 10.1371/journal.pgen.1007001. eCollection 2017 Sep.

8.

The role of TET-mediated DNA hydroxymethylation in prostate cancer.

Smeets E, Lynch AG, Prekovic S, Van den Broeck T, Moris L, Helsen C, Joniau S, Claessens F, Massie CE.

Mol Cell Endocrinol. 2018 Feb 15;462(Pt A):41-55. doi: 10.1016/j.mce.2017.08.021. Epub 2017 Sep 1. Review.

PMID:
28870782
9.

Synthetic lethality between androgen receptor signalling and the PARP pathway in prostate cancer.

Asim M, Tarish F, Zecchini HI, Sanjiv K, Gelali E, Massie CE, Baridi A, Warren AY, Zhao W, Ogris C, McDuffus LA, Mascalchi P, Shaw G, Dev H, Wadhwa K, Wijnhoven P, Forment JV, Lyons SR, Lynch AG, O'Neill C, Zecchini VR, Rennie PS, Baniahmad A, Tavaré S, Mills IG, Galanty Y, Crosetto N, Schultz N, Neal D, Helleday T.

Nat Commun. 2017 Aug 29;8(1):374. doi: 10.1038/s41467-017-00393-y.

10.

Genomic Evolution of Breast Cancer Metastasis and Relapse.

Yates LR, Knappskog S, Wedge D, Farmery JHR, Gonzalez S, Martincorena I, Alexandrov LB, Van Loo P, Haugland HK, Lilleng PK, Gundem G, Gerstung M, Pappaemmanuil E, Gazinska P, Bhosle SG, Jones D, Raine K, Mudie L, Latimer C, Sawyer E, Desmedt C, Sotiriou C, Stratton MR, Sieuwerts AM, Lynch AG, Martens JW, Richardson AL, Tutt A, Lønning PE, Campbell PJ.

Cancer Cell. 2017 Aug 14;32(2):169-184.e7. doi: 10.1016/j.ccell.2017.07.005.

11.

DESNT: A Poor Prognosis Category of Human Prostate Cancer.

Luca BA, Brewer DS, Edwards DR, Edwards S, Whitaker HC, Merson S, Dennis N, Cooper RA, Hazell S, Warren AY; CancerMap Group, Eeles R, Lynch AG, Ross-Adams H, Lamb AD, Neal DE, Sethia K, Mills RD, Ball RY, Curley H, Clark J, Moulton V, Cooper CS.

Eur Urol Focus. 2018 Dec;4(6):842-850. doi: 10.1016/j.euf.2017.01.016. Epub 2017 Mar 6.

12.

New Model for Estimating Glomerular Filtration Rate in Patients With Cancer.

Janowitz T, Williams EH, Marshall A, Ainsworth N, Thomas PB, Sammut SJ, Shepherd S, White J, Mark PB, Lynch AG, Jodrell DI, Tavaré S, Earl H.

J Clin Oncol. 2017 Aug 20;35(24):2798-2805. doi: 10.1200/JCO.2017.72.7578. Epub 2017 Jul 7.

13.

A comparative analysis of whole genome sequencing of esophageal adenocarcinoma pre- and post-chemotherapy.

Noorani A, Bornschein J, Lynch AG, Secrier M, Achilleos A, Eldridge M, Bower L, Weaver JMJ, Crawte J, Ong CA, Shannon N, MacRae S, Grehan N, Nutzinger B, O'Donovan M, Hardwick R, Tavaré S, Fitzgerald RC; Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium.

Genome Res. 2017 Jun;27(6):902-912. doi: 10.1101/gr.214296.116. Epub 2017 May 2. Erratum in: Genome Res. 2017 Oct;27(10 ):1782.

14.

Corrigendum to "Integration of Copy Number and Transcriptomics Provides Risk Stratification in Prostate Cancer: A Discovery and Validation Cohort Study" [EBioMedicine 2 (9) (2015) 1133-1144].

Ross-Adams H, Lamb AD, Dunning MJ, Halim S, Lindberg J, Massie CM, Egevad LA, Russell R, Ramos-Montoya A, Vowler SL, Sharma NL, Kay J, Whitaker H, Clark J, Hurst R, Gnanapragasam VJ, Shah NC, Warren AY, Cooper CS, Lynch AG, Stark R, Mills IG, Grönberg H, Neal DE; CamCaP Study Group.

EBioMedicine. 2017 Mar;17:238. doi: 10.1016/j.ebiom.2017.03.010. Epub 2017 Mar 8. No abstract available.

