publications

    2009

  1. Nolte IM, Wallace C, Newhouse SJ, Waggott D, Fu J, Soranzo N, Gwilliam R, Deloukas P, Savelieva I, Zheng D, Dalageorgou C, Farrall M, Samani NJ, Connell J, Brown M, Dominiczak A, Lathrop M, Zeggini E, Wain LV; Wellcome Trust Case Control Consortium; DCCT/EDIC Research Group, Newton-Cheh C, Eijgelsheim M, Rice K, de Bakker PIW; QTGEN consortium, Pfeufer A, Sanna S, Arking DE; QTSCD consortium, Asselbergs FW, Spector TD, Carter ND, Jeffery S, Tobin M, Caulfield M, Snieder H, Paterson AD, Munroe PB, Jamshidi Y. Common genetic variation near the phospholamban gene is associated with cardiac repolarisation: meta-analysis of three genome-wide association studies. PLoS One. 2009 Jul 9;4(7):e6138.
  2. De Jager PL, Jia X, Wang J, de Bakker PIW, Ottoboni L, Aggarwal NT, Piccio L, Raychaudhuri S, Tran D, Aubin C, Briskin R, Romano S; International MS Genetics Consortium, Baranzini SE, McCauley JL, Pericak-Vance MA, Haines JL, Gibson RA, Naeglin Y, Uitdehaag B, Matthews PM, Kappos L, Polman C, McArdle WL, Strachan DP, Evans D, Cross AH, Daly MJ, Compston A, Sawcer SJ, Weiner HL, Hauser SL, Hafler DA, Oksenberg JR. Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci. Nat Genet. 2009 Jul;41(7):776-82. Epub 2009 Jun 14.
  3. de Bakker PIW, Neale BM, Daly MJ. Meta-analysis of genome-wide association studies. In: Genetics of Complex Human Diseases (Al-Chalabi, Almasy, eds.), pp. XXX-XXX, ISBN XXXXXXXXXX, Cold Spring Harbor Laboratory Press
  4. Walley NM, Julg B, Dickson SP, Fellay J, Ge D, Walker BD, Carrington M, Cohen MS, de Bakker PIW, Goldstein DB, Shianna KV, Haynes BF, Letvin NL, McMichael AJ, Michael NL, Weintrob AC. The Duffy antigen receptor for chemokines null promoter variant does not influence HIV-1 acquisition or disease progression. Cell Host Microbe. 2009 May 8;5(5):408-10.
  5. Newton-Cheh C, Eijgelsheim M, Rice KM, de Bakker PIW, Yin X, Estrada K, Bis JC, Marciante K, Rivadeneira F, Noseworthy PA, Sotoodehnia N, Smith NL, Rotter JI, Kors JA, Witteman JC, Hofman A, Heckbert SR, O'Donnell CJ, Uitterlinden AG, Psaty BM, Lumley T, Larson MG, Stricker BH. Common variants at ten loci influence QT interval duration in the QTGEN Study. Nat Genet. 2009 Apr;41(4):399-406. Epub 2009 Mar 22.
  6. De Jager PL, Baecher-Allan C, Maier LM, Arthur AT, Ottoboni L, Barcellos L, McCauley JL, Sawcer S, Goris A, Saarela J, Yelensky R, Price A, Leppa V, Patterson N, de Bakker PIW, Tran D, Aubin C, Pobywajlo S, Rossin E, Hu X, Ashley CW, Choy E, Rioux JD, Pericak-Vance MA, Ivinson A, Booth DR, Stewart GJ, Palotie A, Peltonen L, Dubois B, Haines JL, Weiner HL, Compston A, Hauser SL, Daly MJ, Reich D, Oksenberg JR, Hafler DA. The role of the CD58 locus in multiple sclerosis. Proc Natl Acad Sci U S A. 2009 Mar 31;106(13):5264-9. Epub 2009 Feb 23.
  7. Kathiresan S, Willer CJ, Peloso GM, Demissie S, Musunuru K, Schadt EE, Kaplan L, Bennett D, Li Y, Tanaka T, Voight BF, Bonnycastle LL, Jackson AU, Crawford G, Surti A, Guiducci C, Burtt NP, Parish S, Clarke R, Zelenika D, Kubalanza KA, Morken MA, Scott LJ, Stringham HM, Galan P, Swift AJ, Kuusisto J, Bergman RN, Sundvall J, Laakso M, Ferrucci L, Scheet P, Sanna S, Uda M, Yang Q, Lunetta KL, Dupuis J, de Bakker PIW, O'Donnell CJ, Chambers JC, Kooner JS, Hercberg S, Meneton P, Lakatta EG, Scuteri A, Schlessinger D, Tuomilehto J, Collins FS, Groop L, Altshuler D, Collins R, Lathrop GM, Melander O, Salomaa V, Peltonen L, Orho-Melander M, Ordovas JM, Boehnke M, Abecasis GR, Mohlke KL, Cupples LA. Common variants at 30 loci contribute to polygenic dyslipidemia. Nat Genet. 2009 Jan;41(1):56-65. Epub 2008 Dec 7.

