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This is a complete list of publications from our project:

Auger, D. L., Gray, A. D., Ream, T. S., Kato, A., Coe, E. H. J., & Birchler, J. A. (2005). Non-additive gene expression in diploid and triploid hybrids of maize. Genetics 169: 389-397.

Auger, D. L., Ream, T. S., & Birchler, J. A. (2004). A test for a metastable epigenetic component of heterosis using haploid induction in maize. Theor Appl Genet, 108(6), 1017-23.

Birchler, J. A., Riddle, N. C., Auger, D. L., Veitia, A., & Veitia R. (2005). Dosage balance in gene regulation: biological implications. Trends in Genetics, in press.

Birchler, J. A., & Auger, D. L. (2004). Biological consequences of dosage dependent gene regulatory mechanisms in multicellular eukaryotes. In: Biology of Dominance. Ed. Veitia, R. Landes Bioscience.

Birchler, J. A., Auger, D. L., & Kato, A. (2004). Cytogenetics of corn. In: Corn: Origin, History, Technology and Production. Ed. Smith, CV, Betran, J, Runge, E. John Wiley and Sons, New York.

Birchler, J. A., Auger, D. L., & Riddle, N. C. (2003). In search of the molecular basis of heterosis. Plant Cell 15: 2236-2239

Birchler, J. A., Bhadra, U., Bhadra, M. P., & Auger, D. L. (2001). Dosage-dependent gene regulation in multicellular eukaryotes: implications for dosage compensation, aneuploid syndromes, and quantitative traits. Dev Biol, 234(2), 275-88.

Black, M. (2002). Statistical issues in the design and analysis of spotted microarray experiments. Ph.D. Dissertation, Department of Statistics, Purdue University, West Lafayette, IN.

Black, M. A., & Doerge, R. W. (2002). Calculation of the minimum number of replicate spots required for detection of significant gene expression fold change in microarray experiments. Bioinformatics, 18(12), 1609-16.

Cao, D., Craig, B.A., & Doerge, R.W. 2005. A model selection based interval mapping method for autopolyploids. Genetics (published ahead of print on January 31, 2005 as doi: 10.1534 / Genetics. 104.035410)

Cao, D., Craig, B.A., & Doerge, R.W. (2004). Interval mapping for autopolyploids. Proceedings of Applied Statistics in Agriculture, Kasas State University. Edited by George Milliken. (in press)

Cao, D., Osborn, T.C. and Doerge, R.W. 2004. Correct estimation of preferential chromosome pairing in polyploids.  Genome Research. 14:1-4.

Chen, Z. J., Wang, J., Tian, L., Lee, H. S., Wang, J. J., Chen, M., Lee, J. J., Josefsson, C., Madlung, A., Watson, B., Pires, J. C., Lippman, Z., Vaughn, M. W., Colot, V., Birchler, J. A., Doerge, R. W., Martienssen, R., Comai, L., & Osborn, T. (2004). The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects. Biological Journal of the Linnean Society, 82, 689-700.

Comai, L. (2000). Genetic and epigenetic interactions in allopolyploid plants. Plant Mol Biol, 43(2-3), 387-99.

Comai, L., Tyagi, A. P., & Lysak, M. A. (2003). FISH analysis of meiosis in Arabidopsis allopolyploids. Chromosome Res, 11(3), 217-26.

Comai, L., Madlung, A., Josefsson, C., & Tyagi, A. (2003). Do the different parental 'heteromes' cause genomic shock in newly formed allopolyploids. Philos Trans R Soc Lond B Biol Sci, 358(1434), 1149-55.

Craig, B. A., Black, M. A., & Doerge, R. W. (2003). Gene Expression Data: The technology and statistical analysis. Journal of Agricultural, Biological and Environmental Statistics, 8(1), 1-28.

Dilkes, P.B., and L. Comai. 2004. A differential dosage hypothesis for parental effects in seed development. Plant Cell 16: 3174-3180.

Dilkes, B., Dobrozsi, S., Scott, R., & Comai, L. The Col blooded killer phenotype: a lethal paternal effect in interploidy crosses. In preparation.

Doerge, R. W. (2002). Mapping and analysis of quantitative trait loci in experimental populations. Nature Reviews Genetics, 3(1), 43-52.

Doerge, R. W. (2004). When are experimental design, replication and analysis of micoarray data important. The Plant Cell, in press.

Gendrel, A. V., Lippman, Z., Yordan, C., Colot, V., & Martienssen, R. A. (2002). Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene DDM1. Science, 297(5588), 1871-73.

