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Publications

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ARTICLES
  1. Camacho N., Van Loo P., Edwards S., Kay J.D., Matthews L., Haase K., Clark J., Dennis N., Thomas S., Kremeyer B., Zamora J., Butler A.P., Gundem G., Merson S., Luxton H., Hawkins S., Ghori M., Marsden L., Lambert A., Karaszi K., Pelvender G., Massie C. E., Kote-Jarai Z., Raine K., Jones D., Howat W. J., Hazell S., Livni N., Fisher C., Ogden C., Kumar P., Thompson A., Nicol D., Mayer E., Dudderidge T., Yu Y., Zhang H., Shah N. C., Gnanapragasam V. J., The CRUK-ICGC Prostate Group, Isaacs W., Visakorpi T., Hamdy F., Berney D., Verrill C., Warren A. Y., Wedge D. C., Lynch A.G., Foster C. S., Lu Y. J., Bova G. S., Whitaker H. C., McDermott U., Neal D. E., Eeles R., Cooper C. S. and Brewer D. S. (2017) 
    Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data PLoS Genetics 

  2. Smeets E, Lynch AG, Prekovica S, Van den Broeck T, Moris L, Helsen C, Joniau S, Claessens F, Massie CE (2017) 
    The role of TET-mediated DNA hydroxymethylation in prostate cancer Molecular and Cellular Endocrinology (online)

  3. Asim M, Tarish F, Zecchini HI, Sanjiv K, Gelali E, Massie CE, Baridi A, Warren AY,  Zhao W, Ogris C, McDuffus L-A, 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 and Helleday T (2017)
    Synthetic lethality between androgen receptor signalling and the PARP pathway in prostate cancer Nature Communications 8, 374

  4. Yates LR, Knappskog S, Wedge D, Farmery JHR,6 Gonzalez S, Martincorena I, Alexandrov LB, Loo PV, Haugland HK, Lilleng PK, Gundem G, Gerstung M, Pappaemmanuil E, Gazinska P, Bhosle SG,Jones,1 Keiran Raine S, Mudie L, Latimer C, Sawyer E, Desmedt C, Sotiriou C, Stratton MR, Sieuwerts AM, Lynch AG, Martens JW, Richardson AL, Tutt A, Lønning PE and Campbell PJ (2017)
    Genomic Evolution of Breast Cancer Metastasis andRelapse Cancer Cell 32, 169–184

  5. Janowitz T, Williams EH, Marshall A, Ainsworth N, Thomas PB, Sammut SJ, Shepherd S, White J, Mark PB, Lynch AG, Jodrell DI, Tavaré S, and Earl H (2017) 
    New Model for Estimating Glomerular Filtration Rate in Patients With CancerJournal of Clinical Oncology (Online ahead of print)

  6. Noorani A*, Bornschein J* Lynch AG*, Secrier M, Achilleos A, Eldridge M, Bower L, Weaver JMJ, Crawte J, Ong C-A, Shannon N, MacRae S, Grehan N, Nutzinger B, O'Donovan M, Hardwick R, Tavaré S, Fitzgerald RC, on behalf of the Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium (2017) 
    A comparative analysis of whole genome sequencing of oesophageal adenocarcinoma pre- and post-chemotherapy. Genome Research (Online ahead of print)

  7. Luca B-A, Brewer DS, Edwards DR, Edward S, Whitaker HC, Merson S, Denis N, Cooper RA, Hazell S, Warren AY, The 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 and Cooper CS (2017)
    DESNT: a Poor Prognosis Category of Human Prostate Cancer. European Urology Focus. (In Press).

  8. Secrier M, Li X, de Silva N, Eldridge MD, Contino G, Bornschein J, MacRae S, Grehan N, O'Donovan M, Miremadi A,  Yang T-P, Bower L, Chettouh H, Crawte J, Galeano-Dalmau N, Grabowska A, Saunders J, Underwood T, Waddell N, Barbour AP, Nutzinger B, Achilleos A, Edwards PAW, Lynch AG, Tavaré S, Fitzgerald RC and the OCCAMS Consortium (2016)
    "Mutational signatures in esophageal adenocarcinoma define etiologically distinct subgroups with therapeutic relevance" Nature Genetics 48 1131-41 doi:10.1038/ng.3659

