N Yi

Summary

Affiliation: University of Alabama at Birmingham
Country: USA

Publications

  1. pmc Evaluation of pooled association tests for rare variant identification
    Wan Yu Lin
    Department of Biostatistics, University of Alabama at Birmingham, 1665 University Boulevard, Birmingham, AL 35294, USA
    BMC Proc 5:S118. 2011
  2. pmc Constitutively decreased TGFBR1 allelic expression is a common finding in colorectal cancer and is associated with three TGFBR1 SNPs
    Boris 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
  3. pmc Association between IL-32 genotypes and outcome in infection-associated acute lung injury
    John J Arcaroli
    Department of Medicine, University of Alabama at Birmingham, 1530 3rd Avenue South, Birmingham, AL 35294 0012, USA
    Crit Care 15:R138. 2011
  4. pmc The role of the fat mass and obesity associated gene (FTO) in breast cancer risk
    Virginia 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
  5. pmc Mapping main, epistatic and sex-specific QTL for body composition in a chicken population divergently selected for low or high growth rate
    Georgina A Ankra-Badu
    Department of Poultry Science Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
    BMC Genomics 11:107. 2010
  6. pmc Bayesian model selection for genome-wide epistatic quantitative trait loci analysis
    Nengjun Yi
    Department of Biostatistics, University of Alabama, Birmingham 35294, USA
    Genetics 170:1333-44. 2005
  7. pmc Bayesian LASSO for quantitative trait loci mapping
    Nengjun Yi
    Department of Biostatistics, University of Alabama, Birmingham, AL 35294 0022, USA
    Genetics 179:1045-55. 2008
  8. pmc Hierarchical generalized linear models for multiple quantitative trait locus mapping
    Nengjun Yi
    Department of Biostatistics, Section on Statistical Genetics, University of Alabama, Birmingham, Alabama 35294 0022, USA
    Genetics 181:1101-13. 2009
  9. pmc A unified Markov chain Monte Carlo framework for mapping multiple quantitative trait loci
    Nengjun Yi
    Section on Statistical Genetics, Department of Biostatistics, University of Alabama, Birmingham, 35294 0022, USA
    Genetics 167:967-75. 2004
  10. pmc Bayesian mapping of genomewide interacting quantitative trait loci for ordinal traits
    Nengjun Yi
    Section on Statistical Genetics, Department of Biostatistics, University of Alabama, Birmingham, Alabama 35294 0022, USA
    Genetics 176:1855-64. 2007

