Statistical and computational pharmacogenomics

Statistical and Computational Pharmacogenomics

Volumn , Issue , 2008, Pages 1-346

  Wu, Rongling ^a   Lin, Min ^b  

^a UNIVERSITY OF FLORIDA   (United States)

^b DUKE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 57749115526     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Book

References (336)

1. Allison, D.B. (1997). Transmission-disequilibrium tests for quantitative traits. American Journal of Human Genetics 60, 676-90.
2. Altshuler, D., L.D. Brooks, A. Chakravarti, F.S. Collins, M.J. Daly, and P. Donnelly (2005). A haplotype map of the human genome. Nature 437, 1299-1320.
3. Andresen, B., J.S. Shiner, and D.E. Uehlinger (2002). Allometric scaling and maximum efficiency in physiological eigen time. Proceedings of the National Academy of Sciences of the United States of America 99, 5822-5824.
4. Andrews, K.L., J.L. Mudd, C. Li, and J.H. Miner (2002). Quantitative trait loci influence renal disease progression in a mouse model of alport syndrome. American Journal of Pathology 160, 721-730.
5. Anholt, R.R.H. and T.F.C. Mackay (2004). Quantitative genetic analyses of complex behaviours in Drosophila. Nature Reviews Genetics 5, 838-849.
6. Attinger, E.O., A. Anne, and D.A. McDonald (1966). Use of fourier series for the analysis of biological systems. Biophysical Journal 6, 291-304.
7. Avraham, S., C.W. Tung, K. Ilic, P. Jaiswal, E.A. Kellogg, S. McCouch, A. Pujar, L. Reiser, S.Y. Rhee, M.M. Sachs, M. Schaeffer, L. Stein, P. Stevens, L. Vincent, F. Zapata, and D. Wareothers (2008). The plant ontology database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Research 36, D449.
8. Bader, J.S. (2001). The relative power of snps and haplotype as genetic markers for ssociation tests. Pharmacogenomics 2, 11-24.
9. Banavar, J.R., A. Maritan, and A. Rinaldo (1999). Size and form in efficient transportation networks. Nature 399, 130-132.
10. Bard, J.B., S.Y. Rhee, and S.M. Ashburner (2005). An ontology for cell types. Genome Biology 6, R21.
11. Barrett, W.W. (1979). A theorem on inverses of tridiagonal matrices. Linear Algebra and its Applications 27, 211-217.
12. Bateson, W. (1909). Mendel’s Principles of Heredity. Cambridge University Press, New York.
13. Beavis, W.D. and P. Keim (1996). Identification of QTL that are affected by environment. In: Genotype by Environment Interactions, edited by Kang, M.S. and Gauch, H. CRC Press, Boca Raton, FL, pp. 123-149.
14. Begum, E., M. Bonno, M. Obata, H. Yamamoto, M. Kawai, and Y. Komada (2006). Emergence of physiological rhythmicity in term and preterm neonates in a neonatal intensive care unit. Journal of Circadian Rhythms 4, doi:10.1186/1740-3391-4-11.
15. Bennett, J.H. (1954). On the theory of random mating. Annals of Eugenics 18, 311-317.
16. Biernacki, C., G. Celeux, and G. Govaert (1999). An improvement of the nec criterion for assessing the number of clusters in a mixture model. Pattern Recognition Letters 20, 267-272.
17. Bookstein, F.L. (1991). Morphometric Tools for Landmark Data: Geometry and Biology. Cambridge University Press, New York.
18. Borlak, J. (2005). Handbook of Toxicogenomics: Strategies and Applications. John Wiley & Sons, New York.
19. Boxenbaum, H. (1982). Interspecies scaling, allometry, physiological time, and the ground plan of pharmacokinetics. Journal of Pharmacokinetics and Pharmacodynamics 10, 201-227.
20. Bradford, G.E. and T.R. Famula (1984). Evidence for a major gene for rapid post-weaning growth in mice. Genetical Research 44, 293-308.
21. Broman, K.W. (2005). The genomes of recombinant inbred lines. Genetics 169, 1133-1146.
22. Brown, E.R., J.G. Ibrahim, and V. DeGruttola (2005). A flexible B-spline model for multiple longitudinal biomarkers and survival. Biometrics 61, 64-73.
23. Brown, G.R., D.L. Bassoni, G.P. Gill, J.R. Fontana, N.C. Wheeler, R.A. Megraw, M.F. Davis, M.M. Sewell, G.A. Tuskan, and D.B. Neale (2003). Identification of quantitative trait loci influencing wood property raits in loblolly pine (Pinus taeda l.). III. QTL verification and candidate gene mapping. Genetics 164, 1537-1546.
24. Brown, J.H. and G.B. West (2000). Scaling in Biology. Oxford University Press, New York.
25. Bruskiewich, R., E.H. Coe, P. Jaiswal, S. McCouch, M. Polacco, L. Stein, L. Vincent, and D. Ware (2002). The plant ontology consortium and plant ontologies. Comparative and Functional Genomics 3, 137-142.
26. Burchard, E.G., E. Ziv, N. Coyle, S.L. Gomez, H. Tang, A.J. Karter, J.L. Mountain, E.J. Perez-Stable, D. Sheppard, and N. Risch (2003). The importance of race and ethnic background in biomedical research and clinical practice. New England Journal of Medicine 348, 1170-1175.
27. Burnham, K.P. and D.R. Anderson (2002). Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach. Springer, New York.
28. Burton, P.R., D.G. Clayton, L.R. Cardon, N. Craddock, P. Deloukas, A. Duncan-son, D.P. Kwiatkowski, M.I. McCarthy, W.H. Ouwehand, N.J. Samani, J.A. Todd, P. Donnelly, J.C. Barrett, P.R. Burton, D. Davison, P. Donnelly, et al. (2007). Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447, 661-678.
29. Calder, W.A. (1996). Size, Function, and Life History. Courier Dover Publications, New York.
30. Calvert, C.C., T.R. Famula, J.F. Bernier, and G.E. Bradford (1985). Serial composition during growth in mice with a major gene for rapid postweaning growth. Growth 49, 246-57.
31. Camp, N.J. (1998). Genomewide transmission/disequilibrium testing: A consideration of the genotype relative risks at disease loci. American Journal of Human Genetics 61, 1424-1430.
32. Cardon, L.R. (2006). Genetics. delivering new disease genes. Science 314, 1403-1405.
33. Carroll, R.J. and D. Ruppert (1984). Power transformations when fitting theoretical models to data. Journal of the American Statistical Association 79, 321-328.
34. Cashio, P., T.V. Lee, and A. Bergmann (2005). Genetic control of programmed cell death in drosophila melanogaster. Seminars in Cell and Developmental Biology 16, 225-235.
35. Celeux, G. and G. Soromenho (1996). An entropy criterion for assessing the number of clusters in a mixture model. Journal of Classification 13, 195-212.
36. Chagnon, Y.C., T. Rankinen, E.E. Snyder, S.J. Weisnagel, L. Perusse, and C. Bouchard (2003). The Human Obesity Gene Map: The 2002 Update. Obesity Research 11, 313-367.
37. Chen, H., J. Chen, and J.D. Kalbfleisch (2004). Testing for a finite mixture model with two components. Journal of the Royal Statistical Society Series B 66, 95115.
38. Cheverud, J.M. (2006). Genetic architecture of quantitative variation. In: Evolutionary Genetics: Concepts and Case Studies, edited by Fox, C.W. and Wolf, J.B. Oxford University Press, Oxford, UK, pp. 288-309.
39. Cheverud, J.M., E.J. Routman, F.A.M. Duarte, B. van Swinderen, K. Cothran, and C. Perel (1996). Quantitative trait loci for murine growth. Genetics 142, 1305-1319.
40. Churchill, G.A. and R.W. Doerge (1994). Empirical threshold values for quantitative trait mapping. Genetics 138, 963-971.
41. Cordell, H.J. (2002). Epistasis: what it means, what it doesn’t mean, and statistical methods to detect it in humans. Human Molecular Genetics 11, 2463-2468.
42. Corva, P.M., S. Horvat, and J.F. Medrano (2001). Quantitative trait loci affecting growth in highgrowth (hg) mice. Mammalian Genome 12, 284-290.
