R.W. Doerge Publications

Prior to 1994 available by request doerge@purdue.edu

1994-2007

1. G.A. Churchill and R.W. Doerge. 1994. Empirical threshold values for quantitative trait mapping. Genetics. 138:963-971.
   
   
2. R.W. Doerge. 1995. Testing for linkage: phase known/phase unknown. Journal of Heredity. 86(1):61-62.
   
   
3. R.W. Doerge. 1995. The relationship between the LOD score and the analysis of variance F-statistic when detecting QTL using single markers. Appendix 1: Locating genes associated with root morphology and drought avoidance in rice via linkage to molecular markers. M.C. Champoux, G. Wang, S. Sarkarung, D.J. Mackill, J.C. O'Toole, N. Huang, S.R. McCouch. Theoretical and Applied Genetics. 90:969-981.
   
   
4. S.R. McCouch and R.W. Doerge. 1995. QTL mapping in rice. Trends in Genetics. Vol. 11, 12:482-487.
   
   
5. R.W. Doerge and G.A. Churchill. 1996. Permutation tests for multiple loci affecting a quantitative character. Genetics. 142:285-294.
   
   
6. R.W. Doerge and A. Rebai. 1996. Significance thresholds for QTL interval mapping tests Heredity. 76:459-464.
   
   
7. M.A. Mutschler, R.W. Doerge, J.P. Kuai, S.C. Liu, B. Liedl, Y. Shapiro. 1996. QTL analysis of the production of acylsugars responsible for pest resistance in the wild tomato lycopersicon pennellii . Theor. Appl. Genet. Vol.92 6:709-719.
   
   
8. R.W. Doerge (Journal of Quantitative Trait Loci. Volume 2. Article 6. 1996). ``Constructing genetic maps by rapid chain delineation''
   
   
9. R.W. Doerge, Z-B. Zeng and B.S. Weir. 1997. Statistical issues in the search for genes affecting quantitative traits in experimental populations. Statistical Science. 12(3):195-219.
   
   
10. G.A. Churchill and R.W. Doerge. 1997. Mapping Quantitative Trait Loci in Experimental Populations. In: Molecular Dissection of Complex Traits. A.H. Paterson (ed). CRC Press: New York.
    
    
11. C. Teuscher, D.M. Rhein, K.D. Livingstone, R.A. Paynter, R.W. Doerge, S.M. Nicholson, and R.W. Melvold. 1997. Evidence that Tmevd2 and eae3 may represent either a common locus or gene complex controlling susceptibility to immunologically mediated demyelination in mice1. Journal of Immunology. 159:4930-4934.
    
    
12. R.J. Roper, R.W. Doerge, S.B. Call, K.S.K. Yung, W.F. Hickey, C. Teuscher. 1998. Autoimmune orchitis, epididymitis, and vastis are immunogenetically distinct lesions. The American Journal of Pathology. Vol. 152, No. 5:1337-1345.
    
    
13. R.W. Doerge. 1998. Statistical threshold values for locating quantitative trait loci. Proceedings of the Tenth Annual Conference on Applied Statistics in Agriculture, Kansas State University. Edited by George Milliken. 10:84-95.
    
    
14. R.J. Roper, J.S. Griffith, C.R. Lyttle, R.W. Doerge, A.W. McNabb, R.E. Broadbent, C. Teuscher. 1999. Interacting quantitative trait loci control phenotypic variation in murine estradiol-regulated responses. Endocrinology. Vol. 140, No. 2: 556-561.
    
    
15. J. Weis, B. McCracken, Y. Ma, D. Fairbairn, R. Roper, J. Weis, J. Zachery, R.W. Doerge, and C. Teuscher. 1999. Identification of quantitative trait loci governing arthritis severity and humoral responses in the murine model of Lyme disease. Journal of Immunology. 162:948-956.
    
    
16. R. J. Butterfield, E. P. Blankenhorn, R. J. Roper, J. F. Zachary, R.W. Doerge, J. Sudweeks, J. Rose, and C. Teuscher. 1999. Genetic analysis of disease subtype and sexual dimorphism in mouse EAE: Relapsing-remitting and monophasic remitting/non-relapsing EAE are immunogenetically distinct. Journal of Immunology. 162:(5)3096-3102.
    
