Publications

    2016

  1. Nicolae DL. "Association Tests for Rare Variants". Annual Review of Genomics and Human Genetics, in press.

  2. Wang J, Gamazon ER, Pierce BL, Stranger BE, Im HK, Gibbons RD, Coc NJ, Nicolae DL and Chen LS. "Imputing Gene Expression in Uncollected Tissues Within and Beyond GTEx". The American Journal of Human Genetics, in press.

  3. Reimherr M and Nicolae D. "Estimating Variance Components in Functional Linear Models with Applications to Genetic Heritability. Journal of the American Statistical Association, in press.

  4. Nicodemus-Johnson J, Naughton KA, Sudi J, Hogarth K, Naurekas ET, Nicolae DL, Sperling AI, Solway J, White SR , Ober C. " enome-wide Methylation Study Identifies an IL-13 Induced Epigenetic Signature in Asthmatic Airways". American Journal of Respiratory and Critical Care Medicine, in press.

  5. Liu Q, Chen LS, Nicolae DL, Pierce BL. "A unified set‐based test with adaptive filtering for gene–environment interaction analyses". Biometrics, in press.


    2015

  6. Loisel D, Du G, Ahluwalia TS, Tisler CJ, Evans MD, Myers RA, Gangnon RE, Moller EK, Bonnelykke K, Bisgaard H, Jackson DJ, Lemanske RF, Nicolae DL, Gern JE, Over C. "Genetic associations with viral respiratory illnesses and asthma control in children". Clinical & Experimental Allergy, 46 (1):112-124.

  7. Gamazon ER, Wheeler HE, Shah KP, Mozaffari SV, Aquino-Michaels K, Carroll RC, Eyler AE, Denny JC, GTEx Consortium, Nicolae DL, Cox NJ, Im HK. "A gene-based association method for mapping traits using reference transcriptome data". Nature Genetics, 47: 1091-1098.

  8. Yan X, Chu J-H, Gomez J, Koenigs M, Holm C, He X, Perez MF, Zhao H, Mane S, Martinez FD, Ober C, Nicolae DL et al. "Noninvasive analysis of the sputum transcriptome discriminates clinical phenotypes of asthma". Am J Respir Crit Care Med, 191:1116-1125.

  9. The GTEx Consortium. "The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans". Science, 348, 6235: 648-660.

  10. 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" Journal of Allergy and Clinical Immunology, 136(3), 678-684.

  11. Brehm JM, Ramratnam SK, Tse SM, Croteau-Chonka DC, Pino-Yanes M, Rosas-Salazar C, Litonjua AA, Raby BA, Boutaoui N, Han Y-Y, et al. "Stress and bronchodilator response in children with asthma." Am J Respir Crit Care Med, 192:47-56.

  12. Livne OE, Han L, Alkorta-Aranburu G, Wentworth-Sheilds W, Abney M, Ober C and Nicolae DL. "PRIMAL: Fast and Accurate Pedigree-based Imputation from Sequence Data in a Founder Population". PLoS Computational Biology, 11(3): e1004139.

  13. 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." Nature Communications, 6:5965.

  14. Pino-Yanes M, Gignoux CR, Galanter JM, et al. "Genome-wide association study and admixture mapping reveal new loci associated with total IgE levels in Latinos." J Allergy Clin Immunol, 135(6):1502-1510.


    2014

  15. 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, Del Rio Navarro B, 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 Medical Genomics, 7(1):48.

  16. 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, 9(6):e99716.

  17. Sharma S, Zhou X, Thibault DM, Himes BE, Liu A, Szefler SJ, Strunk R, Castro M, Hansel NN, Diette GB, Vonakis BM, Adkinson NF Jr, Avila L, Soto-Quiros M, Barraza-Villareal A, Lemanske RF Jr, 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., 134(5), 1153-1162.

  18. 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 Journal, 14(3), 223-228.

  19. King CR and Nicolae DL. "GWAS to Sequencing: Divergence in Study Design and Analysis" Genes, 5(2), 460-476.

  20. 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; on behalf of GRAAD, Gilliland FD, Weiss ST, London SJ, Raby BA, Ober C, Nicolae DL "Genome-wide interaction studies reveal sex-specific asthma risk alleles" Human Molecular Genetics, 23 (19), 5251-5259.

