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Nengjun Yi, Ph.D.

Nengjun Yi, Ph.D. Sir David Cox Endowed Professor in Biostatistics
Department of Biostatistics
Ryals Public Health Bldg, 317F
University of Alabama at Birmingham
Birmingham, AL 35294
Phone: (205) 934-4924
Fax: (205) 975-2540
E-mail: nyi@uab.edu
Full CV


Dr. Yi received his Ph.D. in Population and Quantitative Genetics from Nanjing Forestry University in China. He then completed a post-doctoral fellowship in Statistical Genetics at University of California at Riverside. In 2002, he joined the faculty of the University of Alabama at Birmingham where he is currently Professor in the Department of Biostatistics, the Section on Statistical Genetics. His research interests include statistical genetics, Bayesian statistics, model selection, and Markov chain Monte Carlo (MCMC) algorithms. He is particularly interested in the development of statistical and computational methods for identifying multiple interacting genes for complex traits.

Software

  • BhGLM (Bayesian hierarchical GLMs, with application to genetic data analysis)
     
  • R/qtlbim (QTL Bayesian Interval Mapping)
     

Recent Publications

Click here for listing of recent publications

  • 2013
  • 2012
  • 2011
  • 2010
  • 2009
  • 2008
  • 2007
  • 2006
  • 2005
  • 2004
  • pre 2004
  1. Yi, N. and S. Ma 2012 Hierarchical Shrinkage Priors and Model Fitting Algorithms for High-dimensional Generalized Linear Models. Statistical Applications in Genetics and Molecular Biology 11 (6): 1544-6115. [doi: 10.1515/1544-6115.1803] [PMID:23192052]
     
  2. Wan-Yu Lin, Nengjun Yi, Xiang-Yang Lou, Degui Zhi, Kui Zhang, Guimin Gao, Hemant K. Tiwari, and Nianjun Liu 2013 Haplotype Kernel Association Test as a Powerful Method to Identify Chromosomal Regions Harboring Uncommon Causal Variants. Genetic Epidemiology (in press)
     
  3. Mallick, H. and Nengjun Yi 2013 Bayesian Methods for High Dimensional Linear Models. Journal of Biometrics & Biostatistics (in press)
     
  4. Mallick, H. and Nengjun Yi 2013 Hierarchical Models for Genetic Association Studies. Journal of Biometrics & Biostatistics (in press)
     
  1. Reng-Yun Liu, Ping Chen, Zhe Lei, Jingcheng Miao, Nengjun Yi, Kui Zhang, Boris Pasche, Hong-Tao Zhang 2012 Association between IL6 -174G/C and cancer: a meta-analysis of 103,827 individuals. Experimental and Therapeutic Medicine 3(4): 655-664. [PMID: 22969947] [PMCID: PMC3438703]
     
  2. Jacquelyn W. Zimmerman, Michael J. Pennison, Ivan Brezovich, Nengjun Yi, Celeste T. Yang, Ryne Ramaker, Devin Absher, Richard M. Myers, Niels Kuster, Frederico P. Costa, Alexandre Barbault, Boris Pasche 2012 Cancer cell proliferation is inhibited by specific modulation frequencies. British Journal of Cancer 106, 307–313. [doi:10.1038/bjc.2011.523] [PMID: 22134506] [PMCID: PMC3261663]
     
  3. Ma, Shuangge, Jian Huang, Yang Xie, Nengjun Yi 2011 Identification of Breast Cancer Prognosis Markers using Integrative Sparse Boosting. Methods of Information in Medicine 51(2):152-61. [doi: 10.3414/ME11-02-0019] [PMID: 22344268]
     
  4. Wan-Yu Lin, Nengjun Yi, Degui Zhi, Kui Zhang, Guimin Gao, Hemant K. Tiwari, and Nianjun Liu 2012 Haplotype-based methods for detecting uncommon causal variants with common SNPs. Genetic Epidemiology. [doi: 10.1002/gepi.21650]
     
  5. Jun Chen, Reng-Yun Liu, Lixin Yang, Jun Zhao, Xueying Zhao, Daru Lu, Nengjun Yi, Baohui Han, Xiao-Feng Chen, Kui Zhang, Jun He, Zhe Lei, Yifeng Zhou, Boris Pasche, Xiangdong Li, Hong-Tao Zhang 2012 A two-SNP IL-6 promoter haplotype is associated with increased lung cancer risk. Journal of Cancer Research and Clinical Oncology 139: 231-242.
     
