Integrative Program in Statistical Genetics and Systems Biology

Agronomy and Horticultural Sciences – Crop modeling

Collaborators: Kenneth Boote (Agronomy), Eduardo Vallejos (Horticultural Sciences), James W. Jones, (Agricultural & Biological Engineering)

IFAS Innovation Fund: Discovery of gene functions and their application using a novel statistical approach for integrating functional mapping and crop modeling

USDA/CSREES Hatch Project: Nonparametric and Dynamic Statistical Methods in Agriculture and Genetics

Applied Math – Differential equations, image and shape analysis

Collaborators: Yunmei Chen (Mathematics)

NSF Advances in Biological Informatics (pending): Integrating Differential Equations to Functional Mapping of Biological Rhythms

NSF (pending): Image and Shape

Chen, Y. M., G. F. Fu and R. L. Wu, 2008 Integration of functional mapping and delay differential equations to map the genes that regulate circadian rhythms. International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (peer reviewed; to appear).

Liu, T., X. L. Liu, Y. M. Chen and R. L. Wu, 2007 A unifying differential equation model for functional genetic mapping of circadian rhythms. Theoretical Biology and Medical Modeling 4: 5.

Entomology – Honey bee genetics

Collaborators: Glenn Hall (Entomology)

USDA-NRI: QTL involved in suppression of Varroa mite reproduction on honey bees

Dentistry and Molecular Genetics – SNP modeling, association studies, and pain genetics

Collaborators: Roger Fillingam (Dentistry), Peggy Wallace (Molecular Genetics), Roland Staud (Rheumatology)

NSF-DMS: Statistical Models for Studying the Genetic Architecture of Dynamic Traits

NIH-NINDS: Sex-Related Genetic Influences on Pain and Analgesia

Wang, C. G., Y. Cheng, T. Liu, Q. Li, R. Fillingim, P. Wallace, R. Staud, L. Kaplan and R. L. Wu, 2008 A computational model for sex-specific genetic architecture of complex traits in humans. Molecular Pain 4: 13.

Wen, S., C. Wang, A. Berg, Y. Li, M. Chang, Y. Li, R. Fillingim, M. Wallace, R. Staud, L. Kaplan, R. Wu 2008 Modeling Genetic Imprinting Effects of DNA Sequences with Multilocus Polymorphism Data. (under review).

Yun, C., A. Berg, S. Wu, Y. Li, R. Wu 2008 Computing genetic imprinting expressed by haplotypes. (under review).

Forestry – Gene expression, poplar genetics

Collaborators: Matias Kirst (Forestry)

DOE: Genomic mechanisms of carbon allocation and partitioning in poplar

Ma, C.-X., Q. B. Yu, A. Berg, G. F. Fu, J. S. Yap, A. X. Tan, M. Kirst, Y. H. Cui and R. L. Wu, 2008 A statistical model for testing the pleiotropic control of phenotypic plasticity of a count trait. Genetics 179: 627-636.

Pharmacy Practice – Pharmacogenetics of drug response

Collaborators: Julie Johnson (Pharmacy)

NSF-DMS: Statistical Models for Studying the Genetic Architecture of Dynamic Traits

Lin, M., W. Hou, H. Y. Li, J. A. Johnson and R. L. Wu, 2007 Modeling interactive quantitative trait nucleotides for drug response. Bioinformatics 23: 1251-1257.

Wu, R. L., H. Y. Li, M. Lin, S. G. Terra, C. J. Pepine, S. P. McGorray, D. Johnson and J. A. Johnson, 2006 Genetic variants for human obesity as revealed by linkage disequilibrium mapping.  Current Genomics 7: 463-468.

Lin, M., C. Aqvilonte, J. A. Johnson and R. L. Wu, 2005 Sequencing drug response with HapMap. The Pharmacogenomics Journal 5: 149-156.

Lin, M., R. L. Wu  and J. A. Johnson, 2005 A bivariate functional mapping model for gene identification of drug response for systolic and diastolic blood pressures. Pacific Symposium on Biocomputing (http://helix-web.stanford.edu/psb06/lin.pdf).