    
17. C. Teuscher, R.J. Butterfield, R. Ma, J. Zachary, R.W. Doerge, E.P. Blankenhorn. 1999. Sequence polymorphisms in the chemokines scya1 (TCA-3), scya2 (Monocyte chemattractant protein (MCP-1)), and scya12 (MCP-5) are candidate genes for eae 7, a locus controlling the susceptibility to monophasic remitting/nonrelapsing experimental allergic encephalomyelitus. Journal of Immunology. 163:2262--2266.
    
    
18. S.A. Fennimore, G.E. Shaner, W.E. Nyquist, R.W. Doerge, and M.E. Foley. 1999. A genetic model and molecular markers for wild oat ( Avena fatua L.) seed dormancy. Theoretical and Applied Genetics. (3-4):711-718.
    
    
19. D. Nettleton and R.W. Doerge. 2000. Accounting for variability in the use of permutation testing to detect quantitative trait loci. Biometrics. 56:285-291.
    
    
20. R. Bernardo, J. Romero-Severson, J. Ziegle, J. Hauser, L. Joe, G. Hookstra, and R.W. Doerge. 2000. Parental contribution and coefficient of coancestry among maize inbreds: Pedigree, RFLP, and SSR data. Theoretical and Applied Genetics. 100:552-556.
    
    
21. E.P. Blankenhorn, R.J. Butterfield, R. Rigby, L. Cort, D. Giambrone, P. McDermott, K. McEntee, N. Solowski, N.D. Meeker, J.F. Zachary, R.W. Doerge, and C. Teuscher. 2000. Genetic analysis of the influence of pertussis toxin in EAE susceptibility:an environmental agent can override genetic checkpoints. The Journal of Immunology. 164(6):3420-3425.
    
    
22. R.W. Doerge and Bruce A. Craig. 2000. Model selection for quantitative trait locus analysis in polyploids. Proceedings of the National Academy of Science. 97(14):7951-7956.
    
    
23. R.J. Butterfield, E.P. Blankenhorn, R.J. Roper, J.F. Zachary, R.W. Doerge, and C. Teuscher. 2000. Identification of genetic loci controlling the allergic encephaloeyelitis (EAE). Am. J. Pathol. 157(2):637-646.
    
    
24. R.W. Doerge and Bruce A. Craig. 2000. An Introduction to model selection for quantitative trait locus analysis in polyploids. Proceedings of Applied Statistics in Agriculture, Kansas State University. Edited by George Milliken, pp 13-27.
    
    
25. L.M. McIntyre, C. Coffman, and R.W. Doerge. 2001. Detection and location of a single binary trait locus in experimental populations. Genetical Research. 78:79-92.
    
    
26. Roper, R.J., J.J. Weis, B.A. McCracken, C.B. Green, Y. Ma, K.S. Weber, D. Fairbairn, R.J. Butterfield, M.R. Potter, J.F. Zachary, R.W. Doerge, C. Teuscher. 2001. Susceptibility to experimental lyme arthritis is linked to multiple loci on chromosome 5 in four independent mouse crosses. Genes and Immunity 2(7):388-397.
    
    
27. R.W. Doerge. 2001. Quantitative Trait Loci. Plant Sciences for Students. Macmillan Reference USA, 195-196.
    
    
28. J. Wilbur, J.K. Ghosh, C.H. Nakatsu, S.M. Brouder, and R.W. Doerge. 2001. Statistical Issues in the Analysis of Microbial Communities in Soil. Proceedings of Applied Statistics in Agriculture, Kansas State University. Edited by George Milliken, 129-143.
    
    
29. M.A. Black and R.W. Doerge. 2001. Calculation of the minimum number of replicate spots required for detection of significant gene expression fold changes for cDNA microarrays. Proceedings of Applied Statistics in Agriculture, Kansas State University. Edited by George Milliken, 144-158.
    
