Publications by Yuehua Cui

By year

Peer-referred journal articles (Trainee and *corresponding author)

Theory and Methodology

  1. Wu, C., P-S. Zhong and Y.H. Cui*. (2018) Variable selection in varying-coefficient models for gene-environment interactions. Statistical Applications in Genetics and Molecular Biology (accepted)
  2. Wang, H.L., P-S. Zhong, Y.H. Cui and Y. Li. (2018) Unified empirical likelihood ratio tests for functional concurrent linear models and the phase transition from sparse to dense functional data. [Supplemental files] Journal of the Royal Statistical Society B (in press)

3.       Wu, C., Y. Jiang, J. Ren, Y. Cui and S. Ma. (2018) Dissecting gene-environment interactions: a penalized robust approach accounting for hierarchical structures. Statistics in Medicine (in press)

4.       Wang, H., P-S. Zhong and Y.H. Cui. (2018) Empirical likelihood ratio tests for coefficients in high dimensional heteroscedastic linear models. Statistica Sinica (in press)

5.       Cao, H.Y., Z. Li, H. Yang, Y.H. Cui* and Y. Zhang*. (2017) Longitudinal next-generation sequencing data analysis for rare variants detection with penalized quadratic inference function. Scientific Reports 7: 650. doi:  10.1038/s41598-017-00712-9

6.       Yang, H., S. Li, H. Cao, C. Zhang and Y.H. Cui*. (2017) Predicting disease trait with genomic data: a composite kernel approach. Briefings in Bioinformatics 18(4):591-601.

7.       Zhao, J., S. Li, L. Wang, L. Jiang, R. Yang* and Y.H. Cui*. (2017) Genome-wide random regression analysis for parent-of-origin effects of body composition allometries in mouse. Scientific Reports 7: 45191. doi:10.1038/srep45191.

  1. Liu, X., B. Gao and Y.H. Cui*. (2017) Generalized partial linear varying multi-index coefficient model for gene-environment interactions. Statistical Applications in Genetics and Molecular Biology 16(1): 59-74. doi: 10.1515/sagmb-2016-0045.

9.       Liu, X., H. Wang and Y.H. Cui*. (2016) Statistical identification of gene-gene interactions triggered by nonlinear environmental modulation. Current Genomics 17(5): 388-395.

10.  Li, G. and Y.H. Cui*. (2016) Assessing statistical significance in variance components linkage analysis: a theoretical justification. Journal of Statistical Planning and Inference 178: 70-83 [PDF]

11.  Sa, J., X. Liu, T. He, G. Liu* and Y.H. Cui*. (2016) A nonlinear model for gene-based gene-environment interaction. International Journal of Molecular Sciences 17(6): 882; doi:10.3390/ijms17060882.

12.  Liu, X., Y.H. Cui* and R. Li. (2016) Partial linear varying multi-index coefficient model for integrative gene-environment interactions. [Supplemental file] Statistica Sinica 26: 1037-1060

13.  Li, Z., H.Y. Cao, Y.H. Cui*, Y.B. Zhang*. (2016) Extracting DNA Words Based on the Sequence Features: Non-uniform Distribution and Integrity. Theoretical Biology and Medical Modelling 13:2.

14.  Li, G., Y.H. Cui and H. Zhao. (2015) An empirical Bayes risk prediction model for multiple traits using sequencing data. Statistical Applications in Genetics and Molecular Biology 14(6): 551-73.

  1. Wu, C., X. Shi, Y.H. Cui and S.G. Ma. (2015) A penalized robust semi-parametric approach for gene-environment interactions. Statistics in Medicine 34(30):4016-30.
  2. Gao, B. and Y.H. Cui*. (2015) Learning directed acyclic graphical structures with genetical genomics data. Bioinformatics 31:3953-3960.
  3. Bi, W., G. Kang, Y. Zhao, Y.H. Cui, Y. Li, C.M. Hartford, W. Leung and J-F. Zhang. (2015) SVSI: A fast and powerful set-valued system identification approach to identifying rare variants in sequencing studies for ordered categorical traits. Annals of Human Genetics 79(4): 294-309.
  4. Wu, C., Y.H. Cui and S.G. Ma. (2014) Integrative analysis of gene-environment interactions under a multi-response partially linear varying coefficient model. Statistics in Medicine 33: 4988-4998.
  5. Li, S.*, Y.H. Cui* and R. Romero. (2014) An entropy approach for the dissection of maternal-fetal genotype incompatibility effect. BMC Genetics 15: 66.
  6. He, T., J. Sa, P-S. Zhong and Y.H. Cui*. (2014) Statistical dissection of cytonuclear epistasis subject to genomic imprinting in line crosses. PloS One 9(7): e103018.
  7. Wu, C. and Y.H. Cui*. (2014) Boosting signals in gene-based association studies via efficient SNP selection. Briefings in Bioinformatics 15(2):279-291.