  21. Ahsan H, Halpern J, Kibriya, MG, Pierce, BL et al "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 Epidemiology Biomarkers & Prevention, 23, 658-669.

  22. Reimherr M and Nicolae DL. "A Functional Data Analysis Approach for Genetic Association Studies". The Annals of Applied Statistics, 8(1), 406-429.

  23. 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., 133(1), 248-255.

  24. 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 Journal, 14, 223-228.


    2013

  25. 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, 155(1):70-80.

  26. GTEx Consortium. "The Genotype-Tissue Expression (GTEx) project" Nature Genetics, 45(6), 580-585.

  27. 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 JG. "Genetic variants associated with idiopathic pulmonary fibrosis susceptibility and mortality: a genome-wide association study". The Lancet Respiratory Medicine, 1(4), 309-317.

  28. 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. "Rhinovirus wheezing illness and genetic risk of childhood-onset asthma". New England Journal of Medicine, 368(15), 1398-1407.

  29. Nicodemus-Johnson J, Laxman B, Stern RK, Sudi J, Tierney CN, Norwick L, Hogarth DK, McConville JF, Naureckas ET, Sperling AI, Solway J, Krishnan JA, Nicolae DL, White SR, Ober C. "Maternal asthma and microRNA regulation of soluble HLA-G in the airway". J Allergy Clin Immunol., 131(6), 1496-1503.

  30. Melen E, Granell R, Kogevinas M, Strachan D, Gonzalez JR, Wjst M, Jarvis D, Ege M, Braun-Fahrlander C, Genuneit J, Horak E, Bouzigon E, Demenais F, Kauffmann F, Siroux V, Michel S, von Berg A, Heinzmann A, Kabesch M, Probst-Hensch NM, Curjuric I, Imboden M, Rochat T, Henderson J, Sterne JA, McArdle WL, Hui J, James AL, William Musk A, Palmer LJ, Becker A, Kozyrskyj AL, Chan-Young M, Park JE, Leung A, Daley D, Freidin MB, Deev IA, Ogorodova LM, Puzyrev VP, Celedon JC, Brehm JM, Cloutier MM, Canino G, Acosta-Perez E, Soto-Quiros M, Avila L, Bergström A, Magnusson J, Soderhall C, Kull I, Scholtens S, Marike Boezen H, Koppelman GH, Wijga AH, Marenholz I, Esparza-Gordillo J, Lau S, Lee YA, Standl M, Tiesler CM, Flexeder C, Heinrich J, Myers RA, Ober C, Nicolae DL, Farrall M, Kumar A, Moffatt MF, Cookson WO, Lasky-Su J. "Genome-wide association study of body mass index in 23000 individuals with and without asthma". Clinical and Experimental Allergy, 43(4), 463-474.

  31. Liu Q, Nicolae DL and Chen LS. "Marbled inflation from population structure in gene-based association studies with rare variants" Genetic Epidemiology, 37(3), 286-289.

  32. Himes BE, Sheppard K, Berndt A, Leme AS, Myers RA, Gignoux CR, Levin AM, Gauderman WJ, Yang JJ, Mathias RA, Romieu I, Torgerson DG, Roth LA, Huntsman S, Eng C, Klanderman B, Ziniti J, Senter-Sylvia J, Szefler SJ, Lemanske RF Jr, Zeiger RS, Strunk RC, Martinez FD, Boushey H, Chinchilli VM, Israel E, Mauger D, Koppelman GH, Postma DS, Nieuwenhuis MA, Vonk JM, Lima JJ, Irvin CG, Peters SP, Kubo M, Tamari M, Nakamura Y, Litonjua AA, Tantisira KG, Raby BA, Bleecker ER, Meyers DA, London SJ, Barnes KC, Gilliland FD, Williams LK, Burchard EG, Nicolae DL, Ober C, DeMeo DL, Silverman EK, Paigen B, Churchill G, Shapiro SD, Weiss ST. "Integration of mouse and human genome-wide association data identifies KCNIP4 as an asthma gene". PLoS One, 8(2):e56179.

