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Dan Liviu Nicolae

TitleProfessor
InstitutionUniversity of Chicago
DepartmentMedicine-Genetic Medicine
AddressChicago IL 60637
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    Collapse Overview 
    Collapse overview
    My group works in the areas of statistical genetics and mathematical statistics. Our investigations are motivated by applications to genetics and genomics studies on common/complex diseases, with a focus on asthma. Statistical genetics problems of interest include developing of statistical methodology for sequencing-based data, microbiome,large-scale data integration, networks and systems biology.


    Collapse Biography 
    Collapse education and training
    University of ChicagoPhD06/1999Statistics

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    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. McKennan C, Nicolae D. Accounting for unobserved covariates with varying degrees of estimability in high-dimensional biological data. Biometrika. 2019 Dec; 106(4):823-840. PMID: 31754283.
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    2. Daya M, Rafaels N, Brunetti TM, Chavan S, Levin AM, Shetty A, Gignoux CR, Boorgula MP, Wojcik G, Campbell M, Vergara C, Torgerson DG, Ortega VE, Doumatey A, Johnston HR, Acevedo N, Araujo MI, Avila PC, Belbin G, Bleecker E, Bustamante C, Caraballo L, Cruz A, Dunston GM, Eng C, Faruque MU, Ferguson TS, Figueiredo C, Ford JG, Gan W, Gourraud PA, Hansel NN, Hernandez RD, Herrera-Paz EF, Jiménez S, Kenny EE, Knight-Madden J, Kumar R, Lange LA, Lange EM, Lizee A, Maul P, Maul T, Mayorga A, Meyers D, Nicolae DL, O'Connor TD, Oliveira RR, Olopade CO, Olopade O, Qin ZS, Rotimi C, Vince N, Watson H, Wilks RJ, Wilson JG, Salzberg S, Ober C, Burchard EG, Williams LK, Beaty TH, Taub MA, Ruczinski I, Mathias RA, Barnes KC. Author Correction: Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations. Nat Commun. 2019 Sep 04; 10(1):4082. PMID: 31484942.
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    3. Pividori M, Schoettler N, Nicolae DL, Ober C, Im HK. Shared and distinct genetic risk factors for childhood-onset and adult-onset asthma: genome-wide and transcriptome-wide studies. Lancet Respir Med. 2019 Jun; 7(6):509-522. PMID: 31036433.
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    4. Daya M, Rafaels N, Brunetti TM, Chavan S, Levin AM, Shetty A, Gignoux CR, Boorgula MP, Wojcik G, Campbell M, Vergara C, Torgerson DG, Ortega VE, Doumatey A, Johnston HR, Acevedo N, Araujo MI, Avila PC, Belbin G, Bleecker E, Bustamante C, Caraballo L, Cruz A, Dunston GM, Eng C, Faruque MU, Ferguson TS, Figueiredo C, Ford JG, Gan W, Gourraud PA, Hansel NN, Hernandez RD, Herrera-Paz EF, Jiménez S, Kenny EE, Knight-Madden J, Kumar R, Lange LA, Lange EM, Lizee A, Maul P, Maul T, Mayorga A, Meyers D, Nicolae DL, O'Connor TD, Oliveira RR, Olopade CO, Olopade O, Qin ZS, Rotimi C, Vince N, Watson H, Wilks RJ, Wilson JG, Salzberg S, Ober C, Burchard EG, Williams LK, Beaty TH, Taub MA, Ruczinski I, Mathias RA, Barnes KC. Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations. Nat Commun. 2019 02 20; 10(1):880. PMID: 30787307.
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    5. Sherman RM, Forman J, Antonescu V, Puiu D, Daya M, Rafaels N, Boorgula MP, Chavan S, Vergara C, Ortega VE, Levin AM, Eng C, Yazdanbakhsh M, Wilson JG, Marrugo J, Lange LA, Williams LK, Watson H, Ware LB, Olopade CO, Olopade O, Oliveira RR, Ober C, Nicolae DL, Meyers DA, Mayorga A, Knight-Madden J, Hartert T, Hansel NN, Foreman MG, Ford JG, Faruque MU, Dunston GM, Caraballo L, Burchard EG, Bleecker ER, Araujo MI, Herrera-Paz EF, Campbell M, Foster C, Taub MA, Beaty TH, Ruczinski I, Mathias RA, Barnes KC, Salzberg SL. Author Correction: Assembly of a pan-genome from deep sequencing of 910 humans of African descent. Nat Genet. 2019 02; 51(2):364. PMID: 30647471.
