publications

Click here for a complete list on PubMed.

    2012

  1. Raychaudhuri S, Sandor C, Stahl EA, Freudenberg J, Lee HS, Jia X, Alfredsson L, Padyukov L, Klareskog L, Worthington J, Siminovitch KA, Bae SC, Plenge RM, Gregersen PK, de Bakker PIW. Five amino acids in three HLA proteins explain most of the association between MHC and seropositive rheumatoid arthritis. Nat Genet. 2012 Jan 29. doi: 10.1038/ng.1076. [Epub ahead of print]
  2. 2011

  3. van Es MA, Schelhaas HJ, van Vught PW, Ticozzi N, Andersen PM, Groen EJ, Schulte C, Blauw HM, Koppers M, Diekstra FP, Fumoto K, LeClerc AL, Keagle P, Bloem BR, Scheffer H, van Nuenen BF, van Blitterswijk M, van Rheenen W, Wills AM, Lowe PP, Hu GF, Yu W, Kishikawa H, Wu D, Folkerth RD, Mariani C, Goldwurm S, Pezzoli G, Van Damme P, Lemmens R, Dahlberg C, Birve A, Fernández-Santiago R, Waibel S, Klein C, Weber M, van der Kooi AJ, de Visser M, Verbaan D, van Hilten JJ, Heutink P, Hennekam EA, Cuppen E, Berg D, Brown RH Jr, Silani V, Gasser T, Ludolph AC, Robberecht W, Ophoff RA, Veldink JH, Pasterkamp RJ, de Bakker PIW, Landers JE, van de Warrenburg BP, van den Berg LH. Angiogenin variants in Parkinson disease and amyotrophic lateral sclerosis. Ann Neurol. 2011 Dec;70(6):964-73. doi: 10.1002/ana.22611.
  4. Patsopoulos NA; Bayer Pharma MS Genetics Working Group; Steering Committees of Studies Evaluating IFNβ-1b and a CCR1-Antagonist; ANZgene Consortium; GeneMSA; International Multiple Sclerosis Genetics Consortium, Esposito F, Reischl J, Lehr S, Bauer D, Heubach J, Sandbrink R, Pohl C, Edan G, Kappos L, Miller D, Montalbán J, Polman CH, Freedman MS, Hartung HP, Arnason BG, Comi G, Cook S, Filippi M, Goodin DS, Jeffery D, O'Connor P, Ebers GC, Langdon D, Reder AT, Traboulsee A, Zipp F, Schimrigk S, Hillert J, Bahlo M, Booth DR, Broadley S, Brown MA, Browning BL, Browning SR, Butzkueven H, Carroll WM, Chapman C, Foote SJ, Griffiths L, Kermode AG, Kilpatrick TJ, Lechner-Scott J, Marriott M, Mason D, Moscato P, Heard RN, Pender MP, Perreau VM, Perera D, Rubio JP, Scott RJ, Slee M, Stankovich J, Stewart GJ, Taylor BV, Tubridy N, Willoughby E, Wiley J, Matthews P, Boneschi FM, Compston A, Haines J, Hauser SL, McCauley J, Ivinson A, Oksenberg JR, Pericak-Vance M, Sawcer SJ, De Jager PL, Hafler DA, de Bakker PIW. Genome-wide meta-analysis identifies novel multiple sclerosis susceptibility loci. Ann Neurol. 2011 Dec;70(6):897-912. doi: 10.1002/ana.22609.
  5. Dayyeh BK, Gupta N, Sherman KE, de Bakker PIW, Chung RT; Aids Clinical Trials Group A5178 Study Team. IL28B alleles exert an additive dose effect when applied to HCV-HIV coinfected persons undergoing peginterferon and ribavirin therapy. PLoS One. 2011;6(10):e25753. Epub 2011 Oct 7.