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

  34. Levin AM, Mathias RA, Huang L, Roth LA, Daley D, Myers RA, Himes BE, Romieu I, Yang M, Eng C, Park JE, Zoratti K, Gignoux CR, Torgerson DG, Galanter JM, Huntsman S, Nguyen EA, Becker AB, Chan-Yeung M, Kozyrskyj AL, Kwok PY, Gilliland FD, Gauderman WJ, Bleecker ER, Raby BA, Meyers DA, London SJ, Martinez FD, Weiss ST, Burchard EG, Nicolae DL, Ober C, Barnes KC, Williams LK. "A meta-analysis of genome-wide association studies for serum total IgE in diverse study populations". J Allergy Clin Immunol., 131(4), 1176-1184.


    2012

  35. Chen LS, Hsu L, Gamazon ER, Cox NJ and Nicolae DL. "An exponential combination procedure for set-based association tests in sequencing studies". American Journal of Human Genetics, 91(6), 977-986.

  36. Myers RA, Himes BE, Gignoux CR, Yang JJ, Gauderman WJ, Rebordosa C, Xie J, Torgerson DG, Levin AM, Baurley J, Graves PE, Mathias RA, Romieu I, Roth LA, Conti D, Avila L, Eng C, Vora H, LeNoir MA, Soto-Quiros M, Liu J, Celedón JC, Farber HJ, Kumar R, Avila PC, Meade K, Serebrisky D, Thyne S, Rodriguez-Cintron W, Rodriguez-Santana JR, Borrell LN, Lemanske RF Jr, Bleecker ER, Meyers DA, London SJ, Barnes KC, Raby BA, Martinez FD, Gilliland FD, Williams LK, Burchard EG, Weiss ST, Nicolae DL, Ober C. "Further replication studies of the EVE Consortium meta-analysis identifies 2 asthma risk loci in European Americans". J Allergy Clin Immunol., 30(6), 1294-1301.

  37. Ding D, Scott NM, Thompson EE, Chaiworapongsa T, Torres R, Billstrand C, Murray K, Dexheimer PJ, Ismail M, Kay H, Levy S, Romero R, Lindheimer MD, Nicolae DL, Ober C. "Increased Protein Coding Mutations in the Mitochondrial Genome of African American Women With Preeclampsia". Reproductive Sciences, 19(12), 1343-1351.

  38. Li X, Ampleford EJ, Howard TD, Moore WC, Torgerson DG, Li H, Busse WW, Castro M, Erzurum SC, Israel E, Nicolae DL, Ober C, Wenzel SE, Hawkins GA, Bleecker ER, Meyers DA. "Genome-wide association studies of asthma indicate opposite immunopathogenesis direction from autoimmune diseases". J Allergy Clin Immunol., 130(4), 861–868.

  39. 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, Rodríguez-Santana JR, Rodríguez-Cintrón W, Avila PC, Ford JG, Barnes KC, Burchard EG, Howard TD, Bleecker ER, Meyers DA, Cox NJ, Ober C and Nicolae DL. "Genome-wide ancestry association testing identifies a common European variant on 6q14.1 as a risk factor for asthma in African American subjects". J Allergy Clin Immunol., 130(3), 622-629.

  40. 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 and Ober C. "Resequencing Candidate Genes Implicates Rare Variants in Asthma Susceptibility". American Journal of Human Genetics, 90(20): 273-281.

  41. Im HK, Gamazon ER, Nicolae DL and Cox NJ. "On sharing quantitative trait GWAS results in an era of multiple-omics data and the limits of genomic privacy". American Journal of Human Genetics, 90(4):591-598.

  42. Uricchio LH, Chong JX, Ross KD, Ober and Nicolae DL. "Accurate imputation of rare and common variants in a founder population from a small number of sequenced individuals". Genetic Epidemiology, 36(4), 312-319.

  43. Ostrovnaya I and Nicolae DL. "Estimating the proportion of true null hypotheses under dependence". Statistica Sinica, 22(4), 1689-1716.


    2011

  44. Ionita-Laza I, Makarov V, Yoon S, Raby B, Buxbaum J, Nicolae DL, Lin X. "Finding disease variants in mendelian disorders by using sequence data: methods and applications". American Journal of Human Genetics, 89(6):701-12.