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    6. Barbeira AN, Pividori M, Zheng J, Wheeler HE, Nicolae DL, Im HK. Integrating predicted transcriptome from multiple tissues improves association detection. PLoS Genet. 2019 01; 15(1):e1007889. PMID: 30668570.
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    7. Mozaffari SV, DeCara JM, Shah SJ, Sidore C, Fiorillo E, Cucca F, Lang RM, Nicolae DL, Ober C. Parent-of-origin effects on quantitative phenotypes in a large Hutterite pedigree. Commun Biol. 2019; 2:28. PMID: 30675526.
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    8. Sherman RM, Forman J, Antonescu V, Puiu D, Daya M, Rafaels N, Boorgula MP, Chavan S, Vergara C, Ortega VE, Levin AM, Eng C, Yazdanbakhsh M, Wilson JG, Marrugo J, Lange LA, Williams LK, Watson H, Ware LB, Olopade CO, Olopade O, Oliveira RR, Ober C, Nicolae DL, Meyers DA, Mayorga A, Knight-Madden J, Hartert T, Hansel NN, Foreman MG, Ford JG, Faruque MU, Dunston GM, Caraballo L, Burchard EG, Bleecker ER, Araujo MI, Herrera-Paz EF, Campbell M, Foster C, Taub MA, Beaty TH, Ruczinski I, Mathias RA, Barnes KC, Salzberg SL. Assembly of a pan-genome from deep sequencing of 910 humans of African descent. Nat Genet. 2019 01; 51(1):30-35. PMID: 30455414.
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    9. Croteau-Chonka DC, Chen Z, Barnes KC, Barraza-Villarreal A, Celedón JC, Gauderman WJ, Gilliland FD, Krishnan JA, Liu AH, London SJ, Martinez FD, Millstein J, Naureckas ET, Nicolae DL, White SR, Ober C, Weiss ST, Raby BA. Gene Coexpression Networks in Whole Blood Implicate Multiple Interrelated Molecular Pathways in Obesity in People with Asthma. Obesity (Silver Spring). 2018 12; 26(12):1938-1948. PMID: 30358166.
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    10. Mozaffari SV, Stein MM, Magnaye KM, Nicolae DL, Ober C. Parent of origin gene expression in a founder population identifies two new candidate imprinted genes at known imprinted regions. PLoS One. 2018; 13(9):e0203906. PMID: 30204804.
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    11. Gignoux CR, Torgerson DG, Pino-Yanes M, Uricchio LH, Galanter J, Roth LA, Eng C, Hu D, Nguyen EA, Huntsman S, Mathias RA, Kumar R, Rodriguez-Santana J, Thakur N, Oh SS, McGarry M, Moreno-Estrada A, Sandoval K, Winkler CA, Seibold MA, Padhukasahasram B, Conti DV, Farber HJ, Avila P, Brigino-Buenaventura E, Lenoir M, Meade K, Serebrisky D, Borrell LN, Rodriguez-Cintron W, Thyne S, Joubert BR, Romieu I, Levin AM, Sienra-Monge JJ, Del Rio-Navarro BE, Gan W, Raby BA, Weiss ST, Bleecker E, Meyers DA, Martinez FJ, Gauderman WJ, Gilliland F, London SJ, Bustamante CD, Nicolae DL, Ober C, Sen S, Barnes K, Williams LK, Hernandez RD, Burchard EG. An admixture mapping meta-analysis implicates genetic variation at 18q21 with asthma susceptibility in Latinos. J Allergy Clin Immunol. 2019 Mar; 143(3):957-969. PMID: 30201514.