    8. 2008

  8. Keating BJ, Tischfield S, Murray SS, Bhangale T, Price TS, Glessner JT, Galver L, Barrett JC, Grant SF, Farlow DN, Chandrupatla HR, Hansen M, Ajmal S, Papanicolaou GJ, Guo Y, Li M, Derohannessian S, de Bakker PIW, Bailey SD, Montpetit A, Edmondson AC, Taylor K, Gai X, Wang SS, Fornage M, Shaikh T, Groop L, Boehnke M, Hall AS, Hattersley AT, Frackelton E, Patterson N, Chiang CW, Kim CE, Fabsitz RR, Ouwehand W, Price AL, Munroe P, Caulfield M, Drake T, Boerwinkle E, Reich D, Whitehead AS, Cappola TP, Samani NJ, Lusis AJ, Schadt E, Wilson JG, Koenig W, McCarthy MI, Kathiresan S, Gabriel SB, Hakonarson H, Anand SS, Reilly M, Engert JC, Nickerson DA, Rader DJ, Hirschhorn JN, Fitzgerald GA. Concept, design and implementation of a cardiovascular gene-centric 50 k SNP array for large-scale genomic association studies. PLoS ONE. 2008;3(10):e3583. Epub 2008 Oct 31.
  9. Johnson AD, Handsaker RE, Pulit SL, Nizzari MM, O'Donnell CJ, de Bakker PIW. SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap. Bioinformatics. 2008 Dec 15;24(24):2938-9. Epub 2008 Oct 30. [Go to SNAP]
  10. de Bakker PIW, Ferreira MA, Jia X, Neale BM, Raychaudhuri S, Voight BF. Practical aspects of imputation-driven meta-analysis of genome-wide association studies. Hum Mol Genet. 2008 Oct 15;17(R2):R122-8.
  11. McCarroll SA, Kuruvilla FG, Korn JM, Cawley S, Nemesh J, Wysoker A, Shapero MH, de Bakker PIW, Maller JB, Kirby A, Elliott AL, Parkin M, Hubbell E, Webster T, Mei R, Veitch J, Collins PJ, Handsaker R, Lincoln S, Nizzari M, Blume J, Jones KW, Rava R, Daly MJ, Gabriel SB, Altshuler D. Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet. 2008 Oct;40(10):1166-74. Epub 2008 Sep 7.
  12. Orho-Melander M, Melander O, Guiducci C, Perez-Martinez P, Corella D, Roos C, Tewhey R, Rieder MJ, Hall J, Abecasis G, Tai ES, Welch C, Arnett DK, Lyssenko V, Lindholm E, Saxena R, de Bakker PIW, Burtt N, Voight BF, Hirschhorn JN, Tucker KL, Hedner T, Tuomi T, Isomaa B, Eriksson KF, Taskinen MR, Wahlstrand B, Hughes TE, Parnell LD, Lai CQ, Berglund G, Peltonen L, Vartiainen E, Jousilahti P, Havulinna AS, Salomaa V, Nilsson P, Groop L, Altshuler D, Ordovas JM, Kathiresan S.Common missense variant in the glucokinase regulatory protein gene is associated with increased plasma triglyceride and C-reactive protein but lower fasting glucose concentrations. Diabetes. 2008 Nov;57(11):3112-21. Epub 2008 Aug 4.
  13. Monsuur AJ, de Bakker PIW, Zhernakova A, Pinto D, Verduijn W, Romanos J, Auricchio R, Lopez A, van Heel DA, Crusius JB, Wijmenga C. Effective detection of human leukocyte antigen risk alleles in celiac disease using tag single nucleotide polymorphisms. PLoS ONE. 2008 May 28;3(5):e2270.
  14. Zeggini E, Scott LJ, Saxena R, Voight BF, Marchini JL, Hu T, de Bakker PIW, Abecasis GR, Almgren P, Andersen G, Ardlie K, Boström KB, Bergman RN, Bonnycastle LL, Borch-Johnsen K, Burtt NP, Chen H, Chines PS, Daly MJ, Deodhar P, Ding CJ, Doney AS, Duren WL, Elliott KS, Erdos MR, Frayling TM, Freathy RM, Gianniny L, Grallert H, Grarup N, Groves CJ, Guiducci C, Hansen T, Herder C, Hitman GA, Hughes TE, Isomaa B, Jackson AU, Jørgensen T, Kong A, Kubalanza K, Kuruvilla FG, Kuusisto J, Langenberg C, Lango H, Lauritzen T, Li Y, Lindgren CM, Lyssenko V, Marvelle AF, Meisinger C, Midthjell K, Mohlke KL, Morken MA, Morris AD, Narisu N, Nilsson P, Owen KR, Palmer CN, Payne F, Perry JR, Pettersen E, Platou C, Prokopenko I, Qi L, Qin L, Rayner NW, Rees M, Roix JJ, Sandbaek A, Shields B, Sjögren M, Steinthorsdottir V, Stringham HM, Swift AJ, Thorleifsson G, Thorsteinsdottir U, Timpson NJ, Tuomi T, Tuomilehto J, Walker M, Watanabe RM, Weedon MN, Willer CJ; Wellcome Trust Case Control Consortium, Illig T, Hveem K, Hu FB, Laakso M, Stefansson K, Pedersen O, Wareham NJ, Barroso I, Hattersley AT, Collins FS, Groop L, McCarthy MI, Boehnke M, Altshuler D. Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. Nat Genet. 2008 May;40(5):638-45. Epub 2008 Mar 30.
  15. Sklar P, Smoller JW, Fan J, Ferreira MA, Perlis RH, Chambert K, Nimgaonkar VL, McQueen MB, Faraone SV, Kirby A, de Bakker PIW, Ogdie MN, Thase ME, Sachs GS, Todd-Brown K, Gabriel SB, Sougnez C, Gates C, Blumenstiel B, Defelice M, Ardlie KG, Franklin J, Muir WJ, McGhee KA, MacIntyre DJ, McLean A, VanBeck M, McQuillin A, Bass NJ, Robinson M, Lawrence J, Anjorin A, Curtis D, Scolnick EM, Daly MJ, Blackwood DH, Gurling HM, Purcell SM. Whole-genome association study of bipolar disorder. Mol Psychiatry. 2008 Jun;13(6):558-69. Epub 2008 Mar 4.
  16. Furnham N, de Bakker PIW, Gore S, Burke DF, Blundell TL. Comparative modelling by restraint-based conformational sampling. BMC Struct Biol. 2008 Jan 31;8:7.
  17. Haiman CA, Hsu C, de Bakker PIW, Frasco M, Sheng X, Van Den Berg D, Casagrande JT, Kolonel LN, Le Marchand L, Hankinson SE, Han J, Dunning AM, Pooley KA, Freedman ML, Hunter DJ, Wu AH, Stram DO, Henderson BE. Comprehensive association testing of common genetic variation in DNA repair pathway genes in relationship with breast cancer risk in multiple populations. Hum Mol Genet. 2008 Mar 15;17(6):825-34. Epub 2007 Dec 3.