  6. IBC 50K CAD Consortium: Butterworth AS, Braund PS, Farrall M, Hardwick RJ, Saleheen D, Peden JF, Soranzo N, Chambers JC, Sivapalaratnam S, Kleber ME, Keating B, Qasim A, Klopp N, Erdmann J, Assimes TL, Ball SG, Balmforth AJ, Barnes TA, Basart H, Baumert J, Bezzina CR, Boerwinkle E, Boehm BO, Brocheton J, Bugert P, Cambien F, Clarke R, Codd V, Collins R, Couper D, Cupples LA, de Jong JS, Diemert P, Ejebe K, Elbers CC, Elliott P, Fornage M, Franzosi MG, Frossard P, Garner S, Goel A, Goodall AH, Hengstenberg C, Hunt SE, Kastelein JJ, Klungel OH, Klüter H, Koch K, König IR, Kooner AS, Laaksonen R, Lathrop M, Li M, Liu K, McPherson R, Musameh MD, Musani S, Nelson CP, O'Donnell CJ, Ongen H, Papanicolaou G, Peters A, Peters BJ, Potter S, Psaty BM, Qu L, Rader DJ, Rasheed A, Rice C, Scott J, Seedorf U, Sehmi JS, Sotoodehnia N, Stark K, Stephens J, van der Schoot CE, van der Schouw YT, Thorsteinsdottir U, Tomaszewski M, van der Harst P, Vasan RS, Wilde AA, Willenborg C, Winkelmann BR, Zaidi M, Zhang W, Ziegler A, de Bakker PIW, Koenig W, Mätz W, Trip MD, Reilly MP, Kathiresan S, Schunkert H, Hamsten A, Hall AS, Kooner JS, Thompson SG, Thompson JR, Deloukas P, Ouwehand WH, Watkins H, Danesh J, Samani NJ, Barnes T, Rafelt S, Codd V, Tomaszewski M, Ouwehand WH, Bruinsma N, Dekker LR, Henriques JP, Koch KT, de Winter RJ, Alings M, Allaart CF, Gorgels AP, Verheugt FW, Braund PS, Thompson JR, Samani NJ, Mueller M, Meisinger C, DerOhannessian S, Mehta NN, Ferguson J, Hakonarson H, Matthai W, Wilensky R, Hopewell JC, Parish S, Linksted P, Notman J, Gonzalez H, Young A, Ostley T, Munday A, Goodwin N, Verdon V, Shah S, Cobb L, Edwards C, Mathews C, Gunter R, Benham J, Davies C, Cobb M, Cobb L, Crowther J, Richards A, Silver M, Tochlin S, Mozley S, Clark S, Radley M, Kourellias K, Silveira A, Söderholm B, Olsson P, Barlera S, Tognoni G, Rust S, Assmann G, Heath S, Zelenika D, Gut I, Green F, Farrall M, Peden J, Goel A, Ongen H, Franzosi MG, Lathrop M, Seedorf U, Clarke R, Collins R, Hamsten A, Watkins H, Aly A, Anner K, Björklund K, Blomgren G, Cederschiöld B, Danell-Toverud K, Eriksson P, Grundstedt U, Hamsten A, Heinonen M, Hellénius ML, van't Hooft F, Husman K, Lagercrantz J, Larsson A, Larsson M, Mossfeldt M, Mälarstig A, Olsson G, Sabater-Lleal M, Sennblad B, Silveira A, Strawbridge R, Söderholm B, Öhrvik J, Zaman KS, Mallick NH, Azhar M, Samad A, Ishaq M, Shah N, Samuel M, Schunkert H, König IR, Kathiresan S, Reilly M, Assimes TL, Holm H, Preuss M, Stewart AF, Barbalic M, Gieger C, Absher D, Aherrahrou Z, Allayee H, Altshuler D, Anand S, Andersen K, Anderson JL, Ardissino D, Ball SG, Balmforth AJ, Barnes TA, Becker LC, Becker DM, Berger K, Bis JC, Boekholdt SM, Boerwinkle E, Braund PS, Brown MJ, Burnett MS, Buysschaert I, Carlquist JF, Chen L, Codd V, Davies RW, Dedoussis G, Dehghan A, Demissie S, Devaney J, Do R, Doering A, El Mokhtari NE, Ellis SG, Elosua R, Engert JC, Epstein S, de Faire U, Fischer M, Folsom AR, Freyer J, Gigante B, Girelli D, Gretarsdottir S, Gudnason V, Gulcher JR, Tennstedt S, Halperin E, Hammond N, Hazen SL, Hofman A, Horne BD, Illig T, Iribarren C, Jones GT, Jukema JW, Kaiser MA, Kaplan LM, Kastelein JJ, Khaw KT, Knowles JW, Kolovou G, Kong A, Laaksonen R, Lambrechts D, Leander K, Li M, Lieb W, Diemert P, Lettre G, Loley C, Lotery AJ, Mannucci PM, Maouche S, Martinelli N, McKeown PP, Meisinger C, Meitinger T, Melander O, Merlini PA, Mooser V, Morgan T, Mühleisen TW, Muhlestein JB, Musunuru K, Nahrstaedt J, Nelson CP, Nöthen MM, Olivieri O, Peyvandi F, Patel RS, Patterson CC, Peters A, Qu L, Quyyumi AA, Rader DJ, Rallidis LS, Rice C, Roosendaal FR, Rubin D, Salomaa V, Sampietro ML, Sandhu MS, Schadt E, Schäfer A, Schillert