Terra, S. G., S. P. McGorray, R. Wu, D. M. McNamara, L. H. Cavallari, J. R. Walker, M. R. Wallace, B. D. Johnson, C. N. Bairey-Merz, G. Sopko, C. J. Pepine and J. A. Johnson, 2005 Association between b-adrenergic receptor polymorphisms and their G-protein-coupled receptors with body mass index and obesity in women: a report from the NHLBI-sponsored WISE study. International Journal of Obesity 29: 746-754.

Liu, T., J. A. Johnson, G. Casella and R. L. Wu, 2004 Sequencing complex diseases with HapMap. Genetics 168: 503-511.

Gong, Y., Z. H. Wang, T. Liu, W. Zhao, Y. Zhu, J. A. Johnson and R. L. Wu, 2004 A statistical model for high-resolution mapping of quantitative trait loci affecting pharmacodynamic processes. The Pharmacogenomics Journal 4: 315-321.

Agronomy – Endosperm and polypoid genetics

Collaborators: Maria Gallo (Agronomy)

UF Opportunity Fund: Title

Zhang, L., M. C. K. Yang, M. Gallo-Meagher, X. L. Wang, B. A. Larkins and R. L. Wu, 2004 A statistical model for estimating joint maternal-offspring effects on seed development in autogamous plants. Physiological Genomics 19: 262-269.

Zhao, W., J. Zhu, M. Gallo-Meagher and R. L. Wu, 2004 A unified statistical model for functional mapping of genotype by environment interactions for ontogenetic development. Genetics 168: 1751-1762.

Wu, R. L., C.-X. Ma, M. Gallo-Meagher, R. C. Littell and G. Casella, 2002 Statistical methods for dissecting triploid endosperm traits using molecular markers: An autogamous model. Genetics 162: 875-892.

UC Davis – Genetics of obesity

Collaborators: Juan Medrano (Animal Science)

Wu, R. L., C.-X. Ma, W. Hou, P. Corva and J. F. Medrano, 2005 Functional mapping of quantitative trait loci that interact with the hg gene to regulate growth trajectories in mice. Genetics 171: 239-249.

USDA – Genetics of switchgrass

Collaborators: Christian Tobias (Genomics and Gene Discovery)

USDA-ARS: Linkage Analysis Appropriate for Comparative Genome Analysis and Trait Selection in Switchgrass

Jiahan Li

Princeton – Longitudinal data analysis

Collaborators: Jianqing Fan (Operations Research and Financial Engineering)

Kim, B.-R., L. Zhang, A. Berg, J. Fan and R. L. Wu, 2008 A computational framework for functional clustering of periodic gene expression profiles. Genetics.

Clevland Clinic – SNP discovery and Modelling

Collaborators: Li Zhang (Quantitative Health Sciences), Yaomin Xu (Quantitative Health Sciences)

St. Jude Research Hospital – SNP discovery and Modelling

Collaborators: Wei Zhao (Biostatistics), Song Wu (Biostatistics), Yang Jie (Biostatistics)

Cornell University – Canine genetics

Collaborators: Rory Todhunter (Clinical Sciences)

Liu, T., R. J. Todhunter, S. Wu, W. Hou, R. Mateescu, Z. W. Zhang, N. I. Burton-Wurster, G. M. Acland, G. Lust and R. L. Wu, 2007 A random model for mapping imprinted quantitative trait loci in a structured pedigree: An implication for mapping canine hip dysplasia. Genomics 90: 276-284 (feature article).

Liu, T., R. J. Todhunter, Q. Lu, L. Schoettinger, H. Y. Li, R. C. Littell, S. Bliss, G. Acland, G. Lust and R. L. Wu, 2006 Extent and distribution of zygotic linkage disequilibrium in canine. Genetics 174: 439-453.

Todhunter, R. J., R. Mateescu, G. Lust, N. I. Burton-Wurster, N. L. Dykes, S. P. Bliss, A. J. Williams, M. Vernier-Singer, E. Corey, C. Harjes, R. L. Quaas, Z. Zhang, R. O. Gilbert, D. Volkman, G. Casella, R. L. Wu and G. M. Acland, 2005 Quantitative trait loci for hip dysplasia in a crossbreed canine pedigree.Mammalian Genome 16: 720-730.

Lou, X.-Y., G. Casella, R. J. Todhunter, M. K. C. Yang and Wu, R. L., 2005 A general statistical framework for unifying interval and linkage disequilibrium mapping: Towards high-resolution mapping of quantitative traits. Journal of American Statistical Association 100: 158-171.