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    12. Waage J, Standl M, Curtin JA, Jessen LE, Thorsen J, Tian C, Schoettler N. Author Correction: Genome-wide association and HLA fine-mapping studies identify risk loci and genetic pathways underlying allergic rhinitis. Nat Genet. 2018 09; 50(9):1343. PMID: 30116036.
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    13. Waage J, Standl M, Curtin JA, Jessen LE, Thorsen J, Tian C, Schoettler N. Genome-wide association and HLA fine-mapping studies identify risk loci and genetic pathways underlying allergic rhinitis. Nat Genet. 2018 08; 50(8):1072-1080. PMID: 30013184.
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    14. Gamazon ER, Segrè AV, van de Bunt M, Wen X, Xi HS, Hormozdiari F, Ongen H, Konkashbaev A, Derks EM, Aguet F, Quan J. Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation. Nat Genet. 2018 07; 50(7):956-967. PMID: 29955180.
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    15. Barbeira AN, Dickinson SP, Bonazzola R, Zheng J, Wheeler HE, Torres JM, Torstenson ES, Shah KP, Garcia T, Edwards TL, Stahl EA, Huckins LM. Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics. Nat Commun. 2018 05 08; 9(1):1825. PMID: 29739930.
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    16. Kothari PH, Qiu W, Croteau-Chonka DC, Martinez FD, Liu AH, Lemanske RF, Ober C, Krishnan JA, Nicolae DL, Barnes KC, London SJ, Barraza-Villarreal A, White SR, Naureckas ET, Millstein J, Gauderman WJ, Gilliland FD, Carey VJ, Weiss ST, Raby BA. Role of local CpG DNA methylation in mediating the 17q21 asthma susceptibility gasdermin B (GSDMB)/ORMDL sphingolipid biosynthesis regulator 3 (ORMDL3) expression quantitative trait locus. J Allergy Clin Immunol. 2018 06; 141(6):2282-2286.e6. PMID: 29374573.
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    17. Stein MM, Thompson EE, Schoettler N, Helling BA, Magnaye KM, Stanhope C, Igartua C, Morin A, Washington C, Nicolae D, Bønnelykke K, Ober C. A decade of research on the 17q12-21 asthma locus: Piecing together the puzzle. J Allergy Clin Immunol. 2018 09; 142(3):749-764.e3. PMID: 29307657.
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    18. Jun G, Manning A, Almeida M, Zawistowski M, Wood AR, Teslovich TM, Fuchsberger C, Feng S, Cingolani P, Gaulton KJ, Dyer T, Blackwell TW, Chen H, Chines PS, Choi S, Churchhouse C, Fontanillas P, King R, Lee S, Lincoln SE, Trubetskoy V, DePristo M, Fingerlin T, Grossman R, Grundstad J, Heath A, Kim J, Kim YJ, Laramie J, Lee J, Li H, Liu X, Livne O, Locke AE, Maller J, Mazur A, Morris AP, Pollin TI, Ragona D, Reich D, Rivas MA, Scott LJ, Sim X, Tearle RG, Teo YY, Williams AL, Zöllner S, Curran JE, Peralta J, Akolkar B, Bell GI, Burtt NP, Cox NJ, Florez JC, Hanis CL, McKeon C, Mohlke KL, Seielstad M, Wilson JG, Atzmon G, Below JE, Dupuis J, Nicolae DL, Lehman D, Park T, Won S, Sladek R, Altshuler D, McCarthy MI, Duggirala R, Boehnke M, Frayling TM, Abecasis GR, Blangero J. Evaluating the contribution of rare variants to type 2 diabetes and related traits using pedigrees. Proc Natl Acad Sci U S A. 2018 01 09; 115(2):379-384. PMID: 29279374.
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    19. Demenais F, Margaritte-Jeannin P, Barnes KC, Cookson WOC, Altmüller J, Ang W, Barr RG, Beaty TH, Becker AB, Beilby J, Bisgaard H, Bjornsdottir US, Bleecker E, Bønnelykke K, Boomsma DI, Bouzigon E, Brightling CE, Brossard M, Brusselle GG, Burchard E, Burkart KM, Bush A, Chan-Yeung M, Chung KF, Couto Alves A, Curtin JA, Custovic A, Daley D, de Jongste JC, Del-Rio-Navarro BE, Donohue KM, Duijts L, Eng C, Eriksson JG, Farrall M, Fedorova Y, Feenstra B, Ferreira MA. Multiancestry association study identifies new asthma risk loci that colocalize with immune-cell enhancer marks. Nat Genet. 2018 01; 50(1):42-53. PMID: 29273806.