A, Schreiber S, Schrezenmeir J, Schwartz SM, Siscovick DS, Sivananthan M, Sivapalaratnam S, Smith AV, Smith TB, Snoep JD, Soranzo N, Spertus JA, Stark K, Stefansson K, Stirrups K, Stoll M, Tang WH, Thorgeirsson G, Thorleifsson G, Tomaszewski M, Uitterlinden AG, van Rij AM, Voight BF, Wareham NJ, AWells G, Wichmann HE, Willenborg C, Witteman JC, Wright BJ, Ye S, Ziegler A, Cambien F, Goodall AH, Cupples LA, Quertermous T, März W, Hengstenberg C, Blankenberg S, Ouwehand WH, Hall AS, Deloukas P, Thorsteinsdottir U, Roberts R, Thompson JR, O'Donnell CJ, McPherson R, Erdmann J, Samani NJ, Onland-Moret NC, van Setten J, de Bakker PI, Verschuren WM, Boer JM, Wijmenga C, Hofker MH, Maitland-van der Zee AH, de Boer A, Grobbee DE, Attwood T, Belz S, Braund P, Cambien F, Cooper J, Crisp-Hihn A, Diemert P, Deloukas P, Foad N, Erdmann J, Goodall AH, Gracey J, Gray E, Gwilliams R, Heimerl S, Hengstenberg C, Jolley J, Krishnan U, Lloyd-Jones H, Lugauer I, Lundmark P, Maouche S, Moore JS, Muir D, Murray E, Nelson CP, Neudert J, Niblett D, O'Leary K, Ouwehand WH, Pollard H, Rankin A, Rice CM, Sager H, Samani NJ, Sambrook J, Schmitz G, Scholz M, Schroeder L, Schunkert H, Syvannen AC, Tennstedt S, Wallace C. Large-scale gene-centric analysis identifies novel variants for coronary artery disease. PLoS Genet. 2011 Sep;7(9):e1002260. Epub 2011 Sep 22.
  7. 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. Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis. Nature. 2011 Aug 10;476(7359):214-9. doi: 10.1038/nature10251.
  8. Rotger M, Dalmau J, Rauch A, McLaren P, Bosinger S, Martinez R, Sandler NG, Roque A, Liebner J, Battegay M, Bernasconi E, Descombes P, Erkizia I, Fellay J, Hirschel B, Miró JM, Palou E, Hoffmann M, Massanella M, Blanco J, Woods M, Günthard HF, de Bakker P, Douek DC, Silvestri G, Martinez-Picado J, Telenti A. Comparative transcriptomics of extreme phenotypes of human HIV-1 infection and SIV infection in sooty mangabey and rhesus macaque. J Clin Invest. 2011 Jun 1;121(6):2391-400. doi: 10.1172/JCI45235. Epub 2011 May 9.
  9. McCormack M, Alfirevic A, Bourgeois S, Farrell JJ, Kasperavičiūtė D, Carrington M, Sills GJ, Marson T, Jia X, de Bakker PI, Chinthapalli K, Molokhia M, Johnson MR, O'Connor GD, Chaila E, Alhusaini S, Shianna KV, Radtke RA, Heinzen EL, Walley N, Pandolfo M, Pichler W, Park BK, Depondt C, Sisodiya SM, Goldstein DB, Deloukas P, Delanty N, Cavalleri GL, Pirmohamed M. HLA-A*3101 and carbamazepine-induced hypersensitivity reactions in Europeans. N Engl J Med. 2011 Mar 24;364(12):1134-43.
  10. Zhernakova A, Stahl EA, Trynka G, Raychaudhuri S, Festen EA, Franke L, Westra HJ, Fehrmann RS, Kurreeman FA, Thomson B, Gupta N, Romanos J, McManus R, Ryan AW, Turner G, Brouwer E, Posthumus MD, Remmers EF, Tucci F, Toes R, Grandone E, Mazzilli MC, Rybak A, Cukrowska B, Coenen MJ, Radstake TR, van Riel PL, Li Y, de Bakker PI, Gregersen PK, Worthington J, Siminovitch KA, Klareskog L, Huizinga TW, Wijmenga C, Plenge RM. Meta-Analysis of Genome-Wide Association Studies in Celiac Disease and Rheumatoid Arthritis Identifies Fourteen Non-HLA Shared Loci. PLoS Genet. 2011 Feb;7(2):e1002004. Epub 2011 Feb 24.
  11. Wang JH, Pappas D, De Jager PL, Pelletier D, de Bakker PIW, Kappos L, Polman CH, Multiple Sclerosis Genetics Consortium AA, Chibnik LB, Hafler DA, Matthews PM, Hauser SL, Baranzini SE, Oksenberg JR. Modeling the Cumulative Genetic Risk for Multiple Sclerosis from Genome Wide Association Data. Genome Med. 2011 Jan 18;3(1):3.
  12. Erlich RL, Jia X, Anderson S, Banks E, Gao X, Carrington M, Gupta N, Depristo MA, Henn MR, Lennon NJ, de Bakker PIW. Next-generation sequencing for HLA typing of class I loci. BMC Genomics. 2011 Jan 18;12:42.