    18. 2007

  18. Plenge RM, Cotsapas C, Davies L, Price AL, de Bakker PIW, Maller J, Pe'er I, Burtt NP, Blumenstiel B, DeFelice M, Parkin M, Barry R, Winslow W, Healy C, Graham RR, Neale BM, Izmailova E, Roubenoff R, Parker AN, Glass R, Karlson EW, Maher N, Hafler DA, Lee DM, Seldin MF, Remmers EF, Lee AT, Padyukov L, Alfredsson L, Coblyn J, Weinblatt ME, Gabriel SB, Purcell S, Klareskog L, Gregersen PK, Shadick NA, Daly MJ, Altshuler D. Two independent alleles at 6q23 associated with risk of rheumatoid arthritis. Nat Genet. 2007 Dec;39(12):1477-82. Epub 2007 Nov 4.
  19. The International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007 Oct 18;449(7164):851-61. [Go to HapMap]
  20. de Bakker PIW. 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 [Go to Tagger] [Go to Haploview]
  21. Remmers EF, Plenge RM, Lee AT, Graham RR, Hom G, Behrens TW, de Bakker PIW, Le JM, Lee HS, Batliwalla F, Li W, Masters SL, Booty MG, Carulli JP, Padyukov L, Alfredsson L, Klareskog L, Chen WV, Amos CI, Criswell LA, Seldin MF, Kastner DL, Gregersen PK. STAT4 and the risk of rheumatoid arthritis and systemic lupus erythematosus. N Engl J Med. 2007 Sep 6;357(10):977-86.
  22. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007 Sep;81(3):559-75. Epub 2007 Jul 25. [Go to PLINK]
  23. International Multiple Sclerosis Genetics Consortium: Hafler DA, Compston A, Sawcer S, Lander ES, Daly MJ, De Jager PL, de Bakker PIW, Gabriel SB, Mirel DB, Ivinson AJ, Pericak-Vance MA, Gregory SG, Rioux JD, McCauley JL, Haines JL, Barcellos LF, Cree B, Oksenberg JR, Hauser SL. Risk alleles for multiple sclerosis identified by a genomewide study. N Engl J Med. 2007 Aug 30;357(9):851-62. Epub 2007 Jul 29.
  24. Aarnoudse AJ, Newton-Cheh C, de Bakker PIW, Straus SM, Kors JA, Hofman A, Uitterlinden AG, Witteman JC, Stricker BH. Common NOS1AP variants are associated with a prolonged QTc interval in the Rotterdam Study. Circulation. 2007 Jul 3;116(1):10-6. Epub 2007 Jun 18.
  25. The ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14;447(7146):799-816.
  26. Diabetes Genetics Initiative of Broad Institute of Harvard and MIT, Lund University and Novartis Institutes for BioMedical Research. Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science. 2007 Jun 1;316(5829):1331-6. Epub 2007 Apr 26. [Related info]
  27. de Bakker PIW, Rosand J. In search of genes for stroke. Lancet Neurol. 2007 May;6(5):383-4. No abstract available.