Todhunter, R. J., Y. T. Grohn, S. P. Bliss, A. Wilfand, A. J. Williams, M. Vernier-Singer, N. I. Burton-Wurster, N. L. Dykes, R. L. Wu, G. Casella, G. M. Acland and G. Lust, 2003 Multiple radiographic predictors of hip cartilage lesions in 8-month-old dogs. American Journal of Veterinary Research 64: 1472-1478.

Lou, X.-Y., R. J. Todhunter, M. Lin, Q. Lu, T. Liu, Z. H. Wang, S. Bliss, G. Casella, A. C. Acland, G. Lust and R. L. Wu, 2003 The extent and distribution of linkage disequilibrium in canine. Mammalian Genome 14: 555-564.

Todhunter, R. J., S. P. Bliss, G. Casella, R. L. Wu, G. Lust, N. I. Burton-Wurster, A. J. Williams, R. O. Gilbert, and G. M. Acland, 2003 Genetic structure of susceptibility traits for hip dysplasia and microsatellite informativeness of an outcrossed canine pedigree. Journal of Heredity 94: 39-48.

Bliss, S., R. J. Todhunter, R. Quaas, G. Casella, R. L. Wu, G. Lust, A. J. Williams, S. Hamilton, N. L. Dykes, A. Yeager, R. O. Gilbert, N. I. Burton-Wurster and G. M. Acland, 2002 Quantitative genetics of traits associated with canine hip dysplasia in a canine pedigree constructed by mating dysplastic Labrador Retrievers with unaffected Greyhounds. American Journal of Veterinary Research 63: 1029-1035.

Duke University – Pharmacogenetics

Collaborators: Min Lin (Biostatistics and Bioinformatics)

Wu, R. L., and M. Lin, 2008 Statistical and Computational Pharmacogenomics. Chapman & Hall/CRC, London.

Fred Hutchinson Cancer Research Center – HIV dynamics

Collaborators: Ying Qing Chen (Biostatistics)

Long, F., Y. Q. Chen, J. M. Cheverud and R. L. Wu, 2006 Genetic mapping of allometric scaling laws. Genetical Research 87:207-216. 

Zhao, W., Y. Q. Chen, G. Casella, J. M. Cheverud and R. L Wu, 2005 A nonstationary model for functional mapping of complex traits. Bioinformatics 21: 2469-2477.

Oak Ridge National Laboratory – Poplar genetics

Collaborators: Gerald Tuskan (Plant Genomics), Stan Wullschleger (Plant Genomics), Tongmin Yin (Plant Genomics)

Wu, S., T. Liu, H. Y. Li, T. M. Yin, S. Wullschleger, G. A. Tuskan and R. L. Wu, 2008 An improved approach for mapping quantitative trait loci in a pseudo-testcross design: Revisiting a poplar genome study. Bioinformatics and Biology Insights (invited).

Rutgers University – Polyploid genetics

Collaborators: Stacy Bonos (Plant Pathology)

University of Arizona – Maize genetics

Collaborators: Brian Larkins (Plant Sciences)

Li, Y. C., C. M. Coelho, S. Wu, Y. R. Zeng, Y. Li, B. Hunter, R. A. Dante, B. A. Larkins and R. L. Wu, 2007 A statistical strategy to estimate maternal-zygotic interactions and parent-of-origin effects of QTLs for seed development. PLoS ONE.

Coelho, C. M., 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 Zea mays endosperm. Theoretical and Applied Genetics 115: 1147-1162.

Zhang, L., M. C. K. Yang, M. Gallo-Meagher, X. L. Wang, B. A. Larkins and R. L. Wu, 2004 A statistical model for estimating joint maternal-offspring effects on seed development in autogamous plants. Physiological Genomics 19: 262-269.

Wu, R. L., X.-Y. Lou, C.-X. Ma, X. L. Wang, B. A. Larkins and G. Casella, 2002 An improved genetic model generates high-resolution mapping of QTL for protein quality in maize endosperm. Proceedings of the National Academy of Sciences of the United States of America 99: 11281–11286.