  6. Ana I. Vazquez, M.S. Gustavo de los Campos, Yann C. Klimentidis, Guilherme J.M. Rosa, Daniel Gianola, Nengjun Yi, David B. Allison 2012 A Comprehensive Genetic Approach for Improving Prediction of Skin Cancer Risk in Humans. Genetics 192, 1493–1502. [PMID: 23051645]
     
  7. Banerjee, S. and Yi, N., Identifying QTL for Multiple Complex Traits in Experimental Crosses. In "the Methods in Molecular Biology series" ed. Scott Rifkin. (2012).
     
  1. Yi N, Zhi D. Bayesian analysis of rare variants in genetic association studies. Genet Epidemiol. 2011. 35:57-69. [PMID: 21181897] [DOI: 10.1002/gepi.20554]
     
  2. Virginia Kaklamani, N. Yi, K. Zhang, Maureen Sadim, Kenneth Offit, Carole Oddoux, Harry Ostrer, Christos Mantzoros, Boris Pasche. 2011 Polymorphisms of ADIPOQ and ADIPOR1 and prostate cancer risk. Metabolism. Metabolism 60(9):1234-43. [PMID: 21397927] [PMCID: PMC3134585]
     
  3. Jun Li, Kui Zhang, and Nengjun Yi 2011 A Bayesian hierarchical model for detecting haplotype-haplotype and haplotype-environment interactions in genetic association studies. Human Heredity 71(3): 148-60 [DOI: 10.1159/000324841]. [PMID: 21778734] [PMCID: PMC3153342]
     
  4. Lin WY, Zhang B, Yi N, Gao G, Liu N 2011 Evaluation of Pooled Association Tests for Rare Variants Identification with the Genetic Analysis Workshop 17 Data BMC Proceedings 5 (Suppl 9): S118.
     
  5. Virginia Kaklamani, Nengjun Yi, Maureen Sadim, Kalliopi Siziopikou, Kui Zhang, Yianfei Xu, Sarah Tofilon, Surbhi Agarwal, Boris Pasche and Christos Mantzoros 2011 The role of the fat mass and obesity associated gene (FTO) in breast cancer risk. BMC Medical Genetics, 12:52, [PMID: 21489227] [PMCID: PMC3089782] [DOI: 10.1186/1471-2350-12-52]
     
  6. Yi N, Kaklamani VG, Pasche B. Bayesian analysis of genetic interactions in case-control studies, with application to adiponectin genes and colorectal cancer risk. Ann Hum Genet. 2011 Jan;75(1):90-104. [PMID: 20846215] [DOI: 10.1111/j.1469-1809.2010.00605.x]
     
  7. John J Arcaroli, Nianjun Liu, Nengjun Yi, and Edward Abraham 2011 Association between IL- 32 and outcome in infection-associated acute lung injury. Critical Care 15:R138. [PMID: 21649914]
     
  8. Wu G, Yi N, Absher D, Zhi D (2011) Statistical Quantification of Methylation Levels by Next- Generation Sequencing. PLoS ONE 6(6): e21034. [PMID: 21698242] [PMC3115964] [DOI:10.1371/journal.pone.0021034]
     
  9. Chen, G. B., K. H. Ingram, G. de los Campos, N. Yi, X. Y. Lou, D. Pomp, D. B. Allison. (2011) A two-step modeling strategy for testing and estimating genetic susceptibility to the illeffects of adiposity: Illustration in an outbred F2 mice population. International Journal of Obesity Supplements, S2:21.
     
