Dan Nicolae - Publications

University of Chicago, Chicago, IL 

64 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Gamazon ER, Segrè AV, van de Bunt M, Wen X, Xi HS, Hormozdiari F, Ongen H, Konkashbaev A, Derks EM, Aguet F, Quan J, Nicolae DL, Eskin E, Kellis M, et al. Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation. Nature Genetics. PMID 29955180 DOI: 10.1038/s41588-018-0154-4  0.48
2016 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, ... ... Nicolae DL, et al. A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome. Nature Communications. 7: 12522. PMID 27725671 DOI: 10.1038/ncomms12522  1
2016 Reimherr M, Nicolae D. Estimating Variance Components in Functional Linear Models With Applications to Genetic Heritability Journal of the American Statistical Association. 111: 407-422. DOI: 10.1080/01621459.2015.1016224  1
2015 Liu Q, Chen LS, Nicolae DL, Pierce BL. A unified set-based test with adaptive filtering for gene-environment interaction analyses. Biometrics. PMID 26496228 DOI: 10.1111/biom.12428  1
2015 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. American Journal of Respiratory and Critical Care Medicine. PMID 26474238 DOI: 10.1164/rccm.201506-1243OC  1
2015 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, et al. Genome-wide association study of recalcitrant atopic dermatitis in Korean children. The Journal of Allergy and Clinical Immunology. PMID 25935106 DOI: 10.1016/j.jaci.2015.03.030  1
2015 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, ... ... Nicolae DL, et al. Stress and Bronchodilator Response in Children with Asthma. American Journal of Respiratory and Critical Care Medicine. 192: 47-56. PMID 25918834 DOI: 10.1164/rccm.201501-0037OC  1
2015 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 Computational Biology. 11: e1004139. PMID 25735005 DOI: 10.1371/journal.pcbi.1004139  1
2015 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, ... ... Nicolae DL, et al. Ethnic-specific associations of rare and low-frequency DNA sequence variants with asthma. Nature Communications. 6: 5965. PMID 25591454 DOI: 10.1038/ncomms6965  1
2014 King CR, Nicolae DL. GWAS to Sequencing: Divergence in Study Design and Analysis. Genes. 5: 460-76. PMID 24879455 DOI: 10.3390/genes5020460  1
2014 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, ... ... Nicolae DL, et al. Genome-wide interaction studies reveal sex-specific asthma risk alleles. Human Molecular Genetics. 23: 5251-9. PMID 24824216 DOI: 10.1093/hmg/ddu222  1
2014 Reimherr M, Nicolae D. A functional data analysis approach for genetic association studies Annals of Applied Statistics. 8: 406-429. DOI: 10.1214/13-AOAS692  1
2013 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, ... ... Nicolae D, et al. Genetic variants associated with idiopathic pulmonary fibrosis susceptibility and mortality: a genome-wide association study. The Lancet. Respiratory Medicine. 1: 309-17. PMID 24429156 DOI: 10.1016/S2213-2600(13)70045-6  1
2013 Liu Q, Nicolae DL, Chen LS. Marbled inflation from population structure in gene-based association studies with rare variants. Genetic Epidemiology. 37: 286-92. PMID 23468125 DOI: 10.1002/gepi.21714  1
2013 Reimherr M, Nicolae DL. On quantifying dependence: A framework for developing interpretable measures Statistical Science. 28: 116-130. DOI: 10.1214/12-STS405  1
2012 Ostrovnaya I, Nicolae DL. Estimating the proportion of true null hypotheses under dependence Statistica Sinica. 22: 1689-1716. DOI: 10.5705/ss.2010.255  1
2011 Gamazon ER, Nicolae DL, Cox NJ. A study of CNVs as trait-associated polymorphisms and as expression quantitative trait loci. Plos Genetics. 7: e1001292. PMID 21304891 DOI: 10.1371/journal.pgen.1001292  1
2011 Çalışkan M, Chong JX, Uricchio L, Anderson R, Chen P, Sougnez C, Garimella K, Gabriel SB, dePristo MA, Shakir K, Matern D, Das S, Waggoner D, Nicolae DL, Ober C. Exome sequencing reveals a novel mutation for autosomal recessive non-syndromic mental retardation in the TECR gene on chromosome 19p13. Human Molecular Genetics. 20: 1285-9. PMID 21212097 DOI: 10.1093/hmg/ddq569  1
