G.A. Churchill and R.W. Doerge. 1994. Empirical threshold values for
quantitative trait mapping. Genetics. 138:963-971.
R.W. Doerge. 1995. Testing for linkage: phase known/phase unknown.
Journal of Heredity. 86(1):61-62.
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.
S.R. McCouch and R.W. Doerge. 1995. QTL mapping in rice.
Trends in Genetics. Vol. 11, 12:482-487.
R.W. Doerge and G.A. Churchill. 1996. Permutation tests for multiple loci
affecting a quantitative character. Genetics. 142:285-294.
R.W. Doerge and A. Rebai. 1996. Significance thresholds for QTL interval mapping tests.
Heredity. 76:459-464.
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.
R.W. Doerge. 1996.
Constructing genetic maps by rapid chain delineation. Journal of Quantitative Trait Loci.
Volume 2. Article 6.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
R.W. Doerge. 2001. Quantitative Trait Loci. Plant Sciences for Students. Macmillan Reference USA, 195-196.
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.
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.
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.
R.W. Doerge. 2002. Mapping and analysis of quantitative trait loci in experimental populations.
Nature Reviews Genetics 3:43-52.
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.
R.J. Roper, R.Z. Ma, J.E. Biggins, R.J. Butterfield, S.D. Michael, K.S.K. Tung, R.W. Doerge, and
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.
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.
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.
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.
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.
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.
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.
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.
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.
D. Cao, T.C. Osborn, and R.W. Doerge. 2004. Correct estimation of preferential
chromosome pairing in polyploids. Genome Research. 14:1-4.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
D. Cao, B. Craig, and R.W Doerge. 2005.
A model selection based interval mapping method for autopolyploids.
Genetics. 169: 2371-2382.
M. Bogdan and R.W. Doerge. 2005. Biased estimators of genetic effects
and heritability in interval mapping. Heredity. 95:476-484.
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.
J. Stevens and R.W. Doerge. 2005. Combining Affymetrix microarray results.
BioMed Central Bioinformatics. 6:57.
J. Stevens and R.W. Doerge. 2005. Meta-Analysis combines Affymetrix microarray results
across laboratories. Comparative and Functional Genomics. 6:116-122.
R.A. Martienssen, R.W. Doerge. V. Colot. 2005. Epigenomic mapping in Arabidopsis
using tiling microarrays. Chromosome Research. 13 3:299-308.
B. Munneke, K.A. Schlauch, K. Simonsen, W. Beavis, and R.W. Doerge. 2005. Adding confidence to gene
expression clustering. Genetics. 170: 2003-2011.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
M. Vaughn, M. Tanurdzic, Z. Lippman, H. Jiang, R.
Carrasquillo, V. Colot, R.W. Doerge and R.A. Martienssen. 2007.
Epigenetic natural variation in Arabidopsis thaliana. Public Library of Science (PLoS) Biology. 5(7): e174.
H. van Leeuwen, D.J. Kliebenstein, M.A.L. West, K. Kim, R. van Poecke, F. Katagiri, R.W. Michelmore, R.W. Doerge, and 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.
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.
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.
R.W. Doerge. 2007. Proper experimental design and sound statistical inference win every time: a commentary on 'Statistical design and the analysis of gene expression microarray data' by M. Kathleen Kerr and Gary A. Churchill. Genetics Research. 89(5-6): 505-507.
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.
2008. 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.
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. 64(4):1162-1169.
A.A. Long, E. Kim, H.-T. Leung, E. Woodruff III, L. An, R.W. Doerge, W.L. Pak, and K. Broadie. 2008.
Presynaptic calcium channel localization and calcium-dependent synaptic vesicle exocytosis regulated by the fuseless protien. Journal of Neuroscience. 28: 3668 - 3682.
G.A. Churchill and R.W. Doerge. 2008. Naive application of permutation testing leads to inflated type I error rates. Genetics. 178:609610.
H. Jiang and R.W. Doerge. 2008. Estimating the proportion of true null hypotheses for multiple comparisons. Cancer Informatics. 4:25-32.
H.-T. Leung, J. Tseng-Crank, E. Kim, C. Mahapatra, S. Shino, Y. Zhou, L. An, R.W. Doerge and W.L. Pak. 2008. DAG lipase activity is necessary for TRP channel regulation in Drosophila photoreceptors. Neuron. 58(6):884-896.
