Publications

In the mathematical sciences, author order is typically alphabetical and not indicative of relative contribution to the paper.  For papers where the author order is significant, this is shown.

Papers:
1 Finite particle systems and infection models. Math. Proc. Camb. Phil.  Soc. 94 (1983), 167-182. (With D J A Welsh)

2 The transient behaviour of the Moran model in population genetics. Math. Proc. Camb. Phil. Soc.  95 (1984), 349-358.

3 The antivoter problem: random two colourings of graphs.  In Graph Theory and Combinatorics B. Bollobas (ed.), Academic Press (1984) 133-144. (With D J A Welsh)

4 The Wright-Fisher model with temporally varying selection and population size.  J.  Math. Biol. 23 (1985), 21-29. (With N C Weber)

5 Dual processes and an invariance result for exchangeable models in population genetics.  J. Math. Biol. 23 (1985), 103-118.

6 The ages of alleles and a coalescent. Adv. Appl. Prob. 18 (1986), 1-19. (With S Tavaré)

7 A genealogical approach to variable population size models in population genetics.  J. Appl. Prob. 23 (1986), 283-296.

8 Dual processes in population genetics.  In  Stochastic Spatial Processes, P. Tautu (ed.), Springer Lecture Notes in Mathematics, 1212, (1986),  94-105.

9 Partition structures, Polya urns, the Ewens sampling formula, and the ages of alleles. Theor. Pop. Biol. 30 (1986), 271-288.

10 British rural settlements in the hinterland of connurbations: a classification. Geog. Ann. 69B (1987), 55-63. (With S Harper)

11 A genealogical description of the infinite alleles model.  In Stochastic Models in Biology M. Kimura, G. Kallianpur, and T. Hida (eds), Springer Lecture Notes in Biomathematics, 70, (1987), 27-35. (With S Tavaré)

12 The population genealogy of the infinitely many neutral alleles model. J. Math. Biol. 25 (1987), 381-391. (With S Tavaré)

13 Inter-particle correlation in death processes with application to compartmental models.  Adv. Appl. Prob. 19 (1987), 755-766. (With F Ball)

14 A unified approach to variability in compartmental models. Biometrics 44 (1988), 685-694. (With F Ball)

15 The effect on genetic sampling distributions of correlations in reproduction.  Theor. Pop. Biol. 35 (1989), 22-35. (With P Marjoram)

16 Continuity and weak convergence of ranked and size-biased permutations on the infinite simplex. Stoch. Proc. Appl. 31 (1989), 89-103.  (With P Joyce)

17 On reinforcement-depletion compartmental urn models. Appl. Prob. 26 (1989), 477-489. (With W Whitt)

18 Weak convergence to a Markov chain with an entrance boundary: ancestral processes in population genetics.  Ann. Probab. 19 (1991), 1102-1117

19 Consistent ordered sampling distributions: characterization and convergence. Adv. Appl. Prob. 23 (1991), 229-258. (With P Joyce)

20 Functionals of random mappings: asymptotic and numerical results. Adv. Appl. Prob. 23 (1991), 437-455. (With W Ewens and S Padmadisastra)

21 The heaps process, libraries, and size-biased permutations. J. Appl. Prob. 28 (1991), 437-455.

22 On the functional central limit theorem for the Ewens sampling formula.  Ann. Appl. Prob. 1 (1991), 539-545.  (With T Kurtz and  S Tavaré)

23 Genome mapping with anchored clones: theoretical aspects. Genomics 11 (1991), 799-805.  (W Ewens, C Bell, P Dunn, P Donnelly, E Matallana and J Ecker)

24 Weak convergence of population genealogical processes to the coalescent with ages. Ann. Probab 20 (1992), 322-341. (With P Joyce)

25 Do Eve's alleles live on?  Genet. Res.  60 (1992), 221-234. (With G Watterson)

26 Constant predator-prey ratios: an arithmetical artefact. Ecology 74 (1993), 238-243.  (With G Closs and G Watterson)

27 On conditional intensities and interparticle correlation in non-linear death processes.  Adv. Appl. Prob. 25 (1993), 255-260.  (With T Brown)

28 Correlation and variability in birth processes. J. Appl. Prob. 30 (1993), 275-284.  (With T Kurtz and P Marjoram)

29 On the stochastic approach to cluster size distribution during particle coagulation. I Asymptotic expansion in the deterministic limit.  J. Phys. A. 26 (1993), 2755-2767.  (With S  Simons)

30 On the asymptotic distribution of large prime factors. J. Lond. Math. Soc. 47 (1993), 395-404.  (With G Grimmett)

31 The correlation structure of some epidemic models. Math. Biosci. 117 (1993), 49-76.

32 Pairwise comparisons of mitochondrial DNA sequences in subdivided populations and implications for early human evolution. Genetics 136  (1994), 673-683. (P Marjoram and P Donnelly)