2011 Reimherr M, Nicolae DL. You've gotta be lucky: Coverage and the elusive gene-gene interaction. Annals of Human Genetics. 75: 105-11. PMID 20977438 DOI: 10.1111/j.1469-1809.2010.00615.x  1
2010 King CR, Rathouz PJ, Nicolae DL. An evolutionary framework for association testing in resequencing studies. Plos Genetics. 6: e1001202. PMID 21085648 DOI: 10.1371/journal.pgen.1001202  1
2010 Ratnam S, Bozek G, Nicolae D, Storb U. The pattern of somatic hypermutation of Ig genes is altered when p53 is inactivated. Molecular Immunology. 47: 2611-8. PMID 20691478 DOI: 10.1016/j.molimm.2010.05.291  1
2010 Pluzhnikov A, Below JE, Konkashbaev A, Tikhomirov A, Kistner-Griffin E, Roe CA, Nicolae DL, Cox NJ. Spoiling the whole bunch: quality control aimed at preserving the integrity of high-throughput genotyping. American Journal of Human Genetics. 87: 123-8. PMID 20598280 DOI: 10.1016/j.ajhg.2010.06.005  1
2010 De la Cruz O, Wen X, Ke B, Song M, Nicolae DL. Gene, region and pathway level analyses in whole-genome studies. Genetic Epidemiology. 34: 222-31. PMID 20013942 DOI: 10.1002/gepi.20452  1
2010 Paterson AD, Waggott D, Boright AP, Hosseini SM, Shen E, Sylvestre MP, Wong I, Bharaj B, Cleary PA, Lachin JM, Below JE, Nicolae D, Cox NJ, Canty AJ, et al. A genome-wide association study identifies a novel major locus for glycemic control in type 1 diabetes, as measured by both A1C and glucose. Diabetes. 59: 539-49. PMID 19875614 DOI: 10.2337/db09-0653  1
2010 Thompson EE, Haller G, Pinto JM, Sun Y, Zelano B, Jacob S, McClintock MK, Nicolae DL, Ober C. Sequence variations at the human leukocyte antigen-linked olfactory receptor cluster do not influence female preferences for male odors. Human Immunology. 71: 100-3. PMID 19833159 DOI: 10.1016/j.humimm.2009.10.004  1
2010 Thompson EE, Sun Y, Nicolae D, Ober C. Shades of gray: a comparison of linkage disequilibrium between Hutterites and Europeans. Genetic Epidemiology. 34: 133-9. PMID 19697328 DOI: 10.1002/gepi.20442  1
2010 Song S, Nicolae DL, Song J. Estimating the mixing proportion in a semiparametric mixture model Computational Statistics and Data Analysis. 54: 2276-2283. DOI: 10.1016/j.csda.2010.04.007  1
2009 Storb U, Shen HM, Nicolae D. Somatic hypermutation: processivity of the cytosine deaminase AID and error-free repair of the resulting uracils. Cell Cycle (Georgetown, Tex.). 8: 3097-101. PMID 19738437  1
2009 Krishnaswamy S, Kanteti R, Duke-Cohan JS, Loganathan S, Liu W, Ma PC, Sattler M, Singleton PA, Ramnath N, Innocenti F, Nicolae DL, Ouyang Z, Liang J, Minna J, Kozloff MF, et al. Ethnic differences and functional analysis of MET mutations in lung cancer. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 15: 5714-23. PMID 19723643 DOI: 10.1158/1078-0432.CCR-09-0070  1
2009 Nicolae DL, Ober C. (Too) great expectations: the challenges in replicating asthma disease genes. American Journal of Respiratory and Critical Care Medicine. 179: 1078-9. PMID 19498061 DOI: 10.1164/rccm.200903-0456ED  1
2009 Ober C, Nord AS, Thompson EE, Pan L, Tan Z, Cusanovich D, Sun Y, Nicolae R, Edelstein C, Schneider DH, Billstrand C, Pfaffinger D, Phillips N, Anderson RL, Philips B, ... ... Nicolae DL, et al. Genome-wide association study of plasma lipoprotein(a) levels identifies multiple genes on chromosome 6q. Journal of Lipid Research. 50: 798-806. PMID 19124843 DOI: 10.1194/jlr.M800515-JLR200  1
2009 De la Cruz O, Blekhman R, Zhang X, Nicolae D, Firestein S, Gilad Y. A signature of evolutionary constraint on a subset of ectopically expressed olfactory receptor genes. Molecular Biology and Evolution. 26: 491-4. PMID 19103638 DOI: 10.1093/molbev/msn294  1