M. Tanurdzic, M. Vaughn, H. Jiang, L. Lee, E. Thompson, R.W. Doerge, and R.A. Martienssen. 2008. Epigenomic
consequences of immortalized plant cell suspension culture. Public Library of Science Biology (PLoS Biology). 6(12):2880-2895.
S.-Y. Yoo and R.W. Doerge. Integrating Epigenomics Results. 2008. Epigenomics. A. Ferguson-Smith et al. (eds) Springer-Verlag. 37-52.
R.W. Doerge. 2008. Statistical advances in functional genomics.
R. Varshney and R. Tuberosa (eds.), Genomic Assisted Crop Improvement: Vol 1: Genomics
Approaches and Platforms, 315332. Springer-Verlag.
K. Spach, L. An, M. Blake, E. Blankenhorn, J. Bunn, R. Doerge, B. McElvany, R. Noubade, K. Tung, and C. Teuscher. 2008.
Age, season and stress influence EAE sexual dimorphism in SJL/J mice. Journal of Neuroimmunology. 203(2): 212-212.
P. Jones, T. Archer, S. Baylin, et al. 2008. Moving AHEAD with an international human epigenome project . Nature. 454(7205):711-715.
L. An and R.W. Doerge. 2008. Dynamic clustering of cell-cycle gene expression data. The Proceedings of the Kansas State University Conference on Applied
Statistics in Agriculture. Manhattan, KS. 18-36.
S.-Y. Yoo and R.W. Doerge. 2008. A two-stage approach for estimating the effect of DNA methylation on differential expression using tiling array technology. 2008. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. 124-137.
R.T. Gaeta, S.-Y. Yoo, J.C. Pires, R.W. Doerge, Z.J. Chen, and T.C. Osborn. 2009.
Analysis of gene expression in resynthesized Brassica napus allopolyploids using Arabidopsis
70mer oligo microarrays. Public Library of Science (PLoS) ONE 4(3): e4760. doi:10.1371/journal.pone.0004760
.
M. Bremer and R.W. Doerge. 2009. The KM-Algorithm identifies genes in time series
gene expression data. Advances in Bioinformatics. Volume 2009, Article ID 284251, 10
pages, doi:10.1155/2009/284251.
N. C. Riddle, H. Jiang, L. An, R.W. Doerge, and J.A. Birchler. 2009.
Gene expression analysis at the intersection of ploidy and hybridity in maize. Theoretical and Applied Genetics. 120(2):341-353.
R.W. Doerge and K. Kim. 2009. Statistical challenges in modeling expression quantitative
traits. Proceedings of the 24th International Workshop on Statistical Modelling.
James E. Booth, Editor, pages: 13-22.
G.R. Olbricht, N. Sardesai, S.B. Gelvin, B.A. Craig, and R.W. Doerge. 2009. Statistical
methods for Affymetrix tiling array data. The Proceedings of the Kansas State
University Conference on Applied Statistics in Agriculture. Manhattan, KS. 111-125.
P. L. Auer and R.W. Doerge. 2009. Statistical Issues in next generation sequencing.
The Proceedings of the Kansas State University Conference on Applied Statistics in
Agriculture. Manhattan, KS. 69-84.
A. Lipka, G. McCabe and R.W. Doerge. 2009. Associating SNPs with binary traits.
The Proceedings of the Kansas State University Conference on Applied Statistics in
Agriculture. Manhattan, KS. 5-19.
C. Ochsenfeld, K. Jennings, and R.W. Doerge. 2009. Mapping QTL with Covariates.
The Proceedings of the Kansas State University Conference on Applied Statistics in
Agriculture. Manhattan, KS. 126-140.
D. Pignatta, B.P. Dilkes, S.-Y. Yoo, I.M. Henry, A. Madlung, R.W. Doerge, Z. J. Chen, L. Comai. 2009.
Differential sensitivity of the Arabidopsis thaliana transcriptome and enhancers to the effects of genome doubling.
New Phytologist. 186(1):194-206.
A. Rau, F. Jaffrezic, J.-L. Foulley, and R.W. Doerge. 2009. An empirical bayesian method for estimating
biological networks from temporal microarray data. Statistical Applications in Molecular Biology and Genetics. 9(1) Article 9.
DOI: 10.2202/1544-6115.1513.
M. Bremer and R.W. Doerge. 2010. Statistics at the Bench: A Step-by-Step Handbook
for Biologists. Cold Spring Harbor Press. Cold Spring Harbor, NY.