  9. Thomas B, Kay J, Menon S, Vowler S, Dawson S, Bucklow L, Luxton H, Johnston T, Massie C, Pugh M, Warren AY, Barker P, Burling K, Lynch AG, George A, Burge J, Corcoran M, Stearn A, Lamb A, Sharma N, Shaw G, Neal D and Whitaker HC (2016)
    "Whole blood mRNA in prostate cancer reveals a 4-gene androgen regulated panel" Endocrine Related Cancer

  10. Contino G, Eldridge MD, Secrier M, Bower L, Elliott RF, Weaver J, Lynch AG, Edwards PAW, Fitzgerald RC (2016)
    "Whole-genome sequencing of nine esophageal adenocarcinoma cell linesF1000Research 5:1336 (doi: 10.12688/f1000research.7033.1)

  11. Massie CE, Mills IG, Lynch AG (2017)
    "The Importance of DNA methylation in Prostate Cancer development
    The Journal of Steroid Biochemistry and Molecular Biology 166 1-15

  12. Lynch AG (2016)
    "Decomposition of mutational context signatures using quadratic programming methodsF1000Research 5:1253 (doi: 10.12688/f1000research.8918.1)

  13. 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, Mohammad 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 and Neal D (2016) 
    Choline kinase alpha as an Androgen Receptor Chaperone and Prostate Cancer Therapeutic Target” J. Natl. Cancer Inst. 108 (5): djv371 doi:10.1093/jnci/djv371

  14. Lynch AG (2015)
    "Crambled: A Shiny application to enable intuitive resolution of conflicting cellularity estimatesF1000Research 4:1407 (doi: 10.12688/f1000research.7453.1)

  15. Alioto TS, Buchhalter I, Derdak S, Hutter B, Eldridge M, Hovig E, Heisler LE, Beck TA, Simpson JT, Tonon L, Sertier A-S, Patch A-M, Jäger N, Ginsbach P, Drews R, Paramasivam N, Kabbe R, Chotewutmontri S, Diessl N, Previti C, Schmidt S, Brors B, Feuerbach L, Heinold M, Groebner S, Korshunov A, Tarpey PS, Butler AP, Hinton J, Jones D, Menzies A, Raine K, Shepherd R, Stebbings L, Teague JW, Ribeca P, Castro-Giner F, 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, Letourneau L, Ma S, Seth S, Torrents D, Xi L, Wheeler DA, Lopez-Otin C, Campo E, Campbell PJ, Boutros PC, Puente XS, Gerhard DS, Pfister SM, McPherson JD, Hudson TJ, Schlesner M, Lichter P, Eils R, Jones DTW and Gut IG (2015)
    A comprehensive assessment of somatic mutation detection in cancer using whole genome sequencingNature Communications 6:10001, doi:10.1038/ncomms10001

  16. 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 (2015)
    "The Early Effects of Rapid Androgen Deprivation on Human Prostate Cancer
    .European Urology doi:10.1016/j.eururo.2015.10.042

  17. Ross-Adams H, Lamb AD, Dunning MJ, Halim S, Lindberg J, Massie CE, Egevad LA, Russell R, Ramos-Montoya A, Vowler S, 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, and Neal DE. on behalf of the CamCaP Study Group (2015)
    Integration of copy number and transcriptomics provides risk stratification in prostate cancer: a discovery and validation cohort studyEBioMedicine 2:1133-1144   

  18. 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 on behalf of the Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Study Group. 
    "Whole-genome sequencing provides new insights into the clonal architecture of Barrett's esophagus and esophageal adenocarcinoma", Nature Genetics, 47:1038–1046

  19. Pertega-Gomes N, Vizcaino J, Felisbino S, Warren AY, Shaw G, Kay J, Whitaker H, Lynch AG, Fryer L, Neal DE, and Massie CE. (2015)
    "Epigenetic and oncogenic regulation of SLC16A7 (MCT2) results in protein over-expression, impacting on signalling and cellular phenotypes in prostate cancer" Oncotarget6(25):21675-21684

  20. 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 A-L, ten Hoopen R, Ibrahim AEK, Fuks F and Murrell A (2015)
    "5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancerGenome Biology, 16:69

  21. 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. (2015)
    Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53PLoS Genetics 11(3): e1005053. 