  10. Yi, N., Nianjun Liu, Degui Zhi, Jun Li 2011 Hierarchical Generalized Linear Models for Multiple Groups of Rare and Common Variants: Jointly Estimating Group and Individual-Variants Effects. PLoS Genetics 7(12): e1002382. [DOI:10.1371/journal.pgen.1002382] [PMID: 22144906] P[MCID: PMC3228815]
     
  1. Pasche B, Wisinski KB, Sadim M, Kaklamani V, Pennison MJ, Zeng Q, Bellam N, Zimmerman J, Yi N, Zhang K, Baron J, Stram DO, Hayes MG. Constitutively decreased TGFBR1 allelic expression is a common finding in colorectal cancer and is associated with three TGFBR1 SNPs. J Exp Clin Cancer Res. 2010 May 25;29:57. [PMID: 20500843] [doi: 10.1186/1756-9966-29-57]
     
  2. Pasche B, Yi N. Candidate gene association studies: successes and failures. Curr Opin Genet Dev. 2010 Jun;20(3):257-61. [PMID: 20417090]
     
  3. Li J, Reynolds R, Pomp D, Allison DB, Yi N. Mapping interacting QTL for count phenotypes using hierarchical Poisson and binomial models: an application to reproductive traits in mice. Genet Res (Camb). 2010 Feb;92(1):13-23. [PMID: 20199696]
     
  4. Ankra-Badu GA, Shriner D, Le Bihan-Duval E, Mignon-Grasteau S, Pitel F, Beaumont C, Duclos MJ, Simon J, Porter TE, Vignal A, Cogburn LA, Allison DB, Yi N, Aggrey SE. Mapping main, epistatic and sex-specific QTL for body composition in a chicken population divergently selected for low or high growth rate. BMC Genomics. 2010 Feb 11;11:107. [PMID: 20149241]
     
  5. Yi, N. Statistical Analysis of Genetic Interactions. 2010. Genetics Research 92: 443 -459. [PMID: 21429274]
     
  1. Shriner, D. and N. Yi, 2009 Deviance information criterion (DIC) in Bayesian multiple QTL mapping. Computational Statistics and Data Analysis. 53(5): 1850-1860. [DOI: 10.1016/j.csda.2008.01.016]
     
  2. Yi, N. and Banerjee, S. 2009 Hierarchical generalized linear models for genome-wide interacting QTL mapping. Genetics. 181(3):1101-13 [PMID: 19139143]
  1. Yi, N. and D. Shriner, 2008 Advances in Bayesian multiple QTL mapping in experimental 11 designs. Heredity 100: 240-252. [PMID: 17987056] [DOI: 10.1038/sj.hdy.6801074]
     
  2. Yi, N. and S. Xu, 2008 Bayesian LASSO for quantitative trait loci mapping. Genetics 179: 1045–1055. [PMID: 18505874]
     
  3. Banerjee, S., B.S. Yandell, and N Yi, 2008 Bayesian QTL mapping for multiple traits. Genetics. Genetics 179: 2275-2289 [PMID: 18689903]
     
  4. Yi, N, S. Ding, S. W. Keith, C. S. Coffey, and D. B. Allison, 2008 Bayesian analysis of the effect of intentional weight loss on mortality rate. International Journal of Body Composition Research 6: 185-192.
     
  5. Badu, G., D. Pomp, D. Shriner, D. B. Allison, and N. Yi, 2008 Genetic influences on growth and body composition in mice: multilocus interactions. International Journal of Obesity. [PMID: 18982013] [DOI: 10.1038/ijo.2008.215].
     
  1. Daniel Shriner, Solomon K Musani, and N. Yi, 2007 Statistical methods for multiple QTL mapping in experimental cross. In “Current Topics in Human Genetics: studies in complex diseases” ed. Hong-Wen Deng. World Scientific Publishing Co. Pte. Ltd, Singopore.
     
  2. Solomon K. Musani, Daniel Shriner, Nianjun Liu, Rui Feng, Christopher S. Coffey, Nengjun Yi, Hemant K. Tiwari, & David B. Allison, 2007 Detection of Gene × Gene Interactions in Association Studies of Human Data. Human Heredity 63(2):67-84. [PMID: 17283436]
     
  3. Brian S. Yandell, Tapan Mehta, Samprit Banerjee, Daniel Shriner, Ramprasad Venkataraman, Jee Young Moon, W. Whipple Neely, Hao Wu, Randy von Smith and Nengjun Yi, 2007 R/qtlbim: QTL with Bayesian Interval Mapping in Experimental Crosses. Bioinformatics 23: 641-634. [PMID: 17237038]
     