43. Craft, R.M., J.S. Mogil, and A. Maria Aloisi (2004). Sex differences in pain and analgesia: the role of gonadal hormones. European Journal of Pain 8, 397-411.
44. Crosthwaite, S.K. (2004). Circadian clocks and natural antisense RNA. FEBS Letters 567, 49-54.
45. Cui, Y. H., J. Zhu, and R.L. Wu (2006). Functional mapping for genetic control of programmed cell death. Physiological Genomics 25,458-469.
46. Cuppen, E. (2005). Haplotype-based genetics in mice and rats. Trends in Genetics 21,318-322.
47. Dale, J.K., M. Maroto, M.L. Dequeant, P. Malapert, M. McGrew, and O. Pourquie (2003). Periodic notch inhibition by lunatic fringe underlies the chick segmentation clock. Nature 421, 275-278.
48. Daly, M.J., J.D. Rioux, S.F. Schaffner, T.J. Hudson, and E.S. Lander (2001). Highresolution haplotype structure in the human genome. Nature Genetics 29, 229-232.
49. Darvasi, A. (1998). Experimental strategies for the genetic dissection of complex traits in animal models. Nature Genetics 18, 19-24.
50. Dawson, E., G.R. Abecasis, S. Bumpstead, Y. Chen, S. Hunt, D.M. Beare, J. Pabial, T. Dibling, E. Tinsley, S. Kirby, et al. (2002). A first-generation linkage disequilibrium map of human chromosome 22. Nature 418, 544-548.
51. de Boor, C. (2001). A Practical Guide to Splines. Springer, New York.
52. de Jong, G. (2005). Research reviews: evolution of phenotypic plasticity: patterns of plasticity and the emergence of ecotypes. New Phytologist 166, 101-118.
53. Dempster, A.P., N.M. Laird, and D.B. Rubin (1977). Maximum likelihood from incomplete data via the em algorithm. Journal of the Royal Statistical Society Series B 39, 1-38.
54. Derendorf, H. and B. Meibohm (1999). Modeling of pharmacoki-netic/pharmacodynamic (PK/PD) relationships: concepts and perspectives. Pharmaceutical Research 16, 176-185.
55. DeWan, A., M. Liu, S. Hartman, S.S.M. Zhang, D.T.L. Liu, C. Zhao, P.O.S. Tam, W.M. Chan, D.S.C. Lam, M. Snyder, et al. (2006). HTRA1 promoter polymorphism in wet age-related macular degeneration. Science 314, 989-992.
56. Dewey, T.G. and M. Delle Donne (1998). Non-equilibrium thermodynamics of molecular evolution. Journal of Theoretical Biology 193, 593-599.
57. Diggle, P.J., P. Heagerty, K. Y. Liang, and S. L. Zeger (2002). Analysis of Longitudinal Data. Oxford University Press, Oxford, UK.
58. Diggle, PJ. and A.P. Verbyla (1998). Nonparametric estimation of covariance structure in longitudinal data. Biometrics 54, 401-415.
59. Du, F.X., P. Sorensen, G. Thaller, and I. Hoeschele (2002). Joint linkage disequilibrium and linkage mapping of quantitative trait loci. Proceedings of the 7th World Congress Genetics Applied to Livestock Production 32, 661-668.
60. Duerr, R.H., K.D. Taylor, S.R. Brant, J.D. Rioux, M.S. Silverberg, M.J. Daly, A.H. Steinhart, C. Abraham, M. Regueiro, A. Griffiths, et al. (2006). A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Science 314, 1461-1463.
61. Ebert, T.A. and M.P. Russell (1994). Allometry and model ii non-linear regression. Journal of theoretical biology 168, 367-372.
62. Enquist, B.J., J.H. Brown, and G.B. West (1998). Allometric scaling of plant energetics and population density. Nature 395, 163-165.
63. Enquist, B., G. West, E. Charnov, and J. Brown (1999). Allometric scaling of production and life-history variation in vascular plants. Nature 401, 907-911.
64. Evans, W.E. and J.A. Johnson (2001). Pharmacogenomics: the inherited basis for interindividual differences in drug response. Annual Review of Genomics and Human Genetics 2, 9-39.
65. Evans, W.E. and H.L. McLeod (2003). Pharmacogenomics-drug disposition, drug targets, and side effects. New England Journal of Medicine 348, 538-549.
66. Evans, W.E. and M.V. Relling (1999). Pharmacogenomics: translating functional genomics into rational therapeutics. Science 286,487-491.
67. Eyheramendy, S., J. Marchini, G. McVean, S. Myers, and P. Donnelly (2007). A model-based approach to capture genetic variation for future association studies. Genome Research 17, 88-95.
68. Falconer, D.S. and T.F.C. Mackay (1996). Introduction to Quantitative Genetics (4 ed.). Longman, New York.
69. Fan, J. and R. Li (2004). New estimation and model selection procedures for semiparametric modeling in longitudinal data analysis. Journal of the American Statistical Association 99, 710-724.
70. Feng, M.R., X. Lou, R.R. Brown, and A. Hutchaleelaha (2000). Allometric pharmacokinetic scaling: towards the prediction of human oral pharmacokinetics. Pharmaceutical Research 17,410-418.
71. Ferraty, F. and P. Vieu (2006). Nonparametric Functional Data Analysis: Theory and Practice. Springer-Verlag, New York.
72. Ferreira, E., V. Nunez-AntonNunez-Anton, and J. Rodriguez-Poo (1997). Kernel regression estimates of growth curves using nonstationary correlated errors. Statistics and Probability Letters 34, 413-423.
73. Fillingim, R.B. (2003a). Sex, gender and pain: The biopsychosocial model in action XX vs. XY. The International Journal of Sex Differences in the Study of Health, Disease and Aging 1, 98-101.
74. Fillingim, R.B. (2003b). Sex-related influences on pain: a review of mechanisms and clinical implications. Rehabilitation Psychology 48, 165-174.
75. Fillingim, R.B., L. Kaplan, R. Staud, T.J. Ness, T.L. Glover, C.M. Campbell, J.S. Mogil, and M.R. Wallace (2005). The A118G single nucleotide polymorphism of the jU-opioid receptor gene (OPRM1) is associated with pressure pain sensitivity in humans. Journal of Pain 6, 159-167.
76. Fisher, R.A. (1918). The correlation between relatives on the supposition of mendelian inheritance. Transactions of the Royal Society of Edinburgh 52, 399-433.
77. Flint, J., W. Valdar, S. Shifman, R. Mott, et al. (2005). Strategies for mapping and cloning quantitative trait genes in rodents. Nature Reviews Genetics 6, 271-286.
78. Fogg, G.E. (1987). Algal Cultures and Phytoplankton Ecology. University of Wisconsin Press, Madison, Wisconsin.
79. Foulley, J.L., Quaas R.L., and C. Thaon d’Arnoldi (1998). A link function approach to heterogeneous variance components. Genetics Selection Evolution 30, 27-43.
80. Fraley, C. and A.E. Raftery (1998). How many clusters? which clustering method? answers via model-based cluster analysis. The Computer Journal 41, 578-588.
81. Frank, O. (1926). Die theorie der pulswellen. Z Biol 85, 91-130.
82. Frary, A., T.C. Nesbitt, A. Frary, S. Grandillo, E. Knaap, B. Cong, J. Liu, J. Meller, R. Elber, K.B. Alpert, et al. (2000). fw2. 2: A quantitative trait locus key to the evolution of tomato fruit size. Science 289, 85-88.
83. Frayling, T.M., N.J. Timpson, M.N. Weedon, E. Zeggini, R.M. Freathy, C.M. Lind-gren, J.R.B. Perry, K.S. Elliott, H. Lango, N.W. Rayner, et al. (2007). A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity. Science 316, 889-894.
84. Frazer, K.A., D.G. Ballinger, D.R. Cox, D.A. Hinds, L.L. Stuve, R.A. Gibbs, J.W. Belmont, A. Boudreau, P. Hardenbol, S.M. Leal, S. Pasternak, D.A. Wheeler, T.D. Willis, F. Yu, H. Yang, et al. (2007). A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851-861.