  22. Cooper C, Eeles R, Wedge DC, Loo PV, Gundem G, Alexandrov LB, Kremeyer B, Butler AP, Lynch AG, Camacho N, Massie CE, Kay JD, 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 SJ, Greenman C, Berney D, Hazell S, Livni N, The ICGC Prostate Group, Fisher C, Ogden C, Kumar P, Thompson A, Woodhouse C, Nicol D, Mayer E, Dudderidge T, Shah NC, Gnanapragasam VJ, Voet T, Campbell PJ, Futreal A, Easton D, Warren AY, Foster CS, Stratton MR, Whitaker HC, McDermott U, Brewer D and Neal DE. (2015)
    "Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue" Nature Genetics 47, 367–372

  23. Josephidou M, Lynch AG and Tavaré S. (2015)
    "multiSNV: a probabilistic approach for improving detection of somatic point mutations from multiple related tumour samples" Nucleic Acids Research 43, e61 

  24. 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 A, Tavaré S, Neal DE and Lynch AG. (2015) 
    “HES5 silencing is an early and recurrent change in prostate tumourigenesis” Endocrine-related Cancer 22, 131-144

  25. Cairns J, Lynch AG, Tavaré S. (2014)
    "Quantifying the impact of inter-site heterogeneity on the distribution of ChIP-seq data" Frontiers in Genetics 5:399

  26. 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 M-Q, 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 C, Warren AY, Whitaker H, 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 and Campbell PJ. (2014)
    "Origins and functional consequences of somatic mitochondrial DNA mutations in human cancereLife 
    10.7554/eLife.02935

  27. 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, Fulham 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, ICGC Breast Cancer Group, ICGC Bone Cancer Group, ICGC Prostate Cancer Group, Foster C, Warren AY, Whitaker H, Brewer D, Eeles R, Cooper C, Neal D, Lynch AG, Visakorpi T, Isaacs WB, van 't Veer L, Caldas C, Desmedt C, Sotiriou C, Aparicio S, Foekens J, Eyfjörd JE, Lakhani SR, Thomas G, Myklebost O, Span PN, Børresen-Dale A-L, 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 and Campbell PJ. (2014)
    "Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes" Science 345, DOI:10.1126/science.1251343

  28. Weaver JMJ*, Ross-Innes CS*, Shannon N*, Lynch AG*, Forshew T, Barbera M, Murtaza M, Ong C-AJ, Lao-Sirieix P, Dunning M, Smith L, Smith ML, Anderson CM, 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, and the OCCAMS consortium (2014) 
    "Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis" Nature Genetics 46, 837–843

  29. Whitaker HC, Patel D, Howat WJ, Warren AY, Kay JD, Sangan T, Marioni JC, Mitchell J, Aldridge S, Luxton HJ, Massie C, Lynch AG and Neal DE (2013) "Peroxiredoxin-3 is overexpressed in prostate cancer and promotes cancer cell survival by protecting cells from oxidative stress" British Journal of Cancer 109(4):983-93

  30. Lynch AG, Dunning MJ, Chin S-F, Caldas C, Tavaré S and Curtis C (2012)
    "Calling Sample Mix-ups in Cancer Population Studies" PLoS ONE 7(8):e41815

  31. Curtis C, Shah SP, Chin S-F, 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 A-L, Brenton JD, Tavaré S, Caldas C and Aparicio S (2012) 
    "The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups", Nature 486, 346–352

  32. Ritchie ME, Dunning MJ, Smith ML, Shi W and Lynch AG (2011) 
    "BeadArray Expression Analysis Using Bioconductor ", PLoS Computational Biology 7(12):e1002276 

  33. Massie CE, Lynch AG, Ramos-Montoya A, Boren J, Stark R, Fazli L, Warren A, Scott H, Madhu B, Sharma N, Bon H, Zecchini V, Smith D-M, DeNicola GM, Matthews N, Osborne M, Hadfield J, MacArthur S, Adryan B, Lyons SK, Brindle KM Griffiths J, Gleave ME, Rennie PS, Neal DE and Mills IG (2011) 
    "The androgen receptor fuels prostate cancer by regulating central metabolism and biosynthesis", EMBO Journal 30:2719-2733

  34. Holland D, Burleigh A, Git A, Goldgraben MA, Perez-Mancera PA, Chin S-F, Hurtado A, Bruna A, Ali R, Greenwood W, Dunning MJ, Samarajiwa S, Menon S, Rueda OM, Lynch AG, McKinney S, Ellis IO, Eaves CJ, Carroll JS, Curtis CN, Aparicio S and Caldas C (2011) 
    "ZNF703 is a common Luminal B breast cancer oncogene that differentially regulates luminal and basal progenitors in human mammary epithelium", EMBO Molecular Medicine 3:167-180