15.

Mining Human Prostate Cancer Datasets: The "camcAPP" Shiny App.

Dunning MJ, Vowler SL, Lalonde E, Ross-Adams H, Boutros P, Mills IG, Lynch AG, Lamb AD.

EBioMedicine. 2017 Mar;17:5-6. doi: 10.1016/j.ebiom.2017.02.022. Epub 2017 Mar 2. No abstract available.

16.

Corrigendum: Mutational signatures in esophageal adenocarcinoma define etiologically distinct subgroups with therapeutic relevance.

Secrier M, Li X, de Silva N, Eldridge MD, Contino G, Bornschein J, MacRae S, Grehan N, O'Donovan M, Miremadi A, Yang TP, Bower L, Chettouh H, Crawte J, Galeano-Dalmau N, Grabowska A, Saunders J, Underwood T, Waddell N, Barbour AP, Nutzinger B, Achilleos A, Edwards PA, Lynch AG, Tavaré S, Fitzgerald RC; Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium.

Nat Genet. 2017 Jan 31;49(2):317. doi: 10.1038/ng0217-317a. No abstract available.

PMID:
28138154
17.

Mutational signatures in esophageal adenocarcinoma define etiologically distinct subgroups with therapeutic relevance.

Secrier M, Li X, de Silva N, Eldridge MD, Contino G, Bornschein J, MacRae S, Grehan N, O'Donovan M, Miremadi A, Yang TP, Bower L, Chettouh H, Crawte J, Galeano-Dalmau N, Grabowska A, Saunders J, Underwood T, Waddell N, Barbour AP, Nutzinger B, Achilleos A, Edwards PA, Lynch AG, Tavaré S, Fitzgerald RC; Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium.

Nat Genet. 2016 Oct;48(10):1131-41. doi: 10.1038/ng.3659. Epub 2016 Sep 5. Erratum in: Nat Genet. 2017 Jan 31;49(2):317.

18.

Whole-genome sequencing of nine esophageal adenocarcinoma cell lines.

Contino G, Eldridge MD, Secrier M, Bower L, Fels Elliott R, Weaver J, Lynch AG, Edwards PA, Fitzgerald RC.

F1000Res. 2016 Jun 10;5:1336. doi: 10.12688/f1000research.7033.1. eCollection 2016.

19.

Whole blood mRNA in prostate cancer reveals a four-gene androgen regulated panel.

Thomas BC, Kay JD, Menon S, Vowler SL, Dawson SN, Bucklow LJ, Luxton HJ, Johnston T, Massie CE, Pugh M, Warren AY, Barker P, Burling K, Lynch AG, George A, Burge J, Corcoran M, Stearn S, Lamb AD, Sharma NL, Shaw GL, Neal DE, Whitaker HC.

Endocr Relat Cancer. 2016 Oct;23(10):797-812. doi: 10.1530/ERC-16-0287. Epub 2016 Aug 30.

PMID:
27578825
20.

The importance of DNA methylation in prostate cancer development.

Massie CE, Mills IG, Lynch AG.

J Steroid Biochem Mol Biol. 2017 Feb;166:1-15. doi: 10.1016/j.jsbmb.2016.04.009. Epub 2016 Apr 24. Review.

21.

Choline Kinase Alpha as an Androgen Receptor Chaperone and Prostate Cancer Therapeutic Target.

Asim M, Massie CE, Orafidiya F, Pértega-Gomes N, Warren AY, Esmaeili M, Selth LA, Zecchini HI, Luko K, Qureshi A, Baridi A, Menon S, Madhu B, Escriu C, Lyons S, Vowler SL, Zecchini VR, Shaw G, Hessenkemper W, Russell R, Mohammed H, Stefanos N, Lynch AG, Grigorenko E, D'Santos C, Taylor C, Lamb A, Sriranjan R, Yang J, Stark R, Dehm SM, Rennie PS, Carroll JS, Griffiths JR, Tavaré S, Mills IG, McEwan IJ, Baniahmad A, Tilley WD, Neal DE.

J Natl Cancer Inst. 2015 Dec 11;108(5). doi: 10.1093/jnci/djv371. Print 2016 May.

22.

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.