33 How convincing is DNA evidence? Nature 368  (1994), 285-286.  (With D Balding)

34 Approach to stationarity in the Bernoulli-Laplace diffusion. Adv. Appl. Prob. 26 (1994), 715-727. (With P Lloyd and A Sudbury)

35 The prosecutor's fallacy and DNA evidence.  Crim. Law Rev. (1994), 711-721. (With D Balding)

36 Inference in forensic identification. (with discussion) J. Roy. Stat. Soc. A. 158 (1995), 21-53. (With D Balding)

37 Strong approximations for epidemic models.  Stoch. Proc. Appl. 55 (1995), 1-21. (With F Ball) 

38 Match probability calculations for multi-locus DNA profiles.  Genetica 96 (1995), 55-67.

39 The non-independence of matches at different loci in DNA profiles: quantifying the effect of close relatives on the match probability. Heredity 72 (1995), 26-34 .
 
40 Probability and proof in State v. Skipper: an internet exchange. Jurimetrics 35 (1995), 277-310.  (With RJ Allen, D J Balding, R Friedman, D H Kaye, L H LaRue, R C Park, B Robertson and A Stein)

41 Coalescents and genealogical structure under neutrality.  Ann. Rev. Genet. 29 (1995), 401-421. (With S Tavaré)

42 Inferring identity from DNA profile evidence.  Proc. Natl. Acad. Sci. 92 (1995), 11741-11745. (With D Balding)

43 Interpreting genetic variability: the effects of shared evolutionary history. In Variation in the Human Genome.  Ciba Foundation Symposium 197.  Wiley, Chichester (1996), pp 25-50.

44 ``Quantum spin'' techniques and the exclusion model of diffusion.  Stoch. Proc. Appl. 61 (1996), 205-221. (With P Lloyd and A Sudbury)

45 Evaluating DNA profile evidence when the suspect is identified through a database search.   J. For. Sci. 41 (1996), 599-603. (With D Balding)

46 Estimating the age of the common ancestor of men from the ZFY intron.  Science 272 (1996), 1357-1359.  (P Donnelly, S Tavaré, D Balding and R Griffiths)

47 A countable representation of the Fleming-Viot measure-valued diffusion.  Ann. Prob. 24 (1996), 698-742. (With T Kurtz)

48 The asymptotic behaviour of an urn model arising in population genetics.  Stoch. Proc. Appl. 64 (1996), 1-16.  (With T Kurtz)

49 Optimal sequencing strategies for surveying molecular genetic diversity.  Genetics 144 (1996), 1247-1262. (A Pluzhnikov and P Donnelly)

50 Inferring coalescence times from DNA sequence data. Genetics 145 (1997), 505-518  (S Tavaré, D Balding, R Griffiths and P Donnelly)

51 Human demography and the time since mitochondrial Eve. Progress in Population Genetics and Human Evolution P. Donnelly and S. Tavaré (eds.), Springer-Verlag, (1997), 107-131. (P Marjoram and P. Donnelly)

52 The coalescent process with selfing. Genetics 146 (1997), 1185-1195. (M Nordborg and P Donnelly)

53 Heterogeneity of microsatellite mutations within and between loci, and implications for human demographic histories.  Genetics 148 (1998), 1269-1284. (A DiRienzo, P Donnelly, C Toomajian, B Sisk, A Hill, G Haines, M. Petzl-Erler and D Barch)

54 Genetic evidence that President Thomas Jefferson was the father of one of Sally Hemings' children.  Nature 396 (1998), 27-28. (E.A Foster, M A Jobling, T Zerjal, P de Knijff, P  Donnelly and C. Tyler-Smith).

55 DNA database searches and the legal consumption of scientific evidence.   Michigan Law Review 97 (1999), 931-984. (With R D Friedman)

56 Particle representations for measure-valued population models.  Ann. Prob. 27 (1999), 166-205. (With T Kurtz)

57 The coalescent and microsatellite variability. In Microsatellites: Evolution and Applications D Goldstein and C Schlotterer, eds, Oxford University Press, Oxford (1999),  116-128

58 Conditional genealogies and the age of a neutral mutant.  Theor. Pop. Biol. 56 (1999), 183-201 (C Wiuf and P Donnelly)

59 Genealogical processes for Fleming-Viot models with selection and recombination.   Ann. Appl. Prob. 9 (1999), 1091-1148 (With T Kurtz)

60 Microsatellite mutations and inferences about human evolution. Genetics 154 (2000), 1793-1807 (R Gonser, P Donnelly, G Nicholson, and A DiRienzo).