22.  He, T., P-S. Zhong and Y.H. Cui*. (2014) Gene set association test identifies sex-specific pathways associated with type 2 diabetes. Frontiers in Genetics: Statistical Genetics and Methodology 5: 395.

  1. Dai, H.Y., T. Srivastava, and Y.H. Cui. (2014) A modified generalized fisher method for combining probabilities from dependent tests. Frontiers in Genetics 5:23.
  2. Wu, C. and Y.H. Cui*. (2013) A novel method for identifying nonlinear gene-environment interactions in case-control association studies. Human Genetics 132(12): 1413-1425.
  3. 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. Journal of Proteomics and Genomics Research 1(2): 39-60.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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]
  9. 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)
  10. Wu, C., G.X. Li, J. Zhu, and Y.H. Cui*. (2011) Functional mapping with robust t-distribution. PloS One 6(9): e24902.
  11. 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.
  12. 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].
  13. Li, M.#, R. Romero, W.J. Fu* and Y.H. Cui*. (2010) Mapping haplotype-haplotype interactions with adaptive LASSO. BMC Genetics 11:79 [ PubMed] (#This work was initiated as a class project when M. Li attended my Statistical Genetics class in Fall 2007.)
  14. 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 [PDF] (invited)
  15. 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): 401-414.
  16. 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. [PubMed]
  17. 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]
  18. 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].
  19. 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].
  20. 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)
  21. 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].
  22. 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 5:6. [PubMed].
  23. 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].
  24. 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].
  25. 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].
  26. 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].
  27. 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].
  28. 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].
  29. 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].
  30. 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].
  31. 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].
  32. 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].
  33. Cui, Y.H. and R.L. Wu. (2005) Mapping genome-genome epistasis: A high-dimensional model. Bioinformatics 21(10): 2447-2455 [PubMed].
  34. 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].
  35. 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].
  36. 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]

Applications and Reviews

59.  Zhao, D., J.P. Hamilton, B. Vaillancourt, W. Zhang, G.C. Eizenga, Y.H. Cui, J. Jiang, C.R. Buell, and N. Jiang. (2018) The unique epigenetic features of Pack-MULEs and their impact on chromosomal base composition and expression spectrum. Nucleic Acids Research (accepted)

  1. Wu, D., H. Yang, S.J. Winham, Y. Natanzon, D.C. Koestler, T. Luo, B.L. Fridley, E.L. Goode, Y.B. Zhang and Y.H. Cui*. (2018) Mediation analysis of alcohol consumption, DNA methylation, and epithelial ovarian cancer. Journal of Human Genetics (in press)

61.  Cao, HY, P. Zeng, Z. Li, Y.H. Cui and Y.B. Zhang. (2017) The application of penalized generalized estimating equations in genetic association with longitudinal data. Chinese Journal of Health Statistics 34(4): 534-537.

  1. Cui, Y.H.* and H. Yang. (2017) Dissecting genomic imprinting and genetic conflict from a game theory prospective: Comment on: “Epigenetic game theory: How to compute the epigenetic control of maternal-to-zygotic transition” by Qian Wang et al. Physics of Life Reviews 20: 161-163.

63.  Ren, Yan, J. Jia, J. Sa, L-X. Qiu, Y.H. Cui, Y-A. Zhang, H. Yang, G-F. Liu. (2017) Association between N-terminal proB-type natriuretic peptide and depressive symptoms in patients with acute myocardial infarction. Chinese Medical Journal 130(5): 542-548.