85. Fulker, D.W. and L.R. Cardon (1994). A sib-pair approach to interval mapping of quantitative trait loci. American Journal of Human Genetics 54, 1092-103.
86. Gabriel, K.R. (1962). Ante-dependence analysis of an ordered set of variables. The Annals of Mathematical Statistics 33, 201-212.
87. Gabriel, S.B., S.F. Schaffner, H. Nguyen, J.M. Moore, J. Roy, B. Blumenstiel, J. Higgins, M. DeFelice, A. Lochner, M. Faggart, S.N. Liu-Cordero, C. Rotimi, A. Adeyemo, R. Cooper, R. Ward, E.S. Lander, M.J. Daly, and D. Altshuler(2002). The structure of haplotype blocks in the human genome. Science 296, 2225-2229.
88. Geiger-Thornsberry, G.L. and T.F.C. Mackay (2002). Association of singlenucleotide polymorphisms at the delta locus with genotype by environment interaction for sensory bristle number in Drosophila melanogaster. Genetical Research 79, 211-218.
89. Genet, A.J.H. (2002). A polymorphism in the 151 adrenergic receptor is associated with resting heart rate. American Journal of Human Genetics 70, 935-942.
90. Georges, M. (2007). Mapping, fine mapping, and molecular dissection of quantitative trait loci in domestic animals. Annual Review of Genomics and Human Genetics 8, 131-162.
91. Gibbs, R.A., J.W. Belmont, A. Boudreau, S.M. Leal, P. Hardenbol, S.R. Pasternak, D.A. Wheeler, T.D. Willis, F.L. Yu, H.M. Yang, Z.Q. Zeng, G. Yang, H. R. Hu, W.T. Hu, C.H. Li, W. Lin, et al. (2005). A haplotype map of the human genome. Nature 437, 1299-1320.
92. Gibbs, R.A., J.W. Belmont, P. Hardenbol, T.D. Willis, F. Yu, H. Yang, L.Y. Ch’ang, W. Huang, B. Liu, Y. Shen, P. K.-H. Tam, L.-C. Tsui, M.M.Y. Waye, J.T.-F. Wong, C.Q. Zeng, et al. (2003). The International HapMap Project. Nature 426, 789-796.
93. Gillespie, J.H. and M. Turelli (1989). Genotype-environment interactions and the maintenance of polygenic variation. Genetics 121, 129-138.
94. Giraldo, J. (2003). Empirical models and hill coefficients. Trends in Pharmacological Sciences 24, 63-65.
95. Goldbeter, A. (1995). A model for circadian oscillations in the drosophila period protein (PER). Proceedings: Biological Sciences 261, 319-324.
96. Goldbeter, A. (2002). Computational approaches to cellular rhythms. Nature 420, 238-245.
97. Goldman, S. (1963). Information Theory. Prentice Hall, New York.
98. Gong, Y., Z. Wang, T. Liu, W. Zhao, Y. Zhu, J.A. Johnson, and R.L. Wu (2004). A statistical model for functional mapping of quantitative trait loci regulating drug response. The Pharmacogenomics Journal 4, 315-321.
99. Green, S.A., J. Turki, I.P. Hall, and S.B. Liggett (1995). Implications of genetic variability of human 52-adrenergic receptor structure. Pulmonary Pharmacology 8, 1-10.
100. Greenberg, J.T. (1996). Programmed cell death: away oflife for plants. Proceedings of the National Academy of Sciences of the United States of America 93, 12094-12097.
101. Gregorczyk, A. (1998). Richards plant growth model. Journal of Agronomy and Crop Science 181, 243-247.
102. Gronert, G.A., D.L. Fung, J.H. Jones, S.L. Shafer, S.V. Hildebrand, and E.A. Dis-brow (1995). Allometry of pharmacokinetics and pharmacodynamics of the muscle relaxant metocurine in mammals. American Journal of Physiology-Regulatory, Integrative and Comparative Physiology 268, 85-91.
103. Guenet, J.L. and F. Bonhomme (2003). Wild mice: an ever-increasing contribution to a popular mammalian model. Trends in Genetics 19, 24-31.
104. Guryev, V., B.M.G. Smits, J. van de Belt, M. Verheul, N. Hubner, and E. Cuppen (2006). Haplotype block structure is conserved across mammals. PLoS Genetics 2, e121.
105. Gutteling, E.W., J.A.G. Riksen, J. Bakker, and J.E. Kammenga (2007). Mapping phenotypic plasticity and genotype-environmentinteractions affecting life-history traits in Caenorhabditis elegans. Heredity 98, 28-37.
106. Haddad, J.N. (2004). On the closed form of the covariance matrix and its inverse of the causal ARMA process. Journal of Time Series Analysis 25,443-448.
107. Hall, P., N.I. Fisher, and B. Hoffmann (1994). On the nonparametric estimation of covariance functions. Annals of Statistics 22, 2115-2134.
108. Hardy, G.H. (1908). Mendelian proportions in a mixed population. Science 28(706), 49-50.
109. Hart, J.D. and T.E. Wehrly (1986). Kernel regression estimation using repeated measurements data. Journal of the American Statistical Association 81, 1080-1088.
110. Hastie, T. and R. Tibshirani (1990). Generalized Additive Models. Chapman & Hall/CRC.
111. Ho, D.D., A.U. Neumann, A.S. Perelson, W. Chen, J.M. Leonard, M. Markowitz, et al. (1995). Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection. Nature 373, 123-126.
112. Hochhaus, G. and H. Derendorf (1995). Dose optimization based on pharmacokinetic-pharmacodynamic modeling. In: Handbook of Pharmacokinetic-Pharmacodynamic Correlations, edited by Derendorf, H. and Hochhaus, G. CRC Press, Boca Raton, FL, pp. 79-120.
113. Horvat, S. and J.F. Medrano (1995). Interval mapping of high growth (hg), a major locus that increases weight gain in mice. Genetics 139, 1737-1748.
114. Horvat, S. and J.F. Medrano (2001). Lack of socs2 expression causes the high-growth phenotype in mice. Genomics 72, 209-212.
115. Horvitz, H.R. (2003). Worms, life, and death (Nobel Lecture). ChemBioChem 4, 697-711.
116. Hou, W., C.W. Garvan, R.C. Littell, M. Behnke, F.D. Eyler, and R.L. Wu (2006). A framework to monitor environment-induced major genes for developmental trajectories: implication for a prenatal cocaine exposure study. Statistics In Medicine 25, 4020-4035.
117. Hou, W., C.W. Garvan, W. Zhao, M. Behnke, F.D. Eyler, and R.L. Wu (2005). A general model for detecting genetic determinants underlying longitudinal traits with unequally spaced measurements and nonstationary covariance structure. Biostatistics 6,420-433.
118. Hou, W., J.S.F. Yap, S. Wu, T. Liu, J.M. Cheverud, and R.L. Wu (2007). Haplotyping a quantitative trait with a high-density map in experimental crosses. PLoS ONE 2, e732.
119. Hu, T.M. and W.L. Hayton (2001). Allometric scaling of xenobiotic clearance: uncertainty versus universality. American Association of Pharmaceutical Scientists PharmSci 3, E29.
120. Huang, N., A. Parco, T. Mew, G. Magpantay, S. McCouch, E. Guiderdoni, J. Xu, P. Subudhi, E.R. Angeles, and G.S. Khush (1997). RFLP mapping of isozymes, RAPD and QTLs for grain shape, brown planthopper resistance in a doubled haploid rice population. Molecular Breeding 3, 105-113.
121. Hurvich, C.M. and C.L. Tsai (1989). Regression and time series model selection in small samples. Biometrika 76, 297-307.
122. Ideraabdullah, F.Y., E. de la Casa-Esperon, T.A. Bell, D.A. Detwiler, T. Magnuson, C. Sapienza, and F.P.M. de Villena (2004). Genetic and haplotype diversity among wild-derived mouse inbred strains. Genome Research 14, 1880-1887.
123. Ilic, K., E.A. Kellogg, P. Jaiswal, F. Zapata, P.F. Stevens, L.P. Vincent, S. Avraham, L. Reiser, A. Pujar, M.M. Sachs, et al. (2007). The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Plant Physiology 143, 587-599.