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    20. Igartua C, Mozaffari SV, Nicolae DL, Ober C. Rare non-coding variants are associated with plasma lipid traits in a founder population. Sci Rep. 2017 11 27; 7(1):16415. PMID: 29180722.
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    21. Igartua C, Davenport ER, Gilad Y, Nicolae DL, Pinto J, Ober C. Host genetic variation in mucosal immunity pathways influences the upper airway microbiome. Microbiome. 2017 02 01; 5(1):16. PMID: 28143570.
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    22. Croteau-Chonka DC, Qiu W, Martinez FD, Strunk RC, Lemanske RF, Liu AH, Gilliland FD, Millstein J, Gauderman WJ, Ober C, Krishnan JA, White SR, Naureckas ET, Nicolae DL, Barnes KC, London SJ, Barraza-Villarreal A, Carey VJ, Weiss ST, Raby BA. Gene Expression Profiling in Blood Provides Reproducible Molecular Insights into Asthma Control. Am J Respir Crit Care Med. 2017 01 15; 195(2):179-188. PMID: 27494826.
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    23. Nicodemus-Johnson J, Myers RA, Sakabe NJ, Sobreira DR, Hogarth DK, Naureckas ET, Sperling AI, Solway J, White SR, Nobrega MA, Nicolae DL, Gilad Y, Ober C. DNA methylation in lung cells is associated with asthma endotypes and genetic risk. JCI Insight. 2016 12 08; 1(20):e90151. PMID: 27942592.
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    24. Wheeler HE, Shah KP, Brenner J, Garcia T, Aquino-Michaels K. Survey of the Heritability and Sparse Architecture of Gene Expression Traits across Human Tissues. PLoS Genet. 2016 Nov; 12(11):e1006423. PMID: 27835642.
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    25. Mathias RA, Taub MA, Gignoux CR, Fu W, Musharoff S, O'Connor TD, Vergara C, Torgerson DG, Pino-Yanes M, Shringarpure SS, Huang L, Rafaels N, Boorgula MP, Johnston HR, Ortega VE, Levin AM, Song W, Torres R, Padhukasahasram B, Eng C, Mejia-Mejia DA, Ferguson T, Qin ZS, Scott AF, Yazdanbakhsh M, Wilson JG, Marrugo J, Lange LA, Kumar R, Avila PC, Williams LK, Watson H, Ware LB, Olopade C, Olopade O, Oliveira R, Ober C, Nicolae DL, Meyers D, Mayorga A, Knight-Madden J, Hartert T, Hansel NN, Foreman MG, Ford JG, Faruque MU, Dunston GM, Caraballo L, Burchard EG, Bleecker E, Araujo MI, Herrera-Paz EF, Gietzen K, Grus WE, Bamshad M, Bustamante CD, Kenny EE, Hernandez RD, Beaty TH, Ruczinski I, Akey J. A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome. Nat Commun. 2016 10 11; 7:12522. PMID: 27725671.
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    26. Nicolae DL. Association Tests for Rare Variants. Annu Rev Genomics Hum Genet. 2016 08 31; 17:117-30. PMID: 27147090.
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    27. Wang J, Gamazon ER, Pierce BL, Stranger BE, Im HK, Gibbons RD, Cox NJ, Nicolae DL, Chen LS. Imputing Gene Expression in Uncollected Tissues Within and Beyond GTEx. Am J Hum Genet. 2016 Apr 07; 98(4):697-708. PMID: 27040689.
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    28. Yan X, Chu JH, Gomez J, Koenigs M, Holm C, He X, Perez MF, Zhao H, Mane S, Martinez FD, Ober C, Nicolae DL, Barnes KC, London SJ, Gilliland F, Weiss ST, Raby BA, Cohn L, Chupp GL. Noninvasive Analysis of the Sputum Transcriptome Discriminates Clinical Phenotypes of Asthma. Ann Am Thorac Soc. 2016 Mar; 13 Suppl 1:S104-5. PMID: 27027945.