64.  Zhao, D., J. Hamilton, M. Hardigan, D. Yin, T. He, B. Vaillancourt, M. Reynoso, G.G. Pauluzzi, S. Funkhouser, Y.H. Cui, J. Bailey-Serres, J. Jiang, C.R. Buell and N. Jiang. (2017) Analysis of ribosome-associated mRNAs in rice reveals the importance of transcript size and GC content in translation. G3 7(1): 203-219.

65.  Luo, T., X. Liu and Y.H. Cui*. (2016) A genome-wide association analysis in four populations reveals strong genetic heterogeneity on birth weight. Current Genomics 17(5): 416-426. DOI: 10.2174/1389202917666160726152033 

  1. Cao, H.Y., X. Wei, X. Guo, C. Song, Y. Luo, Y.H. Cui, X. Hu, and Y. Zhang. (2015) Screening high-risk clusters for developing birth defects in mothers in Shanxi Province, China: application of latent class cluster analysis.  BMC Pregnancy and Childbirth 15: 343.
  2. Manrique-Carpintero, N. C., J.J. Coombs, Y.H. Cui, R.E. Veilleux, C. R. Buell, and D. Douches. (2015) Genetic map and QTL analysis of agronomic traits in a diploid potato population using SNP markers. Crop Science 55(16): 2566-2579.

68.  Cui, Y.H.  (2015)  “Statistical methods for QTL mapping” by Z. Chen. Journal of the American Statistical Association. 110(510): 888 (book review)

69.  Habing, G.G., S. Manning, C. Bolin, Y.H. Cui, J. Rudrik, S. Dietrich and J.B. Kaneene. (2015) Within-farm changes in dairy farm associated Salmonella subtypes and comparison to human clinical isolates in Michigan, USA, 2000-2001 and 2009. Applied and Environmental Microbiology 81: 17.

70.  Ren Y, Cui Y.H., Li X, Wang B, Na L, Shi J, Wang L, Qiu L, Zhang K, Liu G, Xu Y. (2015) A co-expression network analysis reveals lncRNA abnormalities in peripheral blood in early-onset schizophrenia. Progress in Neuro-psychopharmacology & Biological Psychiatry 63: 1-5.

71.  Li Z., Y.H. Cui and Y.B. Zhang. (2014) Quantification of the differences in genome sequence distribution. Chinese Journal of Health Statistics 31(4): 554-558.

72.  Humphries, Brock, Z. Wang, A. Oom, T. Fisher, D. Tan, Y.H. Cui, Y. Jiang, and C. Yang. (2014) nMicroRNA-200b targets protein kinase Cα and impairs triple negative breast cancer cell migration and tumor metastasis. Carcinogenesis 35(10): 2254-2263.

73.  Jing, L., C. Qu, H. Yu, T. Wang and Y.H. Cui. (2014) Estimating the sizes of populations at high risk for HIV: A comparison study. PloS One 9(4): e95601.

74.  Wang H., T. He, C. Wu, P.S. Zhong and Y.H. Cui*. (2014) A powerful statistical method identifies novel loci associated with diastolic blood pressure triggered by nonlinear G×E interaction. BMC Proceedings 8(Suppl 1): S61.

75.  Bi, W., G. Kang, Y. Cui, Y. Li, C.M. Hartford, W. Leung, J.F. Zhang. (2014) A new set-valued system identification approach to identifying rare genetic variants for ordered categorical phenotype. BMC Bioinformatics 15(Suppl 10): P29.

76.  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.

77.  Kang, G.L., B. Jiang and Y.H. Cui. (2013) Gene-based genomewide association analysis: a comparison study. Current Genomics 14: 4.

78.  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

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

80.  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. [PubMed]

81.  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)

82.  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].

83.  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.

84.  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.

85.  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.

86.  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.

2000 & earlier (in Chinese with English abstract)

87.  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

88.  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.

89.  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.

90.  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.

91.  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.

Invited book chapters

92.  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.

  1. 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.

Papers submitted

  1. He, T., P-S. Zhong, Y.H. Cui and V. Mandrekar. Tests for high-dimensional nonparametric functions in RKHS with kernel selection and regularization.
  2. Gao, B., X. Liu, H.Z. Li and Y.H. Cui*. Integrative analysis of genetical genomics data incorporating network structures.

Research Highlight

Last Modified in 2017