Henry IM, Dilkes B, Young K, Watson B, Wu H, Comai L. Aneuploidy andgenetic variation in the Arabidopsis thalianatriploid response.Genetics (accepted)

Henry, I., Dilkes, B., Young, K., Watson, B., Wu, H., & Comai, L. (2004). Ploidy-dependent segregation distortion in recombinant inbred lines produced by a triploid Arabidopsis thaliana. Submitted.

Himelblau, E., Lauffer, D., Teutonico, R., Pires, J. C., & Osborn, T. (2004). Rapid-cycling Brassica in research and education. In: Biotechnology in Agriculture and Forestry: Brassica Biotechnology. Ed. Pua, EC and Douglas, CJ. Springer-Verlag Berlin.

Jiang H., Wang J., Tian L., Chen, J., & Doerge, R. W.  Statistical analysis of 70-mer oligonucleotide microarray data from polyploidy experiments using repeated dye-swaps. In Press. The Proceedings of the 2004 Kansas State University Conference on Applied Statistics in Agriculture.

Jiang. H. 2004. A Two-Step Procedure for Multiple Pairwise Comparisons in Microarray Experiments. Department of Statistics, Purdue University. West Lafayette, IN. 47907. USA.

Jiang, H., Wang, J., Tian, L., Chen, Z. J., & Doerge, R. W. (2004). Statistical analysis of 70-mer oligonucleotide microarray from polyploid experiments using repeated dye-swaps. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. In Press.

Johnston, J.S., Pepper, A., Hall, A.E., Chen, Z.J., Hodnett, G., Drabek, J., Lopez, R. & Price, H.J. (2004). Evolution of genome size in the Brassicaceae. Ann. Botany. 95: 229-235

Kato, A. (2002). Chromoseome doubling of haploid maize seedlings using nitrous oxide gas a the flower primordial stage. Z Pflanzenzuecht 121: 370-377.

Lee, H. S., & Chen, Z. J. (2001). Protein-coding genes are epigenetically regulated in Arabidopsis polyploids. Proc Natl Acad Sci U S A, 98(12), 6753-58.

Lee, H. S., Wang, J., Tian, L., Jiang, H., Black, M. A., Madlung, A., Watson, B., Lukens, L., Pires, J. C., Wang, J. J., Comai, L., Osborn, T. C., Doerge, R. W., & Chen, Z. J. (2004). Sensitivity of 70-mer oligonucleotides and cDNAs for microarray analysis of gene expression in Arabidopsis and its related species. Plant Biotechnology Journal, 2, 45-58.

Lippman, Z., Gendrel, A. V., Black, M., Vaughn, M. W., Dedhia, N., McCombie, W. R., Lavine, K., Mittal, V., May, B., Kasschau, K. D., Carrington, J. C., Doerge, R. W., Colot, V., & Martienssen, R. (2004). Role of transposable elements in heterochromatin and epigenetic control. Nature, 430(6998), 471-76.

Lippman, Z., May, B., Yordan, C., Singer, T., & Martienssen, R. (2003). Distinct Mechanisms Determine Transposon Inheritance and Methylation via Small Interfering RNA and Histone Modification. PLoS Biol, 1(3), E67.

Lukens, L., Quijada, P., Udall, J., Pires, E. J. C., Schrantz, M. E., & Osborn, T. (2004). Genome redundancy and plasticity within ancient and recent Brassica crop species. Biological Journal of the Linnean Society, 82, 675-88.

Lukens, L., Zou, F., Lydiate, D., Parkin, I., & Osborn, T. (2003). Comparison of a Brassica oleracea genetic map with the genome of Arabidopsis thaliana. Genetics, 164(1), 359-72.

Lukens, L., Pires, J. C., Leon, E., Vogelzang, R. D., Oslach, L., & Osborn, T. C. (2004). Patterns of sequence loss and cytosine methylation within a population of newly synthesized Brassica napus allopolyploids. In preparation.

Madlung, A., Masuelli, R. W., Watson, B., Reynolds, S. H., Davison, J., & Comai, L. (2002). Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. Plant Physiol, 129(2), 733-46.

Madlung, A., Tyagi, A., Watson, B., Jiang, H., Kagochi, T., Doerge, R. W., Martienssen, R., & Comai, L. (2005). Genomic changes in synthetic Arabidopsis polyploids. Plant Journal 41: 221-230.

Martienssen, R. A., Doerge, R. W., Colot, V. 2005. Epigenomic mapping in Arabidopsis using tiling microarrays.  Chromosome Research. (in press).

Martienssen R.A. (2003). Maintenance of heterochromatin by RNA interference of tandem repeats. Nat. Genet. 35: 213-14.