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    29. Nicodemus-Johnson J, Naughton KA, Sudi J, Hogarth K, Naurekas ET, Nicolae DL, Sperling AI, Solway J, White SR, Ober C. Genome-Wide Methylation Study Identifies an IL-13-induced Epigenetic Signature in Asthmatic Airways. Am J Respir Crit Care Med. 2016 Feb 15; 193(4):376-85. PMID: 26474238.
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    30. Loisel DA, Du G, Ahluwalia TS, Tisler CJ, Evans MD, Myers RA, Gangnon RE, Kreiner-Møller E, Bønnelykke K, Bisgaard H, Jackson DJ, Lemanske RF, Nicolae DL, Gern JE, Ober C. Genetic associations with viral respiratory illnesses and asthma control in children. Clin Exp Allergy. 2016 Jan; 46(1):112-24. PMID: 26399222.
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    31. Liu Q, Chen LS, Nicolae DL, Pierce BL. A unified set-based test with adaptive filtering for gene-environment interaction analyses. Biometrics. 2016 06; 72(2):629-38. PMID: 26496228.
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    32. Gamazon ER, Wheeler HE, Shah KP, Mozaffari SV, Aquino-Michaels K, Carroll RJ, Eyler AE, Denny JC. A gene-based association method for mapping traits using reference transcriptome data. Nat Genet. 2015 Sep; 47(9):1091-8. PMID: 26258848.
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    33. Brehm JM, Ramratnam SK, Tse SM, Croteau-Chonka DC, Pino-Yanes M, Rosas-Salazar C, Litonjua AA, Raby BA, Boutaoui N, Han YY, Chen W, Forno E, Marsland AL, Nugent NR, Eng C, Colón-Semidey A, Alvarez M, Acosta-Pérez E, Spear ML, Martinez FD, Avila L, Weiss ST, Soto-Quiros M, Ober C, Nicolae DL, Barnes KC, Lemanske RF, Strunk RC, Liu A, London SJ, Gilliland F, Sleiman P, March M, Hakonarson H, Duan QL, Kolls JK, Fritz GK, Hu D, Fani N, Stevens JS, Almli LM, Burchard EG, Shin J, McQuaid EL, Ressler K, Canino G, Celedón JC. Stress and Bronchodilator Response in Children with Asthma. Am J Respir Crit Care Med. 2015 Jul 01; 192(1):47-56. PMID: 25918834.
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    34. Yan X, Chu JH, Gomez J, Koenigs M, Holm C, He X, Perez MF, Zhao H, Mane S, Martinez FD, Ober C, Nicolae DL, Barnes KC, London SJ, Gilliland F, Weiss ST, Raby BA, Cohn L, Chupp GL. Noninvasive analysis of the sputum transcriptome discriminates clinical phenotypes of asthma. Am J Respir Crit Care Med. 2015 May 15; 191(10):1116-25. PMID: 25763605.
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    35. Kim KW, Myers RA, Lee JH, Igartua C, Lee KE, Kim YH, Kim EJ, Yoon D, Lee JS, Hirota T, Tamari M, Takahashi A, Kubo M, Choi JM, Kim KE, Nicolae DL, Ober C, Sohn MH. Genome-wide association study of recalcitrant atopic dermatitis in Korean children. J Allergy Clin Immunol. 2015 Sep; 136(3):678-684.e4. PMID: 25935106.
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    36. Livne OE, Han L, Alkorta-Aranburu G, Wentworth-Sheilds W, Abney M, Ober C, Nicolae DL. PRIMAL: Fast and accurate pedigree-based imputation from sequence data in a founder population. PLoS Comput Biol. 2015 Mar; 11(3):e1004139. PMID: 25735005.