  13. Lanktree MB, Guo Y, Murtaza M, Glessner JT, Bailey SD, Onland-Moret NC, Lettre G, Ongen H, Rajagopalan R, Johnson T, Shen H, Nelson CP, Klopp N, Baumert J, Padmanabhan S, Pankratz N, Pankow JS, Shah S, Taylor K, Barnard J, Peters BJ, M Maloney C, Lobmeyer MT, Stanton A, Zafarmand MH, Romaine SP, Mehta A, van Iperen EP, Gong Y, Price TS, Smith EN, Kim CE, Li YR, Asselbergs FW, Atwood LD, Bailey KM, Bhatt D, Bauer F, Behr ER, Bhangale T, Boer JM, Boehm BO, Bradfield JP, Brown M, Braund PS, Burton PR, Carty C, Chandrupatla HR, Chen W, Connell J, Dalgeorgou C, Boer A, Drenos F, Elbers CC, Fang JC, Fox CS, Frackelton EC, Fuchs B, Furlong CE, Gibson Q, Gieger C, Goel A, Grobbee DE, Hastie C, Howard PJ, Huang GH, Johnson WC, Li Q, Kleber ME, Klein BE, Klein R, Kooperberg C, Ky B, Lacroix A, Lanken P, Lathrop M, Li M, Marshall V, Melander O, Mentch FD, J Meyer N, Monda KL, Montpetit A, Murugesan G, Nakayama K, Nondahl D, Onipinla A, Rafelt S, Newhouse SJ, Otieno FG, Patel SR, Putt ME, Rodriguez S, Safa RN, Sawyer DB, Schreiner PJ, Simpson C, Sivapalaratnam S, Srinivasan SR, Suver C, Swergold G, Sweitzer NK, Thomas KA, Thorand B, Timpson NJ, Tischfield S, Tobin M, Tomaszweski M, Verschuren WM, Wallace C, Winkelmann B, Zhang H, Zheng D, Zhang L, Zmuda JM, Clarke R, Balmforth AJ, Danesh J, Day IN, Schork NJ, de Bakker PIW, Delles C, Duggan D, Hingorani AD, Hirschhorn JN, Hofker MH, Humphries SE, Kivimaki M, Lawlor DA, Kottke-Marchant K, Mega JL, Mitchell BD, Morrow DA, Palmen J, Redline S, Shields DC, Shuldiner AR, Sleiman PM, Smith GD, Farrall M, Jamshidi Y, Christiani DC, Casas JP, Hall AS, Doevendans PA, D Christie J, Berenson GS, Murray SS, Illig T, Dorn GW 2nd, Cappola TP, Boerwinkle E, Sever P, Rader DJ, Reilly MP, Caulfield M, Talmud PJ, Topol E, Engert JC, Wang K, Dominiczak A, Hamsten A, Curtis SP, Silverstein RL, Lange LA, Sabatine MS, Trip M, Saleheen D, Peden JF, Cruickshanks KJ, März W, O'Connell JR, Klungel OH, Wijmenga C, Maitland-van der Zee AH, Schadt EE, Johnson JA, Jarvik GP, Papanicolaou GJ; Hugh Watkins on behalf of PROCARDIS, Grant SF, Munroe PB, North KE, Samani NJ, Koenig W, Gaunt TR, Anand SS, van der Schouw YT; Meena Kumari on behalf of the Whitehall II Study and the WHII 50K Group, Soranzo N, Fitzgerald GA, Reiner A, Hegele RA, Hakonarson H, Keating BJ. Meta-analysis of Dense Genecentric Association Studies Reveals Common and Uncommon Variants Associated with Height. Am J Hum Genet. 2011 Jan 7;88(1):6-18. Epub 2010 Dec 30.
  14. Grady BJ, Torstenson ES, McLaren PJ, de Bakker PIW, Haas DW, Robbins GK, Gulick RM, Haubrich R, Ribaudo H, Ritchie MD. Use of biological knowledge to inform the analysis of gene-gene interactions involved in modulating virologic failure with efavirenz-containing treatment regimens in art-naïve actg clinical trials participants. Pac Symp Biocomput. 2011:253-64.