Martienssen R.A. and Colot, V. (2001). DNA methylation and epigenetic inheritance in plants and fungi. Science 293: 1070-1074.

Martienssen R.A. (2001). Chipping away at chromatin. Nature Genetics. 25: 240-241.

Martienssen R.A. and McCombie, W.R., (2001). The first plant genome. Cell 105: 571-574.

Madlung, A., & Comai, L. (2004). The Effect of Stress on Genome Regulation and Structure. Ann Bot 94: 481-495.

May, B., Lippman, Z., & Martienssen, R. (2004). Epigenetic regulation and inheritance of centromeric satellite repeats by RNA interference, histone and DNA methylation. Submitted.

Osborn, T. C., & Lukens, L. (2003). The molecular genetic basis of flowering time variation in Brassica species. In: Biotechnology in Agriculture and Forestry: Brassicas and Legumes from Genome Structure to Breeding. Ed. Nagata, T and Tabata, S. Springer-Verlag Berlin Heidelberg. 52

Osborn, T. C., Pires, J. C., Birchler, J. A., Auger, D. L., Chen, Z. J., Lee, H. S., Comai, L., Madlung, A., Doerge, R. W., Colot, V., & Martienssen, R. A. (2003). Understanding mechanisms of novel gene expression in polyploids. Trends Genet, 19(3), 141-47.

Pires, J. C., Zhao, J., Schrantz, M. E., Leon, E. J., Quijada, P. A., Lukens, L. N., & Osborn, T. C. (2004). Flowering time divergence and genomic rearrangements in resynthesized Brassica polyploids (Brassicaceae). Biological Journal of the Linnean Society, 82, 675-88.

Pontes, O., Neves, N., Silva, M., Lewis, M. S., Madlung, A., Comai, L., Lawrence, R. J., Pikaard, C. S., & Viegas, W. (2004). Rapid genome restructuring accompanies allopolyploid speciation in Arabidopsis suecica. PNAS: in press..

Riddle, N. C., & Birchler, J. A. (2003). Effects of reunited diverged regulatory hierarchies in allopolyploids and species hybrids. Trends Genet, 19(11), 597-600.

Schranz, M. E., & Osborn, T. C. (2004). De novo variation in life-history traits and responses to growth condition of resynthesized polyploid Brassica napus (Brassicaceae). American Journal of Botany, 92, 174-83.

Singer, T., Yordan, C. & Martienssen, R. (2001). Mutator-like transposons in Arabidopsis thaliana are regulated by the chromatin remodeling gene Decrease in DNA Methylation (DDM1). Genes Development 15: 591-602.

Talbert, P. B., Masuelli, R., Tyagi, A. P., Comai, L., & Henikoff, S. (2002). Centromeric localization and adaptive evolution of an Arabidopsis histone H3 variant. Plant Cell, 14(5), 1053-66.

Tian, L., Wang, J., Fong, M. P., Chen, M., Cao, H., Gelvin, S. B., & Chen, Z. J. (2003). Genetic control of developmental changes induced by disruption of Arabidopsis histone deacetylase 1 (AtHD1) expression. Genetics, 165(1), 399-409.

Tian, L., 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 dynamic changes in plant gene regulation and development. Genetics 169: (January issue).

Volpe, T. A., Kidner, C., Hall, I. M., Teng, G., Grewal, S. I., & Martienssen, R. A. (2002). Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science, 297(5588), 1833-37.

Volpe, T., Schramke, V., Hamilton, G. L., White, S. A., Teng, G., Martienssen, R. A., & Allshire, R. C. (2003). RNA interference is required for normal centromere function in fission yeast. Chromosome Res, 11(2), 137-46.

Wang, J., Tian, L., Madlung, A., Lee, H. S., Chen, M., Lee, J. J., Watson, B., Kagochi, T., Comai, L., & Chen, Z. J. (2004). Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids. Genetics, 167(4), 1961-73.

Wang, J., Tian, L., Wang, J. J., Lee, H. S., Lee, J. J., Chen, M., Jiang, H., Watson, B., Madlung, A., Osborn, T. C., Doerge, R. W., Comai, L., & Chen, Z. J. (2004). Transcriptome divergence and allopolyploidy-induced gene regulation in Arabidopsis. Submitted.

Wang, J., Lee, J. J., Lee, H. S., Tian, L., Chen, M., Rao, S., Wei, E. N., Doerge, R. W., Comai, L., & Chen, Z. J. (2004). Methods for genome-wide analysis of gene expression changes in polyploids. Methods in Enzymology. In press.