Research Topics
Genomes and Genes | N YiSummaryAffiliation: University of Alabama at Birmingham Country: USA Publications
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Publications
Constitutively decreased TGFBR1 allelic expression is a common finding in colorectal cancer and is associated with three TGFBR1 SNPsBoris Pasche
Division of Hematology Oncology, The University of Alabama at Birmingham and UAB Comprehensive Cancer Center, Birmingham, AL 35203, USA
J Exp Clin Cancer Res 29:57. 2010..This phenotype was first observed in mice, then in lymphoblastoid cell lines from patients with microsatellite stable colorectal tumors...- Association between IL-32 genotypes and outcome in infection-associated acute lung injuryJohn J Arcaroli
Department of Medicine, University of Alabama at Birmingham, 1530 3rd Avenue South, Birmingham, AL 35294 0012, USA
Crit Care 15:R138. 2011..Our purpose was to investigate variation within the IL-32 promoter and gene, and susceptibility to and outcomes from infection associated acute lung injury (ALI)... - The role of the fat mass and obesity associated gene (FTO) in breast cancer riskVirginia Kaklamani
Cancer Genetics Program, Division of Hematology Oncology, Department of Medicine and Robert H, Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, 676 N St Clair st suite 850, Chicago, IL 60611, USA
BMC Med Genet 12:52. 2011..Our objective was to evaluate tissue expression of FTO in breast and the role of FTO SNPs in predicting breast cancer risk... - Mapping main, epistatic and sex-specific QTL for body composition in a chicken population divergently selected for low or high growth rateGeorgina A Ankra-Badu
Department of Poultry Science Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
BMC Genomics 11:107. 2010..We used Bayesian model selection to comprehensively map main, epistatic and sex-specific QTL in an F2 reciprocal intercross between two chicken lines divergently selected for high or low growth rate... - Bayesian model choice and search strategies for mapping interacting quantitative trait LociNengjun Yi
Department of Biostatistics, University of Alabama, Birmingham, Alabama 35294, USA
Genetics 165:867-83. 2003..Utility and flexibility of the method are demonstrated using both simulated data and a real data set. Sensitivity of posterior inference to prior specifications of the number and genetic effects of QTL is investigated... 
Advances in Bayesian multiple quantitative trait loci mapping in experimental crossesN Yi
Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294 0022, USA
Heredity (Edinb) 100:240-52. 2008..We compare and contrast these methods to clearly describe the relationships among different Bayesian methods. We conclude this review by highlighting some areas of future research...- Bayesian LASSO for quantitative trait loci mappingNengjun Yi
Department of Biostatistics, University of Alabama, Birmingham, AL 35294 0022, USA
Genetics 179:1045-55. 2008..Markov chain Monte Carlo (MCMC) algorithms are developed to simulate the parameters from the posteriors. The methods are illustrated using well-known barley data... - A unified Markov chain Monte Carlo framework for mapping multiple quantitative trait lociNengjun Yi
Section on Statistical Genetics, Department of Biostatistics, University of Alabama, Birmingham, 35294 0022, USA
Genetics 167:967-75. 2004..Finally, we develop strategies to improve the performance of MCMC algorithms... - Stochastic search variable selection for identifying multiple quantitative trait lociNengjun Yi
Department of Biostatistics, University of Alabama, Birmingham 35294 0022, USA
Genetics 164:1129-38. 2003..The results demonstrate that the proposed method works well under typical situations of most QTL studies in terms of number of markers and marker density... - Hierarchical generalized linear models for multiple quantitative trait locus mappingNengjun Yi
Department of Biostatistics, Section on Statistical Genetics, University of Alabama, Birmingham, Alabama 35294 0022, USA
Genetics 181:1101-13. 2009..Our method has been implemented in our freely available package R/qtlbim (www.qtlbim.org), providing a valuable addition to our previous Markov chain Monte Carlo (MCMC) approach... - Bayesian analysis of rare variants in genetic association studiesNengjun Yi
Department of Biostatistics, Section on Statistical Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294 0022, USA
Genet Epidemiol 35:57-69. 2011..We evaluate the proposed method and compare its performance to existing methods on extensive simulated data. The results show that the proposed method performs well under all situations and is more powerful than existing approaches... - Mapping multiple quantitative trait Loci for ordinal traitsNengjun Yi
Department of Biostatistics, University of Alabama at Birmingham, Birmingham, Alabama 35294 0022, USA
Behav Genet 34:3-15. 2004..To this end, we provide a unified approach to mapping multiple QTL for continuous, binary, and ordinal traits. Utility and flexibility of the method are demonstrated using simulated data... - Bayesian analysis of genetic interactions in case-control studies, with application to adiponectin genes and colorectal cancer riskNengjun Yi
Department of Biostatistics, University of Alabama at Birmingham, 35294, USA
Ann Hum Genet 75:90-104. 2011.... - Bayesian mapping of genomewide interacting quantitative trait loci for ordinal traitsNengjun Yi