  35. Cairns J, Spyrou C, Stark R, Smith ML, Lynch AG and Tavaré S (2011) 
    "BayesPeak - An R package for analysing ChIP-seq data", Bioinformatics 27:713-714 

  36. Lynch AG, Hadfield J, Dunning MJ, Osborne M, Thorne NP and Tavaré S (2010) 
    "The cost of reducing starting RNA quantity for Illumina BeadArrays: A bead-level dilution experiment", BMC Genomics 11:540 

  37. Smith ML and Lynch AG (2010) 
    "BeadDataPackR: A Tool to Facilitate the Sharing of Raw Data from Illumina BeadArray Studies", Cancer Informatics 9:217-227 

  38. Dunning MJ, Curtis C, Barbosa-Morais NL, Caldas C, Tavaré S and Lynch AG (2010) 
    "The importance of platform annotation in interpreting microarray data", Lancet Oncology 11:717

  39. Smith ML, Dunning MJ, Tavaré S and Lynch AG (2010) 
    "Identification and correction of previously unreported spatial phenomena using raw Illumina BeadArray data", BMC Bioinformatics 11:208 

  40. Galbraith S, Fagan P, Perkins P, Lynch AG, Booth S (2010) 
    "Does the use of a handheld fan improve chronic dyspnoea? a randomised controlled crossover trial", Journal of Pain and Symptom Management 39:831-8

  41. Ahmed AA, Etemadmoghadam D, Temple J, Lynch AG, Riad M, Australian Ovarian Cancer Study Group, Sharma R, Stewart C, Fereday S, Caldas C, de Fazio A, Bowtell D and Brenton JD (2010) 
    "Driver mutations in TP53 are ubiquitous in high grade serous carcinoma of the ovary", Journal of Pathology 221:49-56

  42. Barbosa-Morais NL, Dunning MJ, Samarajiwa SA, Darot JFJ, Ritchie ME, Lynch AG, Tavaré S. (2010) 
    "A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data", Nucleic Acids Research 38:e17

  43. Curtis CN*, Lynch AG*, Dunning MJ, Spiteri I, Marioni JC, Hadfield J, Chin S-F, Brenton J, Tavaré S and Caldas C (2009) 
    "The pitfalls of platform comparison: DNA copy number array technologies assessed", BMC Genomics 10:588 

  44. Spyrou C, Stark R, Lynch AG, Tavaré S. (2009) 
    "BayesPeak: Bayesian analysis of ChIP-seq data", BMC Bioinformatics 10:299 

  45. Lynch AG, Dunning MJ, Iddawela M, Barbose-Morais NL, Ritchie ME (2009) 
    "Considerations for the processing and analysis of GoldenGate-based two-colour Illumina platforms", Statistical Methods in Medical Research 18:437-452

  46. Wiesner M, Naylor SJ, Copping A, Furlong A, Lynch AG, Parkes M and Hunter JO. (2009)
    "Symptom classification in irritable bowel syndrome as a guide to treatment". Scandinavian Journal of Gastroenterology 44:796-803

  47. Cairns JM, Dunning MJ, Ritchie MR, Russell R, Lynch AG (2008) 
    "BASH: A tool for managing BeadArray spatial artefacts", Bioinformatics 24 2921-2922.

  48. Fanshawe TR*, Lynch AG*, Ellis IO, Green AR, Hanka R (2008) 
    "Assessing agreement between multiple raters with missing rating information, applied to breast cancer tumour grading", PLoS ONE 3(8)

  49. Marioni JC, White M, Tavaré, S, Lynch AG (2008) 
    "Hidden copy number variation in the HapMap population", PNAS 105 (29) 10067-10072

  50. Bernard F, Al-Tamimi YZ, Chafield D, Lynch AG, Matta BF and Menon DK. (2008) 
    "Serum albumin level as a predictor of outcome in traumatic brain injury: Potential for treatment". Journal of Trauma-Injury Infection and Critical Care, 64:872-875

  51. Dunning MJ, Ritchie ME, Barbosa-Morais NL, Tavaré, S, Lynch AG (2008) 
    "Spike-in validation of an Illumina-specific variance stabilizing transformation", BMC Research Notes 2008 1:18 

