publications

    2008

  1. M. Orho-Melander, O. Melander, C. Guiducci, P. Perez-Martinez, D. Corella, C. Roos, R. Tewhey, M.J. Rieder, J. Hall, G. Abecasis, E.S. Tai, C. Welch, D.K. Arnett, V. Lyssenko, E. Lindholm, R. Saxena, P.I.W. de Bakker, N. Burtt, B.F. Voight, J.N. Hirschhorn, K.L. Tucker, T. Hedner, T. Tuomi, B. Isomaa, K.-F. Eriksson, M.-R. Taskinen, B. Wahlstrand, T.E. Hughes, L.D. Parnell, C.-Q. Lai, G. Berglund, L. Peltonen, E. Vartiainen, P. Jousilahti, A.S. Havulinna, V. Salomaa, P. Nilsson, L. Groop, D. Altshuler, J.M. Ordovas, S. Kathiresan (2008) A Common Missense Variant in the Glucokinase Regulatory Protein Gene (GCKR) Is Associated with Increased Plasma Triglyceride and C-Reactive Protein but Lower Fasting Glucose Concentrations. Diabetes. In press.
  2. S.A. McCarroll, F.G. Kuruvilla, J.M. Korn, S. Cawley, J. Nemesh, A. Wysoker, M.H. Shapero, P.I.W. de Bakker, J. Maller, A. Kirby, A.L. Elliott, M. Parkin, E. Hubbell, T. Webster, R. Mei, R. Handsaker, S. Lincoln, M. Nizzari, J. Blume, K. Jones, R. Rava, M.J. Daly, S.B. Gabriel, D. Altshuler (2008) Integrated detection and population-genetic analysis of SNPs and copy-number variation. Nature Genetics. In press.
  3. A.J. Monsuur, P.I.W. de Bakker, A. Zhernakova, D. Pinto, W. Verduijn, J. Romanos, R. Auricchio, A. Lopez, D.A. van Heel, J.B.A. Crusius, C. Wijmenga (2008) Effective detection of human leukocyte antigen risk alleles in celiac disease using tag single nucleotide polymorphisms. PLoS ONE. 3: e2270
  4. E. Zeggini, L.J. Scott, R. Saxena, B.F. Voight, J.L. Marchini, T. Hu, P.I.W. de Bakker, G.R. Abecasis, P. Almgren, G. Andersen, K. Ardlie, K. Bengtsson Bostrom, R.N. Bergman, L.L. Bonnycastle, K. Borch-Johnsen, N.P. Burtt, H. Chen, P.S. Chines, M.J. Daly, P. Deodhar, C. Ding, A.S.F. Doney, W.L. Duren, K.S. Elliott, M.R. Erdos, T.M. Frayling, R.M. Freathy, L. Gianniny, H. Grallert, N. Grarup, C.J. Groves, C. Guiducci, T. Hansen, C. Herder, G.A. Hitman, T.E. Hughes, B. Isomaa, A.U. Jackson, T. Jorgensen, A. Kong, K. Kubalanza, F.G. Kuruvilla, J. Kuusisto, C. Langenberg, H. Lango, T. Lauritzen, Y. Li, C.M. Lindgren, V. Lyssenko, A.F. Marvelle, C. Meisinger, K. Midthjell, K.L. Mohlke, M.A. Morken, A.D. Morris, N. Narisu, P. Nilsson, K.R. Owen, C.N.A. Palmer, F. Payne, J.R.B. Perry, E. Pettersen, C. Platou, I. Prokopenko, L. Qi, L. Qin, N.W. Rayner, M. Rees, J.J. Roix, A. Sandbaek, B. Shields, M. Sjogren, V. Steinthorsdottir, H.M. Stringham, A.J. Swift, G. Thorleifsson, U. Thorsteinsdottir, N.J. Timpson, T. Tuomi, J. Tuomilehto, M. Walker, R.M. Watanabe, M.N. Weedon, C.J. Willer, Wellcome Trust Case Control Consortium, T. Illig, K. Hveem, F.B. Hu, M. Laakso, K. Stefansson, O. Pedersen, N.J. Wareham, I. Barroso, A.T. Hattersley, F.S. Collins, L. Groop, M.I. McCarthy, M. Boehnke, D. Altshuler (2008) Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. Nature Genetics. 40: 638-645
  5. P. Sklar, J.W. Smoller, J. Fan, M.A.R. Ferreira, R.H. Perlis, K. Chambert, V.L. Nimgaonkar, M.B. McQueen, S.V. Faraone, A. Kirby, P.I.W. de Bakker, M.N. Ogdie, M.E. Thase, G.S. Sachs, K. Todd-Brown, S.B. Gabriel, C. Sougnez, C. Gates, B. Blumenstiel, M. Defelice, K.G. Ardlie, J. Franklin, W.J. Muir, K.A. McGhee, D.J. Macintyre, A. McLean, M. Vanbeck, A. McQuillin, N.J. Bass, M. Robinson, J. Lawrence, A. Anjorin, D. Curtis, E.M. Scolnick, M.J. Daly, D.H. Blackwood, H.M. Gurling, S.M. Purcell (2008) Whole-genome association study of bipolar disorder. Molecular Psychiatry. 13: 558-569
  6. N. Furnham, P.I.W. de Bakker, S. Gore, D.F. Burke, T.L. Blundell (2008) Comparative modelling by restraint-based conformational sampling. BMC Structural Biology. 8: 7
  7. C.A. Haiman, C. Hsu, P.I.W. de Bakker, M. Frasco, X. Sheng, D. Van Den Berg, J.T. Casagrande, L.N. Kolonel, L. Le Marchand, S.E. Hankinson, J. Han, A.M. Dunning, K.A. Pooley, M.L. Freedman, D.J. Hunter, A.H. Wu, D.O. Stram, B.E. Henderson (2007) Comprehensive association testing of common genetic variation in DNA repair pathway genes in relationship with breast cancer risk in multiple populations. Human Molecular Genetics. 17: 825-834