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    37. Igartua C, Myers RA, Mathias RA, Pino-Yanes M, Eng C, Graves PE, Levin AM, Del-Rio-Navarro BE, Jackson DJ, Livne OE, Rafaels N, Edlund CK, Yang JJ, Huntsman S, Salam MT, Romieu I, Mourad R, Gern JE, Lemanske RF, Wyss A, Hoppin JA, Barnes KC, Burchard EG, Gauderman WJ, Martinez FD, Raby BA, Weiss ST, Williams LK, London SJ, Gilliland FD, Nicolae DL, Ober C. Ethnic-specific associations of rare and low-frequency DNA sequence variants with asthma. Nat Commun. 2015 Jan 16; 6:5965. PMID: 25591454.
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    38. Pino-Yanes M, Gignoux CR, Galanter JM, Levin AM, Campbell CD, Eng C, Huntsman S, Nishimura KK, Gourraud PA, Mohajeri K, O'Roak BJ, Hu D, Mathias RA, Nguyen EA, Roth LA, Padhukasahasram B, Moreno-Estrada A, Sandoval K, Winkler CA, Lurmann F, Davis A, Farber HJ, Meade K, Avila PC, Serebrisky D, Chapela R, Ford JG, Lenoir MA, Thyne SM, Brigino-Buenaventura E, Borrell LN, Rodriguez-Cintron W, Sen S, Kumar R, Rodriguez-Santana JR, Bustamante CD, Martinez FD, Raby BA, Weiss ST, Nicolae DL, Ober C, Meyers DA, Bleecker ER, Mack SJ, Hernandez RD, Eichler EE, Barnes KC, Williams LK, Torgerson DG, Burchard EG. Genome-wide association study and admixture mapping reveal new loci associated with total IgE levels in Latinos. J Allergy Clin Immunol. 2015 Jun; 135(6):1502-10. PMID: 25488688.
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    39. Bunyavanich S, Schadt EE, Himes BE, Lasky-Su J, Qiu W, Lazarus R, Ziniti JP, Cohain A, Linderman M, Torgerson DG, Eng CS, Pino-Yanes M, Padhukasahasram B, Yang JJ, Mathias RA, Beaty TH, Li X, Graves P, Romieu I, Navarro Bdel R, Salam MT, Vora H, Nicolae DL, Ober C, Martinez FD, Bleecker ER, Meyers DA, Gauderman WJ, Gilliland F, Burchard EG, Barnes KC, Williams LK, London SJ, Zhang B, Raby BA, Weiss ST. Integrated genome-wide association, coexpression network, and expression single nucleotide polymorphism analysis identifies novel pathway in allergic rhinitis. BMC Med Genomics. 2014 Aug 02; 7:48. PMID: 25085501.
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    40. Breton CV, Siegmund KD, Joubert BR, Wang X, Qui W, Carey V, Nystad W, Håberg SE, Ober C, Nicolae D, Barnes KC, Martinez F, Liu A, Lemanske R, Strunk R, Weiss S, London S, Gilliland F, Raby B. Prenatal tobacco smoke exposure is associated with childhood DNA CpG methylation. PLoS One. 2014; 9(6):e99716. PMID: 24964093.
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    41. Sharma S, Zhou X, Thibault DM, Himes BE, Liu A, Szefler SJ, Strunk R, Castro M, Hansel NN, Diette GB, Vonakis BM, Adkinson NF, Avila L, Soto-Quiros M, Barraza-Villareal A, Lemanske RF, Solway J, Krishnan J, White SR, Cheadle C, Berger AE, Fan J, Boorgula MP, Nicolae D, Gilliland F, Barnes K, London SJ, Martinez F, Ober C, Celedón JC, Carey VJ, Weiss ST, Raby BA. A genome-wide survey of CD4(+) lymphocyte regulatory genetic variants identifies novel asthma genes. J Allergy Clin Immunol. 2014 Nov; 134(5):1153-62. PMID: 24934276.
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    42. King CR, Nicolae DL. GWAS to Sequencing: Divergence in Study Design and Analysis. Genes (Basel). 2014 May 28; 5(2):460-76. PMID: 24879455.