124. Jaffrezic, F., R. Thompson, and W.G. Hill (2003). Structured antedependence models for genetic analysis of repeated measures on multiple quantitative traits. Genetical Research 82, 55-65.
125. Jaiswal, P. (2005). Plant ontology (PO): a controlled vocabulary of plant structures and growth stages. Comparative and Functional Genomics 6, 388-397.
126. Jansen, R.C. and P. Stam (1994). High resolution of quantitative traits into multiple loci via interval mapping. Genetics 136, 1447-1455.
127. Jiang, C.J. and Z.B. Zeng (1995). Multiple trait analysis of genetic mapping for quantitative trait loci. Genetics 140, 1111-1127.
128. Johnson, C.G. and D. Marsh (1999). Modelling robot manipulators with multivariate B-splines. Robotica 17, 239-247.
129. Johnson, J.A. (2003). Pharmacogenetics: potential for individualized drug therapy through genetics. Trends in Genetics 19, 660-666.
130. Johnson, J.A. and S.G. Terra (2002). β-adrenergic receptor polymorphisms: cardiovascular disease associations and pharmacogenetics. Pharmaceutical Research 19, 1779-1787.
131. Judson, R., J.C. Stephens, and A. Windemuth (2000). The predictive power of haplotypes in clinical response. Pharmacogenomics 1, 15-26.
132. Kao, C.H. and Z.B. Zeng (1997). General formulas for obtaining the MLEs and the asymptotic variance-covariance matrix in mapping quantitative trait loci when using the EM algorithm. Biometrics 53, 653-665.
133. Kao, C.H., Z.B. Zeng, and R.D. Teasdale (1999). Multiple interval mapping for quantitative trait loci. Genetics 152, 1203-1216.
134. Khor, S. P., K. McCarthy, M. DuPont, K. Murray, and G. Timony (2000). Pharmacokinetics, pharmacodynamics, allometry, and dose selection of rpsgl-ig for phase i trial. Journal of Pharmacology and Experimental Therapeutics 293, 618-624.
135. Kimmel, G. and R. Shamir (2005). GERBIL: genotype resolution and block identification using likelihood. Proceedings of the National Academy of Sciences of the United States of America 102, 158-162.
136. Kirkpatrick, M. and N. Heckman (1989). A quantitative genetic model for growth, shape, reaction norms, and other infinite-dimensional characters. Journal ofMath-ematical Biology 27, 429-450.
137. Klein, R.J., C. Zeiss, E.Y. Chew, J.Y. Tsai, R.S. Sackler, C. Haynes, A.K. Henning, J.P. SanGiovanni, S.M. Mane, S.T. Mayne, et al. (2005). Complement factor h polymorphism in age-related macular degeneration. Science 308, 385-389.
138. Kliebenstein, D.J., A. Figuth, and T. Mitchell-Olds (2002). Genetic architecture of plastic methyl jasmonate responses in Arabidopsis thaliana. Genetics 161, 1685-1696.
139. Klingenberg, C.P. and M. Zimmermann (1992). Static, ontogenetic, and evolutionary allometry: a multivariate comparison in nine species of water striders. The American Naturalist 140, 601-620.
140. Knott, G.D. (2000). Interpolating Cubic Splines. Birkhäuser, Boston, MA.
141. Labrecque, G. and P.M. Belanger (1991). Biological rhythms in the absorption, distribution, metabolism and excretion of drugs. Pharmacology & Therapeutics 52, 95-107.
142. Lakin-Thomas, P.L. and S. Brody (2004). Circadian rhythms in microorganisms: new complexities. Annual Review of Microbiology 58, 489-519.
143. Lander, E.S. and D. Botstein (1989). Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121, 185-199.
144. Lander, E.S. and N.J. Schork (1994). Genetic dissection of complex traits. Science 265, 2037-2048.
145. Large, V., L. Hellstrom, S. Reynisdottir, F. Lonnqvist, P. Eriksson, L. Lannfelt, and P. Arner (1997). Human beta-2 adrenoceptor gene polymorphisms are highly frequent in obesity and associate with altered adipocyte beta-2 adrenoceptor function. Journal of Clinical Investigation 100, 3005-3013.
146. Lee, R.C., R.L. Feinbaum, V. Ambros, et al. (1993). The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843-854.
147. Leips, J. and T.F.C. Mackay (2000). Quantitative trait loci for life span in drosophila melanogaster interactions with genetic background and larval density. Genetics 155, 1773-1788.
148. Leloup, J.C. and A. Goldbeter (1998). A model for circadian rhythms in Drosophila incorporating the formation of a complex between the PER and TIM proteins. Journal of Biological Rhythms 13, 70-83.
149. Leloup, J.C. and A. Goldbeter (2003). Toward a detailed computational model for the mammalian circadian clock. Proceedings of the National Academy of Sciences of the United States of America 100, 7051-7056.
150. Lepist, E.I. and W.J. Jusko (2004). Anti-inflammatory drugs modeling and allo-metric scaling of s (+)-ketoprofen pharmacokinetics and pharmacodynamics: a retrospective analysis. Journal of Veterinary Pharmacology & Therapeutics 27, 211-218.
151. Levi, F., R. Zidani, and J.L. Misset (1997). Randomised multicentre trial of chronotherapy with oxaliplatin, fluorouracil, and folinic acid in metastatic colorectal cancer. Lancet 350, 681-686.
152. Li, C., A. Zhou, and T. Sang (2006a). Rice domestication by reducing shattering. Science 311, 1936-1939.
153. Li, H., Z. Huang, J. Gai, S. Wu, Y. Zeng, Q. Li, and R.L. Wu (2007). A conceptual framework for mapping quantitative trait loci regulating ontogenetic allometry. PLoS ONE 2, doi: 10.1371/journal.pone.0001245.
154. Li, H., B.R. Kim, and R.L. Wu (2006b). Identification of quantitative trait nucleotides that regulate cancer growth: a simulation approach. Journal of Theoretical Biology 242,426-439.
155. Liang, H., H. Wu, and R.J. Carroll (2003). The relationship between virologic and immunologic responses in AIDS clinical research using mixed-effects varying-coefficient models with measurement error. Biostatistics 4, 297-312.
156. Lin, D.Y. and Z. Ying (2001). Semiparametric and nonparametric regression analysis of longitudinal data. Journal of the American Statistical Association 96,103-113.
157. Lin, M., C. Aquilante, J.A. Johnson, and R.L. Wu (2005). Sequencing drug response with HapMap. The Pharmacogenomics Journal 5, 149-156.
158. Lin, M., H. Li, W. Hou, J.A. Johnson, and R.L. Wu (2007). Modeling sequence-sequence interactions for drug response. Bioinformatics 23, 1251-1257.
159. Lin, M. and R.L. Wu (2005). Theoretical basis for the identification of allelic variants that encode drug efficacy and toxicity. Genetics 170, 919-928.
160. Lin, M. and R.L. Wu (2006a). Detecting sequence-sequence interactions for complex diseases. Current Genomics 7, 59-72.
161. Lin, M. and R.L. Wu (2006b). A joint model for nonparametric functional mapping of longitudinal trajectory and time-to-event. BMC Bioinformatics 7, doi: 10.1186/1471-2105-7-138.
162. Lin, M., R.L. Wu, and J.A. Johnson (2006). A bivariate functional mapping model for gene identification of drug response for systolic and diastolic blood pressures. Pacific Symposium on Biocomputing 11, 572-583.
163. Lindblad-Toh, K., E. Winchester, M.J. Daly, D.G. Wang, J.N. Hirschhorn, J.P. Laviolette, K. Ardlie, D.E. Reich, E. Robinson, P. Sklar, et al. (2000). Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse. Nature Genetics 24, 381-386.
164. Liu, T., J.A. Johnson, G. Casella, and R.L. Wu (2004). Sequencing complex diseases with HapMap. Genetics 168, 503-511.
165. Liu, T., X.L. Liu, Y.M. Chen, and R.L. Wu (2007). A computational model for functional mapping of genes that regulate intra-cellular circadian rhythms. Theoretical Biology and Medical Modelling 4, doi: 10.1186/1742-4682-4-5.