  15. 2010

  16. Sotoodehnia N, Isaacs A, de Bakker PIW, Dörr M, Newton-Cheh C, Nolte IM, van der Harst P, Müller M, Eijgelsheim M, Alonso A, Hicks AA, Padmanabhan S, Hayward C, Smith AV, Polasek O, Giovannone S, Fu J, Magnani JW, Marciante KD, Pfeufer A, Gharib SA, Teumer A, Li M, Bis JC, Rivadeneira F, Aspelund T, Köttgen A, Johnson T, Rice K, Sie MP, Wang YA, Klopp N, Fuchsberger C, Wild SH, Mateo Leach I, Estrada K, Völker U, Wright AF, Asselbergs FW, Qu J, Chakravarti A, Sinner MF, Kors JA, Petersmann A, Harris TB, Soliman EZ, Munroe PB, Psaty BM, Oostra BA, Cupples LA, Perz S, de Boer RA, Uitterlinden AG, Völzke H, Spector TD, Liu FY, Boerwinkle E, Dominiczak AF, Rotter JI, van Herpen G, Levy D, Wichmann HE, van Gilst WH, Witteman JC, Kroemer HK, Kao WH, Heckbert SR, Meitinger T, Hofman A, Campbell H, Folsom AR, van Veldhuisen DJ, Schwienbacher C, O'Donnell CJ, Volpato CB, Caulfield MJ, Connell JM, Launer L, Lu X, Franke L, Fehrmann RS, Te Meerman G, Groen HJ, Weersma RK, van den Berg LH, Wijmenga C, Ophoff RA, Navis G, Rudan I, Snieder H, Wilson JF, Pramstaller PP, Siscovick DS, Wang TJ, Gudnason V, van Duijn CM, Felix SB, Fishman GI, Jamshidi Y, Stricker BHCh, Samani NJ, Kääb S, Arking DE. Common variants in 22 loci are associated with QRS duration and cardiac ventricular conduction. Nat Genet. 2010 Dec;42(12):1068-76. Epub 2010 Nov 14. Supplementary Data
  17. The International HIV Controllers Study: Pereyra F, Jia X, McLaren PJ, Telenti A, de Bakker PIW, Walker BD, Ripke S, Brumme CJ, Pulit SL, Carrington M, Kadie CM, Carlson JM, Heckerman D, Graham RR, Plenge RM, Deeks SG, Gianniny L, Crawford G, Sullivan J, Gonzalez E, Davies L, Camargo A, Moore JM, Beattie N, Gupta S, Crenshaw A, Burtt NP, Guiducci C, Gupta N, Gao X, Qi Y, Yuki Y, Piechocka-Trocha A, Cutrell E, Rosenberg R, Moss KL, Lemay P, O'Leary J, Schaefer T, Verma P, Toth I, Block B, Baker B, Rothchild A, Lian J, Proudfoot J, Alvino DM, Vine S, Addo MM, Allen TM, Altfeld M, Henn MR, Le Gall S, Streeck H, Haas DW, Kuritzkes DR, Robbins GK, Shafer RW, Gulick RM, Shikuma CM, Haubrich R, Riddler S, Sax PE, Daar ES, Ribaudo HJ, Agan B, Agarwal S, Ahern RL, Allen BL, Altidor S, Altschuler EL, Ambardar S, Anastos K, Anderson B, Anderson V, Andrady U, Antoniskis D, Bangsberg D, Barbaro D, Barrie W, Bartczak J, Barton S, Basden P, Basgoz N, Bazner S, Bellos NC, Benson AM, Berger J, Bernard NF, Bernard AM, Birch C, Bodner SJ, Bolan RK, Boudreaux ET, Bradley M, Braun JF, Brndjar JE, Brown SJ, Brown K, Brown ST, Burack J, Bush LM, Cafaro V, Campbell O, Campbell J, Carlson RH, Carmichael JK, Casey KK, Cavacuiti C, Celestin G, Chambers ST, Chez N, Chirch LM, Cimoch PJ, Cohen D, Cohn LE, Conway B, Cooper DA, Cornelson B, Cox DT, Cristofano MV, Cuchural G Jr, Czartoski JL, Dahman JM, Daly JS, Davis BT, Davis K, Davod SM, DeJesus E, Dietz CA, Dunham E, Dunn ME, Ellerin TB, Eron JJ, Fangman JJ, Farel CE, Ferlazzo H, Fidler S, Fleenor-Ford A, Frankel R, Freedberg KA, French NK, Fuchs JD, Fuller JD, Gaberman J, Gallant JE, Gandhi RT, Garcia E, Garmon D, Gathe JC Jr, Gaultier CR, Gebre W, Gilman FD, Gilson I, Goepfert PA, Gottlieb MS, Goulston C, Groger RK, Gurley TD, Haber S, Hardwicke R, Hardy WD, Harrigan PR, Hawkins TN, Heath S, Hecht FM, Henry WK, Hladek M, Hoffman RP, Horton JM, Hsu RK, Huhn GD, Hunt P, Hupert MJ, Illeman ML, Jaeger H, Jellinger RM, John M, Johnson JA, Johnson KL, Johnson H, Johnson K, Joly J, Jordan WC, Kauffman CA, Khanlou