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    43. Myers RA, Scott NM, Gauderman WJ, Qiu W, Mathias RA, Romieu I, Levin AM, Pino-Yanes M, Graves PE, Villarreal AB, Beaty TH, Carey VJ, Croteau-Chonka DC, del Rio Navarro B, Edlund C, Hernandez-Cadena L, Navarro-Olivos E, Padhukasahasram B, Salam MT, Torgerson DG, Van den Berg DJ, Vora H, Bleecker ER, Meyers DA, Williams LK, Martinez FD, Burchard EG, Barnes KC, Gilliland FD, Weiss ST, London SJ, Raby BA, Ober C, Nicolae DL. Genome-wide interaction studies reveal sex-specific asthma risk alleles. Hum Mol Genet. 2014 Oct 01; 23(19):5251-9. PMID: 24824216.
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    44. Ahsan H, Halpern J, Kibriya MG, Pierce BL, Tong L, Gamazon E, McGuire V, Felberg A, Shi J, Jasmine F, Roy S, Brutus R, Argos M, Melkonian S, Chang-Claude J, Andrulis I, Hopper JL, John EM, Malone K, Ursin G, Gammon MD, Thomas DC, Seminara D, Casey G, Knight JA, Southey MC, Giles GG, Santella RM, Lee E, Conti D, Duggan D, Gallinger S, Haile R, Jenkins M, Lindor NM, Newcomb P, Michailidou K, Apicella C, Park DJ, Peto J, Fletcher O, dos Santos Silva I, Lathrop M, Hunter DJ, Chanock SJ, Meindl A, Schmutzler RK, Müller-Myhsok B, Lochmann M, Beckmann L, Hein R, Makalic E, Schmidt DF, Bui QM, Stone J, Flesch-Janys D, Dahmen N, Nevanlinna H, Aittomäki K, Blomqvist C, Hall P, Czene K, Irwanto A, Liu J, Rahman N, Turnbull C. A genome-wide association study of early-onset breast cancer identifies PFKM as a novel breast cancer gene and supports a common genetic spectrum for breast cancer at any age. Cancer Epidemiol Biomarkers Prev. 2014 Apr; 23(4):658-69. PMID: 24493630.
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    45. Blair DR, Lyttle CS, Mortensen JM, Bearden CF, Jensen AB, Khiabanian H, Melamed R, Rabadan R, Bernstam EV, Brunak S, Jensen LJ, Nicolae D, Shah NH, Grossman RL, Cox NJ, White KP, Rzhetsky A. A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk. Cell. 2013 Sep 26; 155(1):70-80. PMID: 24074861.
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    46. Hernandez W, Gamazon ER, Aquino-Michaels K, Patel S, O'Brien TJ, Harralson AF, Kittles RA, Barbour A, Tuck M, McIntosh SD, Douglas JN, Nicolae D, Cavallari LH, Perera MA. Ethnicity-specific pharmacogenetics: the case of warfarin in African Americans. Pharmacogenomics J. 2014 Jun; 14(3):223-8. PMID: 24018621.
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    47. Yao TC, Du G, Han L, Sun Y, Hu D, Yang JJ, Mathias R, Roth LA, Rafaels N, Thompson EE, Loisel DA, Anderson R, Eng C, Arruabarrena Orbegozo M, Young M, Klocksieben JM, Anderson E, Shanovich K, Lester LA, Williams LK, Barnes KC, Burchard EG, Nicolae DL, Abney M, Ober C. Genome-wide association study of lung function phenotypes in a founder population. J Allergy Clin Immunol. 2014 Jan; 133(1):248-55.e1-10. PMID: 23932459.
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    48. Noth I, Zhang Y, Ma SF, Flores C, Barber M, Huang Y, Broderick SM, Wade MS, Hysi P, Scuirba J, Richards TJ, Juan-Guardela BM, Vij R, Han MK, Martinez FJ, Kossen K, Seiwert SD, Christie JD, Nicolae D, Kaminski N, Garcia JGN. Genetic variants associated with idiopathic pulmonary fibrosis susceptibility and mortality: a genome-wide association study. Lancet Respir Med. 2013 Jun; 1(4):309-317. PMID: 24429156.
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    73. Reimherr M, Nicolae DL. You've gotta be lucky: Coverage and the elusive gene-gene interaction. Ann Hum Genet. 2011 Jan; 75(1):105-11. PMID: 20977438.
