Publications by Yuehua Cui

(Trainees and *corresponding author)


1.      Wu, C. and Y.H. Cui*. (2013) A novel method for identifying nonlinear gene-environment interactions in case-control association studies. Human Genetics (accepted)

2.      Fu, W.J., M. Li, K. Sun, Y.H. Cui, M. Qian, and R. Romero. (2013) Testing Maternal-Fetal Genotype Incompatibility With Mother-Offspring Pair Data. Proteomics and Genomics Research (in press)

3.      Wu, C. and Y.H. Cui*. (2013) Boosting signals in gene-based association studies via efficient SNP selection. Briefings in Bioinformatics (in press)PDF

4.      Wang H., T. He, C. Wu, P.S. Zhong and Y.H. Cui*. (2013) A powerful statistical method identifies novel loci associated with diastolic blood pressure triggered by nonlinear GxE interaction. BMC Proceedings (in press)

5.      Dang, M-T., C. Gu, J.I. Klavanian, K.A. Jernigan, K.H. Friderici, Y.H. Cui, M. Molina-Molina, J. Ancochea, A. Xaubet, and B.D. Uhal. (2013) Angiotensinogen promoter polymorphisms predict low diffusing capacity in U.S. and Spanish idiopathic pulmonary fibrosis cohorts. Lung 191(4):353-360.  

6.      Kim, D-Y., Y.H. Cui and O. Zhao. (2013) Asymptotic test of mixture model and its applications to QTL interval mapping. Journal of Statistical Planning and Inference 143: 1320-1329.


7.      Geu-Flores, F., N.H. Sherden, V. Courdavault, V. Burlat, W.S. Glenn, C. Wu, E. Nims, Y.H. Cui, and S.E. O’Connor. (2012) An alternative route to cyclic terpenes by reductive cyclization in iridoid biosynthesis. Nature 492: 138–142 doi:10.1038/nature11692.

8.      Wu, C., S. Li and Y.H. Cui*. (2012) Genetic association studies: an information content perspective. Current Genomics 13 (7): 566-573.

9.      Li, S.Y. and Y.H. Cui*. (2012) Gene-centric gene-gene interaction: a model-based kernel machine method. Annals of Applied Statistics [ PDF] 6(3): 1134-1161.

10.  Yang, R.Q., X. Wang, and Y.H. Cui*. (2012) Bayesian inference for genomic imprinting underlying developmental characteristics. Briefings in Bioinformatics [PDF] 13(5): 555-568.

11.  Li, G.X.,C. Wu, , C. Coelho, R. Wu, B.A. Larkins and Y.H. Cui*. (2012) A bivariate variance components model for mapping imprinted quantitative trait loci underlying endosperm traits. Frontiers in Bioscience (Elite Ed) 4: 2464-2475.


12.  Ye, C.Y., Y.H. Cui, C. Wei, R.C. Elston, J. Zhu, and Q. Lu. (2011) A non-parametric method for building predictive genetic tests on high-dimensional data. Human Heredity 71: 161–170 [PDF]

13.  Li, S.Y., B. Williams and Y.H. Cui*. (2011) A combined p-value approach to infer pathway regulations in eQTL mapping. Statistics and Its Interface 4(3): 389-402 [PDF] (invited)

14.  Wu, C., G.X. Li, J. Zhu, and Y.H. Cui*. (2011) Functional mapping with robust t-distribution. PloS One 6(9): e24902.

15.  Ma, S.J., L.J. Yang, R. Romero, and Y.H. Cui*. (2011) Varying coefficient model for gene-environment interaction: a non-linear look. Bioinformatics 27(15): 2119-2126.

16.  Liu, T., C. Tong, J.S. Wu, B. Zhang, Y.H. Cui, Y. Li, Y. Zeng and R.L. Wu. (2011) Haplotype Analysis of Complex Traits in Outcrossing Tree Species: Allele Discovery of Quantitative Trait Loci. In: Genetics, Genomics and Breeding of Poplar (C.P. Joshi, S.P. DiFazio, and C. Kole eds.) Science Publishers, Northants, UK. (invited book chapter)


17.  Li, G.X. and Y.H. Cui*. (2010) A general statistical framework for dissecting parent-of-origin effects underlying triploid endosperm traits in flowering plants. Annals of Applied Statistics 4(3): 1214-1233. [PDF]|[Link to the Journal]. 

18.  Li, M., R. Romero, W.J. Fu and Y.H. Cui*. (2010) Mapping haplotype-haplotype interactions with adaptive LASSO. BMC Genetics 11:79.