Alioto TS, Buchhalter I, Derdak S, Hutter B, Eldridge MD, Hovig E, Heisler LE, Beck TA, Simpson JT, Tonon L, Sertier AS, Patch AM, Jäger N, Ginsbach P, Drews R, Paramasivam N, Kabbe R, Chotewutmontri S, Diessl N, Previti C, Schmidt S, Brors B, Feuerbach L, Heinold M, Gröbner S, Korshunov A, Tarpey PS, Butler AP, Hinton J, Jones D, Menzies A, Raine K, Shepherd R, Stebbings L, Teague JW, Ribeca P, Giner FC, Beltran S, Raineri E, Dabad M, Heath SC, Gut M, Denroche RE, Harding NJ, Yamaguchi TN, Fujimoto A, Nakagawa H, Quesada V, Valdés-Mas R, Nakken S, Vodák D, Bower L, Lynch AG, Anderson CL, Waddell N, Pearson JV, Grimmond SM, Peto M, Spellman P, He M, Kandoth C, Lee S, Zhang J, Létourneau L, Ma S, Seth S, Torrents D, Xi L, Wheeler DA, López-Otín C, Campo E, Campbell PJ, Boutros PC, Puente XS, Gerhard DS, Pfister SM, McPherson JD, Hudson TJ, Schlesner M, Lichter P, Eils R, Jones DT, Gut IG.

Nat Commun. 2015 Dec 9;6:10001. doi: 10.1038/ncomms10001.

23.

The Early Effects of Rapid Androgen Deprivation on Human Prostate Cancer.

Shaw GL, Whitaker H, Corcoran M, Dunning MJ, Luxton H, Kay J, Massie CE, Miller JL, Lamb AD, Ross-Adams H, Russell R, Nelson AW, Eldridge MD, Lynch AG, Ramos-Montoya A, Mills IG, Taylor AE, Arlt W, Shah N, Warren AY, Neal DE.

Eur Urol. 2016 Aug;70(2):214-8. doi: 10.1016/j.eururo.2015.10.042. Epub 2015 Nov 10.

24.

Integration of copy number and transcriptomics provides risk stratification in prostate cancer: A discovery and validation cohort study.

Ross-Adams H, Lamb AD, Dunning MJ, Halim S, Lindberg J, Massie CM, Egevad LA, Russell R, Ramos-Montoya A, Vowler SL, Sharma NL, Kay J, Whitaker H, Clark J, Hurst R, Gnanapragasam VJ, Shah NC, Warren AY, Cooper CS, Lynch AG, Stark R, Mills IG, Grönberg H, Neal DE; CamCaP Study Group.

EBioMedicine. 2015 Jul 29;2(9):1133-44. doi: 10.1016/j.ebiom.2015.07.017. eCollection 2015 Sep. Erratum in: EBioMedicine. 2017 Mar;17 :238.

25.

Whole-genome sequencing provides new insights into the clonal architecture of Barrett's esophagus and esophageal adenocarcinoma.

Ross-Innes CS, Becq J, Warren A, Cheetham RK, Northen H, O'Donovan M, Malhotra S, di Pietro M, Ivakhno S, He M, Weaver JMJ, Lynch AG, Kingsbury Z, Ross M, Humphray S, Bentley D, Fitzgerald RC.

Nat Genet. 2015 Sep;47(9):1038-1046. doi: 10.1038/ng.3357. Epub 2015 Jul 20.

26.

Epigenetic and oncogenic regulation of SLC16A7 (MCT2) results in protein over-expression, impacting on signalling and cellular phenotypes in prostate cancer.

Pertega-Gomes N, Vizcaino JR, Felisbino S, Warren AY, Shaw G, Kay J, Whitaker H, Lynch AG, Fryer L, Neal DE, Massie CE.

Oncotarget. 2015 Aug 28;6(25):21675-84.

27.

Corrigendum: analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue.

Cooper CS, Eeles R, Wedge DC, Van Loo P, Gundem G, Alexandrov LB, Kremeyer B, Butler A, Lynch AG, Camacho N, Massie CE, Kay J, Luxton HJ, Edwards S, Kote-Jarai Z, Dennis N, Merson S, Leongamornlert D, Zamora J, Corbishley C, Thomas S, Nik-Zainal S, Ramakrishna M, O'Meara S, Matthews L, Clark J, Hurst R, Mithen R, Bristow RG, Boutros PC, Fraser M, Cooke S, Raine K, Jones D, Menzies A, Stebbings L, Hinton J, Teague J, McLaren S, Mudie L, Hardy C, Anderson E, Joseph O, Goody V, Robinson B, Maddison M, Gamble S, Greenman C, Berney D, Hazell S, Livni N; ICGC Prostate Group, Fisher C, Ogden C, Kumar P, Thompson A, Woodhouse C, Nicol D, Mayer E, Dudderidge T, Shah NC, Gnanapragasam V, Voet T, Campbell P, Futreal A, Easton D, Warren AY, Foster CS, Stratton MR, Whitaker HC, McDermott U, Brewer DS, Neal DE.

