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Efficiency and power in genetic association studies.
de Bakker PI, Yelensky R, Pe'er I, Gabriel SB, Daly MJ, Altshuler D. de Bakker PI, et al. Nat Genet. 2005 Nov;37(11):1217-23. doi: 10.1038/ng1669. Epub 2005 Oct 23. Nat Genet. 2005. PMID: 16244653
Conformer generation under restraints.
de Bakker PI, Furnham N, Blundell TL, DePristo MA. de Bakker PI, et al. Curr Opin Struct Biol. 2006 Apr;16(2):160-5. doi: 10.1016/j.sbi.2006.02.001. Epub 2006 Feb 17. Curr Opin Struct Biol. 2006. PMID: 16483766 Review.
A genome-wide association study of marginal zone lymphoma shows association to the HLA region.
Vijai J, Wang Z, Berndt SI, Skibola CF, Slager SL, de Sanjose S, Melbye M, Glimelius B, Bracci PM, Conde L, Birmann BM, Wang SS, Brooks-Wilson AR, Lan Q, de Bakker PI, Vermeulen RC, Portlock C, Ansell SM, Link BK, Riby J, North KE, Gu J, Hjalgrim H, Cozen W, Becker N, Teras LR, Spinelli JJ, Turner J, Zhang Y, Purdue MP, Giles GG, Kelly RS, Zeleniuch-Jacquotte A, Ennas MG, Monnereau A, Bertrand KA, Albanes D, Lightfoot T, Yeager M, Chung CC, Burdett L, Hutchinson A, Lawrence C, Montalvan R, Liang L, Huang J, Ma B, Villano DJ, Maria A, Corines M, Thomas T, Novak AJ, Dogan A, Liebow M, Thompson CA, Witzig TE, Habermann TM, Weiner GJ, Smith MT, Holly EA, Jackson RD, Tinker LF, Ye Y, Adami HO, Smedby KE, De Roos AJ, Hartge P, Morton LM, Severson RK, Benavente Y, Boffetta P, Brennan P, Foretova L, Maynadie M, McKay J, Staines A, Diver WR, Vajdic CM, Armstrong BK, Kricker A, Zheng T, Holford TR, Severi G, Vineis P, Ferri GM, Ricco R, Miligi L, Clavel J, Giovannucci E, Kraft P, Virtamo J, Smith A, Kane E, Roman E, Chiu BC, Fraumeni JF, Wu X, Cerhan JR, Offit K, Chanock SJ, Rothman N, Nieters A. Vijai J, et al. Nat Commun. 2015 Jan 8;6:5751. doi: 10.1038/ncomms6751. Nat Commun. 2015. PMID: 25569183 Free PMC article.
A novel MMP12 locus is associated with large artery atherosclerotic stroke using a genome-wide age-at-onset informed approach.
Traylor M, Mäkelä KM, Kilarski LL, Holliday EG, Devan WJ, Nalls MA, Wiggins KL, Zhao W, Cheng YC, Achterberg S, Malik R, Sudlow C, Bevan S, Raitoharju E; METASTROKE, International Stroke Genetics Consortium, Wellcome Trust Case Consortium 2 (WTCCC2), Oksala N, Thijs V, Lemmens R, Lindgren A, Slowik A, Maguire JM, Walters M, Algra A, Sharma P, Attia JR, Boncoraglio GB, Rothwell PM, de Bakker PI, Bis JC, Saleheen D, Kittner SJ, Mitchell BD, Rosand J, Meschia JF, Levi C, Dichgans M, Lehtimäki T, Lewis CM, Markus HS. Traylor M, et al. PLoS Genet. 2014 Jul 31;10(7):e1004469. doi: 10.1371/journal.pgen.1004469. eCollection 2014 Jul. PLoS Genet. 2014. PMID: 25078452 Free PMC article.
Stroke Genetics Network (SiGN) study: design and rationale for a genome-wide association study of ischemic stroke subtypes.
Meschia JF, Arnett DK, Ay H, Brown RD Jr, Benavente OR, Cole JW, de Bakker PI, Dichgans M, Doheny KF, Fornage M, Grewal RP, Gwinn K, Jern C, Conde JJ, Johnson JA, Jood K, Laurie CC, Lee JM, Lindgren A, Markus HS, McArdle PF, McClure LA, Mitchell BD, Schmidt R, Rexrode KM, Rich SS, Rosand J, Rothwell PM, Rundek T, Sacco RL, Sharma P, Shuldiner AR, Slowik A, Wassertheil-Smoller S, Sudlow C, Thijs VN, Woo D, Worrall BB, Wu O, Kittner SJ; NINDS SiGN Study. Meschia JF, et al. Stroke. 2013 Oct;44(10):2694-702. doi: 10.1161/STROKEAHA.113.001857. Epub 2013 Sep 10. Stroke. 2013. PMID: 24021684 Free PMC article. Clinical Trial.
Association study of common genetic variants and HIV-1 acquisition in 6,300 infected cases and 7,200 controls.
McLaren PJ, Coulonges C, Ripke S, van den Berg L, Buchbinder S, Carrington M, Cossarizza A, Dalmau J, Deeks SG, Delaneau O, De Luca A, Goedert JJ, Haas D, Herbeck JT, Kathiresan S, Kirk GD, Lambotte O, Luo M, Mallal S, van Manen D, Martinez-Picado J, Meyer L, Miro JM, Mullins JI, Obel N, O'Brien SJ, Pereyra F, Plummer FA, Poli G, Qi Y, Rucart P, Sandhu MS, Shea PR, Schuitemaker H, Theodorou I, Vannberg F, Veldink J, Walker BD, Weintrob A, Winkler CA, Wolinsky S, Telenti A, Goldstein DB, de Bakker PI, Zagury JF, Fellay J. McLaren PJ, et al. PLoS Pathog. 2013;9(7):e1003515. doi: 10.1371/journal.ppat.1003515. Epub 2013 Jul 25. PLoS Pathog. 2013. PMID: 23935489 Free PMC article.
Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci.
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. Zhernakova A, et al. PLoS Genet. 2011 Feb;7(2):e1002004. doi: 10.1371/journal.pgen.1002004. Epub 2011 Feb 24. PLoS Genet. 2011. PMID: 21383967 Free PMC article.
Meta-analysis of genome-wide association studies.
de Bakker PI, Neale BM, Daly MJ. de Bakker PI, et al. Cold Spring Harb Protoc. 2010 Jun;2010(6):pdb.top81. doi: 10.1101/pdb.top81. Cold Spring Harb Protoc. 2010. PMID: 20516189
Common genetic variation near the phospholamban gene is associated with cardiac repolarisation: meta-analysis of three genome-wide association studies.
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 PI; 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. Nolte IM, et al. PLoS One. 2009 Jul 9;4(7):e6138. doi: 10.1371/journal.pone.0006138. PLoS One. 2009. PMID: 19587794 Free PMC article.
Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates.
Palamara PF, Francioli LC, Wilton PR, Genovese G, Gusev A, Finucane HK, Sankararaman S; Genome of the Netherlands Consortium, Sunyaev SR, de Bakker PI, Wakeley J, Pe'er I, Price AL. Palamara PF, et al. Am J Hum Genet. 2015 Dec 3;97(6):775-89. doi: 10.1016/j.ajhg.2015.10.006. Epub 2015 Nov 12. Am J Hum Genet. 2015. PMID: 26581902 Free PMC article.
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