  45. Torgerson DG, Ampleford EJ, Chiu GY, Gauderman WJ, Gignoux CR, Graves PE, Himes BE, Levin AM, Mathias RA, Hancock DB, Baurley J, Eng C, Stern DA, Celedón 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 WMU, 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, Sierra-Monge JJ, del Rio-Navarro B, Deichmann KA, Heinzmann A, Wenzel SE, Busse WW, Gern JE, Lemanske Jr. RF, Beaty TH, Bleecker ER, Raby BA, Meyers DA, London SJ, Gilliland FD, Burchard EG, Martinez FD, Weiss ST, Williams LK, Barnes KD, Ober C and Nicolae DL. "Meta-analysis of Genome-wide Association Studies of Asthma In Ethnically Diverse North American Populations". Nature Genetics, 43(9):887-892

  46. Wegmann D, Kessner DE, Veeramah KR, Mathias RA, Nicolae DL, Yanek LR, Sun YV, Torgerson DG, Rafaels N, Mosley T, Becker LC, Ruczinski I, Beaty TH, Kardia SL, Meyers DA, Barnes KC, Becker DM, Freimer NB, Novembre J. "Recombination rates in admixed individuals identified by ancestry-based inference". Nature Genetics, 43(9):847-853.

  47. Below JE, Gamazon ER, Morrison JV, Konkashbaev A, Pluzhnikov A, McKeigue PM, Parra EJ, Elbein SC, Hallman DM, Nicolae DL, Bell GI, Cruz M, Cox NJ, Hanis CL. "Genome-wide Meta-analysis for Severe Diabetic Retinopathy". Diabetologia, 54(8):2047-2055.

  48. Grassi MA, Tikhomirov A, Ramalingam S, Below JE, Cox NJ, Nicolae DL. "Genome-wide Meta-analysis for Severe Diabetic Retinopathy". Human Molecular Genetics, 20(12), 2472-2481.

  49. Gamazon ER, Nicolae DL, Cox NJ. "A Study of CNVs As Trait-Associated Polymorphisms and As Expression Quantitative Trait Loci". PLoS Genetics 7(2): e1001292.

  50. Perera MA, Gamazon E, Cavallari LH, Patel SR, Poindexter S, Kittles RA, Nicolae D, Cox NJ. "The Missing Association: Sequencing-Based Discovery of Novel SNPs in VKORC1 and CYP2C9 That Affect Warfarin Dose in African Americans". Clin Pharmacol Ther., 89(3):408-415.

  51. Caliskan 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 Nonsyndromic Mental Retardation in the TECR Gene on Chromosome 19p13". Human Molecular Genetics, 20(7):1285-1289.

  52. Reimherr M and Nicolae DL. "You've Gotta Be Lucky: Coverage and the Elusive Gene-Gene Interaction". Annals of Human Genetics, 75(1), 105-111.


    2010

  53. King CR, Rathouz PJ and Nicolae DL. "An Evolutionary Framework for Association Testing in Resequencing Studies". PLoS Genetics, 6(11):e1001202.

  54. Ratnam S, Bozek G, Nicolae D, Storb U. "The pattern of somatic hypermutation of Ig genes is altered when p53 is inactivated". Mol Immunol., 47(16):2611-8.

  55. 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(1), 123-128.

  56. Song S., Nicolae DL and Song J. "Estimating the mixing proportion in a semiparametric mixture". Computational Statistics and Data Analysis, 54(10), 2276-2283.

  57. Nicolae DL, Gamazon E, Zhang W, Duan S, Dolan ME, Cox NJ. "Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS". PLoS Genetics, 6(4):e1000888.

  58. Gamazon ER, Zhang W, Konkashbaev A, Duan S, Kistner EO, Nicolae DL, Dolan ME, Cox NJ. "SCAN: SNP and copy number annotation". Bioinformatics, 26(2), 259-262.

  59. De la Cruz O, Wen X, Ke B, Song M and Nicolae DL. "Gene, region and pathway level analyses in whole-genome studies". Genetic Epidemiology, 34(3), 222-231.

  60. Paterson AD, Waggott D, Boright AP, Hosseini SM, Shen E, Sylvestre MP, Wong I, Bharaj B, Cleary PA, Lachin JM; MAGIC, Below JE, Nicolae D, Cox NJ, Canty AJ, Sun L, Bull SB; The Diabetes Control and Complications Trial/Epidemiology of Diabetes Interventions and Complications Research Group. "A genome-wide association study identifies a novel major locus for glycemic control in type 1 diabetes, as measured by both HbA1c and glucose". Diabetes, 59(2):539-549.

  61. Thompson EE, Haller G, Pinto JM, Sun Y, Zelano B, Jacob S, McClintock MK, Nicolae DL, Ober C. "Sequence variations at the HLA-linked olfactory receptor cluster do not influence female preferences for male odors". Hum Immunol, 71(1):100-103.

  62. Thompson EE, Sun Y, Nicolae D, Ober C. "`Shades of gray: a comparison of linkage disequilibrium between Hutterites and Europeans". Genetic Epidemiology, 34(2):133-9.


    2009

  63. Storb U, Shen HM, Nicolae D. "Somatic hypermutation: Processivity of the cytosine deaminase AID and error-free repair of the resulting uracils". Cell Cycle 8(19), 3097-3101.

  64. 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, Ferguson MK, Natarajan V, Wang YC, Garcia JG, Vokes EE, Salgia R. " Ethnic differences and functional analysis of MET mutations in lung cancer". Clin Cancer Res., 15(18), 5714-5723.

  65. Nicolae DL and Ober C. "(Too) great expectations: the challenges in replicating asthma disease genes". Am J Respir Crit Care Med., 179(12), 1078-1079.

  66. Song J and Nicolae DL "A sequential clustering algorithm with applications to gene expression data". Journal of the Korean Statistical Society, 38 (2), 175-184.

  67. 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, Rajagopalan R, Hatsukami TS, Rieder MJ, Heagerty PJ, Nickerson DA, Abney M, Marcovina S, Jarvik GP, Scanu AM, Nicolae DL. "Genome-wide association study of plasma Lp(a)levels Identifies multiple genes on chromosome 6q". J Lipid Research, 50(5), 798-806.

  68. 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". Mol Biol Evol., 26(3), 491-494.

  69. Song M, Nicolae DL. "Restricted parameter space models for testing gene-gene interaction". Genetic Epidemiology, 33(5), 386 - 393.

  70. Grassi MA, Mazzulla DA, Knudtson MD, Huang WW, Lee KE, Klein BE, Nicolae DL, Klein R. "Patient Self-Report of Prior Laser Treatment Reliably Indicates Presence of Severe Diabetic Retinopathy" Am J Ophthalmol, 147(3), 501-504.

  71. Nicolae DL, Kurz T and Ober C. "Identifying Disease Genes In Association Studies". In J.C. Bailar III and D.C. Hoaglin, editors, Medical Uses of Statistics, 455--466, The New England Journal and Medicine and Wiley, Hoboken, NJ.

  72. Nicolae DL, Kurz T and Ober C. "Genetic Inference". In J.C. Bailar III and D.C. Hoaglin, editors, Medical Uses of Statistics, 439--454, The New England Journal and Medicine and Wiley, Hoboken, NJ.


    2008

  73. Nicolae DL, Meng XL and Kong A. "Quantifying Relative Incomplete Information for Hypothesis Testing in Statistical and Genetic Studies". Statistical Science, 23(3),287--312.

  74. Nicolae DL, Meng XL and Kong A. "Rejoinder: Quantifying Relative Incomplete Information for Hypothesis Testing in Statistical and Genetic Studies". Statistical Science, 23(3),325--331.

  75. Wen X and Nicolae DL. "Association studies for untyped markers with TUNA". Bioinformatics, 24(3), 435-437.

  76. 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 Jr, Nicolae DL, Elias JA, Chupp GL. "Effect of variation in CHI3L1 on serum YKL-40 level, risk of asthma, and lung function". New England Journal of Medicine, 358(16), 1682-91.

  77. 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(8), 757-766.

  78. 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, Kistner EO, Murtha MT, Regueiro MD, Rotter JI, Schumm LP, Steinhart AH, Targan SR, Xavier RJ; the NIDDK IBD Genetics Consortium, Libioulle C, Sandor C, Lathrop M, Belaiche J, Dewit O, Gut I, Heath S, Laukens D, Mni M, Rutgeerts P, Van Gossum A, Zelenika D, Franchimont D, Hugot JP, de Vos M, Vermeire S, Louis E; the Belgian-French IBD Consortium; the Wellcome Trust Case Control Consortium; the Wellcome Trust Case Control Consortium, Cardon LR, Anderson CA, Drummond H, Nimmo E, Ahmad T, Prescott NJ, Onnie CM, Fisher SA, Marchini J, Ghori J, Bumpstead S, Gwilliam R, Tremelling M, Deloukas P, Mansfield J, Jewell D, Satsangi J, Mathew CG, Parkes M, Georges M, Daly MJ. "Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease". Nature Genetics, 40, 955 - 962.

  79. Tikhomirov A, Konkashbaev A and Nicolae DL. "On Single-Array Genotype Calling Algorithms". 2008 International Conference on BioMedical Engineering and Informatics, 27-30, 459-462.


    2007

  80. Tuvlin JA, Raza SS, Bracamonte S, Julian C, Hanauer SB, Nicolae DL, King AC, Cho JH. "Smoking and inflammatory bowel disease: Trends in familial and sporadic cohorts". Inflamm Bowel Disease, 13(5), 573-579.

  81. 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, Mei L, Nicolae DL, Regueiro M, Schumm LP, Steinhart AH, Rotter JI, Duerr RH, Cho JH, Daly MJ, Brant SR. "Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis". Nature Genetics, 39 (5), 596-604.

  82. Kong A, McCullagh P, Meng XL and Nicolae DL. "Further Explorations of Likelihood Theory for Monte Carlo Integration". in Advances in Statistical Modeling and Inference; Essays in Honor of Kjell Doksum, World Scientific Publishing Company, Imperial College Press.

  83. Zhang X, De la Cruz O, Pinto J, Nicolae D, Firestein S and Gilad Y. "Characterizing the expression of the human olfactory receptor gene family using a novel DNA microarray". Genome Biology, 8(5):R86.

  84. Thompson EE, Pan L, Ostrovnaya I, Weiss LA, Gern JE, Lemanske RF, Nicolae DL, Ober C. "Integrin beta3 genotype influences asthma and allergy phenotypes in the first 6 years of life". J Allergy Clin Immunol, 119(6), 1423-1429.

  85. Tan Z, Randall G, Fan J, Camoretti-Mercado B, Brockman-Schneider R, Pan L, Solway J, Gern JE, Lemanske Jr. RF, Nicolae D, and Ober C. "Allele-Specific Targeting of microRNAs to HLA-G and Risk of Asthma". American Journal of Human Genetics, 81, 829-834.


    2006

  86. Gewirtz AT, Vijay-Kumar M, Brant SR, Duerr RH, Nicolae DL, Cho J. "Dominant-Negative TLR5 Polymorphism Reduces Adaptive Immune Response to Flagellin and negatively associates with Crohn's Disease". Am J Physiol Gastrointest Liver Physiol, 290(6), 1157-1163 .

  87. Achkar JP, Dassopoulos T, Silverberg MS, Tuvlin J, Duerr RH, Brant SR, Siminovitch K, Reddy D, Datta LW, Bayless TM, Zhang L, Barmada MM, Rioux JD, Steinhart HA, McLeod RS, Griffiths AM, Cohen Z, Yang H, Bromfield GP, Schumm P, Hanauer SB, Cho JH, Nicolae DL and the NIDDK IBD Genetics Consortium. "Phenotype-stratified genetic linkage study demonstrates that IBD2 is an extensive ulcerative colitis locus". The American Journal of Gastroenterology, 101, 572-580.

  88. Nicolae DL, Wen X, Voight BF, Cox NJ. "Coverage and characteristics of the Affymetrix GeneChip Human Mapping 100K SNP set". PLoS Genetics, 2(5), e67.

  89. Nicolae DL, Wu X, Miyake K, Cox NJ. "GEL: a novel genotype calling algorithm using empirical likelihood". Bioinformatics, 22(16), 1942-1947.

  90. Nicolae DL. "Quantifying the Amount of MissingInformation in Genetic Association Studies". Genetic Epidemiology, 30(8):703-717.

  91. Nicolae DL. "Testing untyped alleles (TUNA) - applications to genome-wide association studies". Genetic Epidemiology, 30(8): 718-727.

  92. Shen HM, Tanaka A, Bozek G, Nicolae D, Storb U. "Somatic hypermutation and class switch recombination in msh6-/-ung-/- double-knockout mice". The Journal of Immunology, 177(8), 5386--5392.

  93. Duerr RH, Taylor KD, Brant SR, Rioux JD, Silverberg MS, Daly MJ, Steinhart AH, Abraham C, Regueiro M, Griffiths A, Dassopoulos T, Bitton A, Yang H, Targan S, Datta LW, Kistner EO, Schumm LP, Lee A, Gregersen PK, Barmada MM, Rotter JI, Nicolae DL, Cho JH. "A Genome-Wide Association Study Identifies IL23R as an Inflammatory Bowel Disease Gene". Science, 314 (5804), 1461-1463.


    2005 and earlier

  94. Longerich S, Tanaka A, Bozek G, Nicolae D, Storb U (2005) "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(100), 1443-1454.

  95. Nicolae DL (2005) "Information content in gene mapping". in Encyclopedia of Genomics, Proteomics and Bioinformatics, John Wiley & Sons.

  96. 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 (2005) "Gene-environment interaction effects on the development of immune responses in the 1st year of life". American Journal of Human Genetics, 76(4), 696-704.

  97. Nicolae D, Cox NJ, Lester LA, Schneider D, Tan Z, Billstrand C, Kuldanek S, Donfack J, Kogut P, Patel NM, Goodenbour J, Howard T, Wolf R, Koppelman GH, White SR, Parry R, Postma DS, Meyers D, Bleecker ER, Hunt JS, Solway J, Ober C (2005) "Fine Mapping and Positional Candidate Studies Identify HLA-G as an Asthma Susceptibility Gene on Chromosome 6p21". American Journal of Human Genetics, 76(2), 349-357.

  98. Li J, Moran T, Swanson E, Julian C, Harris J, Bonen DK, Hedl M, Nicolae DL, Abraham C, Cho JH (2004) "Regulation of IL-8 and IL-1$\beta$ expression in Crohn's disease associated NOD2/CARD15 mutations". Human Molecular Genetics, 13(16), 1715-1725.

  99. Nicolae DL and Kong A (2004) Measuring the Relative Information in Allele-Sharing Linkage Studies". Biometrics, 60, 368-375.

  100. Barmada MM, Brant SR, Nicolae DL, Achkar JP, Panhuysen CI, Bayless TM, Cho JH, Duerr RH (2004) A genome scan in 260 inflammatory bowel disease-affected relative pairs". Inflammatory Bowel Disease, 10(1), 15-22.

  101. Hoffjan S, Ostrovnaya I, Nicolae D, Newman DL, Nicolae R, Gangnon R, Steiner L, Walker K, Reynolds R, Greene D, Mirel D, Gern JE, Lemanske RF, and Ober C(2004) Genetic variation in immunoregulatory pathways and atopic phenotypes in infancy". J Allergy Clin Immunol, 113, 511-518.

  102. 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, Mikus LD, Rosenthal LA, Ober C, Gangnon R, Lemanske RF (2004) Effects of dog ownership and genotype on immune development and atopy in infancy". J Allergy Clin Immunol, 113, 307-314.

  103. Hoffjan S, Nicolae D, Ober C (2003) Association studies for asthma and atopic diseases: a comprehensive review of the literature". Respiratory Research, 4, 14.

  104. Brant SR, Panhuysen C, 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 (2003) "MDR1 Ala893 Polymorphism Is Associated with Inflammatory Bowel Disease". American Journal of Human Genetics, 73, 1282-1292.

  105. Regunathan A, Glesne DA, Wilson AK, Song J, Nicolae D, Flores T, Bhattacharyya MH (2003) Microarray analysis of changes in bone cell gene expression early after cadmium gavage in mice". Toxicology and Applied Pharmacology, 191, 272-293.

  106. Colilla S, Nicolae D, Pluzhnikov A, Blumenthal MN, Beaty TH, Bleecker ER, Lange EM, Rich SS, Meyers DA, Ober C, Cox NJ (2003) "Evidence for gene-environment interactions in a linkage study of asthma and smoking exposure". J Allergy Clin Immunol, 111, 840-846.

  107. Bonen DK, Ogura Y, Nicolae DL, Inohara N, Saab L, Tanabe T, Chen FF, Foster SJ, Duerr RH, Brant SR, Cho JH, Nunez G (2003) "Crohn's disease-associated NOD2 variants share a signaling defect in response to lipopolysaccharide and peptidoglycan". Gastroenterology, 124, 140-146.

  108. Kong A, McCullagh P, Meng XL, Nicolae D and Tan Z (2003) "A Theory of Statistical Models for Monte Carlo Integration". Journal of Royal Statistical Society Series B, 65, 585-618

  109. Gu Z, Nicolae D, Lu H, Li W-H (2002) "Rapid Divergence in Expression between Duplicate Genes Inferred from Microarray Gene Expression Data". Trends in Genetics}, 18, 609-613.

  110. Michael N, Martin TE, Nicolae D, Kim N, Padjen K, Zhan P, Nguyen H, Pinkert C, Storb U (2002) "Effects of sequence and structure on the hypermutability of immunoglobulin genes". Immunity, 16, 123-134.

  111. Nicolae DL and Cox NJ (2002) "MERLIN...and the Geneticist's Stone?" Nature Genetics, 30, 3-4.

  112. Lachmeijer AM, Arngrimsson R, Bastiaans EJ, Frigge ML, Pals G, Sigurdardottir S, Stefansson H, Palsson B, Nicolae D, Kong A, Aarnoudse JG, Gulcher JR, Dekker GA, ten Kate LP, Stefansson K (2001) "A genome-wide scan for preeclampsia in the Netherlands". Eur J Hum Genet, 9, 758-764.

  113. Ogura Y, Bonen, DK, Inohara N, Nicolae DL, Chen F, Ramos R, Britton H, Moran T, Karaliuskas R, Duerr RH, Achkar JP, Brant SR, Bayless TM, Kirschner BS, Hanauer SB, Nunez G and Cho J (2001) "A Frameshift Mutation in NOD2 Associated with Susceptibility to Crohn's Disease". Nature, 411, 603-606.

  114. Kong A and Nicolae DL (2000) "On a Randomization Procedure". American Journal of Human Genetics, 67, 1352-1355.

  115. Cho JH, Nicolae DL, Ramos R, Fields CT, Rabenau K, Corradino S, Brant SR, Espinosa R, LeBeau M, Hanauer SB, Bodzin J and Bonen DK (2000) "Linkage and Linkage Disequilibrium in Chromosome 1 Band 1p36 in American Chaldeans with Inflammatory Bowel Disease". Human Molecular Genetics, 9, 1425-1432.

  116. Arngrimsson R, Sigurdardottir S, Frigge ML, Bjarnadottir RI, Jonsson T, Stefansson H, Baldursdottir A, Einarsdottir AS, Palsson B, Snorradottir S, Lachmeijer AMA, Nicolae DL, Kong A, Bragason BT, Gulcher JR, Geirsson RT, and Stefansson K (1999) "A Genome-Wide Scan Reveals a Maternal Susceptibility Locus for Pre-eclampsia on Chromosome 2p13". Human Molecular Genetics, 8, 1799-1805.

  117. Nicolae DL, Frigge ML, Cox NJ and Kong A (1998) Discussion to "Multipoint Linkage Analysis Using Affected Relative Pairs and Partially Informative Markers" by Siegmund D and Teng J. Biometrics}, 54, 1271-1274.

  118. Cox N, Frigge M, Nicolae DL, Concannon P, Hanis CL, Bell GI, and Kong A (1999) "Loci on Chromosomes 2 (NIDDM1) and 15 Interact to Increase Susceptibility to Type 2 Diabetes in Mexican Americans". Nature Genetics, 21(2), 213:215.

  119. 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 and Brant SR (1998) "Identification of Novel Susceptibility Loci for Inflammatory Bowel Disease". Proceedings National Academy of Science, 95(13), 7502-7507.

  120. Sweeney P, Nicolae D,Ignacio L, Chen L, Roach M 3rd, Wara W, Marcus KC, Vijayakumar S (1998) "Effect of Subcutaneous Recombinant Human EPO in Cancer Patients Receiving Radiotherapy". British Journal of Cancer, 77(11), 1996-2002.