H, Killian RK, Kim AY, Kim DD, Kinder CA, Kirchner JT, Kogelman L, Kojic EM, Korthuis PT, Kurisu W, Kwon DS, LaMar M, Lampiris H, Lanzafame M, Lederman MM, Lee DM, Lee JM, Lee MJ, Lee ET, Lemoine J, Levy JA, Llibre JM, Liguori MA, Little SJ, Liu AY, Lopez AJ, Loutfy MR, Loy D, Mohammed DY, Man A, Mansour MK, Marconi VC, Markowitz M, Marques R, Martin JN, Martin HL Jr, Mayer KH, McElrath MJ, McGhee TA, McGovern BH, McGowan K, McIntyre D, Mcleod GX, Menezes P, Mesa G, Metroka CE, Meyer-Olson D, Miller AO, Montgomery K, Mounzer KC, Nagami EH, Nagin I, Nahass RG, Nelson MO, Nielsen C, Norene DL, O'Connor DH, Ojikutu BO, Okulicz J, Oladehin OO, Oldfield EC 3rd, Olender SA, Ostrowski M, Owen WF Jr, Pae E, Parsonnet J, Pavlatos AM, Perlmutter AM, Pierce MN, Pincus JM, Pisani L, Price LJ, Proia L, Prokesch RC, Pujet HC, Ramgopal M, Rathod A, Rausch M, Ravishankar J, Rhame FS, Richards CS, Richman DD, Rodes B, Rodriguez M, Rose RC 3rd, Rosenberg ES, Rosenthal D, Ross PE, Rubin DS, Rumbaugh E, Saenz L, Salvaggio MR, Sanchez WC, Sanjana VM, Santiago S, Schmidt W, Schuitemaker H, Sestak PM, Shalit P, Shay W, Shirvani VN, Silebi VI, Sizemore JM Jr, Skolnik PR, Sokol-Anderson M, Sosman JM, Stabile P, Stapleton JT, Starrett S, Stein F, Stellbrink HJ, Sterman FL, Stone VE, Stone DR, Tambussi G, Taplitz RA, Tedaldi EM, Telenti A, Theisen W, Torres R, Tosiello L, Tremblay C, Tribble MA, Trinh PD, Tsao A, Ueda P, Vaccaro A, Valadas E, Vanig TJ, Vecino I, Vega VM, Veikley W, Wade BH, Walworth C, Wanidworanun C, Ward DJ, Warner DA, Weber RD, Webster D, Weis S, Wheeler DA, White DJ, Wilkins E, Winston A, Wlodaver CG, van't Wout A, Wright DP, Yang OO, Yurdin DL, Zabukovic BW, Zachary KC, Zeeman B, Zhao M. The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science. 2010 Dec 10;330(6010):1551-7. Epub 2010 Nov 4. Supplementary Data
  18. Anderson CD, Biffi A, Rahman R, Ross OA, Jagiella JM, Kissela B, Cole JW, Cortellini L, Rost NS, Cheng YC, Greenberg SM, de Bakker PIW, Brown RD Jr, Brott TG, Mitchell BD, Broderick JP, Worrall BB, Furie KL, Kittner SJ, Woo D, Slowik A, Meschia JF, Saxena R, Rosand J; on behalf of the International Stroke Genetics Consortium. Common mitochondrial sequence variants in ischemic stroke. Ann Neurol. 2010 Sep 13. [Epub ahead of print]
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  20. International HapMap 3 Consortium: Altshuler DM, Gibbs RA, Peltonen L, Altshuler DM, Gibbs RA, Peltonen L, Dermitzakis E, Schaffner SF, Yu F, Peltonen L, Dermitzakis E, Bonnen PE, Altshuler DM, Gibbs RA, de Bakker PIW, Deloukas P, Gabriel SB, Gwilliam R, Hunt S, Inouye M, Jia X, Palotie A, Parkin M, Whittaker P, Yu F, Chang K, Hawes A, Lewis LR, Ren Y, Wheeler D, Gibbs RA, Muzny DM, Barnes C, Darvishi K, Hurles M, Korn JM, Kristiansson K, Lee C, McCarrol SA, Nemesh J, Dermitzakis E, Keinan A, Montgomery SB, Pollack S, Price AL, Soranzo N, Bonnen PE, Gibbs RA, Gonzaga-Jauregui C, Keinan A, Price AL, Yu F, Anttila V, Brodeur W, Daly MJ, Leslie S, McVean G, Moutsianas L, Nguyen H, Schaffner SF, Zhang Q, Ghori MJ, McGinnis R, McLaren W, Pollack S, Price AL, Schaffner SF, Takeuchi F, Grossman SR, Shlyakhter I, Hostetter EB, Sabeti PC, Adebamowo CA, Foster MW, Gordon DR, Licinio J, Manca MC, Marshall PA, Matsuda I, Ngare D, Wang VO, Reddy D, Rotimi CN, Royal CD, Sharp RR, Zeng C, Brooks LD, McEwen JE. Integrating common and rare genetic variation in diverse human populations. Nature. 2010 Sep 2;467(7311):52-8.
