Publications

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Journal Article
Pomerantz MM, Ahmadiyeh N, Jia L, Herman P, Verzi MP, Doddapaneni H, Beckwith CA, Chan JA, Hills A, Davis M, Yao K, Kehoe SM, Lenz H-J, Haiman CA, Yan C, Henderson BE, Frenkel B, Barretina J, Bass A, Tabernero J, Baselga J, Regan MM, J Manak R, Shivdasani R, Coetzee GA, Freedman ML. The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer. Nat Genet. 2009 ;41(8):882-4.
Carvalho CMB, Pfundt R, King DA, Lindsay SJ, Zuccherato LW, Macville MVE, Liu P, Johnson D, Stankiewicz P, Brown CW, Shaw CA, Hurles ME, Ira G, Hastings PJ, Brunner HG, Lupski JR. Absence of heterozygosity due to template switching during replicative rearrangements. Am J Hum Genet. 2015 ;96(4):555-64.
Morrison AC, Bray MS, Folsom AR, Boerwinkle E. ADD1 460W allele associated with cardiovascular disease in hypertensive individuals. Hypertension. 2002 ;39(6):1053-7.
Onuchic V, Lurie E, Carrero I, Pawliczek P, Patel RY, Rozowsky J, Galeev T, Huang Z, Altshuler RC, Zhang Z, Harris RA, Coarfa C, Ashmore L, Bertol JW, Fakhouri WD, Yu F, Kellis M, Gerstein M, Milosavljevic A. Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci. Science. 2018 ;361(6409).
Li AH, Morrison AC, Kovar C, L Cupples A, Brody JA, Polfus LM, Yu B, Metcalf GA, Muzny DM, Veeraraghavan N, Liu X, Lumley T, Mosley TH, Gibbs RA, Boerwinkle E. Analysis of loss-of-function variants and 20 risk factor phenotypes in 8,554 individuals identifies loci influencing chronic disease. Nat Genet. 2015 ;47(6):640-2.
Doddapaneni H, Yao J, Lin H, M Walker A, Civerolo EL. Analysis of the genome-wide variations among multiple strains of the plant pathogenic bacterium Xylella fastidiosa. BMC Genomics. 2006 ;7:225.
Maxwell TJ, Ballantyne CM, Cheverud JM, Guild CS, Ndumele CE, Boerwinkle E. APOE modulates the correlation between triglycerides, cholesterol, and CHD through pleiotropy, and gene-by-gene interactions. Genetics. 2013 ;195(4):1397-405.
Klos K, Shimmin L, Ballantyne C, Boerwinkle E, Clark A, Coresh J, Hanis C, Liu K, Sayre S, Hixson J. APOE/C1/C4/C2 hepatic control region polymorphism influences plasma apoE and LDL cholesterol levels. Hum Mol Genet. 2008 ;17(13):2039-46.
Li D, Tanaka M, F Brunicardi C, Fisher WE, Gibbs RA, Gingras M-C. Association between somatostatin receptor 5 gene polymorphisms and pancreatic cancer risk and survival. Cancer. 2011 ;117(13):2863-72.
Schick UM, Auer PL, Bis JC, Lin H, Wei P, Pankratz N, Lange LA, Brody J, Stitziel NO, Kim DS, Carlson CS, Fornage M, Haessler J, Hsu L, Jackson RD, Kooperberg C, Leal SM, Psaty BM, Boerwinkle E, Tracy R, Ardissino D, Shah S, Willer C, Loos R, Melander O, McPherson R, Hovingh K, Reilly M, Watkins H, Girelli D, Fontanillas P, Chasman DI, Gabriel SB, Gibbs RA, Nickerson DA, Kathiresan S, Peters U, Dupuis J, Wilson JG, Rich SS, Morrison AC, Benjamin EJ, Gross MD, Reiner AP. Association of exome sequences with plasma C-reactive protein levels in >9000 participants. Hum Mol Genet. 2015 ;24(2):559-71.
Yu B, Barbalic M, Brautbar A, Nambi V, Hoogeveen RC, Tang W, Mosley TH, Rotter JI, deFilippi CR, O'Donnell CJ, Kathiresan S, Rice K, Heckbert SR, Ballantyne CM, Psaty BM, Boerwinkle E. Association of genome-wide variation with highly sensitive cardiac troponin-T levels in European Americans and Blacks: a meta-analysis from atherosclerosis risk in communities and cardiovascular health studies. Circ Cardiovasc Genet. 2013 ;6(1):82-8.
