Dan L. Nicolae, Ph.D.

Professor

Research Description

My major research interests are in the areas of statistical genetics and mathematical statistics. The problems I am studying are mainly motivated by applications to studies on the genetics of common/complex diseases.

Statistical genetics problems of interest include likelihood applications to complex trait gene detection, genome-wide strategies for testing gene-gene and gene-environment interaction, association with copy-number variation, methods for analysing data from genome-wide association studies at the gene/pathway/network level, and measures of relative information in genetic studies.

The applications I work on focus on finding the genetic and environmental components of asthma, inflammatory bowel disease, and diabetic complications. I am also interested in functional genomics and the analysis of gene expression data.

Mathematical statistics topics I am working on include Bayesian and frequentist ways of measuring the amount of missing data, general measures of information, and artificial likelihoods for hypothesis testing.

Selected Publications

Estimating Variance Components in Functional Linear Models with Applications to Genetic Heritability
Reimherr ML and Nicolae DL (2013)
(2016) Journal of the American Statistical Association, 111(513): 407-422.

Association Tests for Rare Variants.
Nicolae DL
(2016 Aug) Annu Rev Genomics Hum Genet. 2016 Aug 31;17:117-30. doi: 10.1146/annurev-genom-083115-022609. Epub 2016 Apr 21. 27147090

A unified set-based test with adaptive filtering for gene-environment interaction analyses.
Liu Q, Chen LS, Nicolae DL, Pierce BL
(2016 Jun) Biometrics. 2016 Jun;72(2):629-38. doi: 10.1111/biom.12428. Epub 2015 Oct 23. 26496228 (Full Text)

Imputing Gene Expression in Uncollected Tissues Within and Beyond GTEx.
Wang J, Gamazon ER, Pierce BL, Stranger BE, Im HK, Gibbons RD, Cox NJ, Nicolae DL, Chen LS
(2016 Apr) Am J Hum Genet. 2016 Apr 7;98(4):697-708. doi: 10.1016/j.ajhg.2016.02.020. Epub 2016 Mar 31. 27040689 (Full Text)

A gene-based association method for mapping traits using reference transcriptome data.
Gamazon ER, Wheeler HE, Shah KP, Mozaffari SV, Aquino-Michaels K, Carroll RJ, Eyler AE, Denny JC, Nicolae DL, Cox NJ, Im HK
(2015 Sep) Nat Genet. 2015 Sep;47(9):1091-8. doi: 10.1038/ng.3367. Epub 2015 Aug 10. 26258848 (Full Text)

Genome-wide interaction studies reveal sex-specific asthma risk alleles.
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
(2014 Oct) Hum Mol Genet. 2014 Oct 1;23(19):5251-9. doi: 10.1093/hmg/ddu222. Epub 2014 May 13. 24824216 (Full Text)

GWAS to Sequencing: Divergence in Study Design and Analysis.
King CR, Nicolae DL
(2014 May) Genes (Basel). 2014 May 28;5(2):460-76. doi: 10.3390/genes5020460. 24879455 (Full Text)

On Quantifying Dependence: A Frame- work for Developing Interpretable Measures
Reimherr ML and Nicolae DL 
(2013) Statistical Science, 28(1), 116-130.

Rhinovirus wheezing illness and genetic risk of childhood-onset asthma.
Caliskan M, Bochkov YA, Kreiner-Moller E, Bonnelykke K, Stein MM, Du G, Bisgaard H, Jackson DJ, Gern JE, Lemanske RF Jr, Nicolae DL, Ober C
(2013 Apr) N Engl J Med. 2013 Apr 11;368(15):1398-407. doi: 10.1056/NEJMoa1211592. Epub 2013 Mar 27. 23534543 (Full Text)

An exponential combination procedure for set-based association tests in sequencing studies.
Chen LS, Hsu L, Gamazon ER, Cox NJ, Nicolae DL
(2012 Dec) Am J Hum Genet. 2012 Dec 7;91(6):977-86. doi: 10.1016/j.ajhg.2012.09.017. Epub 2012 Nov 15. 23159251 (Full Text)

Genome-wide ancestry association testing identifies a common European variant on 6q14.1 as a risk factor for asthma in African American subjects.
Torgerson DG, Capurso D, Ampleford EJ, Li X, Moore WC, Gignoux CR, Hu D, Eng C, Mathias RA, Busse WW, Castro M, Erzurum SC, Fitzpatrick AM, Gaston B, Israel E, Jarjour NN, Teague WG, Wenzel SE, Rodriguez-Santana JR, Rodriguez-Cintron W, Avila PC, Ford JG, Barnes KC, Burchard EG, Howard TD, Bleecker ER, Meyers DA, Cox NJ, Ober C, Nicolae DL
(2012 Sep) J Allergy Clin Immunol. 2012 Sep;130(3):622-629.e9. doi: 10.1016/j.jaci.2012.03.045. Epub 2012 May 18. 22607992 (Full Text)

Resequencing candidate genes implicates rare variants in asthma susceptibility.
Torgerson DG, Capurso D, Mathias RA, Graves PE, Hernandez RD, Beaty TH, Bleecker ER, Raby BA, Meyers DA, Barnes KC, Weiss ST, Martinez FD, Nicolae DL, Ober C
(2012 Feb) Am J Hum Genet. 2012 Feb 10;90(2):273-81. doi: 10.1016/j.ajhg.2012.01.008. 22325360 (Full Text)

Meta-analysis of genome-wide association studies of asthma in ethnically diverse North American populations.
Torgerson DG, Ampleford EJ, Chiu GY, Gauderman WJ, Gignoux CR, Graves PE, Himes BE, Levin AM, Mathias RA, Hancock DB, Baurley JW, Eng C, Stern DA, Celedon JC, Rafaels N, Capurso D, Conti DV, Roth LA, Soto-Quiros M, Togias A, Li X, Myers RA, Romieu I, Van Den Berg DJ, Hu D, Hansel NN, Hernandez RD, Israel E, Salam MT, Galanter J, Avila PC, Avila L, Rodriquez-Santana JR, Chapela R, Rodriguez-Cintron W, Diette GB, Adkinson NF, Abel RA, Ross KD, Shi M, Faruque MU, Dunston GM, Watson HR, Mantese VJ, Ezurum SC, Liang L, Ruczinski I, Ford JG, Huntsman S, Chung KF, Vora H, Li X, Calhoun WJ, Castro M, Sienra-Monge JJ, del Rio-Navarro B, Deichmann KA, Heinzmann A, Wenzel SE, Busse WW, Gern JE, Lemanske RF Jr, Beaty TH, Bleecker ER, Raby BA, Meyers DA, London SJ, Gilliland FD, Burchard EG, Martinez FD, Weiss ST, Williams LK, Barnes KC, Ober C, Nicolae DL
(2011 Jul) Nat Genet. 2011 Jul 31;43(9):887-92. doi: 10.1038/ng.888. 21804549 (Full Text)

An evolutionary framework for association testing in resequencing studies.
King CR, Rathouz PJ, Nicolae DL
(2010 Nov) PLoS Genet. 2010 Nov 11;6(11):e1001202. doi: 10.1371/journal.pgen.1001202. 21085648 (Full Text)

Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS.
Nicolae DL, Gamazon E, Zhang W, Duan S, Dolan ME, Cox NJ
(2010 Apr) PLoS Genet. 2010 Apr 1;6(4):e1000888. doi: 10.1371/journal.pgen.1000888. 20369019 (Full Text)