61 The mutation rate in the human mtDNA control region.   Am. J. Hum. Genet. 66 (2000), 1599-1609 (S Sigurdardottir, A Helgason, J Gulcher, K Stefanson, and P Donnelly)

62 Inference of population structure using multilocus genotype data.  Genetics 155 (2000), 945-959 (J Pritchard, M Stephens, and P Donnelly)

63 Association mapping in structured populations.  Am. J. Hum. Genet. 67 (2000), 170-181 (J Pritchard, M Stephens, N Rosenberg, and P Donnelly)

64 Inference in molecular population genetics.  J. Roy. Stat. Soc. B.  62 (2000), 605-655. With discussion.  (M Stephens and P Donnelly)

65 Continuum-sites stepping-stone models, coalescing exchangeable partitions, and random trees.   Ann. Prob. 28 (2000), 1063-1110 (With S.N. Evans, K Fleischmann, T G. Kurtz and X Zhou)

66 Convergence to stationarity in the Moran model.   J. Appl. Prob. 37 (2000), 705-717 (With E. Rodrigues)

67 A new statistical method for haplotype reconstruction from population data.  Am. J. Hum. Genet. 68 (2001), 978-989 (M Stephens, N Smith and P Donnelly)

68 Likelihoods and simulation methods for a class of nonneutral population genetics models.  Genetics 159 (2001), 853-867 (M Nordborg, P Joyce and P Donnelly)

69 Estimating recombination rates from population genetic data.  Genetics 159 (2001) 1299-1318 (P Fearnhead and P Donnelly)
 
70 Case-Control Studies of Association in Structured or Admixed Populations. Theor. Pop. Biol. 60 (2001), 227-237 (J K Pritchard and P Donnelly)

71 Approximate likelihood methods for estimating local recombination rates.  J. Roy. Stat. Soc. B.  64 (2002), 657-680. With discussion.  (P.Fearnhead and P Donnelly)

72 Assessing population differentiation and isolation from single-nucleotide polymorphism data.  J. Roy. Stat. Soc. B.  64 (2002), 695-715. With discussion.  (G Nicholson, A V Smith, F Jonsson, O Gustafsson, K Steffanson and P Donnelly)

73 A reassessment of genetic diversity in Icelanders: strong evidence from multiple loci for relative homogeneity caused by genetic drift. Ann. Hum. Genet. 67 (2003) 281-297.  (A Helgason, G Nicholson, K Steffánsson, and P Donnelly)

74 Ancestral inference in population genetics models with selection Aust. N.Z. J. of Stats. 45 (2003) 395-430.  With discussion.  (M Stephens and P Donnelly)
75 A Comparison of Bayesian methods for haplotype reconstruction from population genotype data.   Am. J. Hum. Genet., 73 (2003) 1162-1169, 2003 (M Stephens and P Donnelly)

76 The international HapMap project. Nature 426 (2003) 789-796. (The International HapMap Consortium)
 
77 The effects of human population structure on large genetic association studies. Nature Genetics 36 (2004) 512 - 517.  (J Marchini, L Cardon, M Phillips and P Donnelly).

78 The fine-scale structure of recombination rate variation in the human genome.  Science,  304 (2004) , Issue 5670, 581-584 .  (G McVean, S Myers, S Hunt, P Deloukas, D.Bentley and P Donnelly).

79 Integrating ethics and science in the International HapMap Project.  Nature Reviews Genetics, 5 (2004)  467-475.  (The International HapMap Consortium).

80 High recombination rate in herpes simplex virus type 1 natural populations suggests significant co-infection. Infect. Genet. and Evol., 4 (2004) 115-123.  (R Bowden, H Sakaoka, P Donnelly and R Ward)

81 Application of coalescent methods to reveal fine-scale rate variation and recombination hotspots. Genetics 167 (2004) 2067-2081. (P Fearnhead, R M Harding, J A Schneider, S Myers, and P Donnelly)

82 Comparison of fine scale recombination rates in humans and chimpanzees.  Science 308 (2005) 107-111. (W Winckler, S.Myers, D Richter, R Onofrio, G McDonald, R Bontrop, G McVean, S Gabriel, D Reich, P Donnelly* and D. Altshuler* - joint senior author)

83 Genome-wide strategies for detecting multiple loci that influence complex diseases. Nature Genetics 37 (2005) 413-417 (J Marchini, P Donnelly and L Cardon)

84 Human recombination hot spots hidden in regions of strong marker association. Nature Genetics 37 (2005). 601-606.  (A Jeffreys, R Neumann, M Panayi, S Myers, and P Donnelly)

85 A fine scale map of recombination rates and hotspots across the human genome. Science 309 (2005) 321-324.  (S Myers, L Bottolo, C Freeman, G McVean* and P Donnelly* – joint senior author)

86 A haplotype map of the human genome. Nature 437 (2005). 1299-1320. The International HapMap Consortium.  (D. Altshuler and P. Donnelly corresponding authors.)