  52. Walsh SR, Tang TY, Lynch AG, Sadat U, Carpenter JP, Boyle JR, Gaunt ME (2008) 
    "Suprarenal endograft fixation and medium-term renal function: systematic review and meta-analysis" Journal of Vascular Surgery 47 (6) 1364-1370

  53. Dunning MJ, Barbosa-Morais NL, Lynch AG, Tavaré, S, Ritchie ME (2008) 
    "Statistical issues in the analysis of Illumina data", BMC Bioinformatics 2008 9:85

  54. Burnet NG, Lynch AG, Jefferies SJ, Price SJ, Jones PH, Antoun NM, Xuereb JH and Pohl U (2007)
    "High grade glioma: imaging combined with pathological grade defines management and predicts prognosis". Radiotherapy and Oncology 85:371-378 

  55. Marioni JC, Thorne NP, Valsesia A, Fitzgerald T, Redon R, Fiegler H, Andrews TD, Stranger BE, Lynch AG, Dermitzakis ET, Carter NP, Tavaré S and Hurles ME (2007)  
    "Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization". Genome Biology 8:R228 

  56. Price SJ, Jena R, Green HAL, Kirkby NF, Lynch AG, Coles CE, Pickard JD, Gillard JH and Burnett NG (2007)
    "Early radiotherapy dose response and lack of hypersensitivity effect in normal brain tissue: A sequential dynamic susceptibility imaging study of cerebral perfusion". Clinical Oncology 19:577-587 

  57. Massie CE, Adryan B, Barbosa-Morais NL, Lynch AG, Tran M, Neal DE and Mills IG (2007)
    "New androgen receptor genomic targets show an interaction with the ETS1 transcription factor". EMBO Reports 8:871-878 

  58. Lynch AG, Marioni J and Tavaré S. (2007)
    "Numbers of CNVs and false negative rates will be underestimated if we do not account for the dependence between repeated experiments". American Journal of Human Genetics 81:418-420 

  59. Lynch AG, Neal D, Kelly, J, Burtt G and Thorne N. (2007)
    "Missing channels in two-colour microarray experiments: Combining single-channel and two-channel data". BMC Bioinformatics 8:26 

  60. Robinson AHN, Cullen NP, Chhaya NC, Sri Ram K, and Lynch AG. (2006)
    "Variation of the distal metatarsal articular angle with axial rotation and inclination of the first metatarsal". Foot and Ankle International 27:1036-1040 

  61. Bernard F, Outtrim J, Lynch AG, Menon DK and Matta BF. (2006)
    "Hemodynamic steroid responsiveness is predictive of neurological outcome after traumatic brain injury". Neurocritical Care 5:176-179

  62. Cachón-González MB, Wang S, Lynch A, Ziegler R, Cheng SH and Cox TM. (2006)
    "Effective gene therapy in an authentic model of Tay-Sachs related diseases". PNAS 103:10373-10378

  63. Goodman RS, Taylor CJ, O’Rourke CM, Lynch A, Bradley JA and Key T. (2006)
    "Utility of HLAMatchmaker and single-antigen HLA-antibody detection beads for identification of acceptable mismatches in highly sensitised patients awaiting kidney transplantation". Transplantation 81:1331-1336 

  64. Lynch AG. (2005)
    "The interpretation of negative results demands more caution than exhibited here". Comment on Stenberg AE, Sylvén L, Magnusson CGM and Hultcrantz M, (2004) “Immunological parameters in girls with Turner syndrome.” Journal of Negative Results in BioMedicine 3:6

  65. Callaghan CJ, Lynch AG, Amin I, Fazel M, Lindop MJ, Gaunt ME and Varty K, (2005)
    "Overnight intensive recovery: elective open aortic surgery without a routine ICU bed". European Journal of Vascular and Endovascular Surgery 30:252-258 

  66. Price CJ, Menon DK, Peters AM, Ballinger JR, Barber RW, Balan KK, Lynch A, Xuereb JH, Fryer T, Guadagno JV and Warburton EA (2004)
    "Cerebral neutrophil recruitment, histology and outcome in acute ischemic stroke: an imaging based study". Stroke 35:1659-1664

  67. Sardesai AM, Denny NM, Herrick MJ, Lynch A and Harrop-Griffiths W. (2004)
    "A study of the characteristics of single-injection insulated block needles in a biologic model". Regional Anesthesia and Pain Medicine 29:476-479
* - equal first author

ARTICLES AS NAMED MEMBER OF A CONSORTIUM/GROUP
  1. Noble F, Lloyd MA, Turkington R, Griffiths E, O'Donovan M, O'Neill JR, Mercer S, Parsons SL, Fitzgerald RC, Underwood TJ on behalf of the OCCAMS consortium (2017)
    Multicentre cohort study to define and validate pathological assessment of response to neoadjuvant therapy in oesophagogastric adenocarcinoma. Br J Surg.