    
30. B.A. Craig, O. Vitek, M.A. Black, M. Tanurdzic, R.W. Doerge. 2001. Designing microarray experiments: chips, dips, flips, and skips. Proceedings of Applied Statistics in Agriculture, Kansas State University. Edited by George Milliken, 159-182.
    
    
31. R.W. Doerge. 2002. Mapping and analysis of quantitative trait loci in experimental populations. Nature Reviews Genetics 3:43-52.
    
    
32. J. Wilbur, J.K. Ghosh, C.H. Nakatsu, S.M. Brouder, and R.W. Doerge. 2002. Variable selection in high-dimensional multivariate binary data with application to the analysis of microbial community DNA fingerprints. Biometrics 58:378-386.
    
    
33. R.J. Roper, R.Z. Ma, J.E. Biggins, R.J. Butterfield, S.D. Michael, K.S.K. Tung, R.W. Doerge, an d C. Teuscher. 2002 Interacting quantitative trait loci control loss of peripheral tolerance and susceptibility to autoimmune ovarian dysgenesis after day three thymectomy in mice. Journal of Immunology 168(3):1640-1646.
    
    
34. M.A. Black and RW Doerge. 2002. Calculation of the minimum number of replicate spots required for detection of significant gene expression fold change in microarray experiments. Bioinformatics 18(12):1609-1616.
    
    
35. R.J. Butterfield, R.J. Roper, D.M. Rhein, R.W. Melvold, L.Haynes, R.Z. Ma, R.W. Doerge, C. Teuscher. 2003. Sex specific QTL govern susceptibility to Theiler's murine encephalomyelitis virus-induced demyelination (TMEVD). Genetics 163(3):1041-1046.
    
    
36. B.A. Craig, M.A. Black, and R.W. Doerge. 2003. Gene Expression Data: The technology and statistical analysis. Journal of Agricultural, Biological, and Environmental Statistics (JABES) 8(1):1-28.
    
    
37. T.C. Osborn, J.C. Pires, J.A. Birchler, D.L. Auger, Z.J. Chen, H-S. Lee, L. Comai, A. Madlung, R.W. Doerge, V. Colot, and R.A. Martienssen. 2003. Understanding mechanisms of novel gene expression in polyploids. Trends in Genetics 19(3): 141-147.
    
    
38. Veena, H. Jiang, R.W. Doerge, S.B. Gelvin. 2003. Differential expression of plant genes during the initial stages of Agrobacterium-mediated transformation. The Plant Journal. 35:219-236.
    
    
39. Coffman, C., R.W. Doerge, M. Wayne, L.M. McIntyre. 2003. Intersection tests for single marker QTL analysis can be more powerful than two marker QTL analysis. BioMed Central (BMC) Genetics. 4:10.
    
    
40. O. Abiola, J.M. Angel, P. Avner, A.A. Bachmanov, B. Bennett, E.P. Blankenhorn, D.A. Blizard, V. Bolivar, G.A. Brockmann, W.L. Casley, M. Cook, K.J. Buck, J.-F. Bureau, E.J. Chesler, J.M. Cheverud, G.A. Churchill, J.C. Crabbe, W.E. Crusio, A. Darvasi, P. Demant, R.W. Doerge, R.W. Elliott, C.R. Farber, J. Flint, H. Gershenfeld, J.P. Gibson, W. Gu, G. de Haan, H. Himmelbauer, R. Hitzemann, K. Hunter, H.-C. Hsu, F. Iraqi, R.C. Jansen, T.E. Johnson, G. Kempermann, F. Lammert, L. Lu, K.F. Manly, D.B. Matthews, J.F. Medrano, M. Mehrabian, G. Mittleman, B.A. Mock, J.S. Mogil, X. Montagutelli, G. Morahan, J.D. Mountz, H. Nagase, R.S. Nowakowski, B.F. O'Hara, A.V. Osadchuk, B. Paigen, A.A. Palmer, J.L. Peirce, D. Pomp, G.D. Rosen, M. Rosemann, L.C. Schalkwyk, Z. Seltzer, S. Settle, K. Shimomura, S. Shou, J.M. Sikela, L.D. Siracusa, J.L. Spearow, C. Teuscher, D.W. Threadgill, L.A. Toth, A.A. Toye, C. Vadasz, E. Wakeland, R.W. Williams, G. Van Zant, H.-G. Zhang, F. Zou, L. Flaherty. 2003. The nature and identification of quantitative trait loci: a community's view. Nature Genetics Reviews. 4:911-916.
    