Cincinnati Children's Hospital – Genetic imprinting

Collaborators: Daniel Prows (Human Genetics)

Washington University – Mouse genetics

Collaborators: Cheverud (Anatomy and Neurobiology)

Hou, W., J. S. Yap, S. Wu, T. Liu, J. M. Cheverud and R. L. Wu, 2007 Mapping quantitative trait nucleotides underlying complex traits in a controlled cross. PLoS ONE 2(8): e732. doi:10.1371/journal.pone.0000732.

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.

Cui, Y. H., Q. Lu, J. 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.

Long, F., Y. Q. Chen, J. M. Cheverud and R. L. Wu, 2006 Genetic mapping of allometric scaling laws. Genetical Research 87:207-216. 

Zhao, W., Y. Q. Chen, G. Casella, J. M. Cheverud and R. L Wu, 2005 A nonstationary model for functional mapping of complex traits. Bioinformatics 21: 2469-2477.

Lin, M., C.-X. Ma, W. Zhao, J. M. Cheverud and R. L.Wu, 2005 Mechanistic mapping of ontogenetic growth based on biological principles. Growth, Development and Aging 68: 87-93.

Wu, R. L., Z. H. Wang, W. Zhao and J. M. Cheverud, 2004 A mechanistic model for genetic machinery of ontogenetic growth. Genetics 168: 2383–2394.

Zhao, W., C.-X. Ma, J. M. Cheverud and R. L. Wu, 2004 A unifying statistical model for QTL mapping of genotype-sex interaction for developmental trajectories. Physiological Genomics 19: 218-227.

Shanghai Jiao Tong University – Statistical Genetics

Collaborators: Runqing Yang (Animal Science)

Yang, R. Q., H. J. Gao, X. Wang, J. Zhang, Z.-B. Zeng and R. L. Wu, 2006 A semiparametric model for composite functional mapping of dynamic quantitative traits. Genetics 177: 1859-1870.

Beijing Forestry University – Forest genetics and tree genomics

Collaborators: Zhiyi Zhang (Biological Sciences and Biotechnology)

Genome Institute of Singapore – Cancer genetics

Collaborators: Tian Liu (Statistical Genetics)

INRA – Crop modeling

Collaborators: François Tardieu (Ecophysiology)

Nanjing Agricultural University – Soybean genetics

Collaborators: Junyi Gai (Plant Genetics and Breeding)

Li, H. Y., Z. W. Huang, S. Wu, J. Y. Gai, Y. R. Zeng and R. L. Wu, 2007 A conceptual framework to mapping quantitative trait loci governing ontogenetic allometry. PLoS ONE 2(8): e1245. doi:10.1371/journal.pone.0001245.

Nanjing Forestry University – Forest tree genetics

Collaborators:

Zhejiang Forestry University – Hickory genetics, conifer genetics

Collaborators: Wendy Zeng (Forestry)

NSF of China: Genetic Imprinting in Tree

Zhejiang Department of Science and Technology: Genetics of Nature Population in Hickory Tree

Li, Y. C., C. M. Coelho, S. Wu, Y. R. Zeng, Y. Li, B. Hunter, R. A. Dante, B. A. Larkins and R. L. Wu, 2008 A statistical strategy to estimate maternal-zygotic interactions and parent-of-origin effects of QTLs for seed development. PLoS ONE.

Li, H. Y., Z. W. Huang, S. Wu, J. Y. Gai, Y. R. Zeng and R. L. Wu, 2007 A conceptual framework to mapping quantitative trait loci governing ontogenetic allometry. PLoS ONE 2(8): e1245. doi:10.1371/journal.pone.0001245.

Li, Y. C., Y. Li, S. Wu, K. Han, Z. J. Wang, W. Hou,Y. R. Zeng and R. L. Wu, 2007 Estimation of linkage disequilibria in diploid populations with multilocus dominant markers. Genetics 176: 1879-1892.

Wu, J. S, J. Zhu, Y. R. Zeng and R. L. Wu, 2007 Functional mapping of norm reactions to environmental signals. Genetical Research 89: 27-38.

Wu, R. L., W. Hou, Y. H. Cui, H. Y. Li, T. Liu, S. Wu, C.-X. Ma and Y. R. Zeng, 2007. Mapping the genetic architecture of complex traits with molecular markers. Recent Patents on Nanotechnology 1: 41-49 (invited review article).