Cornes BK, Brody JA, Nikpoor N, Morrison AC, Chu H, Ahn BSoo, Wang S, Dauriz M, Barzilay JI, Dupuis J, Florez JC, Coresh J, Gibbs RA, Kao WHLinda, Liu C-T, McKnight B, Muzny DM, Pankow JS, Reid JG, White CC, Johnson AD, Wong TY, Psaty BM, Boerwinkle E, Rotter JI, Siscovick DS, Sladek R, Meigs JB. Association of levels of fasting glucose and insulin with rare variants at the chromosome 11p11.2-MADD locus: Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium Targeted Sequencing Study. Circ Cardiovasc Genet. 2014 ;7(3):374-382.
Ueda H, Howson JMM, Esposito L, Heward J, Snook H, Chamberlain G, Rainbow DB, Hunter KMD, Smith AN, Di Genova G, Herr MH, Dahlman I, Payne F, Smyth D, Lowe C, Twells RCJ, Howlett S, Healy B, Nutland S, Rance HE, Everett V, Smink LJ, Lam AC, Cordell HJ, Walker NM, Bordin C, Hulme J, Motzo C, Cucca F, J Hess F, Metzker ML, Rogers J, Gregory S, Allahabadia A, Nithiyananthan R, Tuomilehto-Wolf E, Tuomilehto J, Bingley P, Gillespie KM, Undlien DE, Rønningen KS, Guja C, Ionescu-Tîrgovişte C, Savage DA, A Maxwell P, Carson DJ, Patterson CC, Franklyn JA, Clayton DG, Peterson LB, Wicker LS, Todd JA, Gough SCL. Association of the T-cell regulatory gene CTLA4 with susceptibility to autoimmune disease. Nature. 2003 ;423(6939):506-11.
Bis JC, DeStefano A, Liu X, Brody JA, Choi SHoan, Verhaaren BFJ, Debette S, M Ikram A, Shahar E, Butler KR, Gottesman RF, Muzny DM, Kovar CL, Psaty BM, Hofman A, Lumley T, Gupta M, Wolf PA, van Duijn C, Gibbs RA, Mosley TH, Longstreth WT, Boerwinkle E, Seshadri S, Fornage M. Associations of NINJ2 sequence variants with incident ischemic stroke in the Cohorts for Heart and Aging in Genomic Epidemiology (CHARGE) consortium. PLoS One. 2014 ;9(6):e99798.
Voidonikolas G, Kreml SS, Chen C, Fisher WE, F Brunicardi C, Gibbs RA, Gingras M-C. Basic principles and technologies for deciphering the genetic map of cancer. World J Surg. 2009 ;33(4):615-29.
Sedlazeck FJ, Talloji P, von Haeseler A, Bachmair A. Benefit-of-doubt (BOD) scoring: a sequencing-based method for SNP candidate assessment from high to medium read number data sets. Genomics. 2013 ;101(3):204-9.
Grove ML, Yu B, Cochran BJ, Haritunians T, Bis JC, Taylor KD, Hansen M, Borecki IB, L Cupples A, Fornage M, Gudnason V, Harris TB, Kathiresan S, Kraaij R, Launer LJ, Levy D, Liu Y, Mosley T, Peloso GM, Psaty BM, Rich SS, Rivadeneira F, Siscovick DS, Smith AV, Uitterlinden A, van Duijn CM, Wilson JG, O'Donnell CJ, Rotter JI, Boerwinkle E. Best practices and joint calling of the HumanExome BeadChip: the CHARGE Consortium. PLoS One. 2013 ;8(7):e68095.
Fawcett GL, Raveendran M, Deiros DRio, Chen D, Yu F, Harris RA, Ren Y, Muzny DM, Reid JG, Wheeler DA, Worley KC, Shelton SE, Kalin NH, Milosavljevic A, Gibbs RA, Rogers J. Characterization of single-nucleotide variation in Indian-origin rhesus macaques (Macaca mulatta). BMC Genomics. 2011 ;12:311.
Lu JT, Wang Y, Gibbs RA, Yu F. Characterizing linkage disequilibrium and evaluating imputation power of human genomic insertion-deletion polymorphisms. Genome Biol. 2012 ;13(2):R15.