87 Patterns of Eurasian HSV-1 molecular diversity and inferences of human migrations.  Infection, Genetics, and Evolution 6 (2006) 63-74.  (R Bowden, H Sakaoka, R Ward and P Donnelly)

88 The influence of recombination on human genetic diversity.  PLOS Genetics 2 9 (2006) 1375-1385.  (C Spencer, P Deloukas, S Hunt, J Mullikin, S Myers, B Silverman, P Donnelly, D Bentley and G McVean) 

89 A model-based approach to capture genetic variation for future association studies.  Genome Research 17 (2007) 88-95.  (S Eyheramendy, J Marchini, G McVean, S Myers and P  Donnelly)

90 A new multipoint method for genome-wide association studies by imputation of genotypes.  Nature Genetics 39 (2007) 906–913.  (J Marchini, B Howie, S Myers, G McVean and P Donnelly)

91 Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.  Nature 447 (2007) 661-678.  The Wellcome Trust Case Control Consortium.  (Chair: P Donnelly)

92 Replicating genotype-phenotype associations.  Nature 447 (2007) 655-661.  (S Chanock, T Manolio, M Boehnke, E Boerwinkle, D Hunter, G Thomas, J Hirschhorn, G Abecasis, D  Altshuler, J Bailey-Wilson, L Brooks, L Cardon, M Daly, P Donnelly, J Fraumeni, Jr, N Freimer, D Gerhard, C Gunter, A Guttmacher, M Guyer, E Harris, J Hoh, R Hoover, C A Kong, K Merikangas, C Morton, L Palmer, E Phimister, J Rice, J Roberts, C Rotimi, M Tucker, K Vogan, S Wacholder, E Wijsman, D Winn and F Collins)

93 Localization of type 1 diabetes susceptibility to the MHC class 1 genes HLA-B and HLA-A. Nature 450 (7171):887-892 (2007). S Nejentsev, J.M.M Howson, N.M. Walker, J Szeszko, S.F. Field, H.E. Stevens, P. Reynolds, M. Hardy, E. King, J. Masters, J. Hulme, L.M. Maier, D Smyth, R Bailey, J.D. Cooper, G Ribas, R.D. Campbell, The Wellcome Trust Case Control Consortium (Chair: P Donnelly), D.G. Clayton, J.A. Todd.

94 New models of collaboration in genome-wide association studies: the Genetic Association Information Network (GAIN).  Nature Genetics 39 (2007) 1045-1051. 

95 A second generation human haplotype map of over 3.1 million SNPs. Nature 449 (2007) 851-861(Group author Int HapMap Consortium)

96 Association scan of 14,500 nonsynonymous SNPs in four diseases identifies autoimmunity variants. Nature Genetics 39 (2007) 1329-37 Wellcome Trust Case Control Consortium chaired by P Donnelly; Australo-Anglo-American Spondylitis Consortium (TASC).

97 Is mate choice in human MHC-dependent? PLoS Genetics 4 (2008) Article No.: e1000184. (R Chaix, C Cao, P Donnelly)

98 A common sequence motif associated with recombination hot spots and genome instability in humans.  Nature Genetics 40 (2008) 1124 -1129 (S Myers; C Freeman; A Auton; P Donnelly; G McVean)

99 A statistical method for predicting classical HLA alleles from SNP data. American Journal of Human Genetics 82 (2008) 48 -56 (S Leslie, P Donnelly, G McVean)

100 Progress and challenges in genome-wide association studies in humans.  Nature Insight 456 (2008) 728 -731. (P Donnelly)

101  Designing Genome-Wide Association Studies: Sample Size, Power, Imputation, and the Choice of Genotyping Chip. PLoS Genetics 5(5): e1000477 (2009) (C. Spencer, Z. Su, P. Donnelly, J. Marchini)

102 A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies.  Plos Genetics 5.6 (2009) Article: 100529 (B. Howie, P. Donnelly, J. Marchini)

103 Genome-wide and fine-resolution association analysis of malaria in West Africa. Nature Genetics 41, 657-665 (2009) (M Jallow, YY Teo, KS Small, KA Rockett, P Deloukas, TG Clark, K Kivinen, KA Bojang, DJ Conway, M Pinder, G Sirugo, F Sisay-Joof, S Usen, S Auburn, SJ Bumpstead, S Campino, A Coffey, A Dunham, AE Fry, A Green, R Gwilliam, SE Hunt, M Inouye, AE Jeffreys, A Mendy, A Palotie, S Potter, J Ragoussis, J Rogers, K Rowlands, E Somaskantharajah, P Whittaker, C Widden, P Donnelly, B Howie, J Marchini, A Morris, M SanJoaquin, E Akum Achidi, T Agbenyega, A Allen, O Amodu, P Corran, A Djimde, A Dolo, OK Doumbo, C Drakeley, S Dunstan, J Evans, J Farrar, D Fernando, TT Hien, RD Horstmann, M Ibrahim, N Karunaweera, G Kokwaro, KA Koram, M Lemnge, J Makani, K Marsh, P Michon, D Modiano, ME Molyneux, I Mueller, M Parker, N Peshu, CV Plowe, O Puijalon, J Reeder, H Reyburn, EM Riley, A Sakuntabhai, P Singhasivanon, S Sirima, A Tall, TE Taylor, M Thera, M Troye-Blomberg, T N Williams, M Wilson, DP Kwiatkowski, Wellcome Trust Case Control Consortium & Malaria Genomic Epidemiology Network)

104 Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4Aregion. Nature Genetics 41, 1330-1334 (Dec 2009) (The UK IBD Genetics Consortium & the Wellcome Trust Case Control Consortium 2 chaired by P Donnelly).