Nat Genet. 2015 Jun;47(6):689. doi: 10.1038/ng0615-689b. No abstract available.

28.

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.

29.

Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53.

Kirschner K, Samarajiwa SA, Cairns JM, Menon S, Pérez-Mancera PA, Tomimatsu K, Bermejo-Rodriguez C, Ito Y, Chandra T, Narita M, Lyons SK, Lynch AG, Kimura H, Ohbayashi T, Tavaré S, Narita M.

PLoS Genet. 2015 Mar 19;11(3):e1005053. doi: 10.1371/journal.pgen.1005053. eCollection 2015 Mar.

30.

Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue.

Cooper CS, Eeles R, Wedge DC, Van Loo P, Gundem G, Alexandrov LB, Kremeyer B, Butler A, Lynch AG, Camacho N, Massie CE, Kay J, Luxton HJ, Edwards S, Kote-Jarai Z, Dennis N, Merson S, Leongamornlert D, Zamora J, Corbishley C, Thomas S, Nik-Zainal S, O'Meara S, Matthews L, Clark J, Hurst R, Mithen R, Bristow RG, Boutros PC, Fraser M, Cooke S, Raine K, Jones D, Menzies A, Stebbings L, Hinton J, Teague J, McLaren S, Mudie L, Hardy C, Anderson E, Joseph O, Goody V, Robinson B, Maddison M, Gamble S, Greenman C, Berney D, Hazell S, Livni N; ICGC Prostate Group, Fisher C, Ogden C, Kumar P, Thompson A, Woodhouse C, Nicol D, Mayer E, Dudderidge T, Shah NC, Gnanapragasam V, Voet T, Campbell P, Futreal A, Easton D, Warren AY, Foster CS, Stratton MR, Whitaker HC, McDermott U, Brewer DS, Neal DE.

Nat Genet. 2015 Apr;47(4):367-372. doi: 10.1038/ng.3221. Epub 2015 Mar 2. Erratum in: Nat Genet. 2015 Jun;47(6):689.

31.

multiSNV: a probabilistic approach for improving detection of somatic point mutations from multiple related tumour samples.

Josephidou M, Lynch AG, Tavaré S.

Nucleic Acids Res. 2015 May 19;43(9):e61. doi: 10.1093/nar/gkv135. Epub 2015 Feb 26.

32.

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.

33.

Quantifying the impact of inter-site heterogeneity on the distribution of ChIP-seq data.

Cairns J, Lynch AG, Tavaré S.

Front Genet. 2014 Nov 14;5:399. doi: 10.3389/fgene.2014.00399. eCollection 2014.

34.

Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer.

Ju YS, Alexandrov LB, Gerstung M, Martincorena I, Nik-Zainal S, Ramakrishna M, Davies HR, Papaemmanuil E, Gundem G, Shlien A, Bolli N, Behjati S, Tarpey PS, Nangalia J, Massie CE, Butler AP, Teague JW, Vassiliou GS, Green AR, Du MQ, Unnikrishnan A, Pimanda JE, Teh BT, Munshi N, Greaves M, Vyas P, El-Naggar AK, Santarius T, Collins VP, Grundy R, Taylor JA, Hayes DN, Malkin D; ICGC Breast Cancer Group; ICGC Chronic Myeloid Disorders Group; ICGC Prostate Cancer Group, Foster CS, Warren AY, Whitaker HC, Brewer D, Eeles R, Cooper C, Neal D, Visakorpi T, Isaacs WB, Bova GS, Flanagan AM, Futreal PA, Lynch AG, Chinnery PF, McDermott U, Stratton MR, Campbell PJ.

Elife. 2014 Oct 1;3. doi: 10.7554/eLife.02935.

35.

Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes.