166. Liu, T., R.J. Todhunter, Q. Lu, L. Schoettinger, H. Li, R.C. Littell, N. BurtonWurster, G.M. Acland, G. Lust, and R.L. Wu (2006). Modeling extent and distribution of zygotic disequilibrium: implications for a multigenerational canine pedigree. Genetics 174,439-453.
167. Lo, Y., N.R. Mendell, and D.B. Rubin (2001). Testing the number of components in a normal mixture. Biometrika 88, 767-778.
168. Long, F., Y.Q. Chen, J.M. Cheverud, and R.L. Wu (2006). Genetic mapping of allometric scaling laws. Genetical Research 87, 207-216.
169. Lou, X.Y., G. Casella, R.C. Littell, M.C.K. Yang, J.A. Johnson, and R.L. Wu (2003). A haplotype-based algorithm for multilocus linkage disequilibrium mapping of quantitative trait loci with epistasis. Genetics 163, 1533-1548.
170. Lou, X.Y., G. Casella, R.J. Todhunter, M.C.K. Yang, and R.L. Wu (2005). A general statistical framework for unifying interval and linkage disequilibrium mapping: toward high-resolution mapping of quantitative traits. Journal of the American Statistical Association 100, 158-172.
171. Louis, T.A. (1982). Finding the observed information matrix when using the EM algorithm. Journal of the Royal Statistical Society Series B 44, 226-233.
172. Lumer, H. (1937). The consequences of sigmoid growth for relative growth functions. Growth 1, 140-154.
173. Lynch, M. and B. Walsh (1998). Genetics and Analysis of Quantitative Traits. Sin-auer Associates, Sunderland, Massachusetts.
174. Ma, C.X., G. Casella, R.C. Littell, A.I. Khuri, and R.L. Wu (2003). Exponential mapping of quantitative trait loci governing allometric relationships in organisms. Journal of Mathematical Biology 47, 313-324.
175. Ma, C.X., G. Casella, and R.L. Wu (2002). Functional mapping of quantitative trait loci underlying the character process a theoretical framework. Genetics 161, 1751-1762.
176. Mackay, T.F.C. (2001). Quantitative trait loci in Drosophila. Nature Reviews Genetics 2, 11-20.
177. Mager, D.E. and D.R. Abernethy (2007). Use of wavelet and fast fourier transforms in pharmacodynamics. Journal of Pharmacology and Experimental Therapeutics 321, 423-430.
178. Marchini, J., P. Donnelly, and L.R. Cardon (2005). Genome-wide strategies for detecting multiple loci that influence complex diseases. Nature Genetics 37,413-417.
179. Marsh, S. (2005). Pharmacogenetics of colorectal cancer. Expert Opinion on Pharmacotherapy 6, 2607-2616.
180. Marsh, S. and H.L. McLeod (2006). Pharmacogenomics: from bedside to clinical practice. Human Molecular Genetics 15, 89-93.
181. Mason, D.A., J.D. Moore, S.A. Green, and S.B. Liggett (1999). A gain-of-function polymorphism in a g-protein coupling domain of the human 151-adrenergic receptor. Journal ofBiological Chemistry 274, 12670-12674.
182. Mather, K. and J.L. Jinks (1982). Biometrical Genetics (3 ed.). Chapman & Hall, London, UK.
183. McClish, D.K. and J.D. Roberts (2003). Phase I studies of weekly administration of cytotoxic agents: Implications of a mathematical model. Investigational New Drugs 21,299-308.
184. McMahon, T. (1973). Size and shape in biology: elastic criteria impose limits on biological proportions, and consequently on metabolic rates. Science 179, 1201-1204.
185. Meng, X.L. and D.B. Rubin (1991). Using EM to obtain asymptotic variance-covariance matrices: The SEM algorithm. Journal of the American Statistical Association 86, 899-909.
186. Meyer, K. (1998). Estimating covariance functions for longitudinal data using a random regression model. Genetics Selection Evolution 30, 221-240.
187. Meyer, K. (2001). Estimating genetic covariance functions assuming a parametric correlation structure for environmental effects. Genetics Selection Evolution 33, 557-585.
188. Miles, J.S., J.E. Moss, B.A. Taylor, B. Burchell, and C.R. Wolf (1991). Mapping genes encoding drug-metabolizing enzymes in recombinant inbred mice. Genomics 11, 309-316.
189. Mitchison, J.M. (2003). Growth during the cell cycle. International Review of Cytology 226, 165-258.
190. Mogil, J.S., S.P. Richards, L.A. O’Toole, M.L. Helms, S.R. Mitchell, B. Kest, and J.K. Belknap (1997). Identification of a sex-specific quantitative trait locus mediating nonopioid stress-induced analgesia in female mice. Journal ofNeuro-science 17, 7995-8002.
191. Moldenhauer, K. and N. Slaton (2004). Rice growth and development. In: Rice Production Handbook, edited by Slaton, N.A. and Ford, L.B. and Bernhardt, J.L. and Cartwright, R.D. and Gardisser, D. and Gibbons, J. and Huitink, G. and Koen, B. and Lee, F.N. and Miller, D.M. and Norman, R.J. and Siebenmorgen, T. Cooperative Extension Service, Division of Agriculture, University of Kansas, Lawrence, KS, pp. 7-14.
192. Moore, J.H. (2003). The ubiquitous nature of epistasis in determining susceptibility to common human diseases. Human Heredity 56, 73-82.
193. Moore, J.H., P.C. Andrews, N. Barney, and B.C. White (2008).
194. Mueller, T.I. (1986). Geometric Modelling with Multivariate B-splines. Ph. D. thesis, University of Utah, Salt Lake City, Utah.
195. Nabel, E.G. (2003). Cardiovascular disease. New England Journal of Medicine 349, 60-72.
196. Nelder, J.A. and R. Mead (1965). A simplex method for function minimization. Computer Journal 7, 308-313.
197. Newton, H.J. (1988). TIMESLAB: A Time Series Analysis Laboratory. Wadsworth Publishing, New York.
198. Niklas, K.J. (1994). Plant Allometry: The Scaling of Form and Process. University of Chicago Press, Chicago, Illinois.
199. Niklas, K.J. (2006). A phyletic perspective on the allometry of plant biomasspartitioning patterns and functionally equivalent organ-categories. New Phytol-ogist 171, 27-40.
200. Niklas, K.J. and B.J. Enquist (2001). Invariant scaling relationships for interspecific plant biomass production rates and body size. Proceedings of the National Academy of Sciences of the United States of America, 2922-2927.
201. Norberg, E., G.W. Rogers, J. Odegard, J.B. Cooper, and P. Madsen (2006). Short communication: genetic correlation between test-day electrical conductivity of milk and mastitis. Journal of Dairy Science 89, 779-781.
202. Nunez-Anton, V. and G.G. Woodworth (1994). Analysis of longitudinal data with unequally spaced observations and time-dependent correlated errors. Biometrics 50,445-456.
203. Nmiez-Anton, V. and D.L. Zimmerman (2000). Modeling nonstationary longitudinal data. Biometrics 56, 699-705.
204. Ohdo, S., S. Koyanagi, H. Suyama, S. Higuchi, and H. Aramaki (2001). Changing the dosing schedule minimizes the disruptive effects of interferon on clock function. Nature Medicine 7, 356-360.
205. Pan, J.X. and G. Mackenzie (2003). On modelling mean-covariance structures in longitudinal studies. Biometrika 90, 239-244.
206. Park, Y.G., R. Clifford, K.H. Buetow, and K.W. Hunter (2003). Multiple cross and inbred strain haplotype mapping of complex-trait candidate genes. Genome Research 13, 118-121.
207. Patil, N., A.J. Berno, D.A. Hinds, W.A. Barrett, J.M. Doshi, C.R. Hacker, C.R. Kautzer, D.H. Lee, C. Marjoribanks, D.P. McDonough, et al. (2001). Blocks of limited haplotype diversity revealed by high-resolution scanning of human chro-mosome21. Science 294, 1719-1723.
208. Payseur, B.A. et al. (2007). Prospects for association mapping in classical inbred mouse strains. Genetics 175, 1999-2008.