2009 Song M, Nicolae DL. Restricted parameter space models for testing gene-gene interaction. Genetic Epidemiology. 33: 386-93. PMID 19058263 DOI: 10.1002/gepi.20392  1
2009 Song J, Nicolae DL. A sequential clustering algorithm with applications to gene expression data Journal of the Korean Statistical Society. 38: 175-184. DOI: 10.1016/j.jkss.2008.09.006  1
2008 Barrett JC, Hansoul S, Nicolae DL, Cho JH, Duerr RH, Rioux JD, Brant SR, Silverberg MS, Taylor KD, Barmada MM, Bitton A, Dassopoulos T, Datta LW, Green T, Griffiths AM, et al. Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nature Genetics. 40: 955-62. PMID 18587394 DOI: 10.1038/ng.175  1
2008 Ma SF, Flores C, Wade MS, Dudek SM, Nicolae DL, Ober C, Garcia JG. A common cortactin gene variation confers differential susceptibility to severe asthma. Genetic Epidemiology. 32: 757-66. PMID 18521921 DOI: 10.1002/gepi.20343  1
2008 Ober C, Tan Z, Sun Y, Possick JD, Pan L, Nicolae R, Radford S, Parry RR, Heinzmann A, Deichmann KA, Lester LA, Gern JE, Lemanske RF, Nicolae DL, Elias JA, et al. Effect of variation in CHI3L1 on serum YKL-40 level, risk of asthma, and lung function. The New England Journal of Medicine. 358: 1682-91. PMID 18403759 DOI: 10.1056/NEJMoa0708801  1
2008 Wen X, Nicolae DL. Association studies for untyped markers with TUNA. Bioinformatics (Oxford, England). 24: 435-7. PMID 18057020 DOI: 10.1093/bioinformatics/btm603  1
2008 Nicolae DL, Meng XL, Kong A. Rejoinder: Quantifying the fraction of missing information for hypothesis testing in statistical and genetic studies Statistical Science. 23: 325-331. DOI: 10.1214/08-STS244REJ  1
2008 Nicolae DL, Meng XL, Kong A. Quantifying the fraction of missing information for hypothesis testing in statistical and genetic studies Statistical Science. 23: 287-312. DOI: 10.1214/07-STS244  1
2008 Tikhomirov A, Konkashbaev A, Nicolae DL. On single-array genotype calling algorithms Biomedical Engineering and Informatics: New Development and the Future - Proceedings of the 1st International Conference On Biomedical Engineering and Informatics, Bmei 2008. 1: 459-462. DOI: 10.1109/BMEI.2008.107  1
2007 Thompson EE, Pan L, Ostrovnaya I, Weiss LA, Gern JE, Lemanske RF, Nicolae DL, Ober C. Integrin beta 3 genotype influences asthma and allergy phenotypes in the first 6 years of life. The Journal of Allergy and Clinical Immunology. 119: 1423-9. PMID 17556058 DOI: 10.1016/j.jaci.2007.03.029  1
2007 Zhang X, De la Cruz O, Pinto JM, Nicolae D, Firestein S, Gilad Y. Characterizing the expression of the human olfactory receptor gene family using a novel DNA microarray. Genome Biology. 8: R86. PMID 17509148 DOI: 10.1186/gb-2007-8-5-r86  1
2007 Rioux JD, Xavier RJ, Taylor KD, Silverberg MS, Goyette P, Huett A, Green T, Kuballa P, Barmada MM, Datta LW, Shugart YY, Griffiths AM, Targan SR, Ippoliti AF, Bernard EJ, ... ... Nicolae DL, et al. Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis. Nature Genetics. 39: 596-604. PMID 17435756 DOI: 10.1038/ng2032  1
2006 Shen HM, Tanaka A, Bozek G, Nicolae D, Storb U. Somatic hypermutation and class switch recombination in Msh6(-/-)Ung(-/-) double-knockout mice. Journal of Immunology (Baltimore, Md. : 1950). 177: 5386-92. PMID 17015724  1
2006 Nicolae DL. Quantifying the amount of missing information in genetic association studies. Genetic Epidemiology. 30: 703-17. PMID 16986163 DOI: 10.1002/gepi.20181  1
2006 Nicolae DL. Testing untyped alleles (TUNA)-applications to genome-wide association studies. Genetic Epidemiology. 30: 718-27. PMID 16986160 DOI: 10.1002/gepi.20182  1
2006 Nicolae DL, Wu X, Miyake K, Cox NJ. GEL: a novel genotype calling algorithm using empirical likelihood. Bioinformatics (Oxford, England). 22: 1942-7. PMID 16809396 DOI: 10.1093/bioinformatics/btl341  1
2006 Nicolae DL, Wen X, Voight BF, Cox NJ. Coverage and characteristics of the Affymetrix GeneChip Human Mapping 100K SNP set. Plos Genetics. 2: e67. PMID 16680197 DOI: 10.1371/journal.pgen.0020067  1