    
41. D. Cao, B.A. Craig, and R.W. Doerge. 2003. Interval mapping for autopolyploids. Proceedings of Applied Statistics in Agriculture, Kansas State University. Edited by George Milliken, p. 60-72.
    
    
42. D. Cao, T.C. Osborn, and R.W. Doerge. 2004. Correct estimation of preferential chromosome pairing in polyploids. Genome Research. 14:1-4.
    
    
43. M. Bogdan, J.K. Ghosh, and R.W. Doerge. 2004. Modifying the Schwarz Bayesian Information Criterion to locate multiple interacting quantitative trait loci. Genetics. 167:989-999.
    
    
44. H.-S. Lee, J. Wang, L. Tan, H. Jiang, M.A. Black, A. Madlung, L. Lukens, J.C. Pires, L. Comai, T.C. Osborn, R.W. Doerge, Z.J. Chen. 2004. Sensitivity of 70-mer Oligonucleotides and cDNAs for Microarray analysis of gene expression in arabidopsis and its related species. Plant Biotechnology Journal. 2:45-57.
    
    
45. Z.J. Chen, J. Wang, L. Tian, H.-S. Lee, J.J. Wang, M. Chen, J.J. Lee, C. Josefsson, A. Madlung, B. Watson, J.C. Pires, Z. Lippman, M. Vaughn, V. Colot, J.A. Birchler, R.W. Doerge, R.A. Martienssen, L. Comai, and T.C. Osborn. 2004. The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects. Biological Journal of the Linnean Society. 82:689-700.
    
    
46. J. Wang, J.J. Lee, H.-S. Lee, L. Tian, M. Chen, S. Rao, E.N. Wei, R.W. Doerge, L. Comai, Z.J. Chen. 2005. Methods for genome-wide analysis of gene expression changes in polyploids. Methods in Enzymology. 395:570-96.
    
    
47. Z. Lippman, A.-V. Gendrel, M. Black, M. Vaughn, N. Dedhia, W.R. McCombie, K. Lavine, V. Mittal, B. May, K. Kasschau, J.C. Carrington, R.W. Doerge, V. Colot, and R. Martienssen 2004. Transposable elements mediate heterochromatin and epigenetic control. Nature. 430:471-476.
    
    
48. K. Bradley, M.B. Boulware, H. Jiang, R.W. Doerge, and R.L. Meisel. 2004. Sexual experience generates distinct patterns of gene expression in the nucleus accumbens and dorsal striatum of female syrian hamsters. Genes, Brain, and Behavior. 4(1):31-44.
    
    
49. K. Kim, M. West, R.W. Michelmore, D. St. Clair, and R.W. Doerge. 2004. Genetic mapping of gene expression levels: expression level polymorphism analysis for dissecting regulatory networks of plant disease res istance. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture . Manhattan, KS.
    
    
50. D. Cao, B.A. Craig, and R.W. Doerge. 2004. Bayesian quantitative trait mapping of autopolyploi ds. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture . Manhattan, KS.
    
    
51. H. Jiang, J. Wang, L. Tian, Z.J. Chen, and R.W. Doerge. 2004. Statistical analysis of 70-mer ol igonucleotide microarray from poly ploid experiments using repeated dye-swaps. The Proceedings of the Kansas State University Con ference on Applied Statistic s in Agriculture. Manhattan, KS.
    
    
52. The Complex Traits Consortium (see publication 40 for list of members). 2004. The collaborative cross: A community resource for the genetic analysis of complex traits. Nature Genetics. 36(11):1133-7.
    
    
53. L. Tian, M.P. Fong, J.J. Wang, N.E. Wei, H. Jiang, R.W. Doerge, and Z.J, Chen. 2005. Reversible histone acetylation and deacetylation mediate genome-wide, promoter-dependent, and locus-specific changes in gene expression during plant development. Genetics. 169:337-345.
    