    28. 2006

  28. de Bakker PIW, Burtt NP, Graham RR, Guiducci C, Yelensky R, Drake JA, Bersaglieri T, Penney KL, Butler J, Young S, Onofrio RC, Lyon HN, Stram DO, Haiman CA, Freedman ML, Zhu X, Cooper R, Groop L, Kolonel LN, Henderson BE, Daly MJ, Hirschhorn JN, Altshuler D. Transferability of tag SNPs in genetic association studies in multiple populations. Nat Genet. 2006 Nov;38(11):1298-303. Epub 2006 Oct 22.
  29. Rosand J, Bayley N, Rost N, de Bakker PIW. Many hypotheses but no replication for the association between PDE4D and stroke. Nat Genet. 2006 Oct;38(10):1091-2; author reply 1092-3. No abstract available.
  30. de Bakker PIW, McVean G, Sabeti PC, Miretti MM, Green T, Marchini J, Ke X, Monsuur AJ, Whittaker P, Delgado M, Morrison J, Richardson A, Walsh EC, Gao X, Galver L, Hart J, Hafler DA, Pericak-Vance M, Todd JA, Daly MJ, Trowsdale J, Wijmenga C, Vyse TJ, Beck S, Murray SS, Carrington M, Gregory S, Deloukas P, Rioux JD. A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC. Nat Genet. 2006 Oct;38(10):1166-72. Epub 2006 Sep 24. [Related info]
  31. Furnham N, Doré AS, Chirgadze DY, de Bakker PIW, Depristo MA, Blundell TL. Knowledge-based real-space explorations for low-resolution structure determination. Structure. 2006 Aug;14(8):1313-20.
  32. Florez JC, Jablonski KA, Bayley N, Pollin TI, de Bakker PIW, Shuldiner AR, Knowler WC, Nathan DM, Altshuler D; Diabetes Prevention Program Research Group. TCF7L2 polymorphisms and progression to diabetes in the Diabetes Prevention Program. N Engl J Med. 2006 Jul 20;355(3):241-50.
  33. Wiltshire S, de Bakker PIW, Daly MJ. The value of gene-based selection of tag SNPs in genome-wide association studies. Eur J Hum Genet. 2006 Nov;14(11):1209-14. Epub 2006 Jun 28.
  34. Saxena R, de Bakker PIW, Singer K, Mootha V, Burtt N, Hirschhorn JN, Gaudet D, Isomaa B, Daly MJ, Groop L, Ardlie KG, Altshuler D. Comprehensive association testing of common mitochondrial DNA variation in metabolic disease. Am J Hum Genet. 2006 Jul;79(1):54-61. Epub 2006 May 24. [Related info]
  35. Pe'er I, de Bakker PIW, Maller J, Yelensky R, Altshuler D, Daly MJ. Evaluating and improving power in whole-genome association studies using fixed marker sets. Nat Genet. 2006 Jun;38(6):663-7. Epub 2006 May 21. [Related info]
  36. Pe'er I, Chretien YR, de Bakker PIW, Barrett JC, Daly MJ, Altshuler DM. Biases and reconciliation in estimates of linkage disequilibrium in the human genome. Am J Hum Genet. 2006 Apr;78(4):588-603. Epub 2006 Mar 1.
  37. Sun MW, Lee JY, de Bakker PIW, Burtt NP, Almgren P, Råstam L, Tuomi T, Gaudet D, Daly MJ, Hirschhorn JN, Altshuler D, Groop L, Florez JC. Haplotype structures and large-scale association testing of the 5' AMP-activated protein kinase genes PRKAA2, PRKAB1, and PRKAB2 [corrected] with type 2 diabetes. Diabetes. 2006 Mar;55(3):849-55. Erratum in: Diabetes. 2006 Jun;55(6):1904.