    8. 2007

  8. R.M. Plenge, C. Cotsapas, L. Davies, A.L. Price, P.I.W. de Bakker, J. Maller, I. Pe'er, N.P. Burtt, B. Blumenstiel, M. DeFelice, M. Parkin, R. Barry, W. Winslow, C. Healy, R.R. Graham, B.M. Neale, E. Izmailova, R. Roubenoff, A.N. Parker, R. Glass, E.W. Karlson, N. Maher, D.A. Hafler, D.M. Lee, M.F. Seldin, E.F. Remmers, A.T. Lee, L. Padyukov, L. Alfredsson, J. Coblyn, M.E. Weinblatt, S.B. Gabriel, S. Purcell, L. Klareskog, P.K. Gregersen, N.A. Shadick, M.J. Daly, D. Altshuler (2007) Two independent alleles at 6q23 associated with risk of rheumatoid arthritis. Nature Genetics. 357: 977-986
  9. The International HapMap Consortium (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature. 449: 851-861
  10. P.I.W. de Bakker (2007) Selection and evaluation of tag SNPs using Tagger and HapMap. In: Genetic Variation: A Laboratory Manual (Weiner, Gabriel, Stephens, eds.), pp. 283-288, ISBN 0879697806, Cold Spring Harbor Laboratory Press
  11. E.F. Remmers, R.M. Plenge, A.T. Lee, R.R. Graham, G. Hom, T.W. Behrens, P.I.W. de Bakker, J.M. Le, H.-S. Lee, F. Batliwalla, W. Li, S.L. Masters, M.G. Booty, J.P. Carulli, L. Padyukov, L. Alfredsson, L. Klareskog, W.V. Chen, C.I. Amos, L.A. Criswell, M.F. Seldin, D.L. Kastner, P.K. Gregersen (2007) STAT4 and the risk of rheumatoid arthritis and systemic lupus erythematosus. New England Journal of Medicine. 357: 977-986
  12. International Multiple Sclerosis Genetics Consortium (2007) Risk alleles for multiple sclerosis identified by a genomewide study. New England Journal of Medicine. 357: 851-862
  13. S. Purcell, B. Neale, K. Todd-Brown, L. Thomas, M.A.R. Ferreira, D. Bender, J. Maller, P. Sklar, P.I.W. de Bakker, M.J. Daly, P.C. Sham (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics. 81: 559-575
  14. A.L.H.J. Aarnoudse, C. Newton-Cheh, P.I.W. de Bakker, S.M.J.M. Straus, J.A. Kors, A. Hofman, A.G. Uitterlinden, J.C.M. Witteman, B.H.Ch. Stricker (2007) Common NOS1AP variants are associated with a prolonged QTc interval in the Rotterdam Study. Circulation. 116: 10-16
  15. The ENCODE Project Consortium (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816
  16. Diabetes Genetics Initiative of Broad Institute of Harvard and MIT, Lund University and Novartis Institutes for BioMedical Research (2007) Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science. 316: 1331-1336
  17. P.I.W. de Bakker, J. Rosand (2007) In search of genes for stroke. Lancet Neurology. 6: 383-384

