Publications by Yuehua Cui

Invited book chapters
  1. Liu, T., A. Berg, J.S. Wu, B. Zhang, Y.H. Cui, Z.Y. Zhang and R.L. Wu (2009) Haplotype analysis of complex traits in outcrossing tree species: Allele discovery of quantitative trait loci. In: Poplar Genomics (Eds.: S. Joshi and S. DiFazio) Science Publishers of Edenbridge Ltd.
  2. Cui, Y.H., G.X. Li, S.Y. Li and R.L. Wu. 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. (to be published in 2010)
Peer-referred journal articles

Working papers (Trainees and corresponding author*)
  1. Ye, C.Y., Y.H. Cui, R.C. Elston, J. Zhu, and Q. Lu. A novel non-parametric method for building predictive genetic tests, with an application to rheumatoid arthritis.
  2. Li, G.X. and Y.H. Cui*. Assessing statistical significance in variance components linkage analysis.
  3. Yang, R., X. Wang, and Y.H. Cui*. Bayesian inference for genomic imprinting underlying developmental characteristics.
  4. Li, S.Y. and Y.H. Cui*. Correlation matters: a combined p-value approach for inferring enriched genetic pathways in eQTL mapping.
  5. Li, M., R. Romero, W.J. Fu and Y.H. Cui*. Mapping haplotype-haplotype interactions with adaptive LASSO.
  6. Park, H.-B., A. Abhyankar, Y.H. Cui, and H. Luthman. Interaction between nuclear and mitochondrial genes in the GK rat model for type 2 diabetes.
  7. Li, M., K. Sun, Y.H. Cui, M. Qian, R. Romero and W. Fu. Testing maternal-fetal genotype incompatibility with mother-offspring pair data and its application.
  8. Cui, Y.H.*, and D.-Y. Kim. On the limiting distribution of the likelihood ratio test in nucleotide mapping of complex disease. Statistics and Probability Letters (under revision)
Methodology
  1. Li, G.X. and Y.H. Cui*. (2009+) A general statistical framework for dissecting parent-of-origin effects underlying triploid endosperm traits in flowering plants. The Annals of Applied Statistics (minor revision)
  2. Li, S.Y., Q. Lu and Y.H. Cui*. (2009+) A systems biology approach for identifying novel pathway regulators in eQTL mapping. Journal of Biopharmaceutical Statistics (to appear)
  3. Lu, Q, Y.H. Cui, C. Ye, C. Wei and R.C. Elston. (2009+) A bagging optimal roc curve method for predictive genetic tests with an application to rheumatoid arthritis. Journal of Biopharmaceutical Statistics (to appear)
  4. 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 (in press)
  5. 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.
  6. 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. [Link]
  7. 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].
  8. 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].

  9. 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].
  10. 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].
  11. 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].
  12. 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].
  13. 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].

  14. 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 [Link].
  15. Wu, J.S., B. Zhang, Y.H. Cui, W. Zhao, L. Xu, Huang, Y. Zeng, and R. Wu. (2007) Genetic determination of developmental instability: design, model and algorithm. Genetics 176: 1187-1196 [PDF].
  16. 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].
  17. 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].

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

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

  24. 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 [PDF].
  25. 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]
Review
  1. 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].
Applications
  1. 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.
  2. 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.

  3. 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.

  4. Sun, K.L., Y.H. Cui and B. Hauser. (2005) Changes in gene expression during ovule abortion in Arabidopsis. Planta 222: 632-642.
2000 & earlier (in Chinese)
  1. 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
  2. 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.
  3. 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.
  4. 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.
  5. 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.
Last Modified Sept. 2009