Section on Statistical Genetics, Department of Biostatistics, University of Alabama, Birmingham, Alabama 35294 0022, USA
Genetics 176:1855-64. 2007.... - Bayesian model selection for genome-wide epistatic quantitative trait loci analysisNengjun Yi
Department of Biostatistics, University of Alabama, Birmingham 35294, USA
Genetics 170:1333-44. 2005..We illustrate the proposed method by detecting new epistatic QTL for obesity in a backcross of CAST/Ei mice onto M16i... - Hierarchical generalized linear models for multiple groups of rare and common variants: jointly estimating group and individual-variant effectsNengjun Yi
Department of Biostatistics, Section on Statistical Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
PLoS Genet 7:e1002382. 2011..The performance of the proposed procedures is further assessed via simulation studies. The methods are implemented in a freely available R package BhGLM (http://www.ssg.uab.edu/bhglm/)... - Identification of multiple genetic loci that regulate adenovirus gene therapyH G Zhang
Department of Medicine, Division of Clinical Immunology and Rheumatology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
Gene Ther 11:4-14. 2004..0 cM) and Chr 8 (52 and 73.0 cM). These results indicate that different strains of mice exhibit different pathways for effective clearance of AdLacZ depending on genetic polymorphisms and interactions at multiple genetic loci... - Characterization of epistasis influencing complex spontaneous obesity in the BSB modelNengjun Yi
Department of Biostatistics, Section on Statistical Genetics, University of Alabama, Birmingham, Alabama 35294, USA
Genetics 167:399-409. 2004..Chromosomes 6 and 12 have not only main effects but also strong epistatic effects on plasma total cholesterol. Our results emphasize the importance of modeling epistasis for discovery of obesity genes... - Genetic influences on growth and body composition in mice: multilocus interactionsG A Ankra-Badu
Department of Biostatistics, Section on Statistical Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
Int J Obes (Lond) 33:89-95. 2009..Bayesian methodology provides an efficient way of estimating these interactions... - An efficient Bayesian model selection approach for interacting quantitative trait loci models with many effectsNengjun Yi
Department of Biostatistics, Section on Statistical Genetics, University of Alabama, Birmingham, Alabama 35294 0022, USA
Genetics 176:1865-77. 2007..Our method has been implemented in the freely available package R/qtlbim (http://www.qtlbim.org) to facilitate the general usage of the Bayesian methodology for genomewide interacting QTL analysis... - Epistatic interaction between two nonstructural loci on chromosomes 7 and 3 influences hepatic lipase activity in BSB miceNengjun Yi
Department of Biostatistics, Section on Statistical Genetics, University of Alabama, Birmingham, AL 35294, USA
J Lipid Res 45:2063-70. 2004..SPRET/Pt alleles of the QTL on each chromosome promote hepatic lipase activity. The proportion of phenotypic variance explained by the epistatic effect is higher than that explained by the main effect of the QTL on chromosome 7... - Bayesian quantitative trait loci mapping for multiple traitsSamprit Banerjee
Departments of Biostatistics, Section on Statistical Genetics, University of Alabama, Birmingham, AL 35294, USA
Genetics 179:2275-89. 2008..Our methods have been implemented in the freely available package R/qtlbim (http://www.qtlbim.org), which greatly facilitates the general usage of the Bayesian methodology for unraveling the genetic architecture of complex traits... - Candidate gene association studies: successes and failuresBoris Pasche
Division of Hematology Oncology, Department of Medicine, University of Alabama at Birmingham and UAB Comprehensive Cancer Center, Birmingham, AL 35294 3300, USA
Curr Opin Genet Dev 20:257-61. 2010..Together with genome-wide association studies, candidate gene approaches are likely to fill a large gap in our knowledge of the genetic basis of cancer within the next decade... - Mapping interacting QTL for count phenotypes using hierarchical Poisson and binomial models: an application to reproductive traits in miceJun Li
Department of Biostatistics, Section on Statistical Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
Genet Res (Camb) 92:13-23. 2010..The proposed statistical models and methods provide valuable tools for detecting multiple interacting QTLs for complex count phenotypes... - Mapping quantitative trait loci affecting variation in Drosophila triacylglycerol storageMaria De Luca
Department of Environmental Health Sciences, University of Alabama, Birmingham, AL 35294, USA
Obes Res 13:1596-605. 2005..The objective of our study was to identify quantitative trait loci (QTLs) that contribute to variation in triacylglycerol (TAG) storage in two D. melanogaster laboratory strains... - Bayesian analyses of multiple epistatic QTL models for body weight and body composition in miceNengjun Yi
Department of Biostatistics, Section on Statistical Genetics, University of Alabama, Birmingham, AL 35294, USA
Genet Res 87:45-60. 2006..Several main and epistatic effects were shared by the body composition and body weight traits, suggesting that pleiotropy plays an important role in growth and obesity... - Joint tests for quantitative trait loci in experimental crossesT Mark Beasley