209. Perelson, A.S., A.U. Neumann, M. Markowitz, J.M. Leonard, and D.D. Ho (1996). HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time. Science 271, 1582-1586.
210. Perelson, A. S. and P.W. Nelson (1999). Mathematical analysis of HIV-1 dynamics in vivo. SIAM Review 41, 3-44.
211. Phillips, M.S., R. Lawrence, R. Sachidanandam, A.P. Morris, D.J. Balding, M.A. Donaldson, J.F. Studebaker, W.M. Ankener, S.V. Alfisi, F.S. Kuo, et al. (2003). Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots. Nature Genetics 33, 382-387.
212. Pourahmadi, M. (1999). Joint mean-covariance models with applications to longitudinal data: unconstrained parameterisation. Biometrika 86, 677-690.
213. Pourahmadi, M. (2000). Maximum likelihood estimation of generalised linear models for multivariate normal covariance matrix. Biometrika 87,425-435.
214. Prolo, L.M., J.S. Takahashi, and E.D. Herzog (2005). Circadian rhythm generation and entrainment in astrocytes. Journal of Neuroscience 25,404-408.
215. Pujar, A., P. Jaiswal, E.A. Kellogg, K. Ilic, L. Vincent, S. Avraham, P. Stevens, F. Zapata, L. Reiser, S.Y. Rhee, et al. (2006). Whole-plant growth stage ontology for angiosperms and its application in plant biology. Plant Physiology 142, 414-428.
216. Rabinowitz, D. (1997). A transmission disequilibrium test for quantitative trait loci. Human Heredity 47, 342-350.
217. Rae, A.M., M.P.C. Pinel, C. Bastien, M. Sabatti, N.R. Street, J. Tucker, C. Dixon, N. Marron, S.Y. Dillen, and G. Taylor (2007). QTL for yield in bioenergy Populus: identifying G x E interactions from growth at three contrasting sites. Tree Genetics & Genomes, 97-112.
218. Rafalski, A. (2002). Applications of single nucleotide polymorphisms in crop genetics. Current Opinion in Plant Biology 5, 94-100.
219. Raff, R.A. (1998). Evo-devo: the evolution of a new discipline. Genome 280, 1540-1542.
220. Ramsay, J.O. and B.W. Silverman (2002). Applied Functional Data Analysis: Methods and Case Studies. Springer, New York.
221. Reeve, E.C.R. and J.S. Huxley (1945). Some problems in the study of allomet-ric growth, in: Essays on Growth and Form, edited by LeGros Clark, W.E. and Medawa, P.B. Oxford University Press, Oxford, UK, pp. 121-156.
222. Reis, R.E., M.L. Zelditch, and W.L. Fink (1998). Ontogenetic allometry of body shape in the neotropical catfish callichthys (teleostei: siluriformes). Copeia 1998, 177-182.
223. Reppert, S.M. and D.R. Weaver (2002). Coordination of circadian timing in mammals. Nature 418, 935-941.
224. Rha, S.Y., H.C. Jeung, Y.H. Choi, W.I. Yang, J.H. Yoo, B.S. Kim, J.K. Roh, and H.C. Chung (2007). An association between RRM1 haplotype and gemcitabine-induced neutropenia in breast cancer patients. Oncologist 12, 622-630.
225. Rice, J.A. and C.O. Wu (2001). Nonparametric mixed effects models for unequally sampled noisy curves. Biometrics 57, 253-259.
226. Rice, S.H. (1997). The analysis of ontogenetic trajectories: when a change in size or shape is not heterochrony. Proceedings of the National Academy of Sciences of the United States of America 94, 907-912.
227. Rice, S.H. (2002). A general population genetic theory for the evolution of developmental interactions. Proceedings of the National Academy of Sciences of the United States of America 99, 15518-15523.
228. Richards, F.J. (2002). A flexible growth function for empirical use. Journal of Experimental Botany 10, 290-301.
229. Ring, H.Z. and D.L. Kroetz (2002). Candidate gene approach for pharmacogenetic studies. Pharmacogenomics 3, 47-56.
230. Rinn, J.L. and M. Snyder (2005). Sexual dimorphism in mammalian gene expression. Trends in Genetics 21, 298-305.
231. Robb, R.C. (1929). On the nature of heredity size-limitation. II. The growth of parts in relation to the whole. British Journal of Experiental Biology 6, 311-324.
232. Rohlf, F.J. (1998). On applications of geometric morphometrics to studies of ontogeny and phylogeny. Systematic Biology 47, 147-158.
233. Ron, M. and J.I. Weller (2007). From QTL to QTN identification in livestockwinning by points rather than knock-out: a review. Animal Genetics 38,429-439.
234. Rosenbaum, P.R. and D.B. Rubin (1983). The central role of the propensity score in observational studies for causal effects. Biometrika 70, 41-55.
235. Rovery, C., M.V. La, S. Robineau, K. Matsumoto, P. Renesto, and D. Raoult (2005). Preliminary transcriptional analysis of spot gene family and of membrane proteins in rickettsia conorii and rickettsia felis. Annals of the New York Academy of Sciences 1063,79-82.
236. Sax, K. (1923). The association of size differences with seed-coat pattern and pigmentation in Phaseolus vulgaris. Genetics 8, 552-560.
237. Schaeffer, L.R. and J.C.M. Dekkers (1994). Random regression in animal models for test-day production in dairy cattle. Proceedings of 5th World Congress Genetics Applied Livestock Prodouct, Guelph, Canada 18, 443-446.
238. Scheiner, S.M. (1993). Genetics and evolution of phenotypic plasticity. Annual Review of Ecology and Systematics 24, 35-68.
239. Scheiner, S.M. and R.F. Lyman (1989). The genetics of phenotypic plasticity. I. Heritability. Journal of Evolutionary Biology 2, 95-107.
240. Scheper, T., D. Klinkenberg, C. Pennartz, and J. van Pelt (1999). A mathematical model for the intracellular circadian rhythm generator. Journal of Neuroscience 19,40-47.
241. Schlichting, C.D. and H. Smith (2002). Phenotypic plasticity: linking molecular mechanisms with evolutionary outcomes. Evolutionary Ecology 16, 189-211.
242. Schmalhausen, I.I. (1949). Factors of Evolution. Blakiston, Philadelphia, PA.
243. Schmidt-Nielsen, K. (1984). Scaling: Why is Animal Size so Important? Cambridge University Press, Cambridge, UK.
244. Schwarz, G. (1978). Estimating the dimension of a model. Annals of Statistics 6, 461-464.
245. Sebastiani, P., R. Lazarus, S.T. Weiss, L.M. Kunkel, I.S. Kohane, and M.F. Ramoni (2003). Minimal haplotype tagging. Proceedings of the National Academy of Sciences of the United States of America 100, 9900-9905.
246. Seber, G. A. F. and C.J. Wild (1989). Nonlinear Regression. John Wiley & Sons, New York.
247. Shimomura, K., S.S. Low-Zeddies, D.P. King, T.D.L. Steeves, A. Whiteley, J. Kushla, P.D. Zemenides, A. Lin, M.H. Vitaterna, G.A. Churchill, et al. (2001). Genome-wide epistatic interaction analysis reveals complex genetic determinants of circadian behavior in mice. Genome Research 11, 959-980.
248. Sinha, V.K., S.S. De Buck, L.A. Fenu, J.W. Smit, M. Nijsen, R.A. Gilissen, A. Van Peer, K. Lavrijsen, and C.E. Mackie (2008). Predicting oral clearance in humans: how close can we get with allometry? Clinical Pharmacokinetics 47, 35-45.
249. Sladek, R., G. Rocheleau, J. Rung, C. Dina, L. Shen, D. Serre, P. Boutin, D. Vincent, A. Belisle, S. Hadjadj, et al. (2007). A genome-wide association study identifies novel risk loci for type 2 diabetes. Nature 445, 881-885.
250. Smolen, P., D.A. Baxter, and J.H. Byrne (2001). Modeling circadian oscillations with interlocking positive and negative feedback loops. Journal of Neuroscience 21, 6644-6656.
251. Stern, D.L. (1999). The developmental basis for allometry in insects. Development 126, 1091-1101.
252. Sun, Y. and H. Wu (2005). Semiparametric time-varying coefficients regression model for longitudinal data. Scandinavian Journal of Statistics 32, 21-47.