Collaborators

Detail Information

Publications43

  1. pmc Evaluation of pooled association tests for rare variant identification
    Wan Yu Lin
    Department of Biostatistics, University of Alabama at Birmingham, 1665 University Boulevard, Birmingham, AL 35294, USA
    BMC Proc 5:S118. 2011
    ....
  2. pmc Constitutively decreased TGFBR1 allelic expression is a common finding in colorectal cancer and is associated with three TGFBR1 SNPs
    Boris 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...
  3. pmc Association between IL-32 genotypes and outcome in infection-associated acute lung injury
    John 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)...
  4. pmc The role of the fat mass and obesity associated gene (FTO) in breast cancer risk
    Virginia 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...
  5. pmc Mapping main, epistatic and sex-specific QTL for body composition in a chicken population divergently selected for low or high growth rate
    Georgina 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...
  6. pmc Bayesian model selection for genome-wide epistatic quantitative trait loci analysis
    Nengjun 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...
  7. pmc Bayesian LASSO for quantitative trait loci mapping
    Nengjun 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...
  8. pmc Hierarchical generalized linear models for multiple quantitative trait locus mapping
    Nengjun 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...
  9. pmc A unified Markov chain Monte Carlo framework for mapping multiple quantitative trait loci
    Nengjun 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...
  10. pmc Bayesian mapping of genomewide interacting quantitative trait loci for ordinal traits
    Nengjun Yi
    Section on Statistical Genetics, Department of Biostatistics, University of Alabama, Birmingham, Alabama 35294 0022, USA
    Genetics 176:1855-64. 2007
    ....
  11. pmc Bayesian analysis of genetic interactions in case-control studies, with application to adiponectin genes and colorectal cancer risk
    Nengjun Yi
    Department of Biostatistics, University of Alabama at Birmingham, 35294, USA
    Ann Hum Genet 75:90-104. 2011
    ....
  12. ncbi request reprint Mapping multiple quantitative trait Loci for ordinal traits
    Nengjun 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...
  13. pmc Bayesian analysis of rare variants in genetic association studies
    Nengjun 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...
  14. pmc Bayesian model choice and search strategies for mapping interacting quantitative trait Loci
    Nengjun 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...
  15. pmc Stochastic search variable selection for identifying multiple quantitative trait loci
    Nengjun 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...
  16. ncbi request reprint Advances in Bayesian multiple quantitative trait loci mapping in experimental crosses
    N 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...
  17. pmc Hierarchical generalized linear models for multiple groups of rare and common variants: jointly estimating group and individual-variant effects
    Nengjun 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/)...
  18. pmc Characterization of epistasis influencing complex spontaneous obesity in the BSB model
    Nengjun 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...
  19. ncbi request reprint Identification of multiple genetic loci that regulate adenovirus gene therapy
    H 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...
  20. pmc Genetic influences on growth and body composition in mice: multilocus interactions
    G 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...
  21. pmc An efficient Bayesian model selection approach for interacting quantitative trait loci models with many effects
    Nengjun 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...
  22. ncbi request reprint Epistatic interaction between two nonstructural loci on chromosomes 7 and 3 influences hepatic lipase activity in BSB mice
    Nengjun 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...
  23. pmc Bayesian quantitative trait loci mapping for multiple traits
    Samprit 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...
  24. ncbi request reprint Bayesian analyses of multiple epistatic QTL models for body weight and body composition in mice
    Nengjun 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...
  25. pmc Candidate gene association studies: successes and failures
    Boris 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...
  26. pmc Mapping interacting QTL for count phenotypes using hierarchical Poisson and binomial models: an application to reproductive traits in mice
    Jun 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...
  27. pmc Joint tests for quantitative trait loci in experimental crosses
    T 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...
  28. ncbi request reprint Principal component analysis of quantitative trait loci for immune response to adenovirus in mice
    Solomon 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...
  29. ncbi request reprint Detection of gene x gene interactions in genome-wide association studies of human population data
    Solomon 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...
  30. ncbi request reprint Mapping quantitative trait loci affecting variation in Drosophila triacylglycerol storage
    Maria 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...
  31. ncbi request reprint Genetic analysis of the antibody response to AAV2 and factor IX
    Huang 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...
  32. ncbi request reprint Age-related thymic involution in C57BL/6J x DBA/2J recombinant-inbred mice maps to mouse chromosomes 9 and 10
    H 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...
  33. ncbi request reprint Quantitative trait locus (QTL) mapping in aging systems
    Hui 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
    ....
  34. ncbi request reprint Genetic association analysis of 30 genes related to obesity in a European American population
    P Li
    Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
    Int J Obes (Lond) 38:724-9. 2014
    ..We tested candidate genes in pathways related to food intake and energy expenditure for association with body mass index (BMI)...
  35. ncbi request reprint Box-Cox transformation for QTL mapping
    Runqing Yang
    School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 201101, PR China
    Genetica 128:133-43. 2006
    ....
  36. ncbi request reprint Identification of QTL for production traits in chickens
    Christiane 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...
  37. ncbi request reprint Reciprocal hemizygosity analysis of mouse hepatic lipase reveals influence on obesity
    Poupak 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...
  38. ncbi request reprint R/qtlbim: QTL with Bayesian Interval Mapping in experimental crosses
    Brian 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...
  39. ncbi request reprint An EM algorithm for mapping binary disease loci: application to fibrosarcoma in a four-way cross mouse family
    Shizhong 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...
  40. ncbi request reprint Epistasis among genes is a universal phenomenon in obesity: evidence from rodent models
    Craig H Warden
    Rowe Program in Genetics, Department of Pediatrics, University of California, Davis, California 95616, USA
    Nutrition 20:74-7. 2004
  41. ncbi request reprint Linkage analysis of quantitative trait loci in multiple line crosses
    Nengjun 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...
  42. ncbi request reprint Mapping quantitative trait loci with epistatic effects
    Nengjun 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...
  43. ncbi request reprint The Collaborative Cross, a community resource for the genetic analysis of complex traits
    Gary 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 Grants6

  1. Bayesian Methods for Mapping Complex Epistatic Genes
    Nengjun Yi; Fiscal Year: 2005
    ..abstract_text> ..
  2. Bayesian Methods for Mapping Complex Epistatic Genes
    Nengjun Yi; Fiscal Year: 2006
    ..abstract_text> ..
  3. Bayesian Methods for Mapping Complex Epistatic Genes
    Nengjun Yi; Fiscal Year: 2007
    ..abstract_text> ..
  4. Bayesian Methods for Mapping Complex Epistatic Genes
    Nengjun Yi; Fiscal Year: 2009
    ..abstract_text> ..
  5. Bayesian Methods for Genome-Wide Interacting QTL Mapping
    Nengjun Yi; Fiscal Year: 2010
    ..The project is expected to make an important impact on the field of genetics/genomics of complex diseases. ..