    18. 2006

  18. P.I.W. de Bakker, N.P. Burtt, R.R. Graham, C. Guiducci, R. Yelensky, J.A. Drake, T. Bersaglieri, K.L. Penney, J. Butler, S. Young, R.C. Onofrio, H.N. Lyon, D.O. Stram, C.A. Haiman, M.F. Freedman, X. Zhu, R. Cooper, L. Groop, L.N. Kolonel, B.E. Henderson, M.J. Daly, J.N. Hirschhorn, D. Altshuler (2006) Transferability of tag SNPs in genetic association studies in multiple populations. Nature Genetics. 38: 1298-1303
  19. J. Rosand, N. Bayley, N. Rost, P.I.W. de Bakker (2006) Many hypotheses but no replication for the association between PDE4D and stroke. Nature Genetics. 38: 1091-1092
  20. P.I.W. de Bakker, G. McVean, P.C. Sabeti, M.M. Miretti, T. Green, J. Marchini, X. Ke, A.J. Monsuur, P. Whittaker, M. Delgado, J. Morrison, A. Richardson, E.C. Walsh, X. Gao, L. Galver, J. Hart, D.A. Hafler, M. Pericak-Vance, J.A. Todd, M.J. Daly, J. Trowsdale, C. Wijmenga, T.J. Vyse, S. Beck, S.S. Murray, M. Carrington, S. Gregory, P. Deloukas, J.D. Rioux (2006) A high resolution HLA and SNP haplotype map for disease association studies in the extended human MHC. Nature Genetics. 38: 1166-1172.
  21. N. Furnham, A.S. Dore, D.Y. Chirgadze, P.I.W. de Bakker, M.A. DePristo, T.L. Blundell (2006) Knowledge-based real-space explorations for low-resolution structure determination. Structure. 14: 1313-1320
  22. J.C. Florez, K.A. Jablonski, N. Bayley, T.I. Pollin, P.I.W. de Bakker, A.R. Shuldiner, W.C. Knowler, D.M. Nathan, D. Altshuler (2006) TCF7L2 polymorphisms and progression to diabetes in the Diabetes Prevention Program. New England Journal of Medicine. 355: 241-250
  23. S. Wiltshire, P.I.W. de Bakker, M.J. Daly (2006) The value of gene-based selection of tag SNPs in genome-wide association studies. European Journal of Human Genetics. 14: 1209-1214
  24. R. Saxena, P.I.W. de Bakker, K. Synger, V. Mootha, N. Burtt, J.N. Hirschhorn, D. Gaudet, D. Isomaa, M.J. Daly, L. Groop, K.G. Ardlie, D. Altshuler (2006) Comprehensive association testing of common mitochondrial DNA variation in metabolic disease. American Journal of Human Genetics. 79: 54-61
  25. I. Pe'er, P.I.W. de Bakker, J. Maller, R. Yelensky, D. Altshuler, M.J. Daly (2006) Evaluating and improving power in whole-genome association studies using fixed marker sets. Nature Genetics. 38: 663-667
  26. I. Pe'er, Y.R. Chretien, P.I.W. de Bakker, J.C. Barrett, M.J. Daly, D.M. Altshuler (2006) Biases and reconciliation in estimates of linkage disequilibrium in the human genome. American Journal of Human Genetics. 78: 588-603
  27. P.I.W. de Bakker, N. Furnham, T.L. Blundell, M.A. DePristo (2006) Conformer generation under restraints. Current Opinion in Structural Biology. 16: 160-165
  28. M.W. Sun, J.Y. Lee, P.I.W. de Bakker, N.P. Burtt, P. Almgren, L. Råstam, T. Tuomi, D. Gaudet, M.J. Daly, J.N. Hirschhorn, D. Altshuler, L. Groop, J.C. Florez (2006) Haplotype structures and large-scale association testing of the 5' AMP-activated protein kinase genes PRKAA2, PRKAB1 and PRKAB2 with type 2 diabetes. Diabetes. 55: 849-855
  29. P.I.W. de Bakker, R.R. Graham, D. Altshuler, B.E. Henderson, C.A. Haiman (2006) Transferability of tag SNPs to capture common genetic variation in DNA repair genes across multiple populations. In: Pacific Symposium in Biocomputing 2006 (Altman et al., eds.), pp. 478-486, World Scientific Publishing: Singapore
  30. S. Whelan, P.I.W. de Bakker, E. Quevillon, N. Rodriguez, N. Goldman (2006) PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees. Nucleic Acids Research. 34: D327-D331
  31. J.C. Florez, S. Wiltshire, C.M. Agapakis, N.P. Burtt, P.I.W. de Bakker, P. Almgren, K. Bengtsson Bostrom, T. Tuomi, D. Gaudet, M.J. Daly, J.N. Hirschhorn, M.I. McCarthy, D. Altshuler, L. Groop (2006) High-density haplotype structure and association testing of the insulin-degrading enzyme (IDE) gene with type 2 diabetes in 4,206 people. Diabetes. 55: 128-135
  32. E.C. Walsh, P. Sabeti, H.B. Hutcheson, B. Fry, S.F. Schaffner, P.I.W. de Bakker, P. Varilly, A.A. Palma, J. Roy, R. Cooper, C. Winkler, Y. Zeng, G. de The, E.S. Lander, S. O'Brien, D. Altshuler (2006) Searching for signals of evolutionary selection in 168 genes related to immune function. Human Genetics. 119: 92-102