  4. Yi, N., D. Shriner, S. Banerjee, Tapan Mehta, D. Pomp, and Brian S. Yandell, 2007 An efficient Bayesian model selection approach for interacting QTL models with many effects. Genetics 176: 1865–1877. [PMID: 17483424] [DOI: 10.1534/genetics.107.071365 ]
     
  5. Yi, N., S. Banerjee, D. Pomp, and B. S. Yandell, 2007 Bayesian analysis of genome-wide interacting QTL for ordinal traits. Genetics 176: 1855–1864. [PMID: 17507680] [DOI: 10.1534/genetics.107.071142]
     
  6. Hui-Chen Hsu, Lu Lu, N. Yi, G. V. Zant, R. W. Williams and J. D. Mountz, 2007 Quantitative Trait Loci (QTL) Mapping in Aging Systems. Methods Mol Biol. 371:321-48. [PMID: 17634591] [DOI: 10.1007/978-1-59745-361-5]
  1. Yang, R., N. Yi and S. Xu, 2006 Box-Cox transformation for QTL mapping. Genetica 128:133–143. [PMID: 17028946]
     
  2. Yi, N., Denise K. Zinniel, Kyoungmi Kim, Eugene J. Eisen, Alfred Bartolucci, David B. Allison and Daniel Pomp, 2006 Bayesian analysis of multiple epistatic QTL models for body weight and body composition in Mice. Genetical Research 87: 45-60. [PMID: 16545150]
     
  3. Solomon K Musani, Huang-Ge Zhang, Hui-Chen Hsu, N. Yi, David B Allison, and John D. Mountz, 2006 Principal Component Analysis of Quantitative Trait Loci for Adenovirus. Hereditas 143: 189-197. [PMID: 17362354]
     
  1. C. Hansen, N. Yi, Y-M Zhang, S. Xu, Gavora J., and H. Chen, 2005 Identification of QTL for production traits in chicken. Animal Biotechnoloy 16: 67-79. [PMID: 15926264]
     
  2. John D. Mountz, PingAr Yang, Qi Wu, Juling Zhou, Angela Fitgerald, Jennifer Allen, N. Yi, Lu Lu, Robert W. Williams, and Hui-Chen Hsu, 2005 Genetic segregation of spontaneous erosive arthritis and generalized autoimmune disease in BXD2 recombinant inbred strain of mice. Scand J Immunology 61: 128-138. [PMID: 15683449]
     
  3. Huang-Ge Zhang, Katherine A. High, Qi Wu, PingAr Yang, Alex Schlachterman, Shaohua Yu, N. Yi, Hui-Chen Hsu, and John D. Mountz, 2005 Genetic Analysis of the Antibody Response to AAV2 and Factor IX. Molecular Therapy 11(6):866-74. [PMID: 15922957]
     
  4. Maria De Luca, N. Yi, David B. Allison, Jeff Leips, and Douglas M. Ruden, 2005 Mapping Quantitative Trait Loci affecting variation in Drosophila triacylglycerol storage. Obesity Research 13: 1596-1606. [PMID: 16222063]
     
  5. Joseph R. Vasselli, Richard Weindruch, Stephen B. Heymsfield, F. Xavier Pi-Sunyer, Carol N. Boozer, N. Yi, Chenxi Wang, and David B. Allison, 2005 ‘Intentional’ Weight Loss Reduces Mortality Rate in a Rodent Model of Dietary Obesity. Obesity Research 13:693-702. [PMID: 15897478]
     
  6. Yi, N., B. Yandell, G. Churchill, D. Allison, E. J. Eisen and D. Pomp, 2005 Bayesian model selection for genome-wide epistatic analysis. Genetics 170: 1333-1344. [PMID: 15911579]
     
  7. Ruth, J.H., Amin, M.A., Woods, J.M., He, X.,Samuel, S.L., Yi, N., Haas, C.S., Koch, E.A., and Bullard, D.C., 2005 Accelerated Development of Arthritis in Mice Lacking Endothelial Selectins. Arthritis Research & Therapy 7: R959-R970. [PMID: 16207337]
     
  1. G. Churchill (N. Yi among many other authors), 2004 The collaborative cross, a community resource for the genetic analysis of complex traits. Nature Genetics 11: 1133-1137. [PMID: 15514660]
     