105 A Bayesian method for detecting and characterizing allelic heterogeneity and boosting signals in genome-wide association studies. Statistical Science (Nov 2009) 24 (4) 430-450 (Z Su, N Cardin, The Wellcome Trust Case Control Consortium, P Donnelly, J Marchini)

106 Drive against hotspot motifs in primates implicates the PRDM9 gene in meiotic recombination.
Science 2010 Feb 12:327(5967):876-9 (S Myers, R Bowden, A Tumian, RE Bontrop, C Freeman, TS MacFie, G McVean* and P Donnelly* - * joint senior author)

107 Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls  Nature 464 (April 2010) 713-720 (The Wellcome Trust Case Control Consortium, N Craddock, ME Hurles, N Cardin, RD Pearson , V Plagnol, S Robson, D Vukcevic, C Barnes, DF Conrad , E Giannoulatou, C Holmes, JL Marchini, K Stirrups, MD Tobin, LV Wain, C Yau, J Aerts, T Ahmad, TD Andrews, H Arbury, A Attwood, A Auton, SG Ball, AJ Balmforth , JC Barrett, I Barroso, A Barton, AJ Bennett, S Bhaskar, K Blaszczyk, J Bowes, OJ Brand, PS Braund, F Bredin, G Breen, MJ Brown, IN Bruce, J Bull, OS Burren, J Burton, J Byrnes, S Caesar , CM Clee, AJ Coffey, JM Connell,  JD Cooper, AF Dominiczak, K Downes, HE Drummond, D Dudakia, A Dunham, B Ebbs, D Eccles, S Edkins, C Edwards, A Elliot, P Emery, DM Evans , G Evans, S Eyre, A Farmer, IN Ferrier, L Feuk, T Fitzgerald, E Flynn, A Forbes, L Forty, JA Franklyn, RM Freathy, P Gibbs, P Gilbert, O Gokumen, K Gordon-Smith , E Gray, E Green, CJ Groves, D Grozeva, R Gwilliam, A Hall, N Hammond, M Hardy, P Harrison, N Hassanali, H Hebaishi, S Hines, A Hinks, GA Hitman, L Hocking, E Howard , P Howard, JM Howson, D Hughes, S Hunt, JD Isaacs, M Jain, DP Jewell, T Johnson, JD Jolley, IR Jones, LA Jones, G Kirov, CF Langford, H Lango-Allen, GM Lathrop, J Lee, KL Lee, C Lees, K Lewis, CM Lindgren, M Maisuria-Armer, J Maller, J Mansfield, P Martin, DC Massey, WL McArdle, P McGuffin, KE McLay, A Mentzer, ML Mimmack, AE Morgan, AP Morris, C Mowat, S Myers, W Newman, ER Nimmo, MC O'Donovan , A Onipinla, I Onyiah, NR Ovington, MJ Owen, K Palin, K Parnell, D Pernet, JR Perry, A Phillips, D Pinto, NJ Prescott, I Prokopenko, MA Quail, S Rafelt, NW Rayner , R Redon, DM Reid, A Renwick, SM Ring, N Robertson , E Russell, D St Clair, JG Sambrook, JD Sanderson, H Schuilenburg, CE Scott, R Scott, S Seal, S Shaw-Hawkins, BM Shields, MJ Simmonds, DJ Smyth, E Somaskantharajah, K Spanova, S Steer, J Stephens, HE Stevens, MA Stone, Z Su, DP Symmons , JR Thompson , W Thomson, ME Travers, C Turnbull, A Valsesia, M Walker, NM Walker, C Wallace, M Warren-Perry, NA Watkins, J Webster, MN Weedon , AG Wilson,  M Woodburn, BP Wordsworth, AH Young, E Zeggini, NP Carter , TM Frayling, C Lee, G McVean , PB Munroe, A Palotie, SJ Sawcer, SW Scherer, DP Strachan, C Tyler-Smith, MA Brown, PR Burton,  MJ Caulfield, A Compston, M Farrall, SC Gough, AS Hall, AT Hattersley, AV Hill, CG Mathew , M Pembrey, J Satsangi, MR Stratton, J Worthington, P Deloukas, A Duncanson, DP Kwiatkowski, MI McCarthy, W Ouwehand, M Parkes, N Rahman, JA Todd, NJ Samani, and P Donnelly).

108 Failure to validate association between 12p13 variants and ischemic stroke N Engl J Med  2010 Apr 22; 362 (16): 1547-50 (International Stroke Genetics Consortium; Wellcome Trust Case Control Consortium 2 chaired by P Donnelly).