  2. Britton E, Rogerson C, Mehta S, Li Y, Li X, the OCCAMS consortium, Fitzgerald RC, Ang YS, Sharrocks AD (2017)
    Open chromatin profiling identifies AP1 as a transcriptional regulator in oesophageal adenocarcinoma. PLoS Genet. 13(8):e1006879

  3. Fels Elliott DR, Perner J, Li X, Symmons MF, Verstak B, Eldridge M, Bower L, O'Donovan M, Gay NJ, OCCAMS Consortium, Fitzgerald RC (2017)
    Impact of mutations in Toll-like receptor pathway genes on esophageal carcinogenesis. PLoS Genet. 13(5):e1006808.

  4. Behjati S, Gundem G, Wedge DC, Roberts ND, Tarpey PS, Cooke SL, Van Loo P, Alexandrov LB, Ramakrishna M, Davies H, Nik-Zainal S, Hardy C, Latimer C, Raine KM, Stebbings L, Menzies A, Jones D, Shepherd R, Butler AP, Teague JW, Jorgensen M, Khatri B, Pillay N, Shlien A, Futreal PA, Badie C, ICGC Prostate Group, McDermott U, Bova GS, Richardson AL, Flanagan AM, Stratton MR and Campbell PJ (2016)
    "Mutational signatures of ionizing radiation in second malignanciesNature Communications 7, Article number: 12605

  5. Garcia E, Hayden A, Birts C, Britton E, Cowie A, Pickard K, Mellone M, Choh C, Derouet M, Duriez P, Noble F, White MJ, Primrose JN, Strefford JC, Rose-Zerilli M, Thomas GJ, Ang Y,  Sharrocks AD, Fitzgerald RC, Underwood TJ and the OCCAMS consortium (2016)
    "Authentication and characterisation of a new oesophageal adenocarcinoma cell line: MFD-1Scientific Reports 6, Article number: 32417 

  6. Paterson AL, Weaver JMJ, Eldridge MD, Tavaré S, Fitzgerald RC, Edwards PAW and the OCCAMs Consortium (2015)
    "Mobile element insertions are frequent in oesophageal adenocarcinomas and can mislead paired-end sequencing analysisBMC Genomics, 16:473

  7. Ju YS, Tubio JMC, Mifsud W, Fu B, Davies HR, Ramakrishna M, Li Y, Yates L, Gundem G, Tarpey PS, Behjati S, Papaemmanuil E, Martin S, Fullam A, Gerstung M, ICGC Prostate Cancer Working Group, ICGC Bone Cancer Working Group, ICGC Breast Cancer Working Group, Nangalia J, Green AR, Caldas C, Borg A, Tutt A, Lee MTM, van’t Veer LJ, Tan BKT, Aparicio S, Span PN, Martens JWM, Knappskog S, Vincent-Salomon A, Børresen-Dale A-L,  Eyfjörd JE, Flanagan AM, Foster C, Neal DE, Cooper C, Eeles R, Lakhani SR, Desmedt C, Thomas G, Richardson AL,  Purdie CA, Thompson AM, McDermott U, Yang F, Nik-Zainal S, Campbell PJ and Stratton MR (2015)
    "Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells" Genome Research doi:10.1101/gr.190470.115

  8. Gundem G, Van Loo P, Kremeyer B, Alexandrov LB, Tubio JMC, Papaemmanuil E, Brewer DS, Kallio HML, Högnäs G, Annala M, Kivinummi K, Goody V, Latimer C, O'Meara S, Dawson KJ, Isaacs W, Emmert-Buck MR, Nykter M, Foster C, Kote-Jarai Z, Easton D, Whitaker HC, ICGC Prostate UK Group, Neal DE, Cooper CS, Eeles RA, Visakorpi T, Campbell PJ, McDermott U, Wedge DC and Bova GS (2015) 
    "The evolutionary history of lethal metastatic prostate cancer" Nature 520, 353–357