Department of Biostatistics, Section on Statistical Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
Genet Sel Evol 36:601-19. 2004..Joint tests were generally more powerful for one-tailed selection under both backcross and F2 intercross situations. However, joint tests cannot be recommended for one-tailed selective genotyping if segregation distortion is suspected... - Principal component analysis of quantitative trait loci for immune response to adenovirus in miceSolomon K Musani
Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, AL 35294 0007, USA
Hereditas 143:189-97. 2006..01 and 31.01 cM) and 15 (29.21, 36.01, and 56.31 cM). These results illustrate the use of principal component analysis in mapping QTLs using multiple correlated traits... - Detection of gene x gene interactions in genome-wide association studies of human population dataSolomon K Musani
Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
Hum Hered 63:67-84. 2007..Instead, a combination of approaches with the aim of balancing their specific strengths may be the optimal approach to investigate gene x gene interactions in human data... - Genetic analysis of the antibody response to AAV2 and factor IXHuang Ge Zhang
Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, 701 South 19th Street, LHRB 473, Birmingham, AL 35294, USA
Mol Ther 11:866-74. 2005..66) for anti-cF.IX. These results indicate that multiple genetic loci independently regulate the isotype-specific antibody response to the AAV2 capsid and the cF.IX transgene... - Age-related thymic involution in C57BL/6J x DBA/2J recombinant-inbred mice maps to mouse chromosomes 9 and 10H C Hsu
Department of Medicine, Division of Clinical Immunology and Rheumatology, The University of Alabama at Birmingham, Birmingham, AL, USA
Genes Immun 4:402-10. 2003..5 cM) and Chr 3 (D3Mit127 at 70.3 cM). The present study suggests that the initial thymus size and the rate of thymic involution may be influenced by a relatively small number of genetic loci... - Quantitative trait locus (QTL) mapping in aging systemsHui Chen Hsu
Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL, USA
Methods Mol Biol 371:321-48. 2007.... - Linkage analysis of quantitative trait loci in multiple line crossesNengjun Yi
Department of Botany and Plant Sciences, University of California, Riverside, CA 92521-0124, USA
Genetica 114:217-30. 2002..Design I involves two inbred lines and their derived F1, F2, and BC populations. Design II is a half-diallel cross involving three inbred lines. The two designs appear different, but can be handled with the same robust computer program... - Identification of QTL for production traits in chickensChristiane Hansen
USDA, ARS, Avian Disease and Oncology Laboratory, East Lansing, Michigan, USA
Anim Biotechnol 16:67-79. 2005..Two of these regions, one spanning the area of 263/287 cM on GAA01 and the other spanning the area of 23/28 cM on GAA02, were associated with multiple QTL... - Epistasis among genes is a universal phenomenon in obesity: evidence from rodent modelsCraig H Warden
Rowe Program in Genetics, Department of Pediatrics, University of California, Davis, California 95616, USA
Nutrition 20:74-7. 2004 - An EM algorithm for mapping binary disease loci: application to fibrosarcoma in a four-way cross mouse familyShizhong Xu
Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
Genet Res 82:127-38. 2003..All the QTLs detected primarily show dominance effects... - Reciprocal hemizygosity analysis of mouse hepatic lipase reveals influence on obesityPoupak Farahani
Rowe Program in Genetics, University of California, Davis, California 95616, USA
Obes Res 12:292-305. 2004..In the present study, we investigated whether hepatic lipase (Lipc) is an obesity gene, whether Lipc interacts with an unknown gene on chromosome 7, and how HL activity is linked to the chromosome 7 locus... - Mapping quantitative trait loci with epistatic effectsNengjun Yi
Department of Botany and Plant Sciences, University of California, Riverside, CA 92521-0124, USA
Genet Res 79:185-98. 2002..This requires the reversible jump Markov chain Monte Carlo algorithm. The utility of the proposed method is demonstrated through analysis of simulation data... - Box-Cox transformation for QTL mappingRunqing Yang
School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 201101, PR China
Genetica 128:133-43. 2006.... - R/qtlbim: QTL with Bayesian Interval Mapping in experimental crossesBrian S Yandell
Department of Statistics, University of Wisconsin Madison, 1300 University Avenue, Madison, WI 53706, USA
Bioinformatics 23:641-3. 2007..Availability: The package is freely available from cran.r-project.org... - The Collaborative Cross, a community resource for the genetic analysis of complex traitsGary A Churchill
The Jackson Laboratory, 600 Main Street Bar Harbor, Maine 04609, USA
Nat Genet 36:1133-7. 2004..The Collaborative Cross will provide a common reference panel specifically designed for the integrative analysis of complex systems and will change the way we approach human health and disease...
Research Grants
- Bayesian Methods for Mapping Complex Epistatic GenesNengjun Yi; Fiscal Year: 2009..abstract_text> ..
- Bayesian Methods for Genome-Wide Interacting QTL MappingNengjun Yi; Fiscal Year: 2010..The project is expected to make an important impact on the field of genetics/genomics of complex diseases. ..