109 Strong genetic evidence for a selective influence of GABA(A) receptors on a component of the bipolar disorder phenotype Mol Psychiatry (2010 Sep 14) N Craddock, L Jones, IR Jones, G Kirov, EK Green, D Grozeva, V Moskvina, I Nikolov, ML Hamshere , D Vukcevic, S Caesar, K Gordon-Smith, C Fraser, E Russell, N Norton, G Breen, D St Clair, DA Collier, AH Young, IN Ferrier, A Farmer, P McGuffin, PA Holmans , Wellcome Trust Case Control Consortium (WTCCC), P Donnelly, MJ Owen, MC O'Donovan .

110 A map of human genome variation from population-scale sequencing. Nature 467, (28 Oct 2010) 1061-1073 (1000 Genomes Consortium).

111 A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1, Nature Genetics 42, (Nov 2010) 985-990 (Genetic Analysis of Psoriasis Consortium and The Wellcome Trust Case Control Consortium). P Donnelly: joint senior author.

112 Presynaptic NMDARs in the hippocampus facilitate transmitter release at theta frequency, Neuron 68 (6): 1109-1127 (22 Dec 2010) McGuinness L, Taylor C, Taylor RD, Yau C, Langenhan T, Hart ML, Christian H, Tynan PW, Donnelly P, Emptage NJ

113 Dissection of the genetics of Parkinson’s disease identifies an additional association 5’ of SNCA and multiple associated haplotypes at 17q21. Hum Mol Genet 15 Jan 2011, 20 (2) 345-353 (The UK Parkinson’s Disease Consortium and The Wellcome Trust Case Control Consortium 2). P Donnelly: joint senior author.

114 Common variants near ATM are associated with glycemic response to metformin in type 2 diabetes, Nature Genetics 43 (2) 117-U57 Feb 2011 (The GoDARTS and UKPDS Diabetes Pharmacogenetics Study Group and The Wellcome Trust Case Control Consortium 2). P Donnelly: joint senior author.

115 Making Sense of the Data, Science Feb 25 2011, 331 (6020) 1024-1025 (P Donnelly)

116 A genome-wide association study in Europeans and South Asians identifies five new loci for coronary artery disease Nature Genetics advance online publication 6 March 2011; doi:10.1038/ng.782 (The Coronary Artery Disease (C4D) Genetics Consortium).

117 Quantifying the Underestimation of Relative Risks from Genome-Wide Association Studies, PLoS Genetics, 7 (3): e1001337 Mar 2011 (C Spencer, E Hechter, D Vukcevic, P Donnelly)

118 Experiments with the site frequency spectrum. Sainudiin R, Thornton K, Harlow J, Booth J, Stillman M, Yoshida R, Griffiths R, McVean G, Donnelly P. Bull Math Biol. 2011 Apr;73(4):829-72.

119 Disease Model Distortion in Association Studies, Genetic Epidemiology May 2011,  35 (4) 278-290  (D Vukcevic, E Hechter, C Spencer, P Donnelly)

120 A two-stage meta-analysis identifies several new loci for Parkinson's disease. International Parkinson's Disease Genomics Consortium (IPDGC); Wellcome Trust Case Control Consortium 2 (WTCCC2).PLoS Genet. 2011 Jun;7(6):e1002142.

121 Recombination and Population Structure in Salmonella enterica. Didelot X, Bowden R, Street T, Golubchik T, Spencer C, McVean G, Sangal V, Anjum MF, Achtman M, Falush D, Donnelly P. PLoS Genet. 2011 Jul;7(7):e1002191.

122 Interaction between ERAP1 and HLA-B27 in ankylosing spondylitis implicates peptide handling in the mechanism for HLA-B27 in disease susceptibility. Evans DM, Spencer CC, Pointon JJ, Su Z, Harvey D, Kochan G, Opperman U, Dilthey A, Pirinen M, Stone MA, Appleton L, Moutsianis L, Leslie S, Wordsworth T, Kenna TJ, Karaderi T, Thomas GP, Ward MM, Weisman MH, Farrar C, Bradbury LA, Danoy P, Inman RD, Maksymowych W, Gladman D, Rahman P; Spondyloarthritis Research Consortium of Canada (SPARCC), Morgan A, Marzo-Ortega H, Bowness P, Gaffney K, Gaston JS, Smith M, Bruges-Armas J, Couto AR, Sorrentino R, Paladini F, Ferreira MA, Xu H, Liu Y, Jiang L, Lopez-Larrea C, Díaz-Peña R, López-Vázquez A, Zayats T, Band G, Bellenguez C, Blackburn H, Blackwell JM, Bramon E, Bumpstead SJ, Casas JP, Corvin A, Craddock N, Deloukas P, Dronov S, Duncanson A, Edkins S, Freeman C, Gillman M, Gray E, Gwilliam R, Hammond N, Hunt SE, Jankowski J, Jayakumar A, Langford C, Liddle J, Markus HS, Mathew CG, McCann OT, McCarthy MI, Palmer CN, Peltonen L, Plomin R, Potter SC, Rautanen A, Ravindrarajah R, Ricketts M, Samani N, Sawcer SJ, Strange A, Trembath RC, Viswanathan AC, Waller M, Weston P, Whittaker P, Widaa S, Wood NW, McVean G, Reveille JD, Wordsworth BP, Brown MA, Donnelly P*; Australo-Anglo-American Spondyloarthritis Consortium (TASC); Wellcome Trust Case Control Consortium 2 (WTCCC2). (*P Donnelly: joint corresponding author and joint senior author)  Nat Genet. 2011 Jul 10;43(8):761-7. doi: 10.1038/ng.873