Wang QY, Song J, Gibbs RA, Boerwinkle E, Dong JF, Yu FL. Characterizing polymorphisms and allelic diversity of von Willebrand factor gene in the 1000 Genomes. J Thromb Haemost. 2013 ;11(2):261-9.
Weir BA, Woo MS, Getz G, Perner S, Ding L, Beroukhim R, Lin WM, Province MA, Kraja A, Johnson LA, Shah K, Sato M, Thomas RK, Barletta JA, Borecki IB, Broderick S, Chang AC, Chiang DY, Chirieac LR, Cho J, Fujii Y, Gazdar AF, Giordano T, Greulich H, Hanna M, Johnson BE, Kris MG, Lash A, Lin L, Lindeman N, Mardis ER, McPherson JD, Minna JD, Morgan MB, Nadel M, Orringer MB, Osborne JR, Ozenberger B, Ramos AH, Robinson J, Roth JA, Rusch V, Sasaki H, Shepherd F, Sougnez C, Spitz MR, Tsao M-S, Twomey D, Verhaak RGW, Weinstock GM, Wheeler DA, Winckler W, Yoshizawa A, Yu S, Zakowski MF, Zhang Q, Beer DG, Wistuba II, Watson MA, Garraway LA, Ladanyi M, Travis WD, Pao W, Rubin MA, Gabriel SB, Gibbs RA, Varmus HE, Wilson RK, Lander ES, Meyerson M. Characterizing the cancer genome in lung adenocarcinoma. Nature. 2007 ;450(7171):893-8.
Baud A, Hermsen R, Guryev V, Stridh P, Graham D, McBride MW, Foroud T, Calderari S, Diez M, Ockinger J, Beyeen AD, Gillett A, Abdelmagid N, Guerreiro-Cacais AOrtlieb, Jagodic M, Tuncel J, Norin U, Beattie E, Huynh N, Miller WH, Koller DL, Alam I, Falak S, Osborne-Pellegrin M, Martinez-Membrives E, Canete T, Blazquez G, Vicens-Costa E, Mont-Cardona C, Diaz-Moran S, Tobena A, Hummel O, Zelenika D, Saar K, Patone G, Bauerfeind A, Bihoreau M-T, Heinig M, Lee Y-A, Rintisch C, Schulz H, Wheeler DA, Worley KC, Muzny DM, Gibbs RA, Lathrop M, Lansu N, Toonen P, Ruzius FPaul, de Bruijn E, Hauser H, Adams DJ, Keane T, Atanur SS, Aitman TJ, Flicek P, Malinauskas T, E Jones Y, Ekman D, Lopez-Aumatell R, Dominiczak AF, Johannesson M, Holmdahl R, Olsson T, Gauguier D, Hübner N, Fernandez-Teruel A, Cuppen E, Mott R, Flint J. Combined sequence-based and genetic mapping analysis of complex traits in outbred rats. Nat Genet. 2013 ;45(7):767-75.
Yu F, R Hill S, Schaffner SF, Sabeti PC, Wang ET, Mignault AA, Ferland RJ, Moyzis RK, Walsh CA, Reich D. Comment on "Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens". Science. 2007 ;316(5823):370.
Khanna H, Davis EE, Murga-Zamalloa CA, Estrada-Cuzcano A, Lopez I, Hollander AI den, Zonneveld MN, Othman MI, Waseem N, Chakarova CF, Maubaret C, Diaz-Font A, MacDonald I, Muzny DM, Wheeler DA, Morgan M, Lewis LR, Logan CV, Tan PL, Beer MA, Inglehearn CF, Lewis RA, Jacobson SG, Bergmann C, Beales PL, Attié-Bitach T, Johnson CA, Otto EA, Bhattacharya SS, Hildebrandt F, Gibbs RA, Koenekoop RK, Swaroop A, Katsanis N. A common allele in RPGRIP1L is a modifier of retinal degeneration in ciliopathies. Nat Genet. 2009 ;41(6):739-45.
Maheshwari M, Shi J, Badner JA, Skol A, Willour VL, Muzny DM, Wheeler DA, Gerald FR, Detera-Wadleigh S, McMahon FJ, Potash JB, Gershon ES, Liu C, Gibbs RA. Common and rare variants of DAOA in bipolar disorder. Am J Med Genet B Neuropsychiatr Genet. 2009 ;150B(7):960-6.