253. Tafti, M., B. Petit, D. Chollet, E. Neidhart, F. de Bilbao, J.Z. Kiss, P.A. Wood, and P. Franken (2003). Deficiency in short-chain fatty acid beta-oxidation affects theta oscillations during sleep. Nature Genetics 34, 320-325.
254. Takahashi, J.S. (1993). Circadian clocks a la CREM. Nature 365, 299-300.
255. Talkowski, M.E., G. Kirov, M. Bamne, L. Georgieva, G. Torres, H. Mansour, K.V. Chowdari, V. Milanova, J. Wood, L. McClain, K. Prasad, B. Shirts, J. Zhang, M.C. O’Donovan, M.J. Owen, B. Devlin, and V.L. Nimgaonkar (2008). A network of dopaminergic gene variations implicated as risk factors for schizophrenia. Human Molecular Genetics 17, 747-758.
256. Terwilliger, J.D. and T. Hiekkalinna (2006). An utter refutation of the fundamental theorem of the hapmap. The European Journal of Human Genetics 14, 426-437.
257. Togashi, K. and C.Y. Lin (2007). Genetic modification of the lactation curve by bending the eigenvectors of the additive genetic random regression coefficient matrix. Journal of Dairy Science 90, 5753-5758.
258. Toutain, P.L. and P. Lees (2004). Integration and modelling of pharmacokinetic and pharmacodynamic data to optimize dosage regimens in veterinary medicine. Journal of Veterinary Pharmacology and Therapeutics 27,467-477.
259. Ueda, H.R., M. Hagiwara, and H. Kitano (2001). Robust oscillations within the interlocked feedback model of Drosophila circadian rhythm. Journal of Theoretical Biology 210, 401-406.
260. Ungerer, M.C., S.S. Halldorsdottir, M.D. Purugganan, and T.F.C. Mackay (2003). Genotype-environmentinteractions at quantitative trait loci affecting inflorescence development in arabidopsis thaliana. Genetics 165, 353-365.
261. Van der Leeuw, J. (1994). The covariance matrix of ARMA errors in closed form. Journal Econometrics 63, 397-405.
262. Van Der Werf, J.H.J., M.E. Goddard, and K. Meyer (1998). The use of covariance functions and random regressions for genetic evaluation of milk production based on test day records. Journal of Dairy Science 81, 3300-3308.
263. Van Liew, H.D. (1967). Method of exponential peeling. Journal of Theoretical Biology 16, 43-53.
264. Vaughn, T.Y.T., L.S. Pletscher, A. Peripato, K. King-Ellison, E. Adams, C. Erikson, and J.M. Cheverud (1999). Mapping quantitative trait loci for murine growth: a closer look at genetic architecture. Genetical Research 74, 313-322.
265. Via, S., R. Gomulkiewicz, G. De Jong, S.M. Scheiner, C.D. Schlichting, and P.H. Van Tienderen (1995). Adaptive phenotypic plasticity: consensus and controversy. Trends in Ecology & Evolution 10, 212-217.
266. Via, S. and R. Lande (1985). Genotype-environment interaction and the evolution of phenotypic plasticity. Evolution 39, 505-522.
267. von Bertalanffy, L. (1957). Quantitative laws in metabolism and growth. The Quarterly Review of Biology 32, 217-231.
268. Waddington, C.H. (1942). Canalization of development and the inheritance of acquired characters. Nature 150, 563-565.
269. Wade, C.M., E.J. Kulbokas, A.W. Kirby, M.C. Zody, J.C. Mullikin, E.S. Lander, K. Lindblad-Toh, and M.J. Daly (2002). The mosaic structure of variation in the laboratory mouse genome. Nature 420, 574-578.
270. Wall, J. D. and J.K. Pritchard (2003). Haplotype blocks and linkage disequilibrium in the human genome. Nature Reviews Genetics 4, 587-597.
271. Wang, C. G., Y. Cheng, T. Liu, Q Li, R.B. 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.
272. Wang, N. (2003). Marginal nonparametric kernel regression accounting for within-subject correlation. Biometrika 90,43-52.
273. Wang, X., R. Korstanje, D. Higgins, and B. Paigen (2004). Haplotype analysis in multiple crosses to identify a QTL gene. Genome Research 14, 1767-1772.
274. Wang, Z.H. and R.L. Wu (2004). A statistical model for high-resolution mapping of quantitative trait loci determining HIV dynamics. Statistics in Medicine 23, 3033-3051.
275. Watters, J.W. and H.L. McLeod (2003). Using genome-wide mapping in the mouse to identify genes that influence drug response. Trends in Pharmacological Sciences 24, 55-58.
276. Wei, X., S.K. Ghosh, M.E. Taylor, V.A. Johnson, E.A. Emini, P. Deutsch, J.D. Lif-son, S. Bonhoeffer, M.A. Nowak, B.H. Hahn, et al. (1995). Viral dynamics in human immunodeficiency virus type 1 infection. Nature 373, 117-122.
277. Weinberg, W. (1908). Uber den Nachweis der Vererbung beim Menschen. Jahreshefte des Vereins für vaterländische Naturkunde in Württemberg 64, 368-382.
278. Weinshilboum, R. (2003). Inheritance and drug response. New England Journal of Medicine 348, 529-537.
279. Weiss, K.M. and A.G. Clark (2002). Linkage disequilibrium and the mapping of complex human traits. Trends in Genetics 18, 19-24.
280. Weiss, L.A., M. Abney, E.H. Cook, and Carole Ober (2005). Sex-specific genetic architecture of whole blood serotonin levels. American Journal of Human Genetics 76, 33-41.
281. Weiss, L.A., L. Pan, M. Abney, and C. Ober (2006). The sex-specific genetic architecture of quantitative traits in humans. Nature Genetics 38, 218-22.
282. West, G.B. and J.H. Brown (2004). Life’s universal scaling laws. Physics Today 57, 36-42.
283. West, G.B. and J.H. Brown (2005). The origin of allometric scaling laws in biology from genomes to ecosystems: towards a quantitative unifying theory of biological structure and organization. Journal of Experimental Biology 208, 1575-1592.
284. West, G.B., J.H. Brown, and B.J. Enquist (1997). A general model for the origin of allometric scaling laws in biology. Science 276, 122-126.
285. West, G.B., J.H. Brown, and B.J. Enquist (1999a). A general model for the structure and allometry of plant vascular systems. Nature 400, 664-667.
286. West, G.B., J.H. Brown, and B.J. Enquist (1999b). The fourth dimension of life: fractal geometry and allometric scaling of organisms. Science 284, 1677-1679.
287. West, G.B., J.H. Brown, and B.J. Enquist (2001). A general model for ontogenetic growth. Nature 413, 628-31.
288. West-Eberhard, M.J. (2003). Developmental Plasticity and Evolution. Oxford University Press, New York.
289. West-Eberhard, M.J. (2005). Developmental plasticity and the origin of species differences. Proceedings of the National Academy of Sciences of the United States of America 102, 6543-6549.
290. Whitlock, M.C., P.C. Phillips, F.B.G. Moore, and S.J. Tonsor (1995). Multiple fitness peaks and epistasis. Annual Review of Ecology and Systematics 26, 601-629.
291. Wiltshire, T., M.T. Pletcher, S. Batalov, S.W. Barnes, L.M. Tarantino, M.P. Cooke, H. Wu, K. Smylie, A. Santrosyan, N.G. Copeland, et al. (2003). Genome-wide single-nucleotide polymorphism analysis defines haplotype patterns in mouse. Proceedings of the National Academy of Sciences of the United States of America 100, 3380-3385.
292. Wolf, J.B. (2000). Gene interactions from maternal effects. Evolution 54, 1882-1898.
293. Wu, H. and A.A. Ding (1999). Population HIV-1 dynamics in vivo: applicable models and inferential tools for virological data from AIDS clinical trials. Biometrics 55,410-418.
294. Wu, H. and J.T. Zhang (2002). The study of long-term HIV dynamics using semiparametric non-linear mixed-effects models. Statistics in Medicine 21, 3655-3675.