123 Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis. International Multiple Sclerosis Genetics Consortium; Wellcome Trust Case Control Consortium 2, Sawcer S, Hellenthal G, Pirinen M, Spencer CC, Patsopoulos NA, Moutsianas L, Dilthey A, Su Z, Freeman C, Hunt SE, Edkins S, Gray E, Booth DR, Potter SC, Goris A, Band G, Oturai AB, Strange A, Saarela J, Bellenguez C, Fontaine B, Gillman M, Hemmer B, Gwilliam R, Zipp F, Jayakumar A, Martin R, Leslie S, Hawkins S, Giannoulatou E, D'alfonso S, Blackburn H, Boneschi FM, Liddle J, Harbo HF, Perez ML, Spurkland A, Waller MJ, Mycko MP, Ricketts M, Comabella M, Hammond N, Kockum I, McCann OT, Ban M, Whittaker P, Kemppinen A, Weston P, Hawkins C, Widaa S, Zajicek J, Dronov S, Robertson N, Bumpstead SJ, Barcellos LF, Ravindrarajah R, Abraham R, Alfredsson L, Ardlie K, Aubin C, Baker A, Baker K, Baranzini SE, Bergamaschi L, Bergamaschi R, Bernstein A, Berthele A, Boggild M, Bradfield JP, Brassat D, Broadley SA, Buck D, Butzkueven H, Capra R, Carroll WM, Cavalla P, Celius EG, Cepok S, Chiavacci R, Clerget-Darpoux F, Clysters K, Comi G, Cossburn M, Cournu-Rebeix I, Cox MB, Cozen W, Cree BA, Cross AH, Cusi D, Daly MJ, Davis E, de Bakker PI, Debouverie M, D'hooghe MB, Dixon K, Dobosi R, Dubois B, Ellinghaus D, Elovaara I, Esposito F, Fontenille C, Foote S, Franke A, Galimberti D, Ghezzi A, Glessner J, Gomez R, Gout O, Graham C, Grant SF, Guerini FR, Hakonarson H, Hall P, Hamsten A, Hartung HP, Heard RN, Heath S, Hobart J, Hoshi M, Infante-Duarte C, Ingram G, Ingram W, Islam T, Jagodic M, Kabesch M, Kermode AG, Kilpatrick TJ, Kim C, Klopp N, Koivisto K, Larsson M, Lathrop M, Lechner-Scott JS, Leone MA, Leppä V, Liljedahl U, Bomfim IL, Lincoln RR, Link J, Liu J, Lorentzen AR, Lupoli S, Macciardi F, Mack T, Marriott M, Martinelli V, Mason D, McCauley JL, Mentch F, Mero IL, Mihalova T, Montalban X, Mottershead J, Myhr KM, Naldi P, Ollier W, Page A, Palotie A, Pelletier J, Piccio L, Pickersgill T, Piehl F, Pobywajlo S, Quach HL, Ramsay PP, Reunanen M, Reynolds R, Rioux JD, Rodegher M, Roesner S, Rubio JP, Rückert IM, Salvetti M, Salvi E, Santaniello A, Schaefer CA, Schreiber S, Schulze C, Scott RJ, Sellebjerg F, Selmaj KW, Sexton D, Shen L, Simms-Acuna B, Skidmore S, Sleiman PM, Smestad C, Sørensen PS, Søndergaard HB, Stankovich J, Strange RC, Sulonen AM, Sundqvist E, Syvänen AC, Taddeo F, Taylor B, Blackwell JM, Tienari P, Bramon E, Tourbah A, Brown MA, Tronczynska E, Casas JP, Tubridy N, Corvin A, Vickery J, Jankowski J, Villoslada P, Markus HS, Wang K, Mathew CG, Wason J, Palmer CN, Wichmann HE, Plomin R, Willoughby E, Rautanen A, Winkelmann J, Wittig M, Trembath RC, Yaouanq J, Viswanathan AC, Zhang H, Wood NW, Zuvich R, Deloukas P, Langford C, Duncanson A, Oksenberg JR, Pericak-Vance MA, Haines JL, Olsson T, Hillert J, Ivinson AJ, De Jager PL, Peltonen L, Stewart GJ, Hafler DA, Hauser SL, McVean G, Donnelly P*, Compston A. (*P Donnelly: joint corresponding author and joint senior author)  Nature. 2011 Aug 10;476(7359):214-9. doi: 10.1038/nature10251.