  2. Yi, N., 2004 A unified Markov chain Monte Carlo framework for mapping multiple quantitative trait loci. Genetics 167: 967-975. [PMID: 15238545]
     
  3. Yi, N., A. Diament, S. Chiu, J. Fisler and C. Warden, 2004 Epistatic interaction between two nonstructural loci on chromosomes 7 and 3 influences hepatic lipase activity in BSB mice. J Lipid Res 2004; 45:2063-70. [PMID: 15314098]
     
  4. Yi, N., Adam Diament, Sally Chiu, Janis Fisler and Craig Warden, 2004 Characterization of Epistasis influencing complex spontaneous obesity in the BSB model. Genetics 167: 399-409. [PMID: 15166164]
     
  5. Yi, N., S. Xu, V. George and D. B. Allison, 2004 Mapping multiple quantitative trait loci for complex ordinal traits. Behavior Genetics 34: 3-15. [PMID: 14739693]
     
  6. Warden, C., N. Yi and J. Fisler, 2004 Epistasis among genes is a universal phenomenon in obesity: evidence from rodent models. Nutrition 20: 74-77. [PMID: 14698018]
     
  7. Huang-Ge Zhang, Hui-Chen Hsu, N. Yi, PingAr Yang, Qi Wu, David B. Allison and John D. Mountz, 2004 Identification of Multiple Genetic Loci that Regulate Adenovirus Gene Therapy. Gene Therapy 11: 4-14. [PMID: 14681692]
     
  8. Beasley, T. M., D. Yang, N. Yi, D. C. Bullard, C. I. Amos, S. Xu, and D. B. Allison, 2004 Joint Tests for Quantitative Trait Loci in Experimental Crosses. Genetics Selection Evolution 36: 601-619. [PMID: 15496283]
     
  9. Farahani, P., J. S. Fisler, H. Wong, A. L. Diament, N. Yi and C. H. Warden, 2004 Reciprocal hemizygosity analysis of mouse hepatic lipase (Lipc) reveals influence on obesity. Obesity Research 2: 292-306. [PMID: 14981222]
     
  1. Yang, Y., H. Pei and N. Yi, 1991 Shortcut sampling inspection plans and their OC functions. J. Biomathematics, 6(4): 49-52.
     
  2. Yi, N., 1992 A study of precision of several sampling plans. J. Biomathematics, 7(1): 38-42.
     
  3. Yi, N., Y. Yang et al, 1992 Mean precision of multi-stage sampling. J. Biomathematics, 7(4): 169-171.
     
  4. Yang, Y., H. Pei, N. Yi, and Y. Gao, 1994 Optimum allocations of sample size in two-stage sampling plan. J.App.Math., 9(4): 46-50.
     
  5. Yi, N., J. Shi and M. Wang, 1995 Multivariate analysis of genetic differentiation in forest populations. J. Nanjing For. Uni., 4: 7-14.
     
  6. Yi, N., 1995 Comparison of 3P sampling with PSWOR sampling. J.Nanjing For.Uni., 19(1): 89-102.
     
  7. Yi, N. and Y. Yang, 1996 Mean precision of the ratio-type estimator in the two-stage sampling. J. Biomathematics, 11(1): 28-31.
     
  8. Yi, N., J. Shi and M. Wang, 1996 Genetic diversity and multilocus structure in forest trees. Chinese Biodiversity, 4(3): 153-159.
     
  9. Yi, N. "A study on population genetic structure in forest trees", Ph.D. Dissertation, Nanjing Forestry University, 1996.
     
  10. Yin, T, Y. Sun, N. Yi, X. Li, M. Huang and M. Wang,1998 Genome fingerprinting analysis in Populus Deltoides. Acta Botanica Sinica, 40(8):778-780.
     
  11. Yi, N., J. Shi and M. Wang, 1998 Estimation, variance and optimal sampling of multilocus gene diversity. J. Biomathematics, 14: 23-30.
     
  12. Yi, N., J. Shi and M. Wang, 1998 Linkage disequilibrium in populations of Cunninghamia lanceolate (Lamb.) Hook from The People's Republic of China. J. Biomathematics, 15: 11-19.
     