  38. de Bakker PIW, Furnham N, Blundell TL, DePristo MA. Conformer generation under restraints. Curr Opin Struct Biol. 2006 Apr;16(2):160-5. Epub 2006 Feb 17. Review.
  39. de Bakker PIW, Graham RR, Altshuler D, Henderson BE, Haiman CA. Transferability of tag SNPs to capture common genetic variation in DNA repair genes across multiple populations. Pac Symp Biocomput. 2006:478-86.
  40. Whelan S, de Bakker PIW, Quevillon E, Rodriguez N, Goldman N. PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D327-31. [Go to PANDIT]
  41. Florez JC, Wiltshire S, Agapakis CM, Burtt NP, de Bakker PIW, Almgren P, Bengtsson Boström K, Tuomi T, Gaudet D, Daly MJ, Hirschhorn JN, McCarthy MI, Altshuler D, Groop L. High-density haplotype structure and association testing of the insulin-degrading enzyme (IDE) gene with type 2 diabetes in 4,206 people. Diabetes. 2006 Jan;55(1):128-35.
  42. Walsh EC, Sabeti P, Hutcheson HB, Fry B, Schaffner SF, de Bakker PIW, Varilly P, Palma AA, Roy J, Cooper R, Winkler C, Zeng Y, de The G, Lander ES, O'Brien S, Altshuler D. Searching for signals of evolutionary selection in 168 genes related to immune function. Hum Genet. 2006 Mar;119(1-2):92-102. Epub 2005 Dec 14.

    43. 2005

  43. Monsuur AJ, de Bakker PIW, Alizadeh BZ, Zhernakova A, Bevova MR, Strengman E, Franke L, van't Slot R, van Belzen MJ, Lavrijsen IC, Diosdado B, Daly MJ, Mulder CJ, Mearin ML, Meijer JW, Meijer GA, van Oort E, Wapenaar MC, Koeleman BP, Wijmenga C. Myosin IXB variant increases the risk of celiac disease and points toward a primary intestinal barrier defect. Nat Genet. 2005 Dec;37(12):1341-4. Epub 2005 Nov 13.
  44. The International HapMap Consortium. A haplotype map of the human genome. Nature. 2005 Oct 27;437(7063):1299-320. [Go to HapMap]
  45. de Bakker PIW, Yelensky R, Pe'er I, Gabriel SB, Daly MJ, Altshuler D. Efficiency and power in genetic association studies. Nat Genet. 2005 Nov;37(11):1217-23. Epub 2005 Oct 23. [Go to Tagger] [Go to Haploview]
  46. Depristo MA, de Bakker PIW, Johnson RJ, Blundell TL. Crystallographic refinement by knowledge-based exploration of complex energy landscapes. Structure. 2005 Sep;13(9):1311-9.
  47. Winckler W, Burtt NP, Holmkvist J, Cervin C, de Bakker PIW, Sun M, Almgren P, Tuomi T, Gaudet D, Hudson TJ, Ardlie KG, Daly MJ, Hirschhorn JN, Altshuler D, Groop L. Association of common variation in the HNF1alpha gene region with risk of type 2 diabetes. Diabetes. 2005 Aug;54(8):2336-42.
  48. Winckler W, Graham RR, de Bakker PIW, Sun M, Almgren P, Tuomi T, Gaudet D, Hudson TJ, Ardlie KG, Daly MJ, Hirschhorn JN, Groop L, Altshuler D. Association testing of variants in the hepatocyte nuclear factor 4alpha gene with risk of type 2 diabetes in 7,883 people. Diabetes. 2005 Mar;54(3):886-92.