    
54. A. Madlung, A.P. Tyagi, B. Watson, H. Jiang, T. Kagochi, R.W.Doerge, R. Martienssen, L. Comai. 2005. Genomic changes in synthetic Arabidopsis polyploids. Plant Journal. 41(2):221-230.
    
    
55. D. Cao, B. Craig, and R.W Doerge. 2005. A Model Selection Based Interval Mapping Method for Autopolyploids. Genetics. 169: 2371-2382.
    
    
56. M. Bogdan and R.W. Doerge. 2005. Biased estimators of genetic effects and heritability in interval mapping. Heredity. 95:476-484.
    
    
57. C. Coffman, R.W. Doerge, K.L. Simonsen, K. Nichols, C. Duarte, R. Wolfinger, and L.M. McIntyre. 2005. Model Selection in Binary Trait Locus Mapping. Genetics. 170: 1281-1297.
    
    
58. J. Stevens and R.W. Doerge. 2005. Combining Affymetrix microarray results. BioMed Central Bioinformatics. 6:57.
    
    
59. J. Stevens and R.W. Doerge. 2005. Meta-Analysis combines Affymetrix microarray results across laboratories. Comparative and Functional Genomics. 6:116-122.
    
    
60. R.A. Martienssen, R.W. Doerge. V. Colot. 2005. Epigenomic mapping in Arabidopsis using tiling microarrays. Chromosome Research. 13 3:299-308.
    
    
61. B. Munneke, K.A. Schlauch, K. Simonsen, W. Beavis, and R.W. Doerge. 2005. Adding confidence to gene expression clustering. Genetics. 170: 2003-2011.
    
    
62. J. Stevens and R.W. Doerge. 2005. A Bayesian and covariate approach to combine results from multiple microarray studies. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. 133-147.
    
    
63. K. Kim, M. West, R.W. Michelmore, D. St. Clair, and R.W. Doerge. 2005. Old methods for new ideas: using gene expression levels to molecularly dissect complex traits. The Proceedings of the Stadler Genetics Symposium. March 2003. Edited by Perry Gustafson, Randy Shoemaker, and John Snape. Springer, NY. 89-106.
    
    
64. J. Wang, L. Tian, H-S Lee, N.E. Wei, H. Jiang, B. Watson, A. Madlung, T.C. Osborn, R.W. Doerge, L. Comai, and Z.J. Chen. 2006. Genome-wide non-additive gene regulation in Arabidopsis allotetraploids. Genetics. 172: 507-517.
    
    
65. D.J. Kliebenstein, M.A.L. West, H. van Leeuwen, K. Kim, R.W. Doerge, R.W. Michelmore, D.A. St.Clair. 2006. Genomic survey of gene expression diversity in Arabidopsis thaliana. Genetics. 172: 1179-1189.
    
    
66. C. Teuscher, R.W. Doerge, P.D. Fillmore, and E.P. Blankenhorn. 2006. eae36, A locus on mouse chromosome 4 controls susceptibiltiy to experimental allergic encephalomyelitis in older mice and mice immunized in the winter. Genetics. 172: 1147-1153.
    
    
67. M.A.L. West, H. van Leeuwen, A. Kozik, D.J. Kliebenstein, R.W. Doerge, D.A. St. Clair, and R.W. Michelmore. 2006. High-density haplotyping with microarray-based expression and single feature polymorphism markers in Arabidopsis. Genome Research. 16:787-795.
    
    
68. D.J. Kliebenstein, M.A.L. West, H. van Leeuwen, O. Loudet, R.W. Doerge, D.A. St Clair. 2006. Identification of QTLs controlling gene expression networks defined a priori. BMC Bioinformatics. 7(1):308.
    
    
69. L. An, N. Riddle, J. Birchler, and R.W. Doerge. 2006. Clustering a series of replicated polyploid gene expression experiments. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. 52-66.
    
    
70. H. Jiang and R.W. Doerge. 2006. A two-step multiple comparison procedure for a large number of tests and multiple treatments. Statistical Applications in Genetics and Molecular Biology. Vol. 5: Issue 1, Article 28.
    