    33. 2005

  33. A.J. Monsuur, P.I.W. de Bakker, B.Z. Alizadeh, A. Zhernakova, M.R. Bevova, E. Strengman, L. Franke, R. van 't Slot, M.J. van Belzen, I.C.M. Lavrijsen, B. Diosdado, M.J. Daly, C.J.J. Mulder, M.L. Mearin, J.W.R. Meijer, G.A. Meijer, E. van Oort, M.C. Wapenaar, B.F.C. Koeleman, C. Wijmenga (2005) Myosin IXB variant increases the risk of celiac disease and points toward a primary intestinal barrier defect. Nature Genetics. 37: 1341-1344
  34. The International HapMap Consortium (2005) A haplotype map of the human genome. Nature. 437: 1299-1320
  35. P.I.W. de Bakker, R. Yelensky, I. Pe'er, S.B. Gabriel, M.J. Daly, D. Altshuler (2005) Efficiency and power in genetic association studies. Nature Genetics. 37: 1217-1223
  36. M.A. DePristo, P.I.W. de Bakker, R.J.K. Johnson, T.L. Blundell (2005) Crystallographic refinement by knowledge-based exploration of complex energy landscapes. Structure. 13: 1311-1319
  37. W. Winckler, N.P. Burtt, J. Holmkvist, C. Cervin, P.I.W. de Bakker, M. Sun, P. Almgren, T. Tuomi, D. Gaudet, T.J. Hudson, K.G. Ardlie, M.J. Daly, J.N. Hirschhorn, D. Altshuler, L. Groop (2005) Association of common variation in the HNF1-alpha gene region with risk of type 2 diabetes. Diabetes. 54: 2336-2342
  38. W. Winckler, R.R. Graham, P.I.W. de Bakker, M. Sun, P. Almgren, T. Tuomi, D. Gaudet, T.J. Hudson, K.G. Ardlie, M.J. Daly, J.N. Hirschhorn, L. Groop, D. Altshuler (2005) Association testing of the hepatocyte nuclear factor 4-alpha gene with risk of type 2 diabetes in 7,883 people. Diabetes. 54: 886-892