Wu, J. S., B. Zhang, Y. H. Cui, W. Zhao, M. R. Huang, Y. R. Zeng, J. Zhu, and R. L. Wu, 2007 Genetic mapping of developmental instability: Design, model and algorithm. Genetics 176: 1187-1196.

Zeng, Y. R., H. Y. Li, Q. Lu, W. Zhao and R. L. Wu, 2006 A systems biology approach for integrating allometry, ontogeny and plasticity through functional mapping. In: Floriculture, Ornamental and Plant Biotechnology: Advances and Topical Issues. Vol. IV. Edited by Jaime A Teixeira da Silva. Global Science Books, Ikenobe, Japan, pp. 206-212 (invited review article).

Zeng, Y. R., J. S. Wu, and R. L. Wu, 2004 Sequencing Populus: An Impetus for Understanding Tree Biodiversity and Evolution. In: Plant Genome: Biodiversity and Evolution Volume 1, Part B: Phanerogams, A.K. Sharma and A. Sharma (eds). Science Publishers, Inc., Enfield, NH, pp 195-205.

Zhejiang Forestry University -- Phenotypic Plasticity

Collaborators: Jiasheng Wu (Forestry)

NSF of China: Genetics of Reaction Norm

Wu, J. S, J. Zhu, Y. R. Zeng and R. L. Wu, 2007 Functional mapping of norm reactions to environmental signals. Genetical Research 89: 27-38.

Wu, J. S., B. Zhang, Y. H. Cui, W. Zhao, M. R. Huang, Y. R. Zeng, J. Zhu, and R. L. Wu, 2007 Genetic mapping of developmental instability: Design, model and algorithm. Genetics 176: 1187-1196.

Wu, S., J. Yang and R. L. Wu, 2007 Semiparametric functional mapping of quantitative trait loci governing long-term HIV dynamics. Bioinformatics 23: i569-i576.

Wu, S., J. Yang and R. L. Wu, 2006 Multilocus linkage disequilibrium mapping of quantitative trait loci that affect HIV dynamics: A simulation approach. Statistics in Medicine 25: 3826-3849.

Zeng, Y. R., J. S. Wu, and R. L. Wu, 2004 Sequencing Populus: An Impetus for Understanding Tree Biodiversity and Evolution. In: Plant Genome: Biodiversity and Evolution Volume 1, Part B: Phanerogams, A.K. Sharma and A. Sharma (eds). Science Publishers, Inc., Enfield, NH, pp 195-205.

Wu, R. L., C.-X. Ma, J. S. Wu, W. Fang and G. Casella, 2004 Population genetics of heterosis: Effects of Hardy-Weinberg disequilibrium. Silvae Genetica 53: 1-6.

Zhejiang Forestry University – Tree Crop Model

Collaborators: Youjun Huang (Forestry)

Zhejiang University – Plant growth genetics in rice

Collaborators: Jun Zhu (Agriculture and Biotechnology)

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 7: 1, Article 4 (http://www.bepress.com/sagmb/vol7/iss1/art4).

Wu, J. S, J. Zhu, Y. R. Zeng and R. L. Wu, 2007 Functional mapping of norm reactions to environmental signals. Genetical Research 89: 27-38.

Wu, J. S., B. Zhang, Y. H. Cui, W. Zhao, M. R. Huang, Y. R. Zeng, J. Zhu, and R. L. Wu, 2007 Genetic mapping of developmental instability: Design, model and algorithm. Genetics 176: 1187-1196.

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 development. Genetical Research 87: 61-71.

Cui, Y. H., J. Zhu and R. L. Wu, 2006 Functional mapping for genetic control of programmed cell death. Physiological Genomics 25: 458-469.

Zhao, W., J. Zhu, M. Gallo-Meagher and R. L. Wu, 2004 A unified statistical model for functional mapping of genotype by environment interactions for ontogenetic development. Genetics 168: 1751-1762.

Wu, R. L., C.-X. Ma, J. Zhu and G. Casella, 2002 Mapping epigenetic quantitative trait loci (QTL) altering a developmental trajectory. Genome 45: 28-33.

Zhejiang University – Endosperm genetics in rice

Collaborators: Chunhai Shi (Agriculture and Biotechnology)

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 development. Genetical Research 87: 61-71.