Tubio JMC, Li Y, Ju YS, Martincorena I, Cooke SL, Tojo M, Gundem G, Pipinikas CP, Zamora J, Raine K, Menzies A, Roman-Garcia P, Fullam A, Gerstung M, Shlien A, Tarpey PS, Papaemmanuil E, Knappskog S, Van Loo P, Ramakrishna M, Davies HR, Marshall J, Wedge DC, Teague JW, Butler AP, Nik-Zainal S, Alexandrov L, Behjati S, Yates LR, Bolli N, Mudie L, Hardy C, Martin S, McLaren S, O'Meara S, Anderson E, Maddison M, Gamble S, Foster C, Warren AY, Whitaker H, Brewer D, Eeles R, Cooper C, Neal D, Lynch AG, Visakorpi T, Isaacs WB, Veer LV, Caldas C, Desmedt C, Sotiriou C, Aparicio S, Foekens JA, Eyfjörd JE, Lakhani SR, Thomas G, Myklebost O, Span PN, Børresen-Dale AL, Richardson AL, Van de Vijver M, Vincent-Salomon A, Van den Eynden GG, Flanagan AM, Futreal PA, Janes SM, Bova GS, Stratton MR, McDermott U, Campbell PJ; ICGC Breast Cancer Group; ICGC Bone Cancer Group; ICGC Prostate Cancer Group.

Science. 2014 Aug 1;345(6196):1251343. doi: 10.1126/science.1251343.

36.

Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis.

Weaver JMJ, Ross-Innes CS, Shannon N, Lynch AG, Forshew T, Barbera M, Murtaza M, Ong CJ, 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 PAW, Rosenfeld N, Tavaré S, Fitzgerald RC; OCCAMS consortium.

Nat Genet. 2014 Aug;46(8):837-843. doi: 10.1038/ng.3013. Epub 2014 Jun 22.

37.

Peroxiredoxin-3 is overexpressed in prostate cancer and promotes cancer cell survival by protecting cells from oxidative stress.

Whitaker HC, Patel D, Howat WJ, Warren AY, Kay JD, Sangan T, Marioni JC, Mitchell J, Aldridge S, Luxton HJ, Massie C, Lynch AG, Neal DE.

Br J Cancer. 2013 Aug 20;109(4):983-93. doi: 10.1038/bjc.2013.396. Epub 2013 Jul 23.

38.

Variability of computational fluid dynamics solutions for pressure and flow in a giant aneurysm: the ASME 2012 Summer Bioengineering Conference CFD Challenge.

Steinman DA, Hoi Y, Fahy P, Morris L, Walsh MT, Aristokleous N, Anayiotos AS, Papaharilaou Y, Arzani A, Shadden SC, Berg P, Janiga G, Bols J, Segers P, Bressloff NW, Cibis M, Gijsen FH, Cito S, Pallarés J, Browne LD, Costelloe JA, Lynch AG, Degroote J, Vierendeels J, Fu W, Qiao A, Hodis S, Kallmes DF, Kalsi H, Long Q, Kheyfets VO, Finol EA, Kono K, Malek AM, Lauric A, Menon PG, Pekkan K, Esmaily Moghadam M, Marsden AL, Oshima M, Katagiri K, Peiffer V, Mohamied Y, Sherwin SJ, Schaller J, Goubergrits L, Usera G, Mendina M, Valen-Sendstad K, Habets DF, Xiang J, Meng H, Yu Y, Karniadakis GE, Shaffer N, Loth F.

J Biomech Eng. 2013 Feb;135(2):021016. doi: 10.1115/1.4023382.

PMID:
23445061
39.

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.

40.

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.

41.

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.

42.

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.

43.

BayesPeak--an R package for analysing ChIP-seq data.

Cairns J, Spyrou C, Stark R, Smith ML, Lynch AG, Tavaré S.

Bioinformatics. 2011 Mar 1;27(5):713-4. doi: 10.1093/bioinformatics/btq685. Epub 2011 Jan 17.

44.
45.

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.

46.

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
47.

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.

48.

Use of the piggyBac transposon to create HIV-1 gag transgenic insect cell lines for continuous VLP production.

Lynch AG, Tanzer F, Fraser MJ, Shephard EG, Williamson AL, Rybicki EP.

BMC Biotechnol. 2010 Mar 31;10:30. doi: 10.1186/1472-6750-10-30.

49.

Driver mutations in TP53 are ubiquitous in high grade serous carcinoma of the ovary.

Ahmed AA, Etemadmoghadam D, Temple J, Lynch AG, Riad M, Sharma R, Stewart C, Fereday S, Caldas C, Defazio A, Bowtell D, Brenton JD.

J Pathol. 2010 May;221(1):49-56. doi: 10.1002/path.2696.

50.

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.

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