    49. 2004

  49. DePristo MA, de Bakker PIW, Blundell TL. Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography. Structure. 2004 May;12(5):831-8.
  50. Florez JC, Burtt N, de Bakker PIW, Almgren P, Tuomi T, Holmkvist J, Gaudet D, Hudson TJ, Schaffner SF, Daly MJ, Hirschhorn JN, Groop L, Altshuler D. Haplotype structure and genotype-phenotype correlations of the sulfonylurea receptor and the islet ATP-sensitive potassium channel gene region. Diabetes. 2004 May;53(5):1360-8.
  51. de Bakker PIW, Saxena R, Graham RR. 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, Breckenridge, Colorado, USA. Pharmacogenomics. 2004 Mar;5(2):157-61. No abstract available.

    52. 2003

  52. Shetty RP, de Bakker PIW, DePristo MA, Blundell TL. Advantages of fine-grained side chain conformer libraries. Protein Eng. 2003 Dec;16(12):963-9.
  53. DePristo MA, de Bakker PIW, Shetty RP, Blundell TL. Discrete restraint-based protein modeling and the Calpha-trace problem. Protein Sci. 2003 Sep;12(9):2032-46.
  54. Whelan S, de Bakker PIW, Goldman N. Pandit: a database of protein and associated nucleotide domains with inferred trees. Bioinformatics. 2003 Aug 12;19(12):1556-63. [Go to PANDIT]
  55. DePristo MA, de Bakker PIW, Lovell SC, Blundell TL. Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles. Proteins. 2003 Apr 1;51(1):41-55.
  56. de Bakker PIW, DePristo MA, Burke DF, Blundell TL. 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. 2003 Apr 1;51(1):21-40.
  57. Lovell SC, Davis IW, Arendall WB 3rd, de Bakker PIW, Word JM, Prisant MG, Richardson JS, Richardson DC. Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins. 2003 Feb 15;50(3):437-50. [Go to MOLPROBITY]

    58. 2001

  58. Williams MG, Shirai H, Shi J, Nagendra HG, Mueller J, Mizuguchi K, Miguel RN, Lovell SC, Innis CA, Deane CM, Chen L, Campillo N, Burke DF, Blundell TL, de Bakker PIW. Sequence-structure homology recognition by iterative alignment refinement and comparative modeling. Proteins. 2001;Suppl 5:92-7.
  59. de Bakker PIW. 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)]
  60. de Bakker PIW, Bateman A, Burke DF, Miguel RN, Mizuguchi K, Shi J, Shirai H, Blundell TL. HOMSTRAD: adding sequence information to structure-based alignments of homologous protein families. Bioinformatics. 2001 Aug;17(8):748-9. [Go to HOMSTRAD]

    61. 2000

  61. Sánchez R, Pieper U, Mirković N, de Bakker PIW, Wittenstein E, Sali A. MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Res. 2000 Jan 1;28(1):250-3. [Go to MODBASE]

    62. 1999

  62. de Bakker PIW, Hünenberger PH, McCammon JA. Molecular dynamics simulations of the hyperthermophilic protein sac7d from Sulfolobus acidocaldarius: contribution of salt bridges to thermostability. J Mol Biol. 1999 Jan 29;285(4):1811-30.

    63. 1998

  63. de Bakker PIW, Tara S, Briggs JM. 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
  64. de Bakker PIW. HIV-integrase: het volgende doelwit. Pharmaceutisch Weekblad. 133: 982-984 [in Dutch; published by the Royal Dutch Association for the Advancement of Pharmacy (KNMP)]