2006 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, ... ... Nicolae DL, et al. Phenotype-stratified genetic linkage study demonstrates that IBD2 is an extensive ulcerative colitis locus. The American Journal of Gastroenterology. 101: 572-80. PMID 16542294 DOI: 10.1111/j.1572-0241.2006.00451.x  1
2005 Longerich S, Tanaka A, Bozek G, Nicolae D, Storb U. The very 5' end and the constant region of Ig genes are spared from somatic mutation because AID does not access these regions. The Journal of Experimental Medicine. 202: 1443-54. PMID 16301749 DOI: 10.1084/jem.20051604  1
2005 Hoffjan S, Nicolae D, Ostrovnaya I, Roberg K, Evans M, Mirel DB, Steiner L, Walker K, Shult P, Gangnon RE, Gern JE, Martinez FD, Lemanske RF, Ober C. Gene-environment interaction effects on the development of immune responses in the 1st year of life. American Journal of Human Genetics. 76: 696-704. PMID 15726497 DOI: 10.1086/429418  1
2004 Barmada MM, Brant SR, Nicolae DL, Achkar JP, Panhuysen CI, Bayless TM, Cho JH, Duerr RH. A genome scan in 260 inflammatory bowel disease-affected relative pairs. Inflammatory Bowel Diseases. 10: 513-20. PMID 15472510 DOI: 10.1097/00054725-200409000-00004  1
2004 Li J, Moran T, Swanson E, Julian C, Harris J, Bonen DK, Hedl M, Nicolae DL, Abraham C, Cho JH. Regulation of IL-8 and IL-1beta expression in Crohn's disease associated NOD2/CARD15 mutations. Human Molecular Genetics. 13: 1715-25. PMID 15198989 DOI: 10.1093/hmg/ddh182  1
2004 Nicolae DL, Kong A. Measuring the relative information in allele-sharing linkage studies. Biometrics. 60: 368-75. PMID 15180662 DOI: 10.1111/j.0006-341X.2004.00181.x  1
2004 Barmada MM, Brant SR, Nicolae DL, Achkar JP, Panhuysen CI, Bayless TM, Cho JH, Duerr RH. A genome scan in 260 inflammatory bowel disease-affected relative pairs. Inflammatory Bowel Diseases. 10: 15-22. PMID 15058521 DOI: 10.1097/00054725-200401000-00002  1
2004 Gern JE, Reardon CL, Hoffjan S, Nicolae D, Li Z, Roberg KA, Neaville WA, Carlson-Dakes K, Adler K, Hamilton R, Anderson E, Gilbertson-White S, Tisler C, Dasilva D, Anklam K, et al. Effects of dog ownership and genotype on immune development and atopy in infancy. The Journal of Allergy and Clinical Immunology. 113: 307-14. PMID 14767447 DOI: 10.1016/j.jaci.2003.11.017  1
2003 Hoffjan S, Nicolae D, Ober C. Association studies for asthma and atopic diseases: a comprehensive review of the literature. Respiratory Research. 4: 14. PMID 14748924 DOI: 10.1186/1465-9921-4-14  1
2003 Brant SR, Panhuysen CI, Nicolae D, Reddy DM, Bonen DK, Karaliukas R, Zhang L, Swanson E, Datta LW, Moran T, Ravenhill G, Duerr RH, Achkar JP, Karban AS, Cho JH. MDR1 Ala893 polymorphism is associated with inflammatory bowel disease. American Journal of Human Genetics. 73: 1282-92. PMID 14610718 DOI: 10.1086/379927  1
2003 Regunathan A, Glesne DA, Wilson AK, Song J, Nicolae D, Flores T, Bhattacharyya MH. Microarray analysis of changes in bone cell gene expression early after cadmium gavage in mice. Toxicology and Applied Pharmacology. 191: 272-93. PMID 13678660  1
2003 Kong A, McCullagh P, Meng XL, Nicolae D, Tan Z. A theory of statistical models for Monte Carlo integration Journal of the Royal Statistical Society. Series B: Statistical Methodology. 65: 585-604. DOI: 10.1111/1467-9868.00404  1
2002 Gu Z, Nicolae D, Lu HH, Li WH. Rapid divergence in expression between duplicate genes inferred from microarray data. Trends in Genetics : Tig. 18: 609-13. PMID 12446139 DOI: 10.1016/S0168-9525(02)02837-8  1
2002 Michael N, Martin TE, Nicolae D, Kim N, Padjen K, Zhan P, Nguyen H, Pinkert C, Storb U. Effects of sequence and structure on the hypermutability of immunoglobulin genes. Immunity. 16: 123-34. PMID 11825571 DOI: 10.1016/S1074-7613(02)00261-3  1
2002 Nicolae DL, Cox NJ. MERLIN...and the geneticist's stone? Nature Genetics. 30: 3-4. PMID 11753377 DOI: 10.1038/ng0102-3  1
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