  21. de Bakker PIW, Telenti A. Infectious diseases not immune to genome-wide association. Nat Genet. 2010 Sep;42(9):731-2.
  22. Jablonski KA, McAteer JB, de Bakker PIW, Franks PW, Pollin TI, Hanson RL, Saxena R, Fowler S, Shuldiner AR, Knowler WC, Altshuler D, Florez JC; Diabetes Prevention Program Research Group. Common variants in 40 genes assessed for diabetes incidence and response to metformin and lifestyle intervention in the diabetes prevention program. Diabetes. 2010 Oct;59(10):2672-81. Epub 2010 Aug 3.
  23. Eijgelsheim M, Newton-Cheh C, Sotoodehnia N, de Bakker PIW, Müller M, Morrison AC, Smith AV, Isaacs A, Sanna S, Dörr M, Navarro P, Fuchsberger C, Nolte IM, de Geus EJ, Estrada K, Hwang SJ, Bis JC, Rückert IM, Alonso A, Launer LJ, Hottenga JJ, Rivadeneira F, Noseworthy PA, Rice KM, Perz S, Arking DE, Spector TD, Kors JA, Aulchenko YS, Tarasov KV, Homuth G, Wild SH, Marroni F, Gieger C, Licht CM, Prineas RJ, Hofman A, Rotter JI, Hicks AA, Ernst F, Najjar SS, Wright AF, Peters A, Fox ER, Oostra BA, Kroemer HK, Couper D, Völzke H, Campbell H, Meitinger T, Uda M, Witteman JC, Psaty BM, Wichmann HE, Harris TB, Kääb S, Siscovick DS, Jamshidi Y, Uitterlinden AG, Folsom AR, Larson MG, Wilson JF, Penninx BW, Snieder H, Pramstaller PP, van Duijn CM, Lakatta EG, Felix SB, Gudnason V, Pfeufer A, Heckbert SR, Stricker BH, Boerwinkle E, O'Donnell CJ. Genome-wide association analysis identifies multiple loci related to resting heart rate. Hum Mol Genet. 2010 Oct 1;19(19):3885-94. Epub 2010 Jul 16.
  24. Cree BA, Rioux JD, McCauley JL, Gourraud PA, Goyette P, McElroy J, De Jager P, Santaniello A, Vyse TJ, Gregersen PK, Mirel D, Hafler DA, Haines JL, Pericak-Vance MA, Compston A, Sawcer SJ, Oksenberg JR, Hauser SL; IMAGEN; IMSGC. A major histocompatibility Class I locus contributes to multiple sclerosis susceptibility independently from HLA-DRB1*15:01. PLoS One. 2010 Jun 25;5(6):e11296.
  25. International Multiple Sclerosis Genetics Consortium (IMSGC). IL12A, MPHOSPH9/CDK2AP1 and RGS1 are novel multiple sclerosis susceptibility loci. Genes Immun. 2010 Jul;11(5):397-405. Epub 2010 Jun 17.
  26. Biffi A, Anderson CD, Nalls MA, Rahman R, Sonni A, Cortellini L, Rost NS, Matarin M, Hernandez DG, Plourde A, de Bakker PIW, Ross OA, Greenberg SM, Furie KL, Meschia JF, Singleton AB, Saxena R, Rosand J. Principal-component analysis for assessment of population stratification in mitochondrial medical genetics. Am J Hum Genet. 2010 Jun 11;86(6):904-17. Epub 2010 May 27.
  27. de Bakker PIW, Neale BM, Daly MJ. Meta-analysis of genome-wide association studies. Cold Spring Harb Protoc. 2010 Jun;2010(6):pdb.top81.