  13. Yi, N., T. Yin, M. Huang, and L. Zhu, 1998 Mapping quantitative trait loci in forest trees. Progress in Biotechnology (Chinese),18(3): 19-25.
     
  14. Yi, N., T. Yin, Z. Han, M. Huang, and H. Cao, 2000 Genetic variation of RAPD markers in a disease resistant seed orchard of Pinus Elliottii Engelm. Scientia Silvae Sinicae 36: 51-53.
     
  15. Yi, N., 2000 A random model approach to mapping quantitative trait loci using Megagametophte in Conifers. Scientia Silvae Sinicae. 37: 36-41.
     
  16. Li Mei, Shi Jisen, Gan Siming, He Zhenxiang, Li Li, N. Yi, 2001 Correlation between RAPD based parental genetic distance and filial performance of Chinese fir, Forest Research. 14 (1):35-40 (Chinese)
     
  17. Li Mei, Shi Jisen, He Zhenxiang, N. Yi, 2001 Study on molecular genetic variation of superior trees in Chinese fir, SCIENTIA SILVAE SINICAE. 37(4):137-141.
     
  18. Yi, N. and S. Xu, 1999 Mapping quantitative trait loci for complex binary traits in outbred populations. Heredity 82: 668-676. [PMID: 10383689 ]
     
  19. Yi, N. and S. Xu, 1999 A random approach to mapping quantitative trait loci for complex binary traits in outbred populations. Genetics 153: 1029-1040. [PMID: 10511576]
     
  20. Xu, S. and N. Yi, 2000 Mixed model analysis of quantitative trait loci. Proceedings of the National Academy of Sciences of the USA. 97: 14542-14547. [PMID: 11114174]
     
  21. Yi, N. and S. Xu, 2000 Bayesian mapping of quantitative trait loci for complex binary traits. Genetics 155: 1391-1403. [PMID: 10880497]
     
  22. Yi, N. and S. Xu, 2000 Bayesian mapping of quantitative trait loci under the identity-by-descent-based variance component model. Genetics 156: 411-422. [PMID: 10978304]
     
  23. Yi, N. and S. Xu, 2001 Bayesian mapping of quantitative trait loci under complicated mating designs. Genetics 157: 1759-1771. [PMID: 11290729]
     
  24. Xu, S. and Yi, N., 2001 Genetic mapping for complex traits using Bayesian statistics. In “International symposium on mapping and identification of genes for complex polygenic traits and diseases and symposium on application of biological high technology and its products”. Changsha, China.
     
  25. Yi, N. and Xu, S., 2002 Mapping quantitative trait loci with epistatic effects. Genetical Research 79: 185-198.
     
  26. Yi, N. and S. Xu, 2002 Linkage analysis of quantitative trait loci in multiple line crosses. Genetica 114: 217-320. [PMID: 12206360]
     
  27. Yi, N., V. George and D. B. Allison, 2003 Stochastic search variable selection for mapping multiple quantitative trait loci. Genetics 164: 1129-1138. [PMID: 12871920]
     
  28. Yi, N., S. Xu and D. B. Allison, 2003 Bayesian model choice and search strategies for mapping interacting quantitative trait loci. Genetics 165: 867-883. [PMID: 14573494]
     
  29. Xu, S., N. Yi, D. Burke, A. Galeki and R. A. Miller, 2003 An EM algorithm for mapping binary disease loci: application to fibrosarcoma in a four-way cross mouse family. Genetical Research 82: 127-138. [PMID: 14768897]
     
  30. Hsu, H., Zhang, H., Li, L., N. Yi, Yang, P., Wu, Q., Wu, Y., Sun, S., Renda, J., Xu, X., Yang, X., Lu, L., Van Zant, G., Williams, R. W., Allison, D. B., & Mountz, J. D., 2003 Age-related thymic involution in C57BL/6J x DBA/2J recombinant-inbred mice maps to mouse chromosomes 9 and 10.. Genes and Immunity 4: 402-10. [PMID: 12944977]
     
  31. Yi, N. and Xu, S., 2003 Designs and methods to detect QTL for production traits based on random genetic models. In “Poultry breeding and biotechnology”, edited by W. Muir and S. Aggrey. CABI Publishing, Wallingford, UK.