P.L. Auer and R.W. Doerge. 2010. Statistical design and analysis of RNA sequencing data.
Genetics. 185: 405-416.
A.A. Long, C. Mahapatra, H.-T. Leung, E.A. Woodruff III, J. Rohrbough, L. An, R.W. Doerge, M.M. Metzs
tein, S. Shino, W.L. Pak, and K. Broadie. 2010. The nonsense-mediated decay pathway is critical for m
aintaining synapse architecture and synaptic vesicle cycle efficacy. Journal of Cell Science. 3303-3315.
L. Yu and R.W. Doerge. 2010. A semi-nonparametric mixture model for selecting functionally consistent proteins. BMC Bioinformatics. 11:486.
P.L. Auer and R.W. Doerge. 2010. Functional divergence of duplicated genes in the soybean genome.
The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. 171-185.
A. Rau, F. Jaffrezic, J.-L. Foulley, and R.W. Doerge 2010. Approximate Bayesian approaches
for reverse engineering biological networks.
The Proceedings of the Kansas State University Conference on Applied Statistics in
Agriculture. Manhattan, KS. 202-216.
G. Olbricht, B.A. Craig, and R.W. Doerge. 2010. Modeling DNA methylation tiling array data.
The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. 63-84.
S. Srivastava and R.W. Doerge. 2010. A non-parametric empirical Bayes approach for estimating transcript abundance in unreplicated next-generation sequencing data.
The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. 230-244.
T. Achberger, J.C. Fleet, D.E. Salt, and R.W. Doerge. 2010. Introduction to selecting subsets of traits for quantitative trait loci analysis.
The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. 267-286.
P.L. Auer and R.W. Doerge. 2011. A two-stage poisson model for testing RNA-seq data. Statistical Applications in Genetics and Molecular Biology: Vol. 10 : Iss. 1, Article 26.
D. Baumann and R.W. Doerge. 2011. Issues in testing DNA methylation using next-generation sequencing. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. pp1-14.
S. Srivastava and R.W. Doerge. 2011. A hierarchical Bayesian approach for detecting differential gene expression in unreplicated RNA-sequencing data. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. pp166-189.
P.L. Auer, S. Srivastava, and R.W. Doerge. 2012. Differential Expression: The next generation and beyond. Briefings in Functional Genomics. 11(1):57-62.
S. Srivastava and R.W. Doerge. 2012. Purdue Statistics: A journey through time. ``Strength in Numbers: The Rising of Academic Statistics Departments in the United States''. Editors Alan Agresti and Xiao-Li Meng. Springer. pp229-242.
G. Olbricht, B. Craig, and R.W. Doerge. 2012. Incorporating genomic annotation into a hidden markov model for DNA methylation tiling array data. Statistical Applications in Genetics and Molecular Biology. 11(5) DOI: 10.1515/1544-6115.1775.
A. Rau, F. Jaffrezic, J.-L. Foulley and R. W. Doerge. 2012. Reverse engineering gene regulatory networks using approximate Bayesian computation. Statistics and Computing: 22(6):1257-127.
L. An and R.W. Doerge. 2012. Dynamic clustering of gene expression. ISRN Bioinformatics, doi:10.5402/2012/537217.
A.A. Elias, K.R. Robbins, D. Niyogi, J.J. Camberato, R.W. Doerge, and M.R. Tuinstra. 2012. Evaluation of genotype by environment interactions from unreplicated multi-environmental trials of hybrid maize. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. pp1-12.
D. Baumann and R.W. Doerge. 2012. Correcting for amplification bias in next-generation sequencing data. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. pp36-49.
X. Chen and R.W. Doerge. 2012. Towards better FDR procedures for discrete test statistics. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. pp294-303.
S. Srivastava and R.W. Doerge. 2012. The nuances of statistically analyzing next-generation sequencing data. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. pp233-267.
A. Roulin, P.L. Auer, M. Libault, J. Schlueter, A. Farmer, G. May, G. Stacey, R.W. Doerge and S.A. Jackson. 2013. The fate of duplicated genes in a polyploid plant genome. The Plant Journal. 73:143-153.
C.N. Billingsley, J.A. Allen, J.D. Blazek, D.D. Baumann, A. Newbauer, A. Darrah, M. Clement, R.W. Doerge, and R.J. Roper. 2013. Non-trisomic homeobox gene expression during craniofacial development in Down syndrome mice. American Journal of Medical Genetics (in press).
R.W. Doerge Publications