19.  Li, S.Y., Q. Lu and Y.H. Cui*. (2010) A systems biology approach for identifying novel pathway regulators in eQTL mapping. Journal of Biopharmaceutical Statistics 20(2): 373-400. [preprint]

20.  Lu, Q, Y.H. Cui, C. Ye, C. Wei and R.C. Elston. (2010) A bagging optimal roc curve method for predictive genetic tests with an application to rheumatoid arthritis. Journal of Biopharmaceutical Statistics 20(2): 401-453.

21.  Cui, Y.H.*, G.X. Li, S.Y. Li and R.L. Wu. (2010) Designs for Linkage Analysis and Association Studies of Complex Diseases. In: Statistical Methods in Molecular Biology (Eds.: Bang, H, Zhou, XK, Van Epps, H, Mazumdar, M.) Humana Press. (invited book chapter)


22.  Lu, Q, Y. Song, X.F. Wang, S. Won, Y.H. Cui and R.C. Elston. (2009) The effect of multiple genetic variants in predicting the risk of Type 2 Diabetes. BMC Proceedings 3(Suppl 7):S49.

23.  Wan, L. K. Sun, Q. Ding, Y.H. Cui, M. Li, Y. Wen, R. Elston, M. Qian, W.J. Fu. (2009) Hybridization modeling of oligonucleotide SNP arrays for accurate DNA copy number estimation. Nucleic Acids Research 37(17): e117.

24.  Li, S.Y., Q. Lu, W. Fu, R. Romero and Y.H. Cui*. (2009) A regularized regression approach for dissecting genetic conflicts that increase disease risk in pregnancy. Statistical Applications in Genetics and Molecular Biology Vol. 8 : Iss. 1, Article 45. [PubMed]

25.  Li, G.X. and Y.H. Cui*. (2009) A statistical variance components framework for mapping imprinted quantitative trait loci in experimental crosses. Journal of Probability and Statistics vol. 2009, Article ID 689489, doi:10.1155/2009/689489 [PDF].

26.  Cui, Y.H.* and W.Z. Yang. (2009) Zero inflated generalized poisson regression mixture model for mapping quantitative trait loci underlying count trait with many zeros. Journal of Theoretical Biology 256: 276-285 [PubMed].

27.  Cui, Y.H.  (2009) “Multivariate Statistics: Exercises and Solutions” by W. Hardle and Z. Hlavka. Journal of the American Statistical Association 104(488): 1722. (book review)


28.  Cui, Y.H.*, G.L. Kang, K.L. Sun, R. Romero, M. Qian, and W.J. Fu. (2008) Gene-centric genomewide association study via entropy. Genetics 179: 637-650 [Link] | [ PubMed]. (This work was highlighted in Nature Reviews Genetics)

29.  Ma, C-X., Q. Yu, A. Berg, D. Drost, E. Novaes, G. Fu, J.S. Yap, A. Tan, M. Kirst, Y.H. Cui and R.L. Wu. (2008) A statistical model for testing the pleiotropic control of phenotypic plasticity for a count trait. Genetics 179: 627-636. [PubMed].

30.  Cui, Y.H.*, S.Y. Li, and G.X. Li. (2008) Functional mapping imprinted quantitative trait loci underlying developmental characteristics. Theoretical Biology and Medical Modeling 6:5. [PubMed].

31.  Cui, Y.H.*, R.L. Wu, G. Casella, and J. Zhu. (2008) Nonparametric functional mapping quantitative trait loci underlying programmed cell death. Statistical Applications in Genetics and Molecular Biology Vol. 7: Iss. 1, Article 4. [PubMed].

32.  Kang G., W. Yue, J. Zhang, Y.H. Cui, Y. Zuo and D. Zhang. (2008) An entropy-based approach for testing genetic epistasis underlying complex diseases. Journal of Theoretical Biology 250: 362-374 [PubMed].


33.  Cui, Y.H.*, W. Fu, K.L. Sun, R. Romero, and R. Wu. (2007) Mapping nucleotide sequences that encode complex binary disease traits with HapMap. Current Genomics 8(5): 307-322 [PubMed].

34.  Wu, J.S., B. Zhang, Y.H. Cui, W. Zhao, L. Xu, Huang, Y. Zeng, J. Zhu and R. Wu. (2007) Genetic mapping of developmental instability: design, model and algorithm. Genetics 176: 1187-1196 [PDF].

35.  Cintia, M.C., S, Wu, Y. Li, B. Hunter, R.A. Dante, Y.H. Cui, R.L. Wu, and B.A. Larkins. (2007) Identification of quantitative trait loci that affect endoreduplication in maize endosperm. Theoretical and Applied Genetics 115:1147–1162.