    
71. J. M. Ordway, J.A. Bedell, R.W. Citek, A. Nunberg, A. Garrido, R. Kendall, J.R. Stevens, D. Cao, R.W. Doerge, Y. Korshunova, H. Holemon, J. D.McPherson, N. Lakey, J. Leon, R.A. Martienssen, J.A. Jeddeloh. 2006. Comprehensive DNA methylation profiling in a human cancer genome identifies novel epigenetic targets. Carcinogenesis. 27(12):2409-2423.
    
    
72. M.A.L. West, K. Kim, D.J. Kliebenstein, H. van Leeuwen, R.W. Michelmore, R.W. Doerge, D.A. St.Clair. 2007. Global eQTL Mapping Reveals the Complex Genetic Architecture of Transcript Level Variation in Arabidopsis. Genetics. 175: 1441-1450.
    
    
73. R.W. Doerge. 2007. Statistical Advances in Functional Genomics. R. Varshney and R. Tuberosa (eds.), Genomic Assisted Crop Improvement: Vol 1: Genomics Approaches and Platforms, 315-332. Springer-Verlag.
    
    
74. M. Vaughn, M. Tanurdzic, Z. Lippman, H. Jiang, R. Carrasquillo, V. Colot, R.W. Doerge and R.A. Martienssen. 2007. Epigenetic variation in Arabidopsis thaliana. Public Library of Science (PLoS) Biology. 5(7): e174.
    
    
75. H. van Leeuwen, D.J. Kliebenstein, M.A.L. West, K. Kim, R. van Poecke, F. Katagiri, R.W. Michelmore, R.W. Doerge, D.A. St.Clair. 2007. Natural variation among Arabidopsis thaliana accessions for transcriptome response to exogenous salicylic acid. The Plant Cell. 19(7):2099-2110.
    
    
76. J. Zhao, J. Wang, L. An, R.W. Doerge, Z.J. Chen, C. Grau, J. Meng, and T. Osborn. 2007. Analysis of gene expression profiles in response to Sclerotinia sclerotiorum in Brassica napus. Planta. 227(1):13-24.
    
    
77. H.-T. Leung, L. An, J. Tseng-Crank, E. Kim, E.L. Harness, Y. Zhou, J. Kitamoto, G. Li, R.W. Doerge, and W.L. Pak. 2007. Phototransduction in Drosophila: Use of microarrays in cloning genes identified by chemically induced mutations causing ERG defects. In S.J. Fliesler and O.G.Kisselev (eds.), Signal Transduction in the Retina, Taylor and Francis/CRC Press, pp. 195-217.
    
    
78. J.M. Ordway, M.A. Budiman, Y. Korshunova, R.K. Maloney, J.A. Bedell, R.W. Citek, B. Bacher, S. Peterson, T. Rohlfing, J. Hall, R. Brown, N. Lakey, R.W. Doerge, R.A. Martienssen, J. Leon, J.D. McPherson, and J.A. Jeddeloh. 2007. Identification of novel high-frequency DNA methylation changes in breast cancer. Public Library of Science (PLoS) ONE. 12:1314.
    
    
79. M. Bogdan, P. Biecek, R. Cheng, F. Frommlet, J.K. Ghosh, and R.W. Doerge. 2008. Extending the modified Bayesian Information Criterion (mBIC) to dense markers and multiple interval mapping. Biometrics. doi: 10.1111/j.1541-0420.2008.00989.x.
    
    
80. A.A. Long, E. Kim, H.-T. Leung, E. Woodruff III, L. An, R.W. Doerge, W.L. Pak, and K. Broadie. 2008. The presynaptic calcium trigger driving vesicle exocytosis and calcium-dependent facilitation requires the fuseless protein. Journal of Neuroscience. (in press).
    
    
81. G.A. Churchill and R.W. Doerge. 2008. Naive application of permutation testing leads to inflated type I error rates. Genetics. 178:609-610.
    
    
82. H. Jiang and R.W. Doerge. 2008. Estimating the proportion of true null hypotheses for multiple comparisons. Cancer Informatics. 4:25-32.