124 HAPGEN2: simulation of multiple disease SNPs. Su Z, Marchini J, Donnelly P  Bioinformatics. 2011 Aug 15;27(16):2304-5

125 Human metabolic profiles are stably controlled by genetic and environmental variation. Molecular Systems Biology 7:525 (2011) G Nicholson, M Rantalainen, AD Maher, JV Li, D Malmodin, KR Ahmadi, JH Faber, IB Hallgrímsdóttir, A Barrett, H Toft, M Krestyaninova, J Viksna, SG Neogi, M Dumas, U Sarkans, The MolPAGE Consortium, BW Silverman, P Donnelly, JK Nicholson, M Allen, KT Zondervan, JC Lindon, TD Spector, MI McCarthy, E Holmes, D Baunsgaard, CC Holmes.

126 A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection. PLoS Genet 7(9) 2011, Sep 8. G Nicholson, M Rantalainen, JV Li, AD Maher, D Malmodin, KR Ahmadi, JH Faber, A Barrett, JL Min, NW Rayner, H Toft, M Krestyaninova, J Viksna, SG Neogi, M Dumas, U Sarkans, The MolPAGE Consortium, P Donnelly, T Illig, J Adamski, K Suhre, M Allen, KT Zondervan, TD Spector, JK Nicholson, JC Lindon, D Baunsgaard, E Holmes, MI McCarthy, CC Holmes.

127 Bayesian hierarchical mixture modeling to assign copy number from a targeted CNV array. Cardin N, Holmes C; The Wellcome Trust Case Control Consortium, P Donnelly, J Marchini  Genet Epidemiol. 2011 Sep;35(6):536-548. doi: 10.1002/gepi.20604.

128 A robust clustering algorithm for identifying problematic samples in genome-wide association studies. C Bellenguez, A Strange, C Freeman, Wellcome Trust Case Control Consortium, P Donnelly, C Spencer Bioinformatics 03 Nov 2011

129 Pneumococcal genome sequencing tracks a vaccine escape variant formed through a multi-fragment recombination event. T Golubchik, A B Brueggemann, T Street, R E Gertz Jr, C C A Spencer, T Ho, E Giannoulatou, R Link-Gelles, R M Harding, B Beall, T E A Peto, M R Moore, P Donnelly, D W Crook, R Bowden (P Donnelly joint senior author and corresponding author). Nature Genetics published online 29 Jan 2012 doi:10.1038/ng.1072 .

130 Genome-wide association study identifies a variant in HDAC9 associated with large vessel ischemic stroke. The International Stroke Genetics Consortium (ISGC) and The Wellcome Trust Case Control Consortium 2 (WTCCC2). P Donnelly: joint senior author and joint corresponding author. Nature Genetics published online 5 Feb 2012 doi:10.1038/ng.1081.

131 People of the British Isles: Preliminary analysis of genotypes and surnames in a UK-control population. B Winney, A Boumertit, T Day, D Davison, C Echeta, I Evseeva, K Hutnik, S Leslie, K Nicodemus, EC Royrvik, S Tonks, X Yang, J Cheshire, P Longley, P Mateos, A Groom, C Relton, DT Bishop, K Black, E Northwood, L Parkinson, TM Frayling, A Steele, JR Sampson, T King, R Dixon, D Middleton, B Jennings, R Bowden, P Donnelly, W Bodmer. European Journal of Human Genetics 20 (2):203-210 2012.

132 Gene-gene interactions in breast cancer susceptibility. CTurnbull, S Seal, A Renwick, M Warren-Perry, D Hughes, A Elliott, D Pernet, S Peock, J W. Adlard, J Barwell, Jonathan Berg, A F. Brady, C Brewer, G Brice, C Chapman, J Cook, R Davidson, A Donaldson, F Douglas, L Greenhalgh, A Henderson, L  Izatt, A Kumar, F Lalloo, Z Miedzybrodzka, P J Morrison, J Paterson, M Porteous, M T Rogers, S Shanley, L Walker, Breast Cancer Susceptibility Collaboration (UK), EMBRACE, M Ahmed, D Eccles, D G Evans, P Donnelly, D F Easton, M R Stratton, N Rahman. Human Molecular Genetics, 2012, Vol. 21, No. 4 958–962.

133 Genomic Tools for Evolution and Conservation in the Chimpanzee: Pan troglodytes ellioti Is a Genetically Distinct Population. R Bowden, T S MacFie, S Myers, G Hellenthal, E Nerrienet, R E Bontrop, C Freeman, P Donnelly, N I Mundy (P Donnelly: joint senior author and corresponding author). PLoS Genetics, March 2012, Vol 8, Issue 3.

134 Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease. B C Young, T Golubchik, E M Batty, R Fung, H Larner-Svensson, A A Votintseva, R R Miller, H Godwin, K Knox, R G Everitt, Z Iqbal, A J Rimmer, M Cule, C L C Ip, X Didelot, R M Harding, P Donnelly, T E Peto, D W Crook, R Bowden, D J Wilson. Proceedings of the National Academy of Sciences, March 20 2012, Vol 109, no 12, 4550-4555.