  9. Vollana HKM, Rueda OM, Chin S-F, Curtis C, Turashvili G, Shah S, Lingjærde OC, Yuan Y, Ng CK, Dunning MJ, Dick E, Provenzano E, Sammut S, McKinney S, Ellis IO, Pinder S, Purushotham A, Murphy LC, Kristensen VN, METABRIC Group, Brenton JD, Pharoah PDP, Børresen-Dale A-L, Aparicio S and Caldas C. (2014)
    "A tumor DNA complex aberration index is an independent predictor of survival in breast and ovarian cancer" Molecular Oncology 
    9:115-2

CHAPTERS/CONTRIBUTIONS TO BOOKS
  1. Andrews DJ, Lynch AGand Tavaré S. (2016) Using Methylation Patterns for Reconstructing Cell Division Dynamics: Assessing Validation Experiments. In Emerging Trends in Applications and Infrastructures for Computational Biology, Bioinformatics, and Systems Biology Systems and Applications. Tran QN and Arabnia HR editors. pp 3-15 Morgan Kaufmann, Cambridge MA, USA. ISBN 9780128042038

  2. Cairns JM, Lynch AG and Tavaré S. (2013) Statistical aspects of ChIP-seq analysis. In Advances in Statistical Bioinformatics: Models and Integrative Inference for High-Throughput Data. Do K, Qin Z and Vannucci M. editors. pp 138-169 Cambridge University Press. ISBN 1107027527.

  3. Everitt BS and Lynch AG (2010) Two articles in “Encyclopaedic Companion to Medical Statistics. Second Edition”  Everitt, BS and Palmer CR editors. ISBN 0470684194.

  4. Lynch AG (2010)  Twenty-four articles in “Encyclopaedic Companion to Medical Statistics. Second Edition”  Everitt, BS and Palmer CR editors. ISBN 0470684194.

  5. Lynch AG, Smith ML, Dunning MJ, Cairns JM, Barbosa-Morais NL, Tavaré S (2009) "beadarray, BASH and HULK - tools to increase the value of Illumina BeadArray experiments". In A. Gusnato, K.V. Mardia, & C.J. Fallaize (eds), Statistical Tools for Challenges in Bioinformatics. pp. 33-37. Leeds, Leeds University Press. ISBN 9780853162803.

  6. Dunning MJ, Cairns JM, Russell R and Lynch AG (2008) Fortifying the analysis of Illumina data. in Proceedings of the 4th World Conference of the International Association for Statistical Computing. ISBN 9784990444518. 

  7. Lynch AG, Curtis C and Tavaré S (2007) Correcting for probe-design in the analysis of gene-expression microarrays. In S. Barber, P.D. Baxter, & K.V.Mardia (eds), Systems Biology & Statistical Bioinformatics, pp. 83-86. Leeds, Leeds University Press. ISBN 9780853162636.

  8. Everitt BS and Lynch AG (2005) Two articles in “Encyclopaedic Companion to Medical Statistics”  Everitt, BS and Palmer CR editors. ISBN 0340809981.

  9. Lynch AG (2005)  Twenty-four articles in “Encyclopaedic Companion to Medical Statistics”  Everitt, BS and Palmer CR editors. ISBN 0340809981.

  1. Farmery JHR, Smith ML, NIHR BioResource - Rare Diseases and Lynch AG (2017) Telomerecat: A Ploidy-Agnostic Method For Estimating Telomere Length From Whole Genome Sequencing Data bioarxiv

 
OTHER ARTICLES
  1. Dunning MJ, Vowler SL, Lalonde E, Ross-Adams H, Boutros P, Mills IG, Lynch AG, Lamb AD (2017)
    Mining Human Prostate Cancer Datasets: The “camcAPP” Shiny App. EBioMedicine 
    http://dx.doi.org/10.1016/j.ebiom.2017.02.022

  2. Fanshawe TR and Lynch AG (2015)
    The FA Cup draw: the probability of getting four home fixtures in a row. Significance 6th Match 2015

  3. Lynch AG (2003)
    Book Review (Using SPSS for Windows/Doing Statistics with SPSS/Data Analysis Using SPSS for Windows Versions 8-10) Statistics in Medicine 22:2529-2531
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