  28. Price AL, Kryukov GV, de Bakker PIW, Purcell SM, Staples J, Wei LJ, Sunyaev SR. Pooled association tests for rare variants in exon-resequencing studies. Am J Hum Genet. 2010 Jun 11;86(6):832-8. Epub 2010 May 13. Erratum in: Am J Hum Genet. 2010 Jun 11;86(6):982. Supplementary Data
  29. Stahl EA, Raychaudhuri S, Remmers EF, Xie G, Eyre S, Thomson BP, Li Y, Kurreeman FA, Zhernakova A, Hinks A, Guiducci C, Chen R, Alfredsson L, Amos CI, Ardlie KG; BIRAC Consortium, Barton A, Bowes J, Brouwer E, Burtt NP, Catanese JJ, Coblyn J, Coenen MJ, Costenbader KH, Criswell LA, Crusius JB, Cui J, de Bakker PIW, De Jager PL, Ding B, Emery P, Flynn E, Harrison P, Hocking LJ, Huizinga TW, Kastner DL, Ke X, Lee AT, Liu X, Martin P, Morgan AW, Padyukov L, Posthumus MD, Radstake TR, Reid DM, Seielstad M, Seldin MF, Shadick NA, Steer S, Tak PP, Thomson W, van der Helm-van Mil AH, van der Horst-Bruinsma IE, van der Schoot CE, van Riel PL, Weinblatt ME, Wilson AG, Wolbink GJ, Wordsworth BP; YEAR Consortium, Wijmenga C, Karlson EW, Toes RE, de Vries N, Begovich AB, Worthington J, Siminovitch KA, Gregersen PK, Klareskog L, Plenge RM. Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci. Nat Genet. 2010 Jun;42(6):508-14. Epub 2010 May 9. Supplementary Data
  30. International Stroke Genetics Consortium; Wellcome Trust Case-Control Consortium 2. Failure to validate association between 12p13 variants and ischemic stroke. N Engl J Med. 2010 Apr 22;362(16):1547-50. Supplementary Data
  31. Ellinor PT, Lunetta KL, Glazer NL, Pfeufer A, Alonso A, Chung MK, Sinner MF, de Bakker PIW, Mueller M, Lubitz SA, Fox E, Darbar D, Smith NL, Smith JD, Schnabel RB, Soliman EZ, Rice KM, Van Wagoner DR, Beckmann BM, van Noord C, Wang K, Ehret GB, Rotter JI, Hazen SL, Steinbeck G, Smith AV, Launer LJ, Harris TB, Makino S, Nelis M, Milan DJ, Perz S, Esko T, Köttgen A, Moebus S, Newton-Cheh C, Li M, Möhlenkamp S, Wang TJ, Kao WH, Vasan RS, Nöthen MM, MacRae CA, Stricker BH, Hofman A, Uitterlinden AG, Levy D, Boerwinkle E, Metspalu A, Topol EJ, Chakravarti A, Gudnason V, Psaty BM, Roden DM, Meitinger T, Wichmann HE, Witteman JC, Barnard J, Arking DE, Benjamin EJ, Heckbert SR, Kääb S. Common variants in KCNN3 are associated with lone atrial fibrillation. Nat Genet. 2010 Mar;42(3):240-4. Epub 2010 Feb 21.
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  33. 2009

  34. Brown WM, Pierce JJ, Hilner JE, Perdue LH, Lohman K, Lu L, de Bakker PIW, Irenze K, Ziaugra L, Mirel DB; Type I Diabetes Genetics Consortium. Overview of the Rapid Response data. Genes Immun. 2009 Dec;10 Suppl 1:S5-S15.
  35. International MHC and Autoimmunity Genetics Network: Rioux JD, Goyette P, Vyse TJ, Hammarström L, Fernando MM, Green T, De Jager PL, Foisy S, Wang J, de Bakker PIW, Leslie S, McVean G, Padyukov L, Alfredsson L, Annese V, Hafler DA, Pan-Hammarström Q, Matell R, Sawcer SJ, Compston AD, Cree BA, Mirel DB, Daly MJ, Behrens TW, Klareskog L, Gregersen PK, Oksenberg JR, Hauser SL. Mapping of multiple susceptibility variants within the MHC region for 7 immune-mediated diseases. Proc Natl Acad Sci U S A. 2009 Nov 3;106(44):18680-5. Epub 2009 Oct 21.
  36. 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.
  37. 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.
  38. 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.
  39. 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.
  40. 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.
  41. 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.
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  43. 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.
  44. 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.
  45. 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.
  46. 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.
  47. 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.
  48. 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.
  49. 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.
  50. 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.
  51. 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.
  52. 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.
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  54. 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.
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  59. 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.
  60. 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.
  61. 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.
  62. 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
  63. de Bakker PIW, Rosand J. In search of genes for stroke. Lancet Neurol. 2007 May;6(5):383-4.
  64. 2006

  65. 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.
  66. 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.
  67. 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
  68. 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.
  69. 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.
  70. 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.
  71. 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
  72. 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
  73. 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.
  74. 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.
  75. 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.
  76. 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.
  77. 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.
  78. 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.
  79. 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.
  80. 2005

  81. 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.
  82. The International HapMap Consortium. A haplotype map of the human genome. Nature. 2005 Oct 27;437(7063):1299-320.
  83. 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.
  84. 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.
  85. 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.
  86. 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.
  87. 2004

  88. 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.
  89. 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.
  90. 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.
  91. 1998-2003

  92. 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.
  93. 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.
  94. 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.
  95. 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.
  96. 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.
  97. 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.
  98. 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.
  99. 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)]
  100. 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.
  101. 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.
  102. 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.
  103. 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
  104. de Bakker PIW. HIV-integrase: het volgende doelwit. Pharmaceutisch Weekblad. 1998;133:982-984 [in Dutch; published by the Royal Dutch Association for the Advancement of Pharmacy (KNMP)]