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    81. Imielinski M, Baldassano RN, Griffiths A, Russell RK, Annese V, Dubinsky M, Kugathasan S, Bradfield JP, Walters TD, Sleiman P, Kim CE, Muise A, Wang K, Glessner JT, Saeed S, Zhang H, Frackelton EC, Hou C, Flory JH, Otieno G, Chiavacci RM, Grundmeier R, Castro M, Latiano A, Dallapiccola B, Stempak J, Abrams DJ, Taylor K, McGovern D. Common variants at five new loci associated with early-onset inflammatory bowel disease. Nat Genet. 2009 Dec; 41(12):1335-40. PMID: 19915574.
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    105. Achkar JP, Dassopoulos T, Silverberg MS, Tuvlin JA, Duerr RH, Brant SR, Siminovitch K, Reddy D, Datta LW, Bayless TM, Zhang L, Barmada MM, Rioux JD, Steinhart AH, McLeod RS, Griffiths AM, Cohen Z, Yang H, Bromfield GP, Schumm P, Hanauer SB, Cho JH, Nicolae DL. Phenotype-stratified genetic linkage study demonstrates that IBD2 is an extensive ulcerative colitis locus. Am J Gastroenterol. 2006 Mar; 101(3):572-80. PMID: 16542294.
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    106. Gewirtz AT, Vijay-Kumar M, Brant SR, Duerr RH, Nicolae DL, Cho JH. Dominant-negative TLR5 polymorphism reduces adaptive immune response to flagellin and negatively associates with Crohn's disease. Am J Physiol Gastrointest Liver Physiol. 2006 Jun; 290(6):G1157-63. PMID: 16439468.
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    117. Bonen DK, Ogura Y, Nicolae DL, Inohara N, Saab L, Tanabe T, Chen FF, Foster SJ, Duerr RH, Brant SR, Cho JH, Nuñez G. Crohn's disease-associated NOD2 variants share a signaling defect in response to lipopolysaccharide and peptidoglycan. Gastroenterology. 2003 Jan; 124(1):140-6. PMID: 12512038.
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    118. Gu Z, Nicolae D, Lu HH, Li WH. Rapid divergence in expression between duplicate genes inferred from microarray data. Trends Genet. 2002 Dec; 18(12):609-13. PMID: 12446139.
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    120. Nicolae DL, Cox NJ. MERLIN...and the geneticist's stone? Nat Genet. 2002 Jan; 30(1):3-4. PMID: 11753377.
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    123. Cho JH, Nicolae DL, Ramos R, Fields CT, Rabenau K, Corradino S, Brant SR, Espinosa R, LeBeau M, Hanauer SB, Bodzin J, Bonen DK. Linkage and linkage disequilibrium in chromosome band 1p36 in American Chaldeans with inflammatory bowel disease. Hum Mol Genet. 2000 May 22; 9(9):1425-32. PMID: 10814724.
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    124. Cox NJ, Frigge M, Nicolae DL, Concannon P, Hanis CL, Bell GI, Kong A. Loci on chromosomes 2 (NIDDM1) and 15 interact to increase susceptibility to diabetes in Mexican Americans. Nat Genet. 1999 Feb; 21(2):213-5. PMID: 9988276.
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    125. Cho JH, Nicolae DL, Gold LH, Fields CT, LaBuda MC, Rohal PM, Pickles MR, Qin L, Fu Y, Mann JS, Kirschner BS, Jabs EW, Weber J, Hanauer SB, Bayless TM, Brant SR. Identification of novel susceptibility loci for inflammatory bowel disease on chromosomes 1p, 3q, and 4q: evidence for epistasis between 1p and IBD1. Proc Natl Acad Sci U S A. 1998 Jun 23; 95(13):7502-7. PMID: 9636179.
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    126. Sweeney PJ, Nicolae D, Ignacio L, Chen L, Roach M, Wara W, Marcus KC, Vijayakumar S. Effect of subcutaneous recombinant human erythropoietin in cancer patients receiving radiotherapy: final report of a randomized, open-labelled, phase II trial. Br J Cancer. 1998 Jun; 77(11):1996-2002. PMID: 9667681.
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