295. Wu, H. and J. T. Zhang (2006). Nonparametric Regression Methods for Longitudinal Data Analysis: Mixed-Effects Modeling Approaches. John Wiley & Sons, NK.
296. Wu, L. (2002). A joint model for nonlinear mixed-effects models with censoring and covariates measured with error, with application to aids studies. Journal of the American Statistical Association 97, 955-965.
297. Wu, R.L. (1998). The detection of plasticity genes in heterogeneous environments. Evolution 52, 967-977.
298. Wu, R.L., J.E. Grissom, S.E. McKeand, and D.M. O’Malley (2004a). Phenotypic plasticity of fine root growth increases plant productivity in pine seedlings. BMC Ecology 4, doi: 10.1186/1472-6785-4-14.
299. Wu, R.L. and W. Hou (2006). A hyperspace model to decipher the genetic architecture of developmental processes: allometry meets ontogeny. Genetics 172, 627-637.
300. Wu, R.L. and M. Lin (2006). Functional mapping-how to map and study the genetic architecture of dynamic complex traits. Nature Review Genetics 7, 229-237.
301. Wu, R.L., C.X. Ma, and G. Casella (2002b). Joint linkage and linkage disequilibrium mapping of quantitative trait loci in natural populations. Genetics 160, 779-792.
302. Wu, R.L., C.X. Ma, and G. Casella (2007a). Statistical Genetics of Quantitative Traits: Linkage, Maps, and QTL. Springer-Verlag, New York.
303. Wu, R.L., C.X. Ma, M. Chang, R.C. Littell, S.S. Wu, M. Huang, M. Wang, and G. Casella (2002a). A logistic mixture model for detecting major genes governing growth trajectories. Genetical Research 79, 235-245.
304. 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 mutation to regulate growth trajectories in mice. Genetics 171, 239-249.
305. Wu, R.L., C.X. Ma, M. Lin, and G. Casella (2004b). A general framework for analyzing the genetic architecture of developmental characteristics. Genetics 166, 1541-1551.
306. Wu, R.L., C.X. Ma, M. Lin, Z. Wang, and G. Casella (2004c). Functional mapping of quantitative trait loci underlying growth trajectories using a transform-both-sides logistic model. Biometrics 60, 729-738.
307. Wu, R.L., C.X. Ma, R.C. Littell, and G. Casella (2002c). A statistical model for the genetic origin of allometric scaling laws in biology. Journal of Theoretical Biology 219, 121-135.
308. Wu, R.L., C.X. Ma, W. Zhao, and G. Casella (2003). Functional mapping of quantitative trait loci underlying growth rates: a parametric model. Physiological Genomics 14, 241-249.
309. Wu, R.L., Z. Wang, W. Zhao, and J.M. Cheverud (2004d). A mechanistic model for genetic machinery of ontogenetic growth. Genetics 168, 2383-2394.
310. Wu, R.L. and Z.B. Zeng (2001). Joint linkage and linkage disequilibrium mapping in natural populations. Genetics 157, 899-909.
311. Wu, S., J. Yang, C.G. Wang, and R.L. Wu (2007b). A general quantitative genetic model for haplotyping a complex trait in humans. Current Genomics 8, 343-350.
312. Wu, S., J. Yang, and R.L. Wu (2007c). Semiparametric functional mapping of quantitative trait loci governing long-term HIV dynamics. Bioinformatics 23, i569-i576.
313. Wu, W.B. and M. Pourahmadi (2003). Nonparametric estimation of large covariance matrices oflongitudinal data. Biometrika 90, 831-844.
314. Xu, S. and W.R. Atchley (1995). A random model approach to interval mapping of quantitative trait loci. Genetics 141, 1189-1197.
315. Xue, L.G. and L.X. Zhu (2007). Empirical likelihood semiparametric regression analysis for longitudinal data. Biometrika 94, 921-937.
316. Yalcin, B., J. Flint, and R. Mott (2005). Using progenitor strain information to identify quantitative trait nucleotides in outbred mice. Genetics 171, 673-681.
317. Yalcin, B., J. Fullerton, S. Miller, D.A. Keays, S. Brady, A. Bhomra, A. Jefferson, E. Volpi, R.R. Copley, J. Flint, et al. (2004). Unexpected complexity in the haplotypes of commonly used inbred strains of laboratory mice. Proceedings of the National Academy of Sciences of the United States of America 101, 9734-9739.
318. Yang, J., R.L. Wu, and G. Casella (2008). Nonparametric functional mapping of quantitative trait loci. Biometrics (accepted).
319. Yang, R., Q. Tian, and S. Xu (2006). Mapping quantitative trait loci for longitudinal traits in line crosses. Genetics 173, 2339-2356.
320. Zeger, S.L. and PJ. Diggle (1994). Semiparametric models for longitudinal data with application to CD4 cell numbers in HIV seroconverters. Biometrics 50, 689-699.
321. Zelawski, W. and A. Lech (1980). Logistic growth functions and their applicability for characterizing dry matter accumulation in plants. Acta Physiologiae Plantarum 2, 187-194.
322. Zelditch, M.L. and W.L. Fink (1995). Allometry and developmental integration of body growth in a piranha, Pygocentrus nattereri (Teleostei: Ostariophysi). Journal of Morphology 223, 341-355.
323. Zelditch, M.L., W.L. Fink, D.L. Swiderski, and B.L. Lundrigan (1998). On applications of geometric morphometrics to studies of ontogeny and phylogeny: a reply to Rohlf. Systematic Biology 47, 159-167.
324. Zeng, Z.B. (1993). Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci. Proceedings of the National Academy of Sciences of the United States of America 90, 10972-10976.
325. Zeng, Z.B. (1994). Precision mapping of quantitative trait loci. Genetics 136, 1457-1468.
326. Zeng, Z.B., J. Liu, L.F. Stam, C.H. Kao, J.M. Mercer, and C.C. Laurie (2000). Genetic architecture of a morphological shape difference between two drosophila species. Genetics 154, 299-310.
327. Zhang, K., M. Deng, T. Chen, M.S. Waterman, and F. Sun (2002). A dynamic programming algorithm for haplotype block partitioning. Proceedings of the National Academy of Sciences of the United States of America 99, 7335-7339.
328. Zhang, W.K., Y.J. Wang, G.Z. Luo, J.S. Zhang, C.Y. He, X.L. Wu, J.Y. Gai, and S.Y. Chen (2004). QTL mapping of ten agronomic traits on the soybean (Glycine max L. Merr.) genetic map and their association with EST markers. Theoretical and Applied Genetics 108, 1131-1139.
329. Zhao, W., Y.Q. Chen, G. Casella, J.M. Cheverud, and R. Wu (2005). A nonstationary model for functional mapping of complex traits. Bioinformatics 21, 2469-2477.
330. Zhao, W., C.X. Ma, J.M. Cheverud, and R.L. Wu (2004a). A unifying statistical model for QTL mapping of genotype-sex interaction for developmental trajectories. Physiological Genomics 19, 218-227.
331. Zhao, W., R.L. Wu, C.X. Ma, and G. Casella (2004b). A fast algorithm for functional mapping of complex traits. Genetics 167, 2133-2137.
332. Zhao, W., J. Zhu, M. Gallo-Meagher, and R.L. Wu (2004c). A unified statistical model for functional mapping of genotype x environment interactions for ontogenetic development. Genetics 168, 1751-1762.
333. Zhu, Y., W. Hou, and R.L. Wu (2003). A haplotype block model for fine mapping of quantitative trait loci regulating HIV-1 pathogenesis. Computational and Mathematical Methods in Medicine 5, 227-234.
334. Zimmerman, D.L. and V. Ntmez-Anton (2001). Parametric modelling of growth curve data: An overview (with dicussions). Test 10, 1-73.
335. Zondervan, K.T. and L.R. Cardon (2007). Designing candidate gene and genomewide case-control association studies. Nature Protocol 2, 2492-2501.
336. Zuideveld, K.P., P.H. Van der Graaf, L.A. Peletier, and M. Danhof (2007). Allometric scaling of pharmacodynamic responses: application to 5-Ht1A receptor mediated responses from rat to man. Pharmaceutical Research 24, 2031-2039.