    39. 2004

  39. M.A. DePristo, P.I.W. de Bakker, T.L. Blundell (2004) Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography. Structure. 12: 831-838
  40. J.C. Florez, N. Burtt, P.I.W. de Bakker, P. Almgren, T. Tuomi, J. Holmkvist, D. Gaudet, T.J. Hudson, S.F. Schaffner, M.J. Daly, J.N. Hirschhorn, L. Groop, D. Altshuler (2004) Haplotype structure and genotype-phenotype correlations of the sulfonylurea receptor and the islet ATP-sensitive potassium channel gene region. Diabetes. 53: 1360-1368
  41. P.I.W. de Bakker, R. Saxena, R.R. Graham (2004) Variation in the human genome and risk to common disease. Keystone Symposium on 'Human Genome Sequence Variation and the Inherited Basis of Common Diseases'. January 8-13, 2004, Breckenridge, CO. Pharmacogenomics. 5: 157-161

    42. 2003

  42. R.P. Shetty, P.I.W. de Bakker, M.A. DePristo, T.L. Blundell (2003) Advantages of fine-grained side chain conformer libraries. Protein Engineering. 16: 963-969
  43. M.A. DePristo, P.I.W. de Bakker, R.P. Shetty, T.L. Blundell (2003) Discrete restraint-based protein modeling and the Calpha-trace problem. Protein Science. 12: 2032-2046
  44. S. Whelan, P.I.W. de Bakker, N. Goldman (2003) Pandit: a database of protein and associated nucleotide domains with inferred trees. Bioinformatics. 19: 1556-1563
  45. M.A. DePristo, P.I.W. de Bakker, S.C. Lovell, T.L. Blundell (2003) Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles. Proteins: Structure, Function & Genetics. 51: 41-55
  46. P.I.W. de Bakker, M.A. DePristo, D.F. Burke, T.L. Blundell (2003) Ab initio construction of polypeptide fragments: accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model. Proteins: Structure, Function & Genetics. 51: 21-40
  47. S.C. Lovell, I.W. Davis, W.B. Arendall III, P.I.W. de Bakker, J.M. Word, M.G. Prisant, J.S. Richardson, D.C. Richardson (2003) Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins: Structure, Function & Genetics. 50: 437-450

    48. 2001

  48. M.G. Williams, H. Shirai, J. Shi, H.G. Nagendra, J. Mueller, K. Mizuguchi, R.N. Miguel, S.C. Lovell, C.A. Innis, C.M. Deane, L. Chen, N. Campillo, D.F. Burke, T.L. Blundell, P.I.W. de Bakker (2001) Sequence-structure homology recognition by iterative alignment refinement and comparative modelling. Proteins: Structure, Function & Genetics. 45 (Suppl. 5): 92-97
  49. P.I.W. de Bakker (2001) Voorspelling van eiwitstructuren: computer maakt inhaalslag. Fourth Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP4). December 3-7, 2000, Asilomar, CA. Conceptuur. 27: 8-9 [in Dutch; published by the Netherlands Federation for Innovative Drug Research (FIGON)]
  50. P.I.W. de Bakker, A. Bateman, D.F. Burke, R.N. Miguel, K. Mizuguchi, J. Shi, H. Shirai, T.L. Blundell (2001) HOMSTRAD: adding sequence information to structure-based alignments of homologous protein families. Bioinformatics. 17: 748-749

    51. 2000

  51. R. Sanchez, U. Pieper, N. Mirkovic, P.I.W. de Bakker, E. Wittenstein, and A. Sali (2000) MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Research. 28: 250-253

    52. 1999

  52. P.I.W. de Bakker, P.H. Hünenberger, and J.A. McCammon (1999) Molecular dynamics simulations of the hyperthermophilic protein Sac7d from Sulfolobus acidocaldarius: contribution of salt bridges to thermostability. Journal of Molecular Biology. 285: 1811-1830

    53. 1998

  53. P.I.W. de Bakker, S. Tara, and J.M. Briggs (1998) Thermodynamic correlation with kinetic association rates for several mutants of mouse acetylcholinesterase. In: Structure and Function of Cholinesterases and Related Proteins (Doctor et al., eds.), pp. 345-350, ISBN 0306460505, Springer
  54. P.I.W. de Bakker (1998) HIV-integrase: het volgende doelwit. Pharmaceutisch Weekblad. 133: 982-984 [in Dutch; published by the Royal Dutch Pharmaceutical Society (KNMP)]