36.  Cui, Y.H.*, J.M. Cheverud and R.L. Wu. (2007) A statistical model for dissecting genomic imprinting through genetic mapping. Genetica 130: 227-239 [PubMed].

37.  Rice, L., R. Handayani, Y.H. Cui, T. Medrano, Von G. Samedi, H.V. Baker, N.J. Szabo, and K. Shiverick. (2007) Effects of soy isoflavone concentrate on gene expression profiles in LNCaP human prostate cancer cells. Journal of Nutrition 137: 964-972.

38.  Cui, Y.H.* (2007) A statistical framework for genome-wide scanning and testing imprinted quantitative trait loci. Journal of Theoretical Biology 244: 115-126 [PubMed].

39.  Wu, R.L., W. Hou, Y.H. Cui, H.Y. Li, T. Liu, S. Wu, C-X. Ma, and Y. Zeng. (2007) Modeling the genetic architecture of complex traits with molecular markers. Recent Patent on Nanotechnology 1:41-49 (invited review) [PubMed].


40.  Cui, Y.H.*, D.-Y. Kim, and J. Zhu. (2006) On the generalized Poisson regression mixture model for mapping quantitative trait loci with count data. Genetics 174(4): 2159–2172. [PubMed].

41.  Cui, Y.H., J. Zhu, and R.L. Wu. (2006) Functional mapping for genetic control of programmed cell death. Physiological Genomics 25: 458-469 [PubMed].

42.  Cui, Y.H., J. G. Wu, C.H. Shi, J. Zhu, R.C. Littell and R.L. Wu. (2006) Modeling epistatic effects of embryo and endosperm qtl on seed quality traits. Genetical Research 87: 61-71 [PubMed].

43.  Cui, Y.H., Q. Lu, J.M. Cheverud, R.C. Littell and R.L. Wu. (2006) Model for mapping imprinted quantitative trait loci in an inbred F2 design. Genomics 87: 543-551 [PubMed].

44.  Handayani, R., L. Rice, Y.H. Cui, T. Medrano, V.G. Samedi, H. Baker, N.J. Szabo and K. Shiverick. (2006) Soy isoflavones alter expression of genes associated with cancer progression, including IL-8, in androgen-independent PC-3 human prostate cancer cells. Journal of Nutrition 136: 75-82.


45.  Cui, Y.H. and R.L. Wu. (2005) Mapping genome-genome epistasis: A high-dimensional model. Bioinformatics 21(10): 2447-2455 [PubMed].

46.  Sun, K.L., Y.H. Cui and B. Hauser. (2005) Environmental stress alters genes expression and induces ovule abortion: reactive oxygen species appear as ovules commit to abort. Planta 222: 632-642.

47.  Cui, Y.H. and R. L. Wu. (2005) A statistical model for characterizing epistatic control of triploid endosperm triggered by maternal and offspring QTL. Genetical Research 86: 65-76 [PubMed].


48.  Cui, Y. H., G. Casella and R.L. Wu. (2004) Mapping quantitative trait loci interactions from the maternal and offspring genomes. Genetics, 167: 1017-1026 [PubMed].

49.  Lu, Q., Y.H. Cui and R.L. Wu. (2004) A multilocus likelihood approach to joint modeling of linkage, parental diplotype and gene order in a full-sib family. BMC Genetics 5: 20. [PubMed]

2000 and earlier

50.  Sun, K.L., M. Wang and Y.H. Cui. (2000) Study on the Primary Vascular System of the Seedling of Nelumbo Nucifera Gaertn. Acta Botanica Yunnanica, 22(3): 286-290

51.  Cui, Y.H., M. Wang and K.L. Sun. (1999) Study on the Heterogeneity of Endosperm Cell Development in Eucommia ulmoides Oliv. Journal of Agricultural Biotechnology 7(1): 89-93.

52.  Cui, Y.H., M. Wang and K.L. Sun. (1999) Morphology of Gutta-containing Cells in Eucommia ulmoides Oliv. Chinese Bulletin of Botany 16(4): 439-443.

53.  Wang, M., Y.H. Cui and K.L. Sun. (1999) Study on the Programmed Cell Death in the Process of Endosperm Degeneration in Eucommia ulmoides Oliv. Bulletin of Botanical Research 19(4): 401-406.

54.  Zhao, Y.J., W. Zhang, G. C. Li, T. Wang and Y.H. Cui. (1998) Genetic Studies on Several Morphological Index of Columnar Apple Trees. Journal of